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Conco-Biyela T, Malla MA, Olatunji Awolusi O, Allam M, Ismail A, Stenström TA, Bux F, Kumari S. Metagenomics insights into microbiome and antibiotic resistance genes from free living amoeba in chlorinated wastewater effluents. Int J Hyg Environ Health 2024; 258:114345. [PMID: 38471337 DOI: 10.1016/j.ijheh.2024.114345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/15/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024]
Abstract
Free living amoeba (FLA) are among the organisms commonly found in wastewater and are well-established hosts for diverse microbial communities. Despite its clinical significance, there is little knowledge on the FLA microbiome and resistome, with previous studies relying mostly on conventional approaches. In this study we comprehensively analyzed the microbiome, antibiotic resistome and virulence factors (VFs) within FLA isolated from final treated effluents of two wastewater treatment plants (WWTPs) using shotgun metagenomics. Acanthamoeba has been identified as the most common FLA, followed by Entamoeba. The bacterial diversity showed no significant difference (p > 0.05) in FLA microbiomes obtained from the two WWTPs. At phylum level, the most dominant taxa were Proteobacteria, followed by Firmicutes and Actinobacteria. The most abundant genera identified were Enterobacter followed by Citrobacter, Paenibacillus, and Cupriavidus. The latter three genera are reported here for the first time in Acanthamoeba. In total, we identified 43 types of ARG conferring resistance to cephalosporins, phenicol, streptomycin, trimethoprim, quinolones, cephalosporins, tigecycline, rifamycin, and kanamycin. Similarly, a variety of VFs in FLA metagenomes were detected which included flagellar proteins, Type IV pili twitching motility proteins (pilH and rpoN), alginate biosynthesis genes AlgI, AlgG, AlgD and AlgW and Type VI secretion system proteins and general secretion pathway proteins (tssM, tssA, tssL, tssK, tssJ, fha, tssG, tssF, tssC and tssB, gspC, gspE, gspD, gspF, gspG, gspH, gspI, gspJ, gspK, and gspM). To the best of our knowledge, this is the first study of its kind to examine both the microbiomes and resistome in FLA, as well as their potential pathogenicity in treated effluents. Additionally, this study showed that FLA can host a variety of potentially pathogenic bacteria including Paenibacillus, and Cupriavidus that had not previously been reported, indicating that their relationship may play a role in the spread and persistence of antibiotic resistant bacteria (ARBs) and antibiotic resistance genes (ARGs) as well as the evolution of novel pathogens.
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Affiliation(s)
- Thobela Conco-Biyela
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa
| | - Muneer Ahmad Malla
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa
| | - Oluyemi Olatunji Awolusi
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa
| | - Mushal Allam
- NICD Sequencing Core Facility, National Institute for Communicable Diseases, Sandringham, 2192, Pretoria, South Africa; Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates
| | - Arshad Ismail
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa; NICD Sequencing Core Facility, National Institute for Communicable Diseases, Sandringham, 2192, Pretoria, South Africa
| | - Thor A Stenström
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa.
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Ali A, Tabouni M, Kizhakkedath P, Baydoun I, Allam M, John A, Busafared F, Alnuaimi A, Al-Jasmi F, Alblooshi H. Spectrum of genetic variants in bilateral sensorineural hearing loss. Front Genet 2024; 15:1314535. [PMID: 38410152 PMCID: PMC10894970 DOI: 10.3389/fgene.2024.1314535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024] Open
Abstract
Background: Hearing loss (HL) is an impairment of auditory function with identified genetic forms that can be syndromic (30%) or non-syndromic (70%). HL is genetically heterogeneous, with more than 1,000 variants across 150 causative genes identified to date. The genetic diagnostic rate varies significantly depending on the population being tested. Countries with a considerably high rate of consanguinity provide a unique resource for studying rare forms of recessive HL. In this study, we identified genetic variants associated with bilateral sensorineural HL (SNHL) using whole-exome sequencing (WES) in 11 families residing in the United Arab Emirates (UAE). Results: We established the molecular diagnosis in six probands, with six different pathogenic or likely pathogenic variants in the genes MYO15A, SLC26A4, and GJB2. One novel nonsense variant, MYO15A:p.Tyr1962Ter*, was identified in a homozygous state in one family, which has not been reported in any public database. SLC26A4 and GJB2 were found to be the most frequently associated genes in this study. In addition, six variants of uncertain significance (VUS) were detected in five probands in the genes CDH23, COL11A1, ADGRV1, NLRP3, and GDF6. In total, 12 variants were observed in eight genes. Among these variants, eight missense variants (66.7%), three nonsense variants (25.0%), and one frameshift (8.3%) were identified. The overall diagnostic rate of this study was 54.5%. Approximately 45.5% of the patients in this study came from consanguineous families. Conclusion: Understanding the genetic basis of HL provides insight for the clinical diagnosis of hearing impairment cases through the utilization of next-generation sequencing (NGS). Our findings contribute to the knowledge of the heterogeneous genetic profile of HL, especially in a population with a high rate of consanguineous marriage in the Arab population.
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Affiliation(s)
- Amanat Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mohammed Tabouni
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Praseetha Kizhakkedath
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ibrahim Baydoun
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Anne John
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Faiza Busafared
- Department of Otolaryngology, Al Kuwait Hospital, Dubai, United Arab Emirates
| | - Ayesha Alnuaimi
- Department of Otolaryngology, Al Kuwait Hospital, Dubai, United Arab Emirates
| | - Fatma Al-Jasmi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Hiba Alblooshi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Khasawneh LQ, Alsafar H, Alblooshi H, Allam M, Patrinos GP, Ali BR. The diversity and clinical implications of genetic variants influencing clopidogrel bioactivation and response in the Emirati population. Hum Genomics 2024; 18:2. [PMID: 38173046 PMCID: PMC10765826 DOI: 10.1186/s40246-023-00568-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Clopidogrel is a widely prescribed prodrug that requires activation via specific pharmacogenes to exert its anti-platelet function. Genetic variations in the genes encoding its transporter, metabolizing enzymes, and target receptor lead to variability in its activation and platelet inhibition and, consequently, its efficacy. This variability increases the risk of secondary cardiovascular events, and therefore, some variations have been utilized as genetic biomarkers when prescribing clopidogrel. METHODS Our study examined clopidogrel-related genes (CYP2C19, ABCB1, PON1, and P2Y12R) in a cohort of 298 healthy Emiratis individuals. The study used whole exome sequencing (WES) data to comprehensively analyze pertinent variations of these genes, including their minor allele frequencies, haplotype distribution, and their resulting phenotypes. RESULTS Our data shows that approximately 37% (n = 119) of the cohort are likely to benefit from the use of alternative anti-platelet drugs due to their classification as intermediate or poor CYP2C19 metabolizers. Additionally, more than 50% of the studied cohort exhibited variants in ABCB1, PON1, and P2YR12 genes, potentially influencing clopidogrel's transport, enzymatic clearance, and receptor performance. CONCLUSIONS Recognizing these alleles and genotype frequencies may explain the clinical differences in medication response across different ethnicities and predict adverse events. Our findings underscore the need to consider genetic variations in prescribing clopidogrel, with potential implications for implementing personalized anti-platelet therapy among Emiratis based on their genetic profiles.
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Affiliation(s)
- Lubna Q Khasawneh
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box: 15551, Al-Ain, United Arab Emirates
| | - Habiba Alsafar
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Hiba Alblooshi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box: 15551, Al-Ain, United Arab Emirates
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box: 15551, Al-Ain, United Arab Emirates
| | - George P Patrinos
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box: 15551, Al-Ain, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates
- School of Health Sciences, Department of Pharmacy, Laboratory of Pharmacogenomics and Individualized Therapy, University of Patras, Patras, Greece
- Zayed Centre for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box: 15551, Al-Ain, United Arab Emirates.
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates.
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Daoud L, Allam M, Collyns T, Ghazawi A, Saleem A, Al-Marzooq F. Extreme resistance to the novel siderophore-cephalosporin cefiderocol in an extensively drug-resistant Klebsiella pneumoniae strain causing fatal pneumonia with sepsis: genomic analysis and synergistic combinations for resistance reversal. Eur J Clin Microbiol Infect Dis 2023; 42:1395-1400. [PMID: 37828413 DOI: 10.1007/s10096-023-04671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
Cefiderocol (CFDC) is the first-in-class siderophore-cephalosporin. Klebsiella pneumoniae strain that is extremely resistant to CFDC (MIC: 256 µg/ml) was isolated for the first time in the United Arab Emirates from a patient with pneumonia and sepsis. It belonged to sequence-type 14 (ST14), with a novel core genome ST. Resistance was driven by the co-expression of β-lactamases (blaNDM-1, blaOXA-232 and blaCTX-M-15) and a mutation in catecholate-siderophore receptor, utilized by CFDC to enter the bacterial cell. Synergistic combinations (β-lactamase inhibitors, aztreonam plus CFDC) re-sensitized the bacteria to CFDC. Although CFDC resistance is multifactorial, the combination with β-lactamase inhibitors represents a promising approach in resistance reversal for fighting superbugs.
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Affiliation(s)
- Land Daoud
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | | | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | | | - Farah Al-Marzooq
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.
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Shobo CO, Amoako DG, Allam M, Ismail A, Essack SY, Bester LA. A Genomic Snapshot of Antibiotic-Resistant Enterococcus faecalis within Public Hospital Environments in South Africa. Glob Health Epidemiol Genom 2023; 2023:6639983. [PMID: 37342729 PMCID: PMC10279497 DOI: 10.1155/2023/6639983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
Abstract
Enterococci are among the most common opportunistic hospital pathogens. This study used whole-genome sequencing (WGS) and bioinformatics to determine the antibiotic resistome, mobile genetic elements, clone and phylogenetic relationship of Enterococcus faecalis isolated from hospital environments in South Africa. This study was carried out from September to November 2017. Isolates were recovered from 11 frequently touched sites by patients and healthcare workers in different wards at 4 levels of healthcare (A, B, C, and D) in Durban, South Africa. Out of the 245 identified E. faecalis isolates, 38 isolates underwent whole-genome sequencing (WGS) on the Illumina MiSeq platform, following microbial identification and antibiotic susceptibility tests. The tet(M) (31/38, 82%) and erm(C) (16/38, 42%) genes were the most common antibiotic-resistant genes found in isolates originating from different hospital environments which corroborated with their antibiotic resistance phenotypes. The isolates harboured mobile genetic elements consisting of plasmids (n = 11) and prophages (n = 14) that were mostly clone-specific. Of note, a large number of insertion sequence (IS) families were found on the IS3 (55%), IS5 (42%), IS1595 (40%), and Tn3 transposons the most predominant. Microbial typing using WGS data revealed 15 clones with 6 major sequence types (ST) belonging to ST16 (n = 7), ST40 (n = 6), ST21 (n = 5), ST126 (n = 3), ST23 (n = 3), and ST386 (n = 3). Phylogenomic analysis showed that the major clones were mostly conserved within specific hospital environments. However, further metadata insights revealed the complex intraclonal spread of these E. faecalis major clones between the sampling sites within each specific hospital setting. The results of these genomic analyses will offer insights into antibiotic-resistantE. faecalis in hospital environments relevant to the design of optimal infection prevention strategies in hospital settings.
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Affiliation(s)
- Christiana O. Shobo
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- School of Laboratory Medicine and Medical Science, Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4000, South Africa
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Daniel G. Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, UAE
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Linda A. Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
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Elhassan MMO, Adam HBA, Fagir SSAO, Mohamed SB, Khaier MAM, Abdulaziz R, Ismail A, Allam M. Whole-genome sequence data of a Salmonella enterica serovar Rissen sequence type 8877 isolated from cracked table egg in Sudan. Data Brief 2023; 47:109005. [PMID: 36915641 PMCID: PMC10006416 DOI: 10.1016/j.dib.2023.109005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Salmonella enterica serovar Rissen is an emerging and important Salmonella serovar prevalent in live animals and foods from retail markets worldwide. Here, we describe the whole-genome sequence of Salmonella enterica Serovar Rissen Sequence Type 8877 isolated from a cracked table egg in Sudan. The whole-genome sequencing was obtained using Illumina Miseq platform. The quality of the sequenced read, the De novo assembly, and the sequencing typing was conducted by JEKESA pipeline (https://github.com/stanikae/jekesa). The assembled genome was also uploaded to the Center for Genomic Epidemiology web server to determine acquired antibiotic resistance genes, predict the serovar, and the antigenic profile. The genome of Salmonella enterica serovar Rissen 1-M1 was found to harbor 4,689 protein-coding genes, 96 RNA genes, and 115 pseudogenes, as predicted by NCBI Prokaryotic Genome Annotation Pipeline. This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under accession JAPSFB000000000.
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Affiliation(s)
| | - Habiba B A Adam
- College of Veterinary Medicine, University of Bahri, Khartoum, Sudan
| | | | - Sofia B Mohamed
- National University Biomedical Research Institute National University, Khartoum, Sudan
| | - Mona A M Khaier
- College of Veterinary Medicine, University of Bahri, Khartoum, Sudan
| | - Romisa Abdulaziz
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Arshad Ismail
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Singh A, Patel NF, Allam M, Chan WY, Mohale T, Ismail A, Oliver SV. Marked Effects of Larval Salt Exposure on the Life History and Gut Microbiota of the Malaria Vector Anopheles merus (Diptera: Culicidae). Insects 2022; 13:1165. [PMID: 36555074 PMCID: PMC9787035 DOI: 10.3390/insects13121165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Anopheles merus can breed in a range of saltwater concentrations. The consequences of this ability on the life history of adult An. merus are poorly understood. This study examined the effects of exposure to 0, 2.1875, 4.375, 8.75, and 17.5 g/L of sodium chloride on An. merus. The effects on larval development, adult longevity, fertility, and fecundity, as well as deltamethrin tolerance were examined. The effect of larval salt exposure on the expression of defensin-1 in adults was examined by quantitative Real-Time PCR. Finally, the effect of the larval salt concentration on microbial dynamics was assessed by 16S Next Generation Sequencing. High concentrations of saltwater increased larval development time and number of eggs laid, as well as deltamethrin tolerance. Larval exposure to salt also reduced the expression of defensin-1. The exposure also had a significant effect on microbial diversity in larvae and adults. The diversity of larvae decreased once adults emerged. Salt-tolerant bacterial genera predominated in larvae but were absent in adults. High salt concentrations resulted in greater abundance of Plasmodium-protective genera in adults. Although this study was conducted on a laboratory strain of An. merus, these data suggest that osmoregulation has a significant effect on the life history of the species with potential epidemiological consequences.
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Affiliation(s)
- Ashmika Singh
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Nashrin F. Patel
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi 15551, United Arab Emirates
| | - Wai-Yin Chan
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Thabo Mohale
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Shüné V. Oliver
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
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Abuelmaali SA, Jamaluddin JAF, Allam M, Abushama HM, Elnaiem DE, Noaman K, Avicor SW, Ishak IH, Wajidi MFF, Jaal Z, Abu Kassim NF. Genetic Polymorphism and Phylogenetics of Aedes aegypti from Sudan Based on ND4 Mitochondrial Gene Variations. Insects 2022; 13:1144. [PMID: 36555054 PMCID: PMC9785543 DOI: 10.3390/insects13121144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/18/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
This study investigated the genetic differences between Aedes aegypti subspecies (Aedes aegypti aegypti (Aaa) and Aedes aegypti formosus (Aaf)) from Sudan using the NADH dehydrogenase subunit 4 (ND4) mitochondrial gene marker. Nineteen distinct haplotypes of the ND4 were identified in female Aedes aegypti mosquitoes from the study sites. The phylogenetic relationship of the 19 ND4 haplotypes was demonstrated in a median-joining haplotype network tree with Aaa and Aaf populations found to share three haplotypes. The genetic variance (Pairwise FST values) was estimated and found to range from 0.000 to 0.811. Isolation by distance test revealed that geographical distance was correlated to genetic variation (coefficient value (r) = 0.43). The Polar maximum likelihood tree showed the phylogenetic relationship of 91 female Aaa and Aaf from the study sites, with most of the Aaf haplotypes clustered in one group while most of the Aaa haplotypes gathered in another group, but there was an admixture of the subspecies in both clusters, especially the Aaa cluster. The Spatial Analysis of Molecular Variance (SAMOVA) test revealed that the eight populations clustered into two phylogeographic groups/clusters of the two subspecies populations. The 2 Aedes aegypti subspecies seemed not to be totally separated geographically with gene flow among the populations.
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Affiliation(s)
- Sara Abdelrahman Abuelmaali
- 129 Medical Entomology Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
- National Public Health Laboratory, Federal Ministry of Health, Khartoum 11115, Sudan
| | | | - Mushal Allam
- College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 15551 Abu Dhabi, United Arab Emirates
| | - Hind Mohamed Abushama
- Department of Zoology, Faculty of Science, University of Khartoum, Khartoum 321, Sudan
| | - Dia Eldin Elnaiem
- Department of Natural Sciences, University of Maryland Eastern Shore, Maryland, MD 21853, USA
| | - Kheder Noaman
- National Center for Research, Tropical Medicine Research Institute, Khartoum 1304, Sudan
| | - Silas Wintuma Avicor
- Entomology Division, Cocoa Research Institute of Ghana, New Tafo-Akim P.O. Box 8, Ghana
| | - Intan Haslina Ishak
- 129 Medical Entomology Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | | | - Zairi Jaal
- Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Nur Faeza Abu Kassim
- 129 Medical Entomology Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
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Mabasa VV, van Zyl WB, Ismail A, Allam M, Taylor MB, Mans J. Multiple Novel Human Norovirus Recombinants Identified in Wastewater in Pretoria, South Africa by Next-Generation Sequencing. Viruses 2022; 14:v14122732. [PMID: 36560736 PMCID: PMC9788511 DOI: 10.3390/v14122732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The genogroup II genotype 4 (GII.4) noroviruses are a major cause of viral gastroenteritis. Since the emergence of the Sydney_2012 variant, no novel norovirus GII.4 variants have been reported. The high diversity of noroviruses and periodic emergence of novel strains necessitates continuous global surveillance. The aim of this study was to assess the diversity of noroviruses in selected wastewater samples from Pretoria, South Africa (SA) using amplicon-based next-generation sequencing (NGS). Between June 2018 and August 2020, 200 raw sewage and final effluent samples were collected fortnightly from two wastewater treatment plants in Pretoria. Viruses were recovered using skimmed milk flocculation and glass wool adsorption-elution virus recovery methods and screened for noroviruses using a one-step real-time reverse-transcription PCR (RT-PCR). The norovirus BC genotyping region (570-579 bp) was amplified from detected norovirus strains and subjected to Illumina MiSeq NGS. Noroviruses were detected in 81% (162/200) of samples. The majority (89%, 89/100) of raw sewage samples were positive for at least one norovirus, compared with 73% (73/100) of final effluent samples. Overall, a total of 89 different GI and GII RdRp-capsid combinations were identified, including 51 putative novel recombinants, 34 previously reported RdRp-capsid combinations, one emerging novel recombinant and three Sanger-sequencing confirmed novel recombinants.
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Affiliation(s)
- Victor Vusi Mabasa
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Walda Brenda van Zyl
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- National Health Laboratory Service, Tshwane Academic Division, Pretoria 0002, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Maureen Beatrice Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- Correspondence: ; Tel.: +27-12-319-2660
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10
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Neetoo H, Reega K, Manoga ZS, Nazurally N, Bhoyroo V, Allam M, Jaufeerally-Fakim Y, Ghoorah AW, Jaumdally W, Hossen AM, Mayghun F, Ismail A, Hosenally M. Prevalence, Genomic Characterization, and Risk Assessment of Human Pathogenic Vibrio Species in Seafood. J Food Prot 2022; 85:1553-1565. [PMID: 35880931 DOI: 10.4315/jfp-22-064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 07/21/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Pathogenic Vibrio species are largely responsible for human diseases associated with consumption of contaminated seafood. The aim of this study was to determine the prevalence, population densities, species diversity, and molecular characteristics of pathogenic Vibrio in various seafood commodities and the health risks associated with consumption of these contaminated commodities. Samples of finfish and shellfish (oysters and sea urchins) were collected from various regions and analyzed for Vibrio with the most-probable-number (MPN) technique. Genomic DNA of putative Vibrio isolates was analyzed by whole genome sequencing for taxonomic identification and identification of virulence and antimicrobial resistance genes. The risk of Vibrio-related illnesses due to the consumption of contaminated seafood was assessed with Risk Ranger. Populations of presumptive Vibrio were 2.6 to 4.4 log MPN/g and correlated with season; Vibrio levels were significantly higher (P < 0.05) in the summer. Fifteen Vibrio isolates were identified as Vibrio alginolyticus (five isolates), Vibrio parahaemolyticus (six isolates), Vibrio harveyi (two isolates), and Vibrio diabolicus (two isolates). Two of the six V. parahaemolyticus isolates (ST 2504 and ST 2505) from oysters harbored either the tdh gene for thermostable direct hemolysin or the trh gene for thermostable direct hemolysin-related hemolysin. In addition to virulence genes, the shellfish isolates also harbored genes encoding resistance to multiple antibiotics, including tetracycline, penicillin, quinolone, and β-lactams, thus arousing concern. The risk assessment predicted that an estimated 21 cases of V. parahaemolyticus-associated gastroenteritis could occur in the general population annually due to consumption of contaminated oysters. This study highlights both the wide prevalence and diversity of Vibrio in seafood and the potential for certain strains to threaten public health. HIGHLIGHTS
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Affiliation(s)
- Hudaa Neetoo
- Department of Agricultural & Food Science, Faculty of Agriculture, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Keshnee Reega
- Department of Agricultural & Food Science, Faculty of Agriculture, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Zishaan Sheik Manoga
- Department of Agricultural & Food Science, Faculty of Agriculture, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Nadeem Nazurally
- Department of Agricultural & Food Science, Faculty of Agriculture, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Vishwakalyan Bhoyroo
- Department of Agricultural & Food Science, Faculty of Agriculture, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Mushal Allam
- College of Medicine & Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Yasmina Jaufeerally-Fakim
- Department of Agricultural & Food Science, Faculty of Agriculture, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Anisah Wahed Ghoorah
- Department of Digital Technologies, Faculty of Information, Communication and Digital Technologies, National Health Laboratory Services, Johannesburg, South Africa
| | - Wasseem Jaumdally
- Department of Agricultural & Food Science, Faculty of Agriculture, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Aicha Malleck Hossen
- Department of Agricultural & Food Science, Faculty of Agriculture, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Farheen Mayghun
- Department of Agricultural & Food Science, Faculty of Agriculture, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Muzzammil Hosenally
- Department of Economics & Statistics, Faculty of Social Sciences and Humanities, University of Mauritius, Réduit, Mauritius
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11
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Tegally H, San JE, Cotten M, Moir M, Tegomoh B, Mboowa G, Martin DP, Baxter C, Lambisia AW, Diallo A, Amoako DG, Diagne MM, Sisay A, Zekri ARN, Gueye AS, Sangare AK, Ouedraogo AS, Sow A, Musa AO, Sesay AK, Abias AG, Elzagheid AI, Lagare A, Kemi AS, Abar AE, Johnson AA, Fowotade A, Oluwapelumi AO, Amuri AA, Juru A, Kandeil A, Mostafa A, Rebai A, Sayed A, Kazeem A, Balde A, Christoffels A, Trotter AJ, Campbell A, Keita AK, Kone A, Bouzid A, Souissi A, Agweyu A, Naguib A, Gutierrez AV, Nkeshimana A, Page AJ, Yadouleton A, Vinze A, Happi AN, Chouikha A, Iranzadeh A, Maharaj A, Batchi-Bouyou AL, Ismail A, Sylverken AA, Goba A, Femi A, Sijuwola AE, Marycelin B, Salako BL, Oderinde BS, Bolajoko B, Diarra B, Herring BL, Tsofa B, Lekana-Douki B, Mvula B, Njanpop-Lafourcade BM, Marondera BT, Khaireh BA, Kouriba B, Adu B, Pool B, McInnis B, Brook C, Williamson C, Nduwimana C, Anscombe C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Mapanguy CM, Loucoubar C, Onwuamah CK, Ihekweazu C, Malaka CN, Peyrefitte C, Grace C, Omoruyi CE, Rafaï CD, Morang’a CM, Erameh C, Lule DB, Bridges DJ, Mukadi-Bamuleka D, Park D, Rasmussen DA, Baker D, Nokes DJ, Ssemwanga D, Tshiabuila D, Amuzu DSY, Goedhals D, Grant DS, Omuoyo DO, Maruapula D, Wanjohi DW, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Abworo EO, Otieno E, Shumba E, Barasa E, Ahmed EB, Ahmed EA, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Manuel E, Leendertz F, Taweh FM, Wasfi F, Abdelmoula F, Takawira FT, Derrar F, Ajogbasile FV, Treurnicht F, Onikepe F, Ntoumi F, Muyembe FM, Ragomzingba FEZ, Dratibi FA, Iyanu FA, Mbunsu GK, Thilliez G, Kay GL, Akpede GO, van Zyl GU, Awandare GA, Kpeli GS, Schubert G, Maphalala GP, Ranaivoson HC, Omunakwe HE, Onywera H, Abe H, Karray H, Nansumba H, Triki H, Kadjo HAA, Elgahzaly H, Gumbo H, Mathieu H, Kavunga-Membo H, Smeti I, Olawoye IB, Adetifa IMO, Odia I, Ben Boubaker IB, Mohammad IA, Ssewanyana I, Wurie I, Konstantinus IS, Halatoko JWA, Ayei J, Sonoo J, Makangara JCC, Tamfum JJM, Heraud JM, Shaffer JG, Giandhari J, Musyoki J, Nkurunziza J, Uwanibe JN, Bhiman JN, Yasuda J, Morais J, Kiconco J, Sandi JD, Huddleston J, Odoom JK, Morobe JM, Gyapong JO, Kayiwa JT, Okolie JC, Xavier JS, Gyamfi J, Wamala JF, Bonney JHK, Nyandwi J, Everatt J, Nakaseegu J, Ngoi JM, Namulondo J, Oguzie JU, Andeko JC, Lutwama JJ, Mogga JJH, O’Grady J, Siddle KJ, Victoir K, Adeyemi KT, Tumedi KA, Carvalho KS, Mohammed KS, Dellagi K, Musonda KG, Duedu KO, Fki-Berrajah L, Singh L, Kepler LM, Biscornet L, de Oliveira Martins L, Chabuka L, Olubayo L, Ojok LD, Deng LL, Ochola-Oyier LI, Tyers L, Mine M, Ramuth M, Mastouri M, ElHefnawi M, Mbanne M, Matsheka MI, Kebabonye M, Diop M, Momoh M, Lima Mendonça MDL, Venter M, Paye MF, Faye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina MG, Owusu M, Wiley MR, Tatfeng MY, Ayekaba MO, Abouelhoda M, Beloufa MA, Seadawy MG, Khalifa MK, Matobo MM, Kane M, Salou M, Mbulawa MB, Mwenda M, Allam M, Phan MVT, Abid N, Rujeni N, Abuzaid N, Ismael N, Elguindy N, Top NM, Dia N, Mabunda N, Hsiao NY, Silochi NB, Francisco NM, Saasa N, Bbosa N, Murunga N, Gumede N, Wolter N, Sitharam N, Ndodo N, Ajayi NA, Tordo N, Mbhele N, Razanajatovo NH, Iguosadolo N, Mba N, Kingsley OC, Sylvanus O, Femi O, Adewumi OM, Testimony O, Ogunsanya OA, Fakayode O, Ogah OE, Oludayo OE, Faye O, Smith-Lawrence P, Ondoa P, Combe P, Nabisubi P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Okokhere PO, Bejon P, Dussart P, Bester PA, Mbala PK, Kaleebu P, Abechi P, El-Shesheny R, Joseph R, Aziz RK, Essomba RG, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Neto Rodrigues RMDESA, Audu RA, Carr RAA, Gargouri S, Masmoudi S, Bootsma S, Sankhe S, Mohamed SI, Femi S, Mhalla S, Hosch S, Kassim SK, Metha S, Trabelsi S, Agwa SH, Mwangi SW, Doumbia S, Makiala-Mandanda S, Aryeetey S, Ahmed SS, Ahmed SM, Elhamoumi S, Moyo S, Lutucuta S, Gaseitsiwe S, Jalloh S, Andriamandimby SF, Oguntope S, Grayo S, Lekana-Douki S, Prosolek S, Ouangraoua S, van Wyk S, Schaffner SF, Kanyerezi S, Ahuka-Mundeke S, Rudder S, Pillay S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Mohale T, Le-Viet T, Velavan TP, Schindler T, Maponga TG, Bedford T, Anyaneji UJ, Chinedu U, Ramphal U, George UE, Enouf V, Nene V, Gorova V, Roshdy WH, Karim WA, Ampofo WK, Preiser W, Choga WT, Ahmed YA, Ramphal Y, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Ouma AEO, von Gottberg A, Githinji G, Moeti M, Tomori O, Sabeti PC, Sall AA, Oyola SO, Tebeje YK, Tessema SK, de Oliveira T, Happi C, Lessells R, Nkengasong J, Wilkinson E. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Science 2022; 378:eabq5358. [PMID: 36108049 PMCID: PMC9529057 DOI: 10.1126/science.abq5358] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022]
Abstract
Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Matthew Cotten
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Bryan Tegomoh
- The Biotechnology Centre of the University of Yaoundé I, Yaoundé, Cameroon
- CDC Foundation, Atlanta, Georgia, Nebraska Department of Health and Human Services, Lincoln, NE, USA
| | - Gerald Mboowa
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | | | - Amadou Diallo
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | | | - Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abdel-Rahman N. Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Abdou Salam Gueye
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Abdoul K. Sangare
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Abdoul-Salam Ouedraogo
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | - Abdualmoniem O. Musa
- Faculty of Medicine and Health Sciences, Kassala University, Kassala City, Sudan
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
- General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan
| | | | - Abe G. Abias
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | | | - Adamou Lagare
- Center for Medical and Sanitary Research (CERMES), Niamey, Niger
| | | | - Aden Elmi Abar
- Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti, Republic of Djibouti
| | - Adeniji A. Johnson
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeola Fowotade
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeyemi O. Oluwapelumi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- The Pirbright Institute, Woking, UK
| | - Adrienne A. Amuri
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Agnes Juru
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ahmed Sayed
- Genomics and Epigenomics Program, Research Department CCHE57357, Cairo, Egypt
| | - Akano Kazeem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Aladje Balde
- Laboratório de Biologia Molecular Jean Piaget, Bissau, Guinea-Bissau
- University Jean Piaget in Guinea-Bissau, Bissau, Guinea-Bissau
| | - Alan Christoffels
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
- SAMRC Bioinformatics Unit, SA Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | | | - Allan Campbell
- Central Public Health Reference Laboratories, Freetown, Sierra Leone
| | - Alpha K. Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
| | - Amadou Kone
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Amel Naguib
- Central Public Health Laboratories (CPHL), Cairo, Egypt
| | | | | | | | - Anges Yadouleton
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
| | - Anika Vinze
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anise N. Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Apporach and Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia
| | - Arash Iranzadeh
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arisha Maharaj
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Armel L. Batchi-Bouyou
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Marien Ngouabi, Brazzaville, Republic of the Congo
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Augustina A. Sylverken
- Kwame Nkrumah University of Science and Technology, Department of Theoretical and Applied Biology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Augustine Goba
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Ayoade Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Ayotunde E. Sijuwola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Baba Marycelin
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria
| | - Babatunde L. Salako
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Bamidele S. Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bankole Bolajoko
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Bassirou Diarra
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Belinda L. Herring
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | | | - Bernard Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
- Département de Parasitologie-Mycologie Université des Sciences de la Santé (USS), Libreville, Gabon
| | - Bernard Mvula
- National HIV Reference Laboratory, Community Health Sciences Unit, Ministry of Health, Lilongwe, Malawi
| | | | | | - Bouh Abdi Khaireh
- National Medical and Molecular Biology Laboratory, Ministry of Health, Djibouti, Republic of Djibouti
- Africa CDC, Rapid Responder, Team Djibouti, Djibouti, Djibouti
| | - Bourema Kouriba
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Bright Adu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Brigitte Pool
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
| | - Bronwyn McInnis
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Cara Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Carolyn Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Catherine Anscombe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal G. Akoua-Koffi
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
- UFR Sciences Médicales, Universite Alassane Ouattara, Bouaké, Côte d’Ivoire
| | - Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | - Chastel M. Mapanguy
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Faculty of Science and Techniques, University Marien Ngouabi, Brazzaville, Republic of the Congo
| | | | - Chika K. Onwuamah
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Chikwe Ihekweazu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Christian N. Malaka
- Laboratoire des Arbovirus, Fièvres Hémorragiques virales, Virus Emergents et Zoonoses, Institut Pasteur de Bangui, Bangui, Central African Republic
| | | | - Chukwa Grace
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Chukwuma E. Omoruyi
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Clotaire D. Rafaï
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Collins M. Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Cyril Erameh
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Daniel B. Lule
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | | | - Daniel Mukadi-Bamuleka
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | - Danny Park
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David A. Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | | | - David J. Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Deogratius Ssemwanga
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Dominic S. Y. Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Dominique Goedhals
- PathCare Vermaak, Pretoria, South Africa and Division of Virology, University of the Free State, Bloemfontein, South Africa
| | - Donald S. Grant
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | | | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Dorcas W. Wanjohi
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | | | - Eddy K. Lusamaki
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
| | | | | | - Edith N. Ngabana
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Edward O. Abworo
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Edward Otieno
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Edwin Shumba
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Edwine Barasa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - El Bara Ahmed
- INRSP, Nouakchott, Mauritania
- Faculté de Médecine de Nouakchott, Nouakchott, Mauritani
| | - Elhadi A. Ahmed
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
| | - Emmanuel Lokilo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | | | - Eromon Philomena
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Etilé A. Anoh
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | - Eusebio Manuel
- Direcção Nacional da Saúde Pública, Ministério da Saúde, Luanda, Angola
| | | | - Fahn M. Taweh
- National Public Health Reference Laboratory–National Public Health Institute of Liberia, Monrovia, Liberia
| | - Fares Wasfi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
| | - Fatma Abdelmoula
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | | | - Fawzi Derrar
- National Influenza Centre, Institut Pasteur d’Algérie, Algiers, Algeria
| | - Fehintola V. Ajogbasile
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Florette Treurnicht
- Department of Virology, National Health Laboratory Service (NHLS), Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Folarin Onikepe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Francine Ntoumi
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Francisca M. Muyembe
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | - Fred A. Dratibi
- WHO Int Comoros, Moroni, Union of Comoros
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Fred-Akintunwa Iyanu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Gabriel K. Mbunsu
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | | | - George O. Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Gert U. van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Grace S. Kpeli
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | | | - Gugu P. Maphalala
- Ministry of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
| | | | - Hannah E. Omunakwe
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Nigeria
| | - Harris Onywera
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hela Karray
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Henda Triki
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
| | | | - Hesham Elgahzaly
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Hota Mathieu
- Doctoral School of Technical and Environmental Sciences, Department of Biology and Human Health, N’Djamena, Chad
| | - Hugo Kavunga-Membo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | - Ibtihel Smeti
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Idowu B. Olawoye
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ifedayo M. O. Adetifa
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ilhem Boutiba Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
| | - Iluoreh Ahmed Mohammad
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Isatta Wurie
- College of Medicine and Allied Health Science, University of Sierra Leone, Freetown, Sierra Leone
| | | | | | - James Ayei
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | - Janaki Sonoo
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
| | - Jean-Claude C. Makangara
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Jean-Jacques M. Tamfum
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Jean-Michel Heraud
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Jessica N. Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Joana Morais
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
- Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
| | | | - John D. Sandi
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - John K. Odoom
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - John O. Gyapong
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - John T. Kayiwa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Johnson C. Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Joicymara S. Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
| | - Jones Gyamfi
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | - Joseph H. K. Bonney
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Joseph Nyandwi
- National Institute of Public Health, Bujumbura, Burundi
- Faculty of Medicine, University of Burundi, Bujumbura, Burundi
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Joyce M. Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | | | - Judith U. Oguzie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Julia C. Andeko
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | - Katherine J. Siddle
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Kayode T. Adeyemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Kefentse A. Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
| | | | | | | | | | - Kwabena O. Duedu
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Lamia Fki-Berrajah
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Lenora M. Kepler
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Leon Biscornet
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
| | | | | | - Luicer Olubayo
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
| | - Lul Deng Ojok
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | - Lul Lojok Deng
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | | | - Lynn Tyers
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Magalutcheemee Ramuth
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
| | - Maha Mastouri
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Mahmoud ElHefnawi
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
| | - Maimouna Mbanne
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | - Mamadou Diop
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mambu Momoh
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
| | | | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Marietou F. Paye
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Martin Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | | | - Matoke-Muhia Damaris
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Maximillian G. Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Insitute, Ifakara, Tanzania
| | - Michael Owusu
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael R. Wiley
- University of Nebraska Medical Center (UNMC), Omaha, NE, USA
- PraesensBio, Lincoln, NE, USA
| | - Mirabeau Y. Tatfeng
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
| | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | | | - Mohamed G. Seadawy
- Biological Prevention Department, Ministry of Defence, Cairo, Egypt
- Faculty of Science, Fayoum University, Fayoum, Egypt
| | | | | | - Mouhamed Kane
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | | | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - My V. T. Phan
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- High Institute of Biotechnology of Monastir, University of Monastir, Rue Taher Haddad 5000, Monastir, Tunisia
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Nadir Abuzaid
- Department of Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Sudan
| | - Nalia Ismael
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | | | | | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nédio Mabunda
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Nei-yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Ngiambudulu M. Francisco
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Nicholas Bbosa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | | | - Nicksy Gumede
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Nikita Sitharam
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Nnaemeka Ndodo
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Nnennaya A. Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Noël Tordo
- Institut Pasteur de Guinée, Conarky, Guinea
| | - Nokuzola Mbhele
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Nosamiefan Iguosadolo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Nwando Mba
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Ojide C. Kingsley
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Okogbenin Sylvanus
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Oladiji Femi
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences. College of Health Sciences. University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olubusuyi M. Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olumade Testimony
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Olusola A. Ogunsanya
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Oluwatosin Fakayode
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
| | - Onwe E. Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ope-Ewe Oludayo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | - Patricia Nabisubi
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | | | - Paul E. Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Peter Kojo Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Peter O. Okokhere
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- Department of Medicine, Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Edo State, Nigeria
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Phillip A. Bester
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | - Placide K. Mbala
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Pontiano Kaleebu
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Priscilla Abechi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
- Infectious Hazards Preparedness, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
| | - Rageema Joseph
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ramy Karam Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt, Cairo, Egypt
| | - René G. Essomba
- National Public Health Laboratory, Ministry of Public Health of Cameroon, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
| | - Reuben Ayivor-Djanie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Richard Njouom
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
| | - Richard O. Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Rosa Maria D. E. S. A. Neto Rodrigues
- Coordenadora da rede do Diagnóstico Tuberculose/HIV/COVID-19 na Instituição - Laboratório Nacional de Referência da Tuberculose em São Tomé e Príncipe, São Tomé, São Tomé and Principe
- Ponto focal para Melhoria da qualidade dos Laboratórios (SLIPTA) ao nível de São Tomé e Príncipe, São Tomé, São Tomé and Principe
| | - Rosemary A. Audu
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Rosina A. A. Carr
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Saba Gargouri
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Saibu Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Salma Mhalla
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
- Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia
| | - Salome Hosch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Samar Kamal Kassim
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Samar Metha
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sameh Trabelsi
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
| | - Sara Hassan Agwa
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Sarah Wambui Mwangi
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Seydou Doumbia
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Sheila Makiala-Mandanda
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Sherihane Aryeetey
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | - Siham Elhamoumi
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Silvia Lutucuta
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simbirie Jalloh
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Sobajo Oguntope
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Sonia Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Soumeya Ouangraoua
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
| | - Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Stephen F. Schaffner
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Stephen Kanyerezi
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Steve Ahuka-Mundeke
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Susan Nabadda
- Central Public Health Laboratories (CPHL), Kampala, Uganda
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | | | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | - Tapfumanei Mashe
- National Microbiology Reference Laboratory, Harare, Zimbabwe
- World Health Organization, Harare, Zimbabwe
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Thirumalaisamy P. Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- University of Basel, Basel, Switzerland
| | - Tongai G. Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugwu Chinedu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
| | - Uwem E. George
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | - Vishvanath Nene
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Vivianne Gorova
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
| | | | - Wasim Abdul Karim
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - William K. Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yahaya Ali Ahmed
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Yajna Ramphal
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Yemaachi Biotech, Accra, Ghana
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yvan Butera
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Africa Pathogen Genomics Initiative (Africa PGI)
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- The Biotechnology Centre of the University of Yaoundé I, Yaoundé, Cameroon
- CDC Foundation, Atlanta, Georgia, Nebraska Department of Health and Human Services, Lincoln, NE, USA
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
- West African Health Organisation, Bobo-Dioulasso, Burkina Faso
- Faculty of Medicine and Health Sciences, Kassala University, Kassala City, Sudan
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
- General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan
- MRC Unit The Gambia at LSHTM, Fajara, Gambia
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
- Libyan Biotechnology Research Center, Tripoli, Libya
- Center for Medical and Sanitary Research (CERMES), Niamey, Niger
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti, Republic of Djibouti
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- The Pirbright Institute, Woking, UK
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Genomics and Epigenomics Program, Research Department CCHE57357, Cairo, Egypt
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- Laboratório de Biologia Molecular Jean Piaget, Bissau, Guinea-Bissau
- University Jean Piaget in Guinea-Bissau, Bissau, Guinea-Bissau
- SAMRC Bioinformatics Unit, SA Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
- Quadram Institute Bioscience, Norwich, UK
- Central Public Health Reference Laboratories, Freetown, Sierra Leone
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Central Public Health Laboratories (CPHL), Cairo, Egypt
- National Institute of Public Health, Bujumbura, Burundi
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Apporach and Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Marien Ngouabi, Brazzaville, Republic of the Congo
- Kwame Nkrumah University of Science and Technology, Department of Theoretical and Applied Biology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
- Département de Parasitologie-Mycologie Université des Sciences de la Santé (USS), Libreville, Gabon
- National HIV Reference Laboratory, Community Health Sciences Unit, Ministry of Health, Lilongwe, Malawi
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
- National Medical and Molecular Biology Laboratory, Ministry of Health, Djibouti, Republic of Djibouti
- Africa CDC, Rapid Responder, Team Djibouti, Djibouti, Djibouti
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- National Health Laboratory Service (NHLS), Cape Town, South Africa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
- University of Nebraska Medical Center (UNMC), Omaha, NE, USA
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
- UFR Sciences Médicales, Universite Alassane Ouattara, Bouaké, Côte d’Ivoire
- School of Public Health, Pwani University, Kilifi, Kenya
- Faculty of Science and Techniques, University Marien Ngouabi, Brazzaville, Republic of the Congo
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
- Laboratoire des Arbovirus, Fièvres Hémorragiques virales, Virus Emergents et Zoonoses, Institut Pasteur de Bangui, Bangui, Central African Republic
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- PATH, Lusaka, Zambia
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- Uganda Virus Research Institute, Entebbe, Uganda
- PathCare Vermaak, Pretoria, South Africa and Division of Virology, University of the Free State, Bloemfontein, South Africa
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Macha Research Trust, Choma, Zambia
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- INRSP, Nouakchott, Mauritania
- Faculté de Médecine de Nouakchott, Nouakchott, Mauritani
- Rwanda National Reference Laboratory, Kigali, Rwanda
- Robert Koch-Institute, Berlin, Germany
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France
- Direcção Nacional da Saúde Pública, Ministério da Saúde, Luanda, Angola
- National Public Health Reference Laboratory–National Public Health Institute of Liberia, Monrovia, Liberia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
- National Influenza Centre, Institut Pasteur d’Algérie, Algiers, Algeria
- Department of Virology, National Health Laboratory Service (NHLS), Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
- Ministère de Santé Publique et de la Solidarité Nationale, Ndjamena, Chad
- WHO Int Comoros, Moroni, Union of Comoros
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
- Ministry of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Nigeria
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
- Central Public Health Laboratories (CPHL), Kampala, Uganda
- Institut Pasteur de Côte d’Ivoire, Departement des Virus Epidemiques, Abidjan, Côte d’Ivoire
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
- Doctoral School of Technical and Environmental Sciences, Department of Biology and Human Health, N’Djamena, Chad
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
- College of Medicine and Allied Health Science, University of Sierra Leone, Freetown, Sierra Leone
- Namibia Institute of Pathology, Windhoek, Namibia
- National Institute of Hygiene, Lomé, Togo
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
- WHO Burundi, Gitega, Burundi
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
- Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
- WHO South Sudan, Juba, South Sudan
- Faculty of Medicine, University of Burundi, Bujumbura, Burundi
- Pasteur Network, Institut Pasteur, Paris, France
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- Instituto Nacional de Saúde Pública, Praia, Cape Verde
- Zambia National Public Health Institute, Lusaka, Zambia
- Public Health Institute of Malawi, Lilongwe, Malawi
- National Health Laboratory, Gaborone, Botswana
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
- Ministry of Health and Wellness, Gaborone, Botswana
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- National Reference Laboratory Lesotho, Maseru, Lesotho
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Insitute, Ifakara, Tanzania
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- PraesensBio, Lincoln, NE, USA
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
- Biological Prevention Department, Ministry of Defence, Cairo, Egypt
- Faculty of Science, Fayoum University, Fayoum, Egypt
- Molecular Pathology Lab, Children’s Cancer Hospital, Cairo, Egypt
- Laboratoire Biolim FSS/Université de Lomé, Lomé, Togo
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
- High Institute of Biotechnology of Monastir, University of Monastir, Rue Taher Haddad 5000, Monastir, Tunisia
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Department of Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Sudan
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Institut Pasteur de Guinée, Conarky, Guinea
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences. College of Health Sciences. University of Ilorin, Ilorin, Kwara State, Nigeria
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Mayotte Hospital Center, Mayotte, France
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
- Department of Medicine, Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Edo State, Nigeria
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
- Infectious Hazards Preparedness, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt, Cairo, Egypt
- National Public Health Laboratory, Ministry of Public Health of Cameroon, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
- Coordenadora da rede do Diagnóstico Tuberculose/HIV/COVID-19 na Instituição - Laboratório Nacional de Referência da Tuberculose em São Tomé e Príncipe, São Tomé, São Tomé and Principe
- Ponto focal para Melhoria da qualidade dos Laboratórios (SLIPTA) ao nível de São Tomé e Príncipe, São Tomé, São Tomé and Principe
- National Public Health Reference Laboratory (NPHRL), Mogadishu, Somalia
- Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia
- University of Basel, Basel, Switzerland
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
- World Health Organization, Harare, Zimbabwe
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Yemaachi Biotech, Accra, Ghana
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Ahmed E. O. Ouma
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Matshidiso Moeti
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Pardis C. Sabeti
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Samuel O. Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Yenew K. Tebeje
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - John Nkengasong
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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12
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Mendes A, Lentsoane O, Allam M, Khumalo Z, Ismail A, Coetzer JAW, Venter M. Phylogenetic Characterisation of the Full Genome of a Bagaza Virus Isolate from Bird Fatalities in South Africa. Viruses 2022; 14:v14071476. [PMID: 35891456 PMCID: PMC9324014 DOI: 10.3390/v14071476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 12/10/2022] Open
Abstract
Bagaza virus (BAGV), a member of the Ntaya serogroup in the Flavivirus genus of the Flaviviridae, was isolated from the brain tissue of a Himalayan monal pheasant that died following neurological signs in Pretoria, South Africa in 2016. Next-generation sequencing was carried out on this isolate resulting in a genome sequence of 10980nt. The full genome sequence of this isolate, designated ZRU96-16, shared 98% nucleotide identity with a BAGV isolate found in Culex univitattus mosquitoes from Namibia and 97% nucleotide identity with a Spanish BAGV sequence isolated from an infected partridge. In total, seven amino acid variations were unique to ZRU96-16 after alignment with other BAGV and Israel turkey meningoencephalomyelitis (ITV) genomes. The 3′UTR sequence of ZRU96-16 was resolved with sufficient detail to be able to annotate the variable and conserved sequence elements within this region. Multiple sequence alignment of the 3′UTR suggested that it could be useful in lineage designation as more similar viruses carried similar mutations across this region, while also retaining certain unique sites. Maximum likelihood phylogenetic analysis revealed two clusters containing both BAGV and ITVs from Europe, the Middle East and Africa. Broadly, temporal clustering separated isolates into two groups, with one cluster representing viruses from the 1960–2000’s and the other from 2010 onwards. This suggests that there is consistent exchange of BAGV and ITV between Europe and Africa. This investigation provides more information on the phylogenetics of an under-represented member of the Flaviviridae and provides an avenue for more extensive research on its pathogenesis and geographic expansion.
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Affiliation(s)
- Adriano Mendes
- Zoonotic Arbo- and Respiratory Virus Research Program, Centre for Viral Zoonoses, University of Pretoria, Pretoria 0007, South Africa; (A.M.); (O.L.)
| | - Olivia Lentsoane
- Zoonotic Arbo- and Respiratory Virus Research Program, Centre for Viral Zoonoses, University of Pretoria, Pretoria 0007, South Africa; (A.M.); (O.L.)
| | - Mushal Allam
- Sequencing Core Facility, National Institute of Communicable Disease, Johannesburg 2192, South Africa; (M.A.); (Z.K.); (A.I.)
| | - Zamantungwaka Khumalo
- Sequencing Core Facility, National Institute of Communicable Disease, Johannesburg 2192, South Africa; (M.A.); (Z.K.); (A.I.)
| | - Arshad Ismail
- Sequencing Core Facility, National Institute of Communicable Disease, Johannesburg 2192, South Africa; (M.A.); (Z.K.); (A.I.)
| | - Jacobus A. W. Coetzer
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria 0001, South Africa;
| | - Marietjie Venter
- Zoonotic Arbo- and Respiratory Virus Research Program, Centre for Viral Zoonoses, University of Pretoria, Pretoria 0007, South Africa; (A.M.); (O.L.)
- Correspondence: ; Tel.: +27-832-930-884
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13
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Ali DE, Allam M, Altayb HN, Mursi D, Adalla MA, Mohammed NO, Khaier MAM, Salih MH, Abusalab S, Abbas MA. A prevalence and molecular characterization of novel pathogenic strains of Macrococcus caseolyticus isolated from external wounds of donkeys in Khartoum State -Sudan. BMC Vet Res 2022; 18:197. [PMID: 35614464 PMCID: PMC9131596 DOI: 10.1186/s12917-022-03297-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
A pathogenic strain of Macrococcus caseolyticus (M. caseolyticus) was isolated from wounds infection during an investigation on donkeys in Khartoum State. (122) samples were collected from external wounds (head, abdomen, back and leg) during different seasons. One isolate (124B) was identified using whole-genome sequence analysis. RAST software identified 31 virulent genes of disease and defense, including methicillin-resistant genes, TatR family and ANT(4')-Ib. Plasmid rep22 was identified by PlasmidFindet-2.0 Server and a CRISPR. MILST-2.0 predicted many novel alleles. NCBI notated the genome as a novel M. caseolyticus strain (DaniaSudan). The MLST-tree-V1 revealed that DaniaSudan and KM0211a strains were interrelated. Strain DaniaSudan was resistant to ciprofloxacin, ceftazidime, erythromycin, oxacillin, clindamycin and kanamycin. Mice modeling showed bacteremia and many clinical signs (swelling, allergy, wounds, and hair loss). Enlargement, hyperemia, adhesions and abscesses were observed in many organs.Constructive conclusionThe prevalence of the strain was 4.73%, with significant differences between collection seasons and locations of wounds. A highly significant association between doses (105 CFU/ml, 102 CFU/ml, Intra-peritoneum and sub-cutaneous) and swelling, developing of allergy and loss of hair (p = 0.001, p = 0.000 and p = 0.005) respectively were seen.This result represents the first report of pathogenic strains of M. caseolyticus worldwide.
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Affiliation(s)
- Dania E Ali
- Animal Resources Research Corporation, Sudan Academy of Science, Khartoum, Sudan.
| | - Mushal Allam
- Department of Genetics and Genomics, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Hisham N Altayb
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, 21452, Saudi Arabia
| | - D Mursi
- Central Laboratory, Ministry of Higher Education and Scientific Research, Khartoum, Sudan
| | - M A Adalla
- Central Veterinary Research Laboratory, Department of Biological Products, Animal Resources Research Corporation, Khartoum, Sudan
| | - N O Mohammed
- Ahfad Center for Science and Technology, Ahfad University for Women, Omdurman, Sudan
| | - Mona A M Khaier
- Department of Molecular Biology and Bioinformatics, University of Bahri, Khartoum, Sudan
| | - Manal H Salih
- Central Veterinary Research Laboratory, Department of Pathology, Animal Resources Research Corporation, Khartoum, Sudan
| | - Sarah Abusalab
- Department of Preventive Medicine and Veterinary Public Health, Faculty of Veterinary Medicine, University of Khartoum, Khartoum, Sudan
| | - M A Abbas
- Department of Microbiology, Faculty of Veterinary Medicine, University of Khartoum, Khartoum, Sudan
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14
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Nogbou ND, Ramashia M, Nkawane GM, Allam M, Obi CL, Musyoki AM. Whole-Genome Sequencing of a Colistin-Resistant Acinetobacter baumannii Strain Isolated at a Tertiary Health Facility in Pretoria, South Africa. Antibiotics (Basel) 2022; 11:594. [PMID: 35625238 PMCID: PMC9138137 DOI: 10.3390/antibiotics11050594] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Acinetobacter baumannii's (A. baumannii) growing resistance to all available antibiotics is of concern. The study describes a colistin-resistant A. baumannii isolated at a clinical facility from a tracheal aspirate sample. Furthermore, it determines the isolates' niche establishment ability within the tertiary health facility. METHODS An antimicrobial susceptibility test, conventional PCR, quantitative real-time PCR, phenotypic evaluation of the efflux pump, and whole-genome sequencing and analysis were performed on the isolate. RESULTS The antimicrobial susceptibility pattern revealed a resistance to piperacillin/tazobactam, ceftazidime, cefepime, cefotaxime/ceftriaxone, imipenem, meropenem, gentamycin, ciprofloxacin, trimethoprim/sulfamethoxazole, tigecycline, and colistin. A broth microdilution test confirmed the colistin resistance. Conventional PCR and quantitative real-time PCR investigations revealed the presence of adeB, adeR, and adeS, while mcr-1 was not detected. A MIC of 0.38 µg/mL and 0.25 µg/mL was recorded before and after exposure to an AdeABC efflux pump inhibitor. The whole-genome sequence analysis of antimicrobial resistance-associated genes detected beta-lactam: blaOXA-66; blaOXA-23; blaADC-25; blaADC-73; blaA1; blaA2, and blaMBL; aminoglycoside: aph(6)-Id; aph(3″)-Ib; ant(3″)-IIa and armA) and a colistin resistance-associated gene lpsB. The whole-genome sequence virulence analysis revealed a biofilm formation system and cell-cell adhesion-associated genes: bap, bfmR, bfmS, csuA, csuA/B, csuB, csuC, csuD, csuE, pgaA, pgaB, pgaC, and pgaD; and quorum sensing-associated genes: abaI and abaR and iron acquisition system associated genes: barA, barB, basA, basB, basC, basD, basF, basG, basH, basI, basJ, bauA, bauB, bauC, bauD, bauE, bauF, and entE. A sequence type classification based on the Pasteur scheme revealed that the isolate belongs to sequence type ST2. CONCLUSIONS The mosaic of the virulence factors coupled with the resistance-associated genes and the phenotypic resistance profile highlights the risk that this strain is at this South African tertiary health facility.
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Affiliation(s)
- Noel-David Nogbou
- Microbiological Pathology Department, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa; (N.-D.N.); (M.R.); (G.M.N.)
| | - Mbudzeni Ramashia
- Microbiological Pathology Department, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa; (N.-D.N.); (M.R.); (G.M.N.)
| | - Granny Marumo Nkawane
- Microbiological Pathology Department, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa; (N.-D.N.); (M.R.); (G.M.N.)
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates;
| | - Chikwelu Lawrence Obi
- School of Sciences and Technology, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa;
| | - Andrew Munyalo Musyoki
- Microbiological Pathology Department, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa; (N.-D.N.); (M.R.); (G.M.N.)
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15
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Lapidot R, Faits T, Ismail A, Allam M, Khumalo Z, MacLeod W, Kwenda G, Mupila Z, Nakazwe R, Segrè D, Johnson WE, Thea DM, Mwananyanda L, Gill CJ. Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study. Gates Open Res 2022. [DOI: 10.12688/gatesopenres.13561.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background: Infants suffering from lower respiratory tract infections (LRTIs) have distinct nasopharyngeal (NP) microbiome profiles that correlate with severity of disease. Whether these profiles precede the infection or a consequence of it, is unknown. In order to answer this question, longitudinal studies are needed. Methods: We conducted an analysis of a longitudinal prospective cohort study of 1,981 Zambian mother-infant pairs who underwent NP sampling from 1-week through 14-weeks of age at 2-3-week intervals. Ten of the infants in the cohort who developed LRTI were matched 1:3 with healthy comparators. We completed 16S rRNA gene sequencing on the samples each of these infants contributed, as well as from baseline samples of the infants’ mothers, and characterized the normal maturation of the healthy infant NP microbiome, compared to infants who developed LRTI. Results: The infant NP microbiome maturation was characterized by transitioning from Staphylococcus dominant to respiratory-genera dominant profiles during the first three months of life, similar to what is described in the literature. Interestingly, infants who developed LRTI had NP dysbiosis before infection, in most cases as early as the first week of life. Dysbiosis was characterized by the presence of Novosphingobium, Delftia, high relative abundance of Anaerobacillus, Bacillus, and low relative abundance of Dolosigranulum, compared to the healthy controls. Mothers of infants with LRTI also had low relative abundance of Dolosigranulum in their baseline samples compared to mothers of infants that did not develop an LRTI. Conclusions: Our results suggest that NP microbiome dysbiosis precedes LRTI in young infants and may be present in their mothers as well. Early dysbiosis may play a role in the causal pathway leading to LRTI or could be a marker of other pathogenic forces that directly lead to LRTI.
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Wadhwa M, Kang HN, Thorpe R, Knezevic I, Aprea P, Bielsky MC, Ekman N, Heim HK, Joung J, Kurki P, Lacana E, Njue C, Nkansah E, Savkina M, Thorpe R, Yamaguchi T, Wadhwa M, Wang J, Weise M, Wolff-Holz E, Allam M, Bahaa H, Sayed M, Al-Oballi A, Alshahrani A, Baek D, Kim J, Chua H, Gangakhedkar J, Jagtap MP, Lyaskovsky T, Okudaira S, Ondee W, Sotomayor P, Ricra JS, Uviase J, Ahmed F, Rajendran Y, Defendi HT, Cho SO, Qu A, Acha V, Gencoglu M, Ho K, Baldrighi M, Schiestl M, Watson K, Spitzer E, Chong S, Fukushima A, Kang HN, Knezevic I, Pante G, Simao M. WHO informal consultation on revision of guidelines on evaluation of similar biotherapeutic products, virtual meeting, 30 June – 2 July 2021. Biologicals 2022; 76:1-9. [PMID: 35466023 PMCID: PMC9109723 DOI: 10.1016/j.biologicals.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/28/2022] [Accepted: 03/29/2022] [Indexed: 11/26/2022] Open
Abstract
The WHO informal consultation was held to promote the revision of WHO guidelines on evaluation of similar biotherapeutic products (SBPs) adopted by the Expert Committee on Biological Standardization (ECBS) in 2009. It was agreed in the past consultations that the evaluation principles in the guidelines are still valid, but a review was recommended to provide more clarity and case-by-case flexibility. The opportunity was therefore taken to review the experience and identify areas where the current guidance could be more permissive without compromising its basic principles, and where additional explanation could be provided regarding the possibility of reducing the amount of data needed for regulatory approval. The meeting participants applauded the leading role taken by the WHO in providing a much-needed streamlined approach for development and evaluation of SBPs which will provide efficient and cost-effective product development and increase patient access to treatments. It was recognized that the principles as currently described in the draft WHO guidelines are based on sound science and experience gained over the last fifteen years of biosimilar approvals. However, since these guidelines when finalised will constitute the global standard for biosimilar evaluation and assist national regulatory authorities in establishing revised guidance and regulatory practice in this complex area, it was felt that further revision and clarity on certain perspectives in specific areas was necessary to dispel uncertainties arising in the current revised version. This report describes the principles in the draft guidelines, including topics discussed and consensus reached. WHO guidelines serve as a basis for the development of national regulatory framework for biosimilars. Revision of guidelines is to provide more flexibility and clarification on data required for regulatory approval. Revised guidelines would contribute to improving consistency on regulatory decision and patient access to treatments.
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17
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Turumtay H, Allam M, Sandalli A, Turumtay EA, Genç H, Sandalli C. Characteristics in the whole-genome sequence of Klebsiella pneumoniae ST147 from Turkey. Acta Microbiol Immunol Hung 2022. [PMID: 35195536 DOI: 10.1556/030.2022.01690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/12/2022] [Indexed: 11/19/2022]
Abstract
The study aimed to analyze antibiotic resistance determinants in a carbapenem-resistant Klebsiella pneumoniae by whole-genome sequencing (WGS). K. pneumoniae was isolated from a urine sample and it was characterized by 16S rDNA sequencing in Turkey. This strain was named as Kpn Rize-53-TR. Antimicrobial susceptibility testing was performed for seventeen antibiotics by VITEK-2 and the result was confirmed by MIC. The whole genome of isolate was sequenced by Illumina and was analysed by bioinformatic tools for MLST, replicon types, and antimicrobial resistance genes. The whole genome data was submitted to NCBI. The isolate was found to be resistant to all tested β-lactam antibiotics and the highest MIC values were found for piperacillin, piperacillin/tazobactam (≥128). No resistance to colistin and moderate susceptibility to amikacin and tetracycline was observed. The isolate carried 12 resistance genes belonging to 10 resistance classes; ere(A), fosA, oqxB, cmlA1, aac(a)-IIa, bla KPC-2, bla TEM-1A, bla SHV-67, bla CTX-M-15, bla OXA-1-2-9. Mutations were detected in gyrA (83Y) and parC (80I) genes. Clonal subtype of the isolate was ST147, and it had wzi420 and wzc38 alleles. Its serotype was O3/O3a. The bla KPC-2 was firstly found in both ST147 clonal group in Turkey and in serotype O3/O3a in the world. By plasmid replicon typing, five plasmids IncFII(K), Col(BS512), IncR, IncFIA(HI1) and IncFIB(pQil) were determined in Kpn Rize-53-TR and bla KPC-2 was located on IncFII(K) plasmid. The presence of bla KPC-2 on the plasmid with other resistance genes accelerates its own spread together with other resistance genes.
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Affiliation(s)
- Halbay Turumtay
- 1 Karadeniz Technical University, Department of Energy System Engineering, 61830, Trabzon, Turkey
- 2 Joint BioEnergy Institute, Feedstocks Division, Emeryville, CA 94608, USA
| | - Mushal Allam
- 3 Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Aytül Sandalli
- 4 Recep Tayyip Erdoğan University, Department of Biology, 53020, Rize, Turkey
| | | | - Hacer Genç
- 6 Rize Tea Research and Application Center (ÇAYMER), 53100, Rize, Turkey
| | - Cemal Sandalli
- 4 Recep Tayyip Erdoğan University, Department of Biology, 53020, Rize, Turkey
- 7 Firtina Research Group, Fener Mahallesi, VillaKent Konutları, 53020 Rize, Turkey
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Ramsamy Y, Mlisana KP, Amoako DG, Abia ALK, Ismail A, Allam M, Mbanga J, Singh R, Essack SY. Mobile genetic elements-mediated Enterobacterales-associated carbapenemase antibiotic resistance genes propagation between the environment and humans: A One Health South African study. Sci Total Environ 2022; 806:150641. [PMID: 34606866 DOI: 10.1016/j.scitotenv.2021.150641] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
We, (1) studied carbapenem-resistant Enterobacterales (CRE) in the environment, humans, and animals, within the same geographical area and, (2) delineated the isolates' resistome, mobilome, virulome, and phylogeny. Following ethical approval, 587 samples (humans = 230, pigs = 345, and water = 12) were collected and cultured on CRE selective media. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK 2 automated platform. The resistomes, virulomes, mobilomes, and phylogenies were ascertained by whole genome sequencing. Nineteen (3.2%), i.e., 15/19 humans and 4/19 environmental, but no pig, CRE were obtained. CREs included Klebsiella pneumoniae 9/19 (47%), Enterobacter hormaechei 6/19 (32%), Klebsiella quasipneumoniae 2/19 (11%), a novel ST498 Citrobacter freundii 1/19 (5%) and Serratia marcescens 1/19 (5%). Eleven isolates were extensively drug-resistant; eight were multidrug-resistant. Sixteen CRE harbored the blaOXA-181, blaOXA-48, blaOXA-484, blaNDM-1, and blaGES-5 genes. Multiple species/clones carried blaOXA-48 and blaNDM-1 carbapenemase-encoding genes with respective mobile genetic elements (MGEs). The IncFIB(K) plasmid replicon was found in most human K. pneumoniae strains (7/9) and all environmental K. quasipneumoniae isolates; most K. pneumoniae produced OXA-181 (5/9). The (Col440I) plasmid replicon, identified in 11 (26.82%) isolates, mainly E. hormaechei (n = 6), predominated both sectors. Most β-lactamase-encoding genes were associated with class 1 integrons IntI1, insertion sequences (IS) (IS91, IS5075, IS30, IS3000, IS3, IS19, ISKpn19, IS5075) and transposons (Tn3). The IncL/M(pMU407) and IncL/M(pOXA48) plasmid replicons were found exclusively in K. pneumoniae; all but one of these strains produced OXA-181. Also, the Klebsiella spp. harbored 80 virulence genes. Phylogenomic clustered identified isolates with other carbapenemase-producing K. pneumoniae, E. hormaechei, S. marcescens, and C. freundii from different South African sources (animals, environment, and humans). We delineated the resistome, mobilome, virulome, and phylogeny of carbapenemase-producing Enterobacterales in humans and environment, highlighting antibiotic resistance genes propagation via MGEs across sectors, emphasizing a One Health approach to AMR.
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Affiliation(s)
- Yogandree Ramsamy
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Medical Microbiology, National Health Laboratory Services, Durban, South Africa; Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Koleka P Mlisana
- Medical Microbiology, National Health Laboratory Services, Durban, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Joshua Mbanga
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Ravesh Singh
- Medical Microbiology, National Health Laboratory Services, Durban, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Singh A, Allam M, Kwenda S, Khumalo ZTH, Ismail A, Oliver SV. The dynamic gut microbiota of zoophilic members of the Anopheles gambiae complex (Diptera: Culicidae). Sci Rep 2022; 12:1495. [PMID: 35087127 PMCID: PMC8795440 DOI: 10.1038/s41598-022-05437-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 12/17/2021] [Indexed: 11/11/2022] Open
Abstract
The gut microbiota of mosquitoes plays a critical role in the life history of the animal. There is a growing body of research characterising the gut microbiota of a range of mosquito species, but there is still a paucity of information on some members of the Anopheles gambiae complex. In this study, the gut microbiota of four laboratory strains were characterised. SENN (Anopheles arabiensis—insecticide susceptible major vector), SENN DDT (Anopheles arabiensis—insecticide resistant major vector), MAFUS (Anopheles merus—minor vector) and SANGWE (Anopheles quadriannulatus—non-vector) were used in this study. The microbiota of fourth instar larvae, 3-day old, 15-day old non-blood fed and 15-day old blood fed females were characterised by MALDI-TOF mass spectroscopy and 16 s rRNA gene sequencing by next generation sequencing. The four strains differed in species richness but not diversity. The major vectors differ in β-diversity from that of the minor and non-vectors. There was no difference in α- or β-diversity in 15 non-blood fed females and 15-day old females that had 3 blood meals before day 15. These differences may be related to a mixture of the effect of insecticide resistance phenotype as well as a potential relationship to vector competence to a limited extent. Bacterial diversity is affected by species and age. There is also a potential relationship between the differences in gut microbiota and capacity to transmit parasites. This genetic background of the mosquitoes, however, play a major role, and must be considered in this relationship.
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Affiliation(s)
- Ashmika Singh
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Stanford Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Zamantungwa T H Khumalo
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Shüné V Oliver
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. .,Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Naicker SD, Maphanga TG, Chow NA, Allam M, Kwenda S, Ismail A, Govender NP. Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolates. Emerg Microbes Infect 2021; 10:1300-1308. [PMID: 34176429 PMCID: PMC8253216 DOI: 10.1080/22221751.2021.1944323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/01/2021] [Accepted: 06/13/2021] [Indexed: 11/07/2022]
Abstract
In South Africa, Candida auris was the third most common cause of candidemia in 2016-2017. We performed single nucleotide polymorphism (SNP) genome-wide analysis of 115 C. auris isolates collected between 2009 and 2018 from national laboratory-based surveillance, an environmental survey at four hospitals and a colonization study during a neonatal unit outbreak. The first known South African C. auris strain from 2009 clustered in clade IV. Overall, 98 strains clustered within clade III (85%), 14 within clade I (12%) and three within clade IV (3%). All environmental and colonizing strains clustered in clade III. We also identified known clade-specific resistance mutations in the ERG11 and FKS1 genes. Identification of clade I strains between 2016 and 2018 suggests introductions from South Asia followed by local transmission. SNP analysis characterized most C. auris strains into clade III, the clade first reported from South Africa, but the presence of clades I and IV strains also suggest early introductions from other regions.
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Affiliation(s)
- Serisha D. Naicker
- National Institute for Communicable Diseases (Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses), a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tsidiso G. Maphanga
- National Institute for Communicable Diseases (Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses), a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nancy A. Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mushal Allam
- National Institute for Communicable Diseases (Core Sequencing Facility), a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stanford Kwenda
- National Institute for Communicable Diseases (Core Sequencing Facility), a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- National Institute for Communicable Diseases (Core Sequencing Facility), a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nelesh P. Govender
- National Institute for Communicable Diseases (Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses), a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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21
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Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, Martin DP, Rasmussen DA, Zekri ARN, Sangare AK, Ouedraogo AS, Sesay AK, Priscilla A, Kemi AS, Olubusuyi AM, Oluwapelumi AOO, Hammami A, Amuri AA, Sayed A, Ouma AEO, Elargoubi A, Ajayi NA, Victoria AF, Kazeem A, George A, Trotter AJ, Yahaya AA, Keita AK, Diallo A, Kone A, Souissi A, Chtourou A, Gutierrez AV, Page AJ, Vinze A, Iranzadeh A, Lambisia A, Ismail A, Rosemary A, Sylverken A, Femi A, Ibrahimi A, Marycelin B, Oderinde BS, Bolajoko B, Dhaala B, Herring BL, Njanpop-Lafourcade BM, Kleinhans B, McInnis B, Tegomoh B, Brook C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Peyrefitte C, Daubenberger C, Morang’a CM, Nokes DJ, Amoako DG, Bugembe DL, Park D, Baker D, Doolabh D, Ssemwanga D, Tshiabuila D, Bassirou D, Amuzu DSY, Goedhals D, Omuoyo DO, Maruapula D, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Shumba E, El Fahime E, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Leendertz F, Ajili F, Enoch FO, Wasfi F, Abdelmoula F, Mosha FS, Takawira FT, Derrar F, Bouzid F, Onikepe F, Adeola F, Muyembe FM, Tanser F, Dratibi FA, Mbunsu GK, Thilliez G, Kay GL, Githinji G, van Zyl G, Awandare GA, Schubert G, Maphalala GP, Ranaivoson HC, Lemriss H, Anise H, Abe H, Karray HH, Nansumba H, Elgahzaly HA, Gumbo H, Smeti I, Ayed IB, Odia I, Ben Boubaker IB, Gaaloul I, Gazy I, Mudau I, Ssewanyana I, Konstantinus I, Lekana-Douk JB, Makangara JCC, Tamfum JJM, Heraud JM, Shaffer JG, Giandhari J, Li J, Yasuda J, Mends JQ, Kiconco J, Morobe JM, Gyapong JO, Okolie JC, Kayiwa JT, Edwards JA, Gyamfi J, Farah J, Nakaseegu J, Ngoi JM, Namulondo J, Andeko JC, Lutwama JJ, O’Grady J, Siddle K, Adeyemi KT, Tumedi KA, Said KM, Hae-Young K, Duedu KO, Belyamani L, Fki-Berrajah L, Singh L, Martins LDO, Tyers L, Ramuth M, Mastouri M, Aouni M, el Hefnawi M, Matsheka MI, Kebabonye M, Diop M, Turki M, Paye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina M, Nwando M, Owusu M, Wiley MR, Youtchou MT, Ayekaba MO, Abouelhoda M, Seadawy MG, Khalifa MK, Sekhele M, Ouadghiri M, Diagne MM, Mwenda M, Allam M, Phan MVT, Abid N, Touil N, Rujeni N, Kharrat N, Ismael N, Dia N, Mabunda N, Hsiao NY, Silochi NB, Nsenga N, Gumede N, Mulder N, Ndodo N, Razanajatovo NH, Iguosadolo N, Judith O, Kingsley OC, Sylvanus O, Peter O, Femi O, Idowu O, Testimony O, Chukwuma OE, Ogah OE, Onwuamah CK, Cyril O, Faye O, Tomori O, Ondoa P, Combe P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Dussart P, Bester PA, Mbala PK, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Carr RAA, El Kabbaj S, Gargouri S, Masmoudi S, Sankhe S, Lawal SB, Kassim S, Trabelsi S, Metha S, Kammoun S, Lemriss S, Agwa SHA, Calvignac-Spencer S, Schaffner SF, Doumbia S, Mandanda SM, Aryeetey S, Ahmed SS, Elhamoumi S, Andriamandimby S, Tope S, Lekana-Douki S, Prosolek S, Ouangraoua S, Mundeke SA, Rudder S, Panji S, Pillay S, Engelbrecht S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Aanniz T, Mohale T, Le-Viet T, Schindler T, Anyaneji UJ, Chinedu U, Ramphal U, Jessica U, George U, Fonseca V, Enouf V, Gorova V, Roshdy WH, Ampofo WK, Preiser W, Choga WT, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Sall AA, Rebai A, von Gottberg A, Kouriba B, Williamson C, Bridges DJ, Chikwe I, Bhiman JN, Mine M, Cotten M, Moyo S, Gaseitsiwe S, Saasa N, Sabeti PC, Kaleebu P, Tebeje YK, Tessema SK, Happi C, Nkengasong J, de Oliveira T. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science 2021; 374:423-431. [PMID: 34672751 PMCID: PMC7613315 DOI: 10.1126/science.abj4336] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/03/2021] [Indexed: 01/05/2023]
Abstract
The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.
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Affiliation(s)
- Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diego Cuadros
- Department of Geography and GIS, University of Cincinnati, Cincinnati, OH, USA
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - David A. Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Abdel-Rahman N. Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Abdoul K. Sangare
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Abdoul-Salam Ouedraogo
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | - Abechi Priscilla
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Adedotun-Sulaiman Kemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Adeyemi O. O. Oluwapelumi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Adnène Hammami
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Adrienne A. Amuri
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Ahmad Sayed
- Genomics Research Program, Children’s Cancer Hospital, Cairo, Egypt
| | - Ahmed E. O. Ouma
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Aida Elargoubi
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Nnennaya A. Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ajogbasile F. Victoria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Akano Kazeem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Ali A. Yahaya
- World Health Organization, Africa Region, Brazzaville Congo
| | - Alpha K. Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Montpellier University/IRD/INSERM, Montpellier, France
| | - Amadou Diallo
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Kone
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amel Chtourou
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | | | - Anika Vinze
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Arash Iranzadeh
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arnold Lambisia
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Audu Rosemary
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ayoade Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Baba Marycelin
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bamidele S. Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bankole Bolajoko
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | | | - Bronwyn Kleinhans
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Bronwyn McInnis
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Bryan Tegomoh
- The Biotechnology Center of the University of Yaoundé I, Cameroon and CDC Foundation, Yaounde, Cameroon
| | - Cara Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal G. Akoua-Koffi
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | - Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | | | | | - Collins M. Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - D. James Nokes
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Danny Park
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | | | - Deelan Doolabh
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Deogratius Ssemwanga
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diarra Bassirou
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Dominic S. Y. Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Dominique Goedhals
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | | | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | | | - Eddy K. Lusamaki
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edgar Simulundu
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | - Edith N. Ngabana
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edwin Shumba
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Elmostafa El Fahime
- Functional Genomic Platform/National Centre for Scientific and Technical Research (CNRST), Rabat, Morocco
| | - Emmanuel Lokilo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
| | | | - Eromon Philomena
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Etilé A. Anoh
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | | | - Faida Ajili
- Research Unit of Autoimmune Diseases UR17DN02, Military Hospital of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Fakayode O. Enoch
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
| | - Fares Wasfi
- Laboratory of Clinical Virology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Fatma Abdelmoula
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | | | | | - Fawzi Derrar
- National Influenza Centre, Viral Respiratory Laboratory, Algiers, Algeria
| | - Feriel Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Folarin Onikepe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Fowotade Adeola
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Francisca M. Muyembe
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Frank Tanser
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | | | - Gabriel K. Mbunsu
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | - George Githinji
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Gugu P. Maphalala
- Institution and Department, Ministry Of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
| | | | - Hajar Lemriss
- Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco
| | - Happi Anise
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hela H. Karray
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | - Hesham A. Elgahzaly
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Ibtihel Smeti
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ikhlas B. Ayed
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Ilhem Boutiba Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, 1006 Tunis, Tunisia
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Imed Gaaloul
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Inbal Gazy
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Innocent Mudau
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Jean B. Lekana-Douk
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | - Jean-Claude C. Makangara
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Jacques M. Tamfum
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Michel Heraud
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jingjing Li
- Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Joana Q. Mends
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | - John M. Morobe
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - John O. Gyapong
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Johnson C. Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John T. Kayiwa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Johnathan A. Edwards
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jones Gyamfi
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | | | - Joyce M. Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Julia C. Andeko
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | - Kayode T. Adeyemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Kefentse A. Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
| | - Khadija M. Said
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Kim Hae-Young
- New York University Grossman School of Medicine, New York City, NY, USA
| | - Kwabena O. Duedu
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Lahcen Belyamani
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Lamia Fki-Berrajah
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Lynn Tyers
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Magalutcheemee Ramuth
- Virology/Molecular Biology Department, Central Health Laboratory, Ministry of Health and Wellness, Mauritius
| | - Maha Mastouri
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Mahjoub Aouni
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Mahmoud el Hefnawi
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo Egypt
| | | | | | - Mamadou Diop
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Manel Turki
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Marietou Paye
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | | | - Matoke-Muhia Damaris
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Maureen W. Mburu
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Maximillian Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Institute, Dar-es-Salaam, Tanzania
| | - Mba Nwando
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Michael Owusu
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Mirabeau T. Youtchou
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
| | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Mohamed G. Seadawy
- Biological Prevention Department, Main Chemical Laboratories, Egypt Army, Cairo, Egypt
| | | | - Mooko Sekhele
- National Reference Laboratory Lesotho, Maseru, Lesotho
| | - Mouna Ouadghiri
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | | | | | - Mushal Allam
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - My V. T. Phan
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
| | - Nadia Touil
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Najla Kharrat
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Nalia Ismael
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nedio Mabunda
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Nei-yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Ngoy Nsenga
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicksy Gumede
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | | | | | - Nosamiefan Iguosadolo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Oguzie Judith
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ojide C. Kingsley
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | - Oladiji Femi
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olawoye Idowu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Olumade Testimony
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Omoruyi E. Chukwuma
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Onwe E. Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Chika K. Onwuamah
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | | | - Paul E. Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Paulo Arnaldo
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Peter K. Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Phillip A. Bester
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | - Placide K. Mbala
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Reuben Ayivor-Djanie
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Richard Njouom
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
| | - Richard O. Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Rosina A. A. Carr
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Saâd El Kabbaj
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Saba Gargouri
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Salako B. Lawal
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Samar Kassim
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Sameh Trabelsi
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
| | - Samar Metha
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Sami Kammoun
- CHU Hedi Chaker Sfax, Service de Pneumologie, Tunis, Tunisia
| | - Sanaâ Lemriss
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Sara H. A. Agwa
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | | | | | - Seydou Doumbia
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Sheila M. Mandanda
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | - Sobajo Tope
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Sonia Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Soumeya Ouangraoua
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
| | - Steve A. Mundeke
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Susan Nabadda
- Central Public Health Laboratories (CPHL), Kampala, Uganda
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Tarik Aanniz
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugwu Chinedu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
| | - Uwanibe Jessica
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Uwem George
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | - Vivianne Gorova
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
| | | | - William K. Ampofo
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yvan Butera
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Bourema Kouriba
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | - Carolyn Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | | | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Matthew Cotten
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ngonda Saasa
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | | | - Yenew K. Tebeje
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John Nkengasong
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
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22
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Goolam Mahomed T, Peters RPH, Allam M, Ismail A, Mtshali S, Goolam Mahomed A, Ueckermann V, Kock MM, Ehlers MM. Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa. Sci Rep 2021; 11:19758. [PMID: 34611216 PMCID: PMC8492659 DOI: 10.1038/s41598-021-99127-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.
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Affiliation(s)
- T. Goolam Mahomed
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - R. P. H. Peters
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.442327.40000 0004 7860 2538Foundation for Professional Development, Research Unit, East London, South Africa
| | - M. Allam
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - A. Ismail
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - S. Mtshali
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | | | - V. Ueckermann
- grid.49697.350000 0001 2107 2298Department of Internal Medicine, University of Pretoria, Pretoria, South Africa
| | - M. M. Kock
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
| | - M. M. Ehlers
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
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23
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Richter L, du Plessis EM, Duvenage S, Allam M, Ismail A, Korsten L. Whole Genome Sequencing of Extended-Spectrum- and AmpC- β-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa. Front Microbiol 2021; 12:734649. [PMID: 34659162 PMCID: PMC8517129 DOI: 10.3389/fmicb.2021.734649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase- (AmpC) producing Enterobacterales in irrigation water and associated irrigated fresh produce represents risks related to the environment, food safety, and public health. In South Africa, information about the presence of ESBL/AmpC-producing Enterobacterales from non-clinical sources is limited, particularly in the water-plant-food interface. This study aimed to characterize 19 selected MDR ESBL/AmpC-producing Escherichia coli (n=3), Klebsiella pneumoniae (n=5), Serratia fonticola (n=10), and Salmonella enterica (n=1) isolates from spinach and associated irrigation water samples from two commercial spinach production systems within South Africa, using whole genome sequencing (WGS). Antibiotic resistance genes potentially encoding resistance to eight different classes were present, with bla CTX-M-15 being the dominant ESBL encoding gene and bla ACT-types being the dominant AmpC encoding gene detected. A greater number of resistance genes across more antibiotic classes were seen in all the K. pneumoniae strains, compared to the other genera tested. From one farm, bla CTX-M-15-positive K. pneumoniae strains of the same sequence type 985 (ST 985) were present in spinach at harvest and retail samples after processing, suggesting successful persistence of these MDR strains. In addition, ESBL-producing K. pneumoniae ST15, an emerging high-risk clone causing nosocomical outbreaks worldwide, was isolated from irrigation water. Known resistance plasmid replicon types of Enterobacterales including IncFIB, IncFIA, IncFII, IncB/O, and IncHI1B were observed in all strains following analysis with PlasmidFinder. However, bla CTX-M-15 was the only β-lactamase resistance gene associated with plasmids (IncFII and IncFIB) in K. pneumoniae (n=4) strains. In one E. coli and five K. pneumoniae strains, integron In191 was observed. Relevant similarities to human pathogens were predicted with PathogenFinder for all 19 strains, with a confidence of 0.635-0.721 in S. fonticola, 0.852-0.931 in E. coli, 0.796-0.899 in K. pneumoniae, and 0.939 in the S. enterica strain. The presence of MDR ESBL/AmpC-producing E. coli, K. pneumoniae, S. fonticola, and S. enterica with similarities to human pathogens in the agricultural production systems reflects environmental and food contamination mediated by anthropogenic activities, contributing to the spread of antibiotic resistance genes.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Erika M. du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
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24
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Lukhele ST, Kwatra G, Ismail A, Allam M, Dangor Z, Madhi SA. Investigation of Possible Nosocomial-Associated Invasive Group B Streptococcus Disease Using Whole-Genome Sequencing: A Report of 3 Cases. J Pediatric Infect Dis Soc 2021; 10:880-882. [PMID: 34129035 DOI: 10.1093/jpids/piab042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/20/2021] [Indexed: 11/13/2022]
Abstract
We investigated possible nosocomial transmission of 3 invasive cases of Group B Streptococcus serotype III disease in newborns delivered in the same facility. All cases were of the same sequence type and clonal complex. Genomic variation was detected within the core genome and capsular region, indicating different sources of acquisition.
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Affiliation(s)
- Sindiswa T Lukhele
- South African Medical Research Council: Vaccines and Infectious Diseases Analytical Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science/National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- South African Medical Research Council: Vaccines and Infectious Diseases Analytical Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science/National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa.,Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Ziyaad Dangor
- South African Medical Research Council: Vaccines and Infectious Diseases Analytical Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science/National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council: Vaccines and Infectious Diseases Analytical Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science/National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
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Mitchev N, Singh R, Allam M, Kwenda S, Ismail A, Garrett N, Ramsuran V, Niehaus AJ, Mlisana KP. Antimicrobial Resistance Mechanisms, Multilocus Sequence Typing, and NG-STAR Sequence Types of Diverse Neisseria gonorrhoeae Isolates in KwaZulu-Natal, South Africa. Antimicrob Agents Chemother 2021; 65:e0075921. [PMID: 34280016 PMCID: PMC8448096 DOI: 10.1128/aac.00759-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/13/2021] [Indexed: 01/08/2023] Open
Abstract
Antimicrobial resistance (AMR) is a major challenge to managing infectious diseases. Africa has the highest incidence of gonorrhoea, but there is a lack of comprehensive data from sparse surveillance programs. This study investigated the molecular epidemiology and AMR profiles of Neisseria gonorrhoeae isolates in KwaZulu-Natal province (KZN), South Africa. Repository isolates from patients attending public health care clinics for sexually transmitted infection (STI) care were used for phenotypic and genotypic analysis. An Etest was performed to determine antimicrobial susceptibility. Whole-genome sequencing (WGS) was used to determine epidemiology and to predict susceptibility by detecting resistance-associated genes and mutations. Among the 61 isolates, multiple sequence types were identified. Six isolates were novel, as determined by multilocus sequence typing. N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) determined 48 sequence types, of which 35 isolates had novel antimicrobial profiles. Two novel penA alleles and eight novel mtrR alleles were identified. Point mutations were detected in gyrA, parC, mtrR, penA, ponA, and porB1. This study revealed a high prevalence of AMR (penicillin 67%, tetracycline 89%, and ciprofloxacin 52%). However, spectinomycin, cefixime, ceftriaxone, and azithromycin remained 100% effective. This study is one of the first to comprehensively describe the epidemiology and AMR of N. gonorrhoeae in KZN, South Africa and Africa, using WGS. KZN has a wide strain diversity and most of these sequence types have been detected in multiple countries; however, more than half of our isolates have novel antimicrobial profiles. Continued surveillance is crucial to monitor the emergence of resistance to cefixime, ceftriaxone, and azithromycin.
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Affiliation(s)
- Nireshni Mitchev
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ravesh Singh
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- National Health Laboratory Service, Durban, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Stanford Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- School of Nursing and Public Health, Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Abraham J. Niehaus
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Koleka P. Mlisana
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- National Health Laboratory Service, Johannesburg, South Africa
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Schneider C, Allam M, Stoyanov D, Hawkes DJ, Gurusamy K, Davidson BR. Performance of image guided navigation in laparoscopic liver surgery - A systematic review. Surg Oncol 2021; 38:101637. [PMID: 34358880 DOI: 10.1016/j.suronc.2021.101637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/04/2021] [Accepted: 07/24/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Compared to open surgery, minimally invasive liver resection has improved short term outcomes. It is however technically more challenging. Navigated image guidance systems (IGS) are being developed to overcome these challenges. The aim of this systematic review is to provide an overview of their current capabilities and limitations. METHODS Medline, Embase and Cochrane databases were searched using free text terms and corresponding controlled vocabulary. Titles and abstracts of retrieved articles were screened for inclusion criteria. Due to the heterogeneity of the retrieved data it was not possible to conduct a meta-analysis. Therefore results are presented in tabulated and narrative format. RESULTS Out of 2015 articles, 17 pre-clinical and 33 clinical papers met inclusion criteria. Data from 24 articles that reported on accuracy indicates that in recent years navigation accuracy has been in the range of 8-15 mm. Due to discrepancies in evaluation methods it is difficult to compare accuracy metrics between different systems. Surgeon feedback suggests that current state of the art IGS may be useful as a supplementary navigation tool, especially in small liver lesions that are difficult to locate. They are however not able to reliably localise all relevant anatomical structures. Only one article investigated IGS impact on clinical outcomes. CONCLUSIONS Further improvements in navigation accuracy are needed to enable reliable visualisation of tumour margins with the precision required for oncological resections. To enhance comparability between different IGS it is crucial to find a consensus on the assessment of navigation accuracy as a minimum reporting standard.
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Affiliation(s)
- C Schneider
- Department of Surgical Biotechnology, University College London, Pond Street, NW3 2QG, London, UK.
| | - M Allam
- Department of Surgical Biotechnology, University College London, Pond Street, NW3 2QG, London, UK; General surgery Department, Tanta University, Egypt
| | - D Stoyanov
- Department of Computer Science, University College London, London, UK; Centre for Medical Image Computing (CMIC), University College London, London, UK
| | - D J Hawkes
- Centre for Medical Image Computing (CMIC), University College London, London, UK; Wellcome / EPSRC Centre for Surgical and Interventional Sciences (WEISS), University College London, London, UK
| | - K Gurusamy
- Department of Surgical Biotechnology, University College London, Pond Street, NW3 2QG, London, UK
| | - B R Davidson
- Department of Surgical Biotechnology, University College London, Pond Street, NW3 2QG, London, UK
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Mbanga J, Amoako DG, Abia ALK, Allam M, Ismail A, Essack SY. Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South Africa. Front Microbiol 2021; 12:648454. [PMID: 34194401 PMCID: PMC8236953 DOI: 10.3389/fmicb.2021.648454] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/19/2021] [Indexed: 12/21/2022] Open
Abstract
We investigated the antibiotic resistome, mobilome, virulome, and phylogenomic lineages of Enterococcus spp. obtained from a wastewater treatment plant and its associated waters using whole-genome sequencing (WGS) and bioinformatics tools. The whole genomes of Enterococcus isolates including Enterococcus faecalis (n = 4), Enterococcus faecium (n = 5), Enterococcus hirae (n = 2), and Enterococcus durans (n = 1) with similar resistance patterns from different sampling sites and time points were sequenced on an Illumina MiSeq machine. Multilocus sequence typing (MLST) analysis revealed two E. faecalis isolates that had a common sequence type ST179; the rest had unique sequence types ST841, and ST300. The E. faecium genomes belonged to 3 sequence types, ST94 (n = 2), ST361 (n = 2), and ST1096 (n = 1). Detected resistance genes included those encoding tetracycline [tet(S), tet(M), and tet(L)], and macrolides [msr(C), msr(D), erm(B), and mef(A)] resistance. Antibiotic resistance genes were associated with insertion sequences (IS6, ISL3, and IS982), and transposons (Tn3 and Tn6000). The tet(M) resistance gene was consistently found associated with a conjugative transposon protein (TcpC). A total of 20 different virulence genes were identified in E. faecalis and E. faecium including those encoding for sex pheromones (cCF10, cOB1, cad, and came), adhesion (ace, SrtA, ebpA, ebpC, and efaAfs), and cell invasion (hylA and hylB). Several virulence genes were associated with the insertion sequence IS256. No virulence genes were detected in E. hirae and E. durans. Phylogenetic analysis revealed that all Enterococcus spp. isolates were more closely related to animal and environmental isolates than clinical isolates. Enterococcus spp. with a diverse range of resistance and virulence genes as well as associated mobile genetic elements (MGEs) exist in the wastewater environment in South Africa.
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Affiliation(s)
- Joshua Mbanga
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Daniel G. Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
| | - Akebe L. K. Abia
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
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Mbanga J, Amoako DG, Abia ALK, Allam M, Ismail A, Essack SY. Genomic Insights of Multidrug-Resistant Escherichia coli From Wastewater Sources and Their Association With Clinical Pathogens in South Africa. Front Vet Sci 2021; 8:636715. [PMID: 33718473 PMCID: PMC7952442 DOI: 10.3389/fvets.2021.636715] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/01/2021] [Indexed: 01/09/2023] Open
Abstract
There is limited information on the comparative genomic diversity of antibiotic-resistant Escherichia coli from wastewater. We sought to characterize environmental E. coli isolates belonging to various pathotypes obtained from a wastewater treatment plant (WWTP) and its receiving waters using whole-genome sequencing (WGS) and an array of bioinformatics tools to elucidate the resistomes, virulomes, mobilomes, clonality, and phylogenies. Twelve multidrug-resistant (MDR) diarrheagenic E. coli isolates were obtained from the final effluent of a WWTP, and the receiving river upstream and downstream of the WWTP were sequenced on an Illumina MiSeq machine. The multilocus sequence typing (MLST) analysis revealed that multiple sequence types (STs), the most common of which was ST69 (n = 4) and ST10 (n = 2), followed by singletons belonging to ST372, ST101, ST569, ST218, and ST200. One isolate was assigned to a novel ST ST11351. A total of 66.7% isolates were positive for β-lactamase genes with 58.3% harboring the bla TEM1B gene and a single isolate the blaCTX-M-14 and blaCTX-M-55 extended-spectrum β-lactamase (ESBL) genes. One isolate was positive for the mcr-9 mobilized colistin resistance gene. Most antibiotic resistance genes (ARGs) were associated with mobile genetic support: class 1 integrons (In22, In54, In191, and In369), insertion sequences (ISs), and/or transposons (Tn402 or Tn21). A total of 31 virulence genes were identified across the study isolates, including those responsible for adhesion (lpfA, iha, and aggR), immunity (air, gad, and iss), and toxins (senB, vat, astA, and sat). The virulence genes were mostly associated with IS (IS1, IS3, IS91, IS66, IS630, and IS481) or prophages. Co-resistance to heavy metal/biocide, antibiotics were evident in several isolates. The phylogenomic analysis with South African E. coli isolates from different sources (animals, birds, and humans) revealed that isolates from this study mostly clustered with clinical isolates. Phylogenetics linked with metadata revealed that isolates did not cluster according to source but according to ST. The occurrence of pathogenic and MDR isolates in the WWTP effluent and the associated river is a public health concern.
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Affiliation(s)
- Joshua Mbanga
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Daniel G. Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Akebe L. K. Abia
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
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Ramsamy Y, Amoako DG, Abia ALK, Allam M, Ismail A, Mtshali PS, Mlisana KP, Essack SY. First genome sequence of Aeromonas hydrophilia novel sequence type 658 strain isolated from livestock in South Africa. J Glob Antimicrob Resist 2021; 24:175-177. [PMID: 33460845 DOI: 10.1016/j.jgar.2020.12.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/13/2020] [Accepted: 12/24/2020] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES The underlying resistance mechanisms, defence systems, mobilome, virulome, clonality and global phylogenetic relationship of a novel sequence type (ST) 658 Aeromonas hydrophilia (A34a) isolated from a pig abattoir in South Africa was determined using whole-genome sequence (WGS) technology. METHODS Following isolation on chromogenic agar (CHROMID® CARBA SMART), microbial identification and antibiotic susceptibility testing were performed using a VITEK®2 platform. Genotyping involved WGS performed with an Illumina MiSeq platform. RESULTS The antibiotic resistome agreed with the resistance phenotype of the isolate and included antibiotic resistance determinants for β-lactams (blaCPHA3 and blaOXA-724). BLASTn analysis of resistome-encoding contigs affirmed chromosomally-mediated resistance. BURST algorithmic analysis identified the novel ST658 as a satellite variant. Virulome analysis predicted virulence genes of Aeromonas whose expression are critical for establishing infection in the host. Global phylogenomic analyses showed strain A34a is closely related to two international isolates from Sri Lanka (Ae25) and the USA (RU34A), although there is little to suggest that it was imported from abroad. CONCLUSION This is the first report on the genomic analysis of a novel ST658 A. hydrophilia, offering useful insights into its pathogenicity and global phylogenetics.
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Affiliation(s)
- Yogandree Ramsamy
- Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; National Health Laboratory Service, South Africa; Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Phillip Senzo Mtshali
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | | | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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30
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Ahmeidi AA, Musa A, Ahmed HS, Elahmar AA, Goota RB, Ahmed IA, Ali AH, Allam M, Hassan MO. Inflammatory markers as predictors of mortality in COVID-19 infection. Afr J Lab Med 2020; 9:1298. [PMID: 33392056 PMCID: PMC7756526 DOI: 10.4102/ajlm.v9i1.1298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/07/2020] [Indexed: 01/08/2023] Open
Affiliation(s)
- Awadia A Ahmeidi
- Department Hematology, Faculty of Medical Laboratory Science, University of Science and Technology, Khartoum, Sudan
| | | | - Hend S Ahmed
- Department Hematology and Blood Transfusion, Faculty of Medical Laboratory Science, Omdurman Ahlia University, Khartoum, Sudan
| | - Adel A Elahmar
- Communicable Disease Center, Harmad Medical Corporation, Doha, Qatar
| | | | - Ibtihal A Ahmed
- Faculty of Medical Laboratory Science, Ibn Sina University, Khartoum, Sudan
| | - Abdelhakam H Ali
- Department Microbiology, Faculty of Medical Laboratory Science, University of Al Butana, Rufaa, Sudan
| | - Mushal Allam
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mozan O Hassan
- Department Hematology and Blood Transfusion, Faculty of Medical Laboratory Science, Omdurman Ahlia University, Khartoum, Sudan
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31
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Mubarak A, Mustafa M, Allam M, Babiker A, Mukhtar M. Molecular approaches for identification of Bulinus species from White and Blue Nile, Sudan. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.1279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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32
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Hassan MO, Osman AA, Elbasit HEA, Hassan HE, Rufai H, Satti MMM, Elnegoumi M, Idris R, Musa A, Ali AH, Zroog SA, Altayb ADA, Khairy A, Allam M, Abdelhalim ATI. Convalescent plasma as a treatment modality for coronavirus disease 2019 in Sudan. Transfus Apher Sci 2020; 59:102918. [PMID: 32900597 PMCID: PMC7450236 DOI: 10.1016/j.transci.2020.102918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/28/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a disease spreading rapidly in Sudan, the rest of the African continent and the world with no known definitive treatment or vaccines. However, among many treatment interventions being tested globally, beneficial effects and clinical improvements have been reported when convalescent plasma is used for treating COVID-19 patients. We prepared a guiding protocol for treating early to moderate COVID-19 patients with plasma transfusion from convalescent COVID-19 patients. This protocol was deduced based on previously published reports and studies that evaluated and tested convalescent plasma as a prospective therapy for COVID-19 patients. The protocol covers instructions on patient and donor selection criteria, plasma harvesting, plasma product specifications, dosage and precautions for convalescent plasma collection and transfusion process. Altogether, we prepared a treatment protocol that is tailored to the context of Sudan to be adopted by Sudan's health authority. Moreover, it will also provide reference for researchers to design open label clinical trials for convalescent plasma transfusion.
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Affiliation(s)
- Mozan Osman Hassan
- Faculty of Medical Laboratory Science, Omdurman Ahlia University, Sudan.
| | - Asma Ahmed Osman
- Faculty of Medicine and Health Science, Omdurman Islamic University, Sudan
| | | | | | - Hala Rufai
- National Blood Transfusion Services, Federal Ministry of Health, Sudan
| | - Maria M M Satti
- National Blood Transfusion Services, Federal Ministry of Health, Sudan
| | - Musab Elnegoumi
- Diseases Control Directorate, Federal Ministry of Health, Sudan
| | - Roaa Idris
- University of Wolverhampton, United Kingdom
| | | | - Abdelhakam H Ali
- Faculty of Medical Laboratory Science, University of Al Butana, Sudan
| | - Susan Ali Zroog
- Faculty of Applied Medical Science, University of Al Butana, Sudan
| | | | - Amna Khairy
- Diseases Control Directorate, Federal Ministry of Health, Sudan
| | - Mushal Allam
- National Institute for Communicable Diseases, National Health Laboratory Service, South Africa
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Ismail H, Govender NP, Singh-Moodley A, van Schalkwyk E, Shuping L, Moema I, Feller G, Mogokotleng R, Strasheim W, Lowe M, Mpembe R, Naicker S, Maphanga TG, De Abreu C, Ismail F, Ismail N, Allam M, Ismail A, Singh T, Matuka O, Duba T, Perovic O. An outbreak of cutaneous abscesses caused by Panton-Valentine leukocidin-producing methicillin-susceptible Staphylococcus aureus among gold mine workers, South Africa, November 2017 to March 2018. BMC Infect Dis 2020; 20:621. [PMID: 32831057 PMCID: PMC7446146 DOI: 10.1186/s12879-020-05352-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/16/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND We aimed to describe an outbreak of cutaneous abscesses caused by Panton-Valentine leukocidin (PVL)-producing methicillin-susceptible Staphylococcus aureus (MSSA) among gold mine workers. METHODS In February 2018, we retrospectively reviewed a random sample of 50 medical records from 243 cases and conducted face-to-face interviews using a structured questionnaire. Pus aspirates were sent to the National Institute for Communicable Diseases from prospectively-identified cases (November 2017-March 2018). Nasopharyngeal swabs were collected during a colonisation survey in February 2018. Staphylococcus aureus isolates were screened with a conventional PCR for lukS/F-PV. Pulsed-field gel electrophoresis (PFGE) was performed to determine the genetic relatedness among the isolates. A sample of isolates were selected for whole genome sequencing (WGS). We conducted an assessment on biological risks associated with mining activities. RESULTS From January 2017 to February 2018, 10% (350/3582) of mine workers sought care for cutaneous abscesses. Forty-seven medical files were available for review, 96% were male (n = 45) with a mean age of 43 years (SD = 7). About 52% (24/46) were involved in stoping and 28% (13/47) worked on a particular level. We cultured S. aureus from 79% (30/38) of cases with a submitted specimen and 14% (12/83) from colonisation swabs. All isolates were susceptible to cloxacillin. Seventy-one percent of S. aureus isolates (30/42) were PVL-PCR-positive. Six PFGE clusters were identified, 57% (21/37) were closely related. WGS analysis found nine different sequence types. PFGE and WGS analysis showed more than one cluster of S. aureus infections involving closely related isolates. Test reports for feed and product water of the mine showed that total plate counts were above the limits of 1000 cfu/ml, coliform counts > 10 cfu/100 ml and presence of faecal coliforms. Best practices were poorly implemented as some mine workers washed protective clothing with untreated water and hung them for drying at the underground surface. CONCLUSIONS PVL-producing MSSA caused an outbreak of cutaneous abscesses among underground workers at a gold mining company. To our knowledge, no other outbreaks of PVL-producing S. aureus involving skin and soft tissue infections have been reported in mining facilities in South Africa. We recommend that worker awareness of infection prevention and control practices be strengthened.
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Affiliation(s)
- Husna Ismail
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa.
| | - Nelesh P Govender
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Faculty of Health Sciences, University of Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa
| | - Ashika Singh-Moodley
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Faculty of Health Sciences, University of Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa
| | - Erika van Schalkwyk
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Liliwe Shuping
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Itumeleng Moema
- South African Field Epidemiology Training Programme, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Gal Feller
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Ruth Mogokotleng
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Wilhelmina Strasheim
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Michelle Lowe
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Ruth Mpembe
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Serisha Naicker
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Tsidiso G Maphanga
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Cecilia De Abreu
- Centre for Tuberculosis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Farzana Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Tanusha Singh
- Faculty of Health Sciences, University of Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa.,Immunology and Microbiology, National Institute for Occupational Health, a division of the National Health Laboratory Service, 25 Hospital Street, Constitution Hill, Johannesburg, 2000, South Africa
| | - Onnicah Matuka
- Immunology and Microbiology, National Institute for Occupational Health, a division of the National Health Laboratory Service, 25 Hospital Street, Constitution Hill, Johannesburg, 2000, South Africa
| | - Thabang Duba
- Immunology and Microbiology, National Institute for Occupational Health, a division of the National Health Laboratory Service, 25 Hospital Street, Constitution Hill, Johannesburg, 2000, South Africa
| | - Olga Perovic
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Faculty of Health Sciences, University of Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa
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Owusu-Darko R, Allam M, Ismail A, Ferreira CAS, de Oliveira SD, Buys EM. Comparative Genome Analysis of Bacillus sporothermodurans with Its Closest Phylogenetic Neighbor, Bacillus oleronius, and Bacillus cereus and Bacillus subtilis Groups. Microorganisms 2020; 8:microorganisms8081185. [PMID: 32759699 PMCID: PMC7464528 DOI: 10.3390/microorganisms8081185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/26/2022] Open
Abstract
Bacillus sporothermodurans currently possesses one of the most highly heat-resistant spores (HRS), which can withstand ultra-high temperature (UHT) processing. Determination of multiple whole genome sequences of B. sporothermodurans provided an opportunity to perform the first comparative genome analysis between strains and with B. oleronius, B. cereus, and B. subtilis groups. In this study, five whole genome sequences of B. sporothermodurans strains, including those belonging to the HRS clone (SAD and BR12) normally isolated from UHT milk, were compared with the aforementioned Bacillus species for gene clusters responsible for heat resistance. In the phylogenomic analysis, B. sporothermodurans, with its closest phylogenetic neighbor, B. oleronius, clustered with B. thermoamylovorans and B. thermotolerans. Heat shock proteins GrpE, GroES, GroEL, and DnaK presented identical sequences for all B. sporothermodurans strains, indicating that differences in functional efficiency are not involved in the thermal resistance variations. However, comparing all species evaluated, B. sporothermodurans exhibited a different gene configuration in the chromosomal region of the heat shock protein GrpE. Furthermore, only B. sporothermodurans strains presented the stage II sporulation protein P gene located in this region. Multisequence alignment and phylogenetic analysis of the ClpB protein showed differences for HRS and non-HRS strains. The study identified ClpC, ClpE, and ClpX as the three ATPases putatively involved in protein disaggregation in B. sporothermodurans. Bacillussporothermodurans exhibits high homology with other Bacillus species in the DnaK, DnaJ, GroEL, and GroES cluster of genes involved in heat resistance. The data presented here pave the way to select and evaluate the phenotypic effects of genes putatively involved in heat resistance.
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Affiliation(s)
- Rodney Owusu-Darko
- Department of Consumer and Food Sciences, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa;
| | - Mushal Allam
- National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg 2131, South Africa; (M.A.); (A.I.)
| | - Arshad Ismail
- National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg 2131, South Africa; (M.A.); (A.I.)
| | - Carlos A. S. Ferreira
- Laboratory of Immunology and Microbiology, School of Health and Life Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, Brazil;
| | - Sílvia D. de Oliveira
- Laboratory of Immunology and Microbiology, School of Health and Life Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, Brazil;
- Correspondence: (S.D.d.O.); (E.M.B.)
| | - Elna M. Buys
- Department of Consumer and Food Sciences, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa;
- Correspondence: (S.D.d.O.); (E.M.B.)
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35
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Valley-Omar Z, Cloete A, Pieterse R, Walaza S, Salie-Bassier Y, Smith M, Govender N, Seleka M, Hellferscee O, Mtshali PS, Allam M, Ismail A, Anthony T, Seutloali M, McCarthy K, van Helden L, Cohen C, Treurnicht FK. Human surveillance and phylogeny of highly pathogenic avian influenza A(H5N8) during an outbreak in poultry in South Africa, 2017. Influenza Other Respir Viruses 2020; 14:266-273. [PMID: 32058677 PMCID: PMC7182598 DOI: 10.1111/irv.12724] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/19/2019] [Accepted: 01/15/2020] [Indexed: 12/14/2022] Open
Abstract
Background In June 2017, an outbreak of the highly pathogenic avian influenza A(H5N8) was detected in commercial poultry farms in South Africa, which rapidly spread to all nine South African provinces. Objectives We conducted active surveillance for the transmission of influenza A(H5N8) to humans working with infected birds during the South African outbreak. Methods Influenza A(H5N8)‐positive veterinary specimens were used to evaluate the ability of real‐time PCR‐based assays to detect contemporary avian influenza A(H5N8) strains. Whole genome sequences were generated from these specimens by next‐generation sequencing for phylogenetic characterization and screening for mammalian‐adaptive mutations. Results Human respiratory samples from 74 individuals meeting our case definition, all tested negative for avian influenza A(H5) by real‐time PCR, but 2 (3%) were positive for human influenza A(H3N2). 54% (40/74) reported wearing personal protective equipment including overalls, boots, gloves, masks, and goggles. 94% (59/63) of veterinary specimens positive for H5N8 were detected on an influenza A(H5) assay for human diagnostics. A commercial H5N8 assay detected H5 in only 6% (3/48) and N8 in 92% (44/48). Thirteen (13/25; 52%) A(H5N8) genomes generated from veterinary specimens clustered in a single monophyletic clade. These sequences contained the NS (P42S) and PB2 (L89V) mutations noted as markers of mammalian adaptation. Conclusions Diagnostic assays were able to detect and characterize influenza A(H5N8) viruses, but poor performance is reported for a commercial assay. Absence of influenza A(H5N8) in humans with occupational exposure and no clear impression of molecular adaptation for mammalian infection suggest that this avian pathogen continues to be low‐risk human pathogen.
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Affiliation(s)
- Ziyaad Valley-Omar
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Department of Pathology, Division of Medical Virology, University of Cape Town, South Africa
| | - Alicia Cloete
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Reneé Pieterse
- Department of Agriculture, Western Cape Provincial Veterinary Laboratory, Stellenbosch, South Africa
| | - Sibongile Walaza
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Yusrah Salie-Bassier
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mikhail Smith
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nevashan Govender
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mpho Seleka
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Orienka Hellferscee
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Phillip Senzo Mtshali
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Tasneem Anthony
- Department of Agriculture, Western Cape Provincial Veterinary Laboratory, Stellenbosch, South Africa
| | - Michelle Seutloali
- Department of Agriculture, Western Cape Provincial Veterinary Laboratory, Stellenbosch, South Africa
| | - Kerrigan McCarthy
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Lesley van Helden
- Veterinary Services, Western Cape Department of Agriculture, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Florette Kathleen Treurnicht
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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36
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Thomas J, Govender N, McCarthy KM, Erasmus LK, Doyle TJ, Allam M, Ismail A, Ramalwa N, Sekwadi P, Ntshoe G, Shonhiwa A, Essel V, Tau N, Smouse S, Ngomane HM, Disenyeng B, Page NA, Govender NP, Duse AG, Stewart R, Thomas T, Mahoney D, Tourdjman M, Disson O, Thouvenot P, Maury MM, Leclercq A, Lecuit M, Smith AM, Blumberg LH. Outbreak of Listeriosis in South Africa Associated with Processed Meat. N Engl J Med 2020; 382:632-643. [PMID: 32053299 PMCID: PMC7301195 DOI: 10.1056/nejmoa1907462] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND An outbreak of listeriosis was identified in South Africa in 2017. The source was unknown. METHODS We conducted epidemiologic, trace-back, and environmental investigations and used whole-genome sequencing to type Listeria monocytogenes isolates. A case was defined as laboratory-confirmed L. monocytogenes infection during the period from June 11, 2017, to April 7, 2018. RESULTS A total of 937 cases were identified, of which 465 (50%) were associated with pregnancy; 406 of the pregnancy-associated cases (87%) occurred in neonates. Of the 937 cases, 229 (24%) occurred in patients 15 to 49 years of age (excluding those who were pregnant). Among the patients in whom human immunodeficiency virus (HIV) status was known, 38% of those with pregnancy-associated cases (77 of 204) and 46% of the remaining patients (97 of 211) were infected with HIV. Among 728 patients with a known outcome, 193 (27%) died. Clinical isolates from 609 patients were sequenced, and 567 (93%) were identified as sequence type 6 (ST6). In a case-control analysis, patients with ST6 infections were more likely to have eaten polony (a ready-to-eat processed meat) than those with non-ST6 infections (odds ratio, 8.55; 95% confidence interval, 1.66 to 43.35). Polony and environmental samples also yielded ST6 isolates, which, together with the isolates from the patients, belonged to the same core-genome multilocus sequence typing cluster with no more than 4 allelic differences; these findings showed that polony produced at a single facility was the outbreak source. A recall of ready-to-eat processed meat products from this facility was associated with a rapid decline in the incidence of L. monocytogenes ST6 infections. CONCLUSIONS This investigation showed that in a middle-income country with a high prevalence of HIV infection, L. monocytogenes caused disproportionate illness among pregnant girls and women and HIV-infected persons. Whole-genome sequencing facilitated the detection of the outbreak and guided the trace-back investigations that led to the identification of the source.
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Affiliation(s)
- Juno Thomas
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Nevashan Govender
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Kerrigan M McCarthy
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Linda K Erasmus
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Timothy J Doyle
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Mushal Allam
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Arshad Ismail
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Ntsieni Ramalwa
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Phuti Sekwadi
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Genevie Ntshoe
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Andronica Shonhiwa
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Vivien Essel
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Nomsa Tau
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Shannon Smouse
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Hlengiwe M Ngomane
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Bolele Disenyeng
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Nicola A Page
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Nelesh P Govender
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Adriano G Duse
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Rob Stewart
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Teena Thomas
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Deon Mahoney
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Mathieu Tourdjman
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Olivier Disson
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Pierre Thouvenot
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Mylène M Maury
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Alexandre Leclercq
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Marc Lecuit
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Anthony M Smith
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
| | - Lucille H Blumberg
- From the Centre for Enteric Diseases (J.T., N.R., P.S., N.T., S.S., H.M.N., B.D., N.A.P., A.M.S.), the Division of Public Health Surveillance and Response (N.G., K.M.M., L.K.E., G.N., A.S., V.E., L.H.B.), the Sequencing Core Facility (M.A., A.I.), and the Centre for Healthcare-Associated Infections and Antimicrobial Resistance (N.P.G.), National Institute for Communicable Diseases, National Health Laboratory Service, the University of the Witwatersrand (K.M.M., N.P.G., A.G.D., T.T., A.M.S.), and the School of Pathology, National Health Laboratory Service (A.G.D., R.S., T.T.), Johannesburg, the Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Pretoria (T.J.D.), the University of Pretoria, Tshwane (N.R., G.N., N.A.P.), and the University of Stellenbosch, Stellenbosch (L.H.B.) - all in South Africa; Deon Mahoney Consulting, Melbourne, VIC, Australia (D.M.); and Santé Publique France, the French Public Health Agency, Saint-Maurice (M.T.), and Institut Pasteur, Biology of Infection Unit, INSERM Unité 1117 and National Reference Center-WHO Collaborating Center for Listeria (O.D., P.T., M.M.M., A.L., M.L.), and Université de Paris, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Institut Imagine (M.L.), Paris - all in France
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Ramsamy Y, Mlisana KP, Amoako DG, Allam M, Ismail A, Singh R, Abia ALK, Essack SY. Pathogenomic Analysis of a Novel Extensively Drug-Resistant Citrobacter freundii Isolate Carrying a bla NDM-1 Carbapenemase in South Africa. Pathogens 2020; 9:pathogens9020089. [PMID: 32024012 PMCID: PMC7168644 DOI: 10.3390/pathogens9020089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
Pathogenomic analysis was performed on a novel carbapenem-resistant Citrobacter freundii isolate (H2730R) from a rectal swab of an adult male patient admitted to a tertiary hospital, Durban, South Africa. H2730R was identified using selective media and API 20e kit. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK II. H2730R was whole-genome sequenced on the Illumina MiSeq platform. H2730R was resistant to all tested antibiotics except tigecycline and was defined as ST498 by the C. freundii multilocus sequence typing (MLST) database. The estimated pathogenic potential predicted a higher probability (Pscore ≈ 0.875), supporting H2730R as a human pathogen. H2730R harbored 25 putative acquired resistance genes, 4 plasmid replicons, 4 intact prophages, a class 1 integron (IntI1), 2 predominant insertion sequences (IS3 and IS5), numerous efflux genes, and virulome. BLASTn analysis of the blaNDM-1 encoding contig (00022) and its flanking sequences revealed the blaNDM-1 was located on a plasmid similar to the multireplicon p18-43_01 plasmid reported for the spread of carbapenem resistance in South Africa. Phylogenomic analysis showed clustering of H2730R with CF003/CF004 strains in the same clade, suggesting a possible association between C. freundii strains/clones. Acquiring the p18-43_01 plasmid containing blaNDM-1, the diversity, and complex resistome, virulome, and mobilome of this pathogen makes its incidence very worrying regarding mobilized resistance. This study presents the background genomic information for future surveillance and tracking of the spread of carbapenem-resistant Enterobacteriaceae in South Africa.
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Affiliation(s)
- Yogandree Ramsamy
- Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
- National Health Laboratory Services, Durban 4000, South Africa;
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.L.K.A.); (S.Y.E.)
- Correspondence:
| | | | - Daniel G. Amoako
- Infection Genomics and Applied Bioinformatics Division, Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa; (M.A.); (A.I.)
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa; (M.A.); (A.I.)
| | - Ravesh Singh
- Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
- National Health Laboratory Services, Durban 4000, South Africa;
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.L.K.A.); (S.Y.E.)
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.L.K.A.); (S.Y.E.)
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Ramsamy Y, Mlisana KP, Allam M, Amoako DG, Abia ALK, Ismail A, Singh R, Kisten T, Swe Han KS, Muckart DJJ, Hardcastle T, Suleman M, Essack SY. Genomic Analysis of Carbapenemase -Producing Extensively Drug-Resistant Klebsiella pneumoniae Isolates Reveals the Horizontal Spread of p18-43_01 Plasmid Encoding blaNDM-1 in South Africa. Microorganisms 2020; 8:microorganisms8010137. [PMID: 31963608 PMCID: PMC7023316 DOI: 10.3390/microorganisms8010137] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/11/2020] [Accepted: 01/17/2020] [Indexed: 12/12/2022] Open
Abstract
Whole-genome sequence (WGS) analyses were employed to investigate the genomic epidemiology of extensively drug-resistant Klebsiella pneumoniae strains, focusing on the carbapenem resistance-encoding determinants, mobile genetic support, clonal and epidemiological relationships. A total of ten isolates were obtained from patients admitted to the intensive care unit (ICU) in a public hospital in South Africa. Five isolates were from rectal swabs of colonized patients and five from blood cultures of patients with invasive carbapenem-resistant infections. Following microbial identification and antibiotic susceptibility tests, the isolates were subjected to WGS on the Illumina MiSeq platform. All the isolates showed genotypic resistance to tested β-lactams (NDM-1, OXA-1, CTX-M-15, TEM-1B, SHV-1) and other antibiotics. All but one isolate belonged to the ST152 with a novel sequence type, ST3136, differing by a single-locus variant. The isolates had the same plasmid multilocus sequence type (IncF[K12:A-:B36]) and capsular serotype (KL149), supporting the epidemiological linkage between the clones. Resistance to carbapenems in the 10 isolates was conferred by the blaNDM-1 mediated by the acquisition of multi-replicon [ColRNAI, IncFIB(pB171), Col440I, IncFII, IncFIB(K) and IncFII(Yp)] p18-43_01 plasmid. These findings suggest that the acquisition of blaNDM-1-bearing plasmid structure (p18-43_01), horizontal transfer and clonal dissemination facilitate the spread of carbapenemases in South Africa. This emphasizes the importance of targeted infection control measures to prevent dissemination.
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Affiliation(s)
- Yogandree Ramsamy
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.L.K.A.); (S.Y.E.)
- Medical Microbiology, National Health Laboratory Services, Durban 4000, South Africa; (K.P.M.); (R.S.)
- Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Correspondence: (Y.R.); (D.G.A.)
| | - Koleka P. Mlisana
- Medical Microbiology, National Health Laboratory Services, Durban 4000, South Africa; (K.P.M.); (R.S.)
- Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa; (M.A.); (A.I.)
| | - Daniel G. Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.L.K.A.); (S.Y.E.)
- Correspondence: (Y.R.); (D.G.A.)
| | - Akebe L. K. Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.L.K.A.); (S.Y.E.)
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa; (M.A.); (A.I.)
| | - Ravesh Singh
- Medical Microbiology, National Health Laboratory Services, Durban 4000, South Africa; (K.P.M.); (R.S.)
- Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Theroshnie Kisten
- School of Clinical Medicine, Discipline of Anaesthetics & Critical Care, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
- Inkosi Albert Luthuli Central Hospital, Department of Critical Care, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Khine Swe Swe Han
- Medical Microbiology, National Health Laboratory Services, Durban 4000, South Africa; (K.P.M.); (R.S.)
- Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - David J. Jackson Muckart
- Inkosi Albert Luthuli Central Hospital, Department of Surgery & Trauma Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (D.J.J.M.); (T.H.)
| | - Timothy Hardcastle
- Inkosi Albert Luthuli Central Hospital, Department of Surgery & Trauma Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (D.J.J.M.); (T.H.)
| | - Moosa Suleman
- Ahmed Al-Kadi Private Hospital, Durban 4000, South Africa;
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.L.K.A.); (S.Y.E.)
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Schneider C, Thompson S, Totz J, Song Y, Allam M, Sodergren MH, Desjardins AE, Barratt D, Ourselin S, Gurusamy K, Stoyanov D, Clarkson MJ, Hawkes DJ, Davidson BR. Comparison of manual and semi-automatic registration in augmented reality image-guided liver surgery: a clinical feasibility study. Surg Endosc 2020; 34:4702-4711. [PMID: 32780240 PMCID: PMC7524854 DOI: 10.1007/s00464-020-07807-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND The laparoscopic approach to liver resection may reduce morbidity and hospital stay. However, uptake has been slow due to concerns about patient safety and oncological radicality. Image guidance systems may improve patient safety by enabling 3D visualisation of critical intra- and extrahepatic structures. Current systems suffer from non-intuitive visualisation and a complicated setup process. A novel image guidance system (SmartLiver), offering augmented reality visualisation and semi-automatic registration has been developed to address these issues. A clinical feasibility study evaluated the performance and usability of SmartLiver with either manual or semi-automatic registration. METHODS Intraoperative image guidance data were recorded and analysed in patients undergoing laparoscopic liver resection or cancer staging. Stereoscopic surface reconstruction and iterative closest point matching facilitated semi-automatic registration. The primary endpoint was defined as successful registration as determined by the operating surgeon. Secondary endpoints were system usability as assessed by a surgeon questionnaire and comparison of manual vs. semi-automatic registration accuracy. Since SmartLiver is still in development no attempt was made to evaluate its impact on perioperative outcomes. RESULTS The primary endpoint was achieved in 16 out of 18 patients. Initially semi-automatic registration failed because the IGS could not distinguish the liver surface from surrounding structures. Implementation of a deep learning algorithm enabled the IGS to overcome this issue and facilitate semi-automatic registration. Mean registration accuracy was 10.9 ± 4.2 mm (manual) vs. 13.9 ± 4.4 mm (semi-automatic) (Mean difference - 3 mm; p = 0.158). Surgeon feedback was positive about IGS handling and improved intraoperative orientation but also highlighted the need for a simpler setup process and better integration with laparoscopic ultrasound. CONCLUSION The technical feasibility of using SmartLiver intraoperatively has been demonstrated. With further improvements semi-automatic registration may enhance user friendliness and workflow of SmartLiver. Manual and semi-automatic registration accuracy were comparable but evaluation on a larger patient cohort is required to confirm these findings.
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Affiliation(s)
- C. Schneider
- Division of Surgery & Interventional Science, Royal Free Campus, University College London, Pond Street, London, NW3 2QG UK
| | - S. Thompson
- Wellcome / EPSRC Centre for Surgical and Interventional Sciences (WEISS), University College London, London, UK ,Centre for Medical Image Computing (CMIC), University College London, London, UK ,Department of Medical Physics and Bioengineering, University College London, London, UK
| | - J. Totz
- Wellcome / EPSRC Centre for Surgical and Interventional Sciences (WEISS), University College London, London, UK ,Centre for Medical Image Computing (CMIC), University College London, London, UK ,Department of Medical Physics and Bioengineering, University College London, London, UK
| | - Y. Song
- Wellcome / EPSRC Centre for Surgical and Interventional Sciences (WEISS), University College London, London, UK ,Centre for Medical Image Computing (CMIC), University College London, London, UK ,Department of Medical Physics and Bioengineering, University College London, London, UK
| | - M. Allam
- Division of Surgery & Interventional Science, Royal Free Campus, University College London, Pond Street, London, NW3 2QG UK
| | - M. H. Sodergren
- Centre for Medical Image Computing (CMIC), University College London, London, UK
| | - A. E. Desjardins
- Wellcome / EPSRC Centre for Surgical and Interventional Sciences (WEISS), University College London, London, UK ,Department of Medical Physics and Bioengineering, University College London, London, UK
| | - D. Barratt
- Wellcome / EPSRC Centre for Surgical and Interventional Sciences (WEISS), University College London, London, UK ,Centre for Medical Image Computing (CMIC), University College London, London, UK ,Department of Medical Physics and Bioengineering, University College London, London, UK
| | - S. Ourselin
- Wellcome / EPSRC Centre for Surgical and Interventional Sciences (WEISS), University College London, London, UK ,Centre for Medical Image Computing (CMIC), University College London, London, UK ,Department of Medical Physics and Bioengineering, University College London, London, UK
| | - K. Gurusamy
- Division of Surgery & Interventional Science, Royal Free Campus, University College London, Pond Street, London, NW3 2QG UK ,Wellcome / EPSRC Centre for Surgical and Interventional Sciences (WEISS), University College London, London, UK ,Department of Hepatopancreatobiliary and Liver Transplant Surgery, Royal Free Hospital, London, UK
| | - D. Stoyanov
- Wellcome / EPSRC Centre for Surgical and Interventional Sciences (WEISS), University College London, London, UK ,Centre for Medical Image Computing (CMIC), University College London, London, UK ,Department of Computer Science, University College London, London, UK
| | - M. J. Clarkson
- Wellcome / EPSRC Centre for Surgical and Interventional Sciences (WEISS), University College London, London, UK ,Centre for Medical Image Computing (CMIC), University College London, London, UK ,Department of Medical Physics and Bioengineering, University College London, London, UK
| | - D. J. Hawkes
- Wellcome / EPSRC Centre for Surgical and Interventional Sciences (WEISS), University College London, London, UK ,Centre for Medical Image Computing (CMIC), University College London, London, UK ,Department of Medical Physics and Bioengineering, University College London, London, UK
| | - B. R. Davidson
- Division of Surgery & Interventional Science, Royal Free Campus, University College London, Pond Street, London, NW3 2QG UK ,Wellcome / EPSRC Centre for Surgical and Interventional Sciences (WEISS), University College London, London, UK ,Department of Hepatopancreatobiliary and Liver Transplant Surgery, Royal Free Hospital, London, UK
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Founou RC, Founou LL, Allam M, Ismail A, Essack SY. Draft genome sequence of a clinical Acinetobacter haemolyticus isolate from South Africa. J Glob Antimicrob Resist 2019; 20:16-17. [PMID: 31655135 DOI: 10.1016/j.jgar.2019.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 10/07/2019] [Accepted: 10/15/2019] [Indexed: 10/25/2022] Open
Abstract
OBJECTIVES Here we describe the draft genome sequence of a clinical Acinetobacter haemolyticus isolate (A109R1B4) from a rectal swab of a hospitalised patient in South Africa. METHODS Genomic DNA from the isolate was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using Qiagen CLC Genomics Workbench. The assembled contigs were annotated and antimicrobial resistance genes and sequence type were identified. RESULTS The genome comprised 281 contigs with a total assembly length of 3 371 389bp, a G+C content of 39.9% and an N50 value of 58 196bp, and reference coverage was 93.08 while the coverage was 88.08. A total of 3387 genes, 3292 coding sequences (CDS), 3175 coding genes and 95 RNA genes were detected. The antimicrobial resistance genes blaOXA-264 and aac(6')-Ig were detected. CONCLUSION The genome sequence reported will serve as a reference point for molecular epidemiological studies of antibiotic-resistant A. haemolyticus in Africa.
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Affiliation(s)
- Raspail Carrel Founou
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Clinical Microbiology, Centre of Expertise and Biological Diagnostic of Cameroon (CEDBCAM), Yaoundéé, Cameroon.
| | - Luria Leslie Founou
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Food Safety and Environmental Health, Centre of Expertise and Biological Diagnostic of Cameroon (CEDBCAM), Yaoundé, Cameroon
| | - Mushal Allam
- National Institute for Communicable Diseases Sequencing Core Facility, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Arshad Ismail
- National Institute for Communicable Diseases Sequencing Core Facility, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Mohale T, Wolter N, Allam M, Nzenze SA, Madhi SA, du Plessis M, von Gottberg A. Genomic differences among carriage and invasive nontypeable pneumococci circulating in South Africa. Microb Genom 2019; 5. [PMID: 31617841 PMCID: PMC6861859 DOI: 10.1099/mgen.0.000299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Most pneumococci express a polysaccharide capsule, a key virulence factor and target for pneumococcal vaccines. However, pneumococci showing no serological evidence of capsule expression [nontypeable pneumococci (NTPn)] are more frequently isolated from carriage studies than in invasive disease. Limited data exist about the population structure of carriage NTPn from the African continent. We aimed to characterize carriage NTPn and compare them to previously described invasive NTPn. Carriage and invasive NTPn isolates were obtained from South African cross-sectional studies (2009 and 2012) and laboratory-based surveillance for invasive pneumococcal disease (2003–2013), respectively. Isolates were characterized by capsular locus sequence analysis, multilocus sequence typing, antimicrobial non-susceptibility patterns and phylogenetic analysis. NTPn represented 3.7 % (137/3721) of carriage isolates compared to 0.1 % (39/32 824) of invasive isolates (P<0.001), and 24 % (33/137) of individuals were co-colonized with encapsulated pneumococci. Non-susceptibility to cotrimoxazole [84 % (112/133) vs 44 % (17/39)], penicillin [77 % (102/133) vs 36 % (14/39)], erythromycin [53 % (70/133) vs 31 % (12/39)] and clindamycin [36 % (48/133) vs 18 % (7/39)] was higher (P=0.03) among carriage than invasive NTPn. Ninety-one per cent (124/137) of carriage NTPn had complete deletion of the capsular locus and 9 % (13/137) had capsule genes, compared to 44 % (17/39) and 56 % (22/39) of invasive NTPn, respectively. Carriage NTPn were slightly less diverse [Simpson’s diversity index (D)=0.92] compared to invasive NTPn [D=0.97]. Sixty-seven per cent (92/137) of carriage NTPn belonged to a lineage exclusive to NTPn strains compared to 23 % (9/39) of invasive NTPn. We identified 293 and 275 genes that were significantly associated with carriage and invasive NTPn, respectively. NTPn isolates detected in carriage differed from those causing invasive disease, which may explain their success in colonisation or in causing invasive disease.
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Affiliation(s)
- Thabo Mohale
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Susan A Nzenze
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Research Chair, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Research Chair, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Anne von Gottberg
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
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Youssef G, Mekkawy D, El-Fayoumy N, Abbas A, Allam M. P1817Assessment of carotid stiffness indices in patients with ischemic stroke. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz748.0569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Arterial stiffness is considered as an emerging new important risk factor for stoke development. Measuring carotid stiffness is easy and non-invasive and thus can be widely applicable.
Purpose
To evaluate the carotid stiffness indices in patients with ischemic stroke compared to normal healthy subjects.
Methods
Included in this study are 60 patients (group 1) with ischemic stroke and 60 healthy control subjects (group 2). Participants were exposed to routine clinical examination and Duplex assessment of both carotid arteries. A specific wall tracking system was used for the semiautomatic calculation of the carotid stiffness indices, which included; compliance coefficient (CC), distensibility coefficient (DC), carotid pulse wave velocity (PWV) and carotid intima media thickness (IMT). Results from both carotid arteries were averaged and data from group 1 patients were compared to group 2 subjects.
Results
The mean age was (60.1±6.9 years) in group 1 compared to (60.1±6.6 years) in group 2 (p=0.9). A significant difference was found between both groups in all carotid stiffness indices; including average CC (0.64±0.29 vs 0.82±0.36 m2/kpa, p=0.004); average DC (11.69±5.42 vs 18.61±11.87 1/kpa, p<0.001); average PWV (16.5±0.6 vs 12.5±3.7 m/s, p<0.001) and average IMT (0.78±0.13 vs 0.68±0.18 mm, p=0.001). Only the carotid PWV was found to be a predictor of vascular stroke (p=0.001)
Conclusion
Patients with vascular stroke have higher carotid stiffness indices than age matched control subjects. Measuring carotid stiffness indices in patients who have atherosclerotic risk factors may help predict those at risk of vascular stroke and thus guide a tighter and a more efficient risk factors control.
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Affiliation(s)
- G Youssef
- Cairo University Hospitals, CardioVascular Department, Cairo, Egypt
| | - D Mekkawy
- Cairo University Hospitals, Neurology Department, Cairo, Egypt
| | - N El-Fayoumy
- Cairo University Hospitals, Neurology Department, Cairo, Egypt
| | - A Abbas
- Cairo University Hospitals, Neurology Department, Cairo, Egypt
| | - M Allam
- Cairo University Hospitals, Neurology Department, Cairo, Egypt
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Amoako DG, Somboro AM, Abia ALK, Allam M, Ismail A, Bester LA, Essack SY. Genome Mining and Comparative Pathogenomic Analysis of An Endemic Methicillin-Resistant Staphylococcus Aureus (MRSA) Clone, ST612-CC8-t1257-SCCmec_IVd(2B), Isolated in South Africa. Pathogens 2019; 8:E166. [PMID: 31569754 PMCID: PMC6963616 DOI: 10.3390/pathogens8040166] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/19/2022] Open
Abstract
This study undertook genome mining and comparative genomics to gain genetic insights into the dominance of the methicillin-resistant Staphylococcus aureus (MRSA) endemic clone ST612-CC8-t1257-SCCmec_IVd(2B), obtained from the poultry food chain in South Africa. Functional annotation of the genome revealed a vast array of similar central metabolic, cellular and biochemical networks within the endemic clone crucial for its survival in the microbial community. In-silico analysis of the clone revealed the possession of uniform defense systems, restriction-modification system (type I and IV), accessory gene regulator (type I), arginine catabolic mobile element (type II), and type 1 clustered, regularly interspaced, short palindromic repeat (CRISPR)Cas array (N = 7 ± 1), which offer protection against exogenous attacks. The estimated pathogenic potential predicted a higher probability (average Pscore ≈ 0.927) of the clone being pathogenic to its host. The clone carried a battery of putative virulence determinants whose expression are critical for establishing infection. However, there was a slight difference in their possession of adherence factors (biofilm operon system) and toxins (hemolysins and enterotoxins). Further analysis revealed a conserved environmental tolerance and persistence mechanisms related to stress (oxidative and osmotic), heat shock, sporulation, bacteriocins, and detoxification, which enable it to withstand lethal threats and contribute to its success in diverse ecological niches. Phylogenomic analysis with close sister lineages revealed that the clone was closely related to the MRSA isolate SHV713 from Australia. The results of this bioinformatic analysis provide valuable insights into the biology of this endemic clone.
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Affiliation(s)
- Daniel Gyamfi Amoako
- Infection Genomics and Applied Bioinformatics Division, Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal; Durban 4000, South Africa.
| | - Anou M Somboro
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal; Durban 4000, South Africa.
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa.
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa.
| | - Linda A Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal; Durban 4000, South Africa.
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
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Smith AM, Tau NP, Kalule BJ, Nicol MP, McCulloch M, Jacobs CA, McCarthy KM, Ismail A, Allam M, Kleynhans J. Shiga toxin-producing Escherichia coli O26:H11 associated with a cluster of haemolytic uraemic syndrome cases in South Africa, 2017. Access Microbiol 2019; 1:e000061. [PMID: 32974561 PMCID: PMC7472548 DOI: 10.1099/acmi.0.000061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/22/2019] [Indexed: 01/17/2023] Open
Abstract
INTRODUCTION Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens that may cause diarrhoeal outbreaks and occasionally are associated with haemolytic-uraemic syndrome (HUS). We report on STEC O26:H11 associated with a cluster of four HUS cases in South Africa in 2017. METHODOLOGY All case-patients were female and aged 5 years and under. Standard microbiological tests were performed for culture and identification of STEC from specimens (human stool and food samples). Further analysis of genomic DNA extracted from bacterial cultures and specimens included PCR for specific virulence genes, whole-genome sequencing and shotgun metagenomic sequencing. RESULTS For 2/4 cases, stool specimens revealed STEC O26:H11 containing eae, stx2a and stx2b virulence genes. All food samples were found to be negative for STEC. No epidemiological links could be established between the HUS cases. Dried meat products were the leading food item suspected to be the vehicle of transmission for these cases, as 3/4 case-patients reported they had eaten this. However, testing of dried meat products could not confirm this. CONCLUSION Since STEC infection does not always lead to severe symptoms, it is possible that many more cases were associated with this cluster and largely went unrecognized.
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Affiliation(s)
- Anthony M. Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nomsa P. Tau
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Bosco J. Kalule
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P. Nicol
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Mignon McCulloch
- Red Cross Children’s Hospital, University of Cape Town, Cape Town, South Africa
| | - Charlene A. Jacobs
- Communicable Disease Control, Department of Health, Cape Town, South Africa
| | - Kerrigan M. McCarthy
- Division of Public Health Surveillance and Response, NICD, NHLS, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, NICD, NHLS, Johannesburg, South Africa
| | - Mushal Allam
- Sequencing Core Facility, NICD, NHLS, Johannesburg, South Africa
| | - Jackie Kleynhans
- South African Field Epidemiology Training Programme, NICD, NHLS, Johannesburg, South Africa
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Agyepong N, Govinden U, Owusu-Ofori A, Amoako DG, Allam M, Janice J, Pedersen T, Sundsfjord A, Essack S. Genomic characterization of multidrug-resistant ESBL-producing Klebsiella pneumoniae isolated from a Ghanaian teaching hospital. Int J Infect Dis 2019; 85:117-123. [DOI: 10.1016/j.ijid.2019.05.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/13/2019] [Accepted: 05/20/2019] [Indexed: 10/26/2022] Open
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Amoako DG, Somboro AM, Abia ALK, Allam M, Ismail A, Bester L, Essack SY. Genomic analysis of methicillin-resistant Staphylococcus aureus isolated from poultry and occupational farm workers in Umgungundlovu District, South Africa. Sci Total Environ 2019; 670:704-716. [PMID: 30909047 DOI: 10.1016/j.scitotenv.2019.03.110] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
This study detected methicillin-resistant Staphylococcus aureus (MRSA) isolates circulating in poultry and farm workers at an intensive poultry production system in uMgungundlovu, South Africa and established the genetic relatedness and characteristics of the isolates using whole genome sequencing (WGS). A total of 145 S. aureus were isolated from poultry (120) and occupational workers (25) in the "farm to fork" continuum (farm, transport, slaughterhouse, and retail points). Twelve MRSA (12/145; 8.3%) isolates were found in the poultry food-chain. MRSA isolates were subjected to antibiotic susceptibility testing against a panel of 20 antibiotics using the broth dilution method and their whole genome was sequenced via the Illumina MiSeq. All the MRSA isolates were multi-drug resistant (MDR) and carried the mecA gene on the SCCmec mobile genetic element (MGE). The majority (11/12) of the MRSA isolates circulating between humans and animals in the continuum belonged to a human-associated clone, ST612-CC8-t1257-SCCmec_IVd (2B), previously reported in South Africa. Other MGEs present in the isolates included: plasmid replicons based on Rep 7 and 20, insertion sequences (IS1182), and prophages (phi2958PVL). Genomic analysis identified a distinct acquired antibiotic resistome in the clone, which accurately predicted the phenotypic antibiograms. Phylogenetic analysis clustered the isolates within the major cluster (I), suggesting the spread of the local dominant multidrug resistance MRSA clone ST612-CC8-t1257-SCCmec_IVd (2B) between humans and animals along the 'farm to fork' continuum. The findings of this study suggest the need to establish appropriate control measures to curb the spread of MDR-MRSA in the food chain.
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Affiliation(s)
- Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Anou Moise Somboro
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Pretoria, South Africa.
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Pretoria, South Africa.
| | - Linda Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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Founou LL, Founou RC, Allam M, Ismail A, Finyom Djoko C, Essack SY. Genome analysis of methicillin-resistant Staphylococcus aureus isolated from pigs: Detection of the clonal lineage ST398 in Cameroon and South Africa. Zoonoses Public Health 2019; 66:512-525. [PMID: 31124311 DOI: 10.1111/zph.12586] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/28/2019] [Accepted: 05/05/2019] [Indexed: 01/16/2023]
Abstract
Food animals are considered reservoirs of methicillin-resistant Staphylococcus aureus (MRSA) and are implicated in their zoonotic transmission in the farm-to-plate continuum. LA-MRSA has been reported as a zoonotic agent that has the potential to spread to humans and may cause infections in at-risk groups. In this study, whole genome sequencing was used to describe the genetic environment (resistance mechanisms, virulence factors and mobile genetic elements) and investigate the genetic lineages of MRSA isolates from pigs in Cameroonian and South African abattoirs. During March-October 2016, 288 nasal and rectal pooled samples from 432 pigs as well as nasal and hand swabs from 82 humans were collected. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were de novo-assembled using the Qiagen CLC Genomics Workbench and SPAdes. The assembled contigs were annotated, and antibiotic resistance genes, virulence factors, plasmids, SCCmec and phage elements were identified with ResFinder, Virulence Finder, PlasmidFinder, SCCmec Finder and PHAST, respectively. Core genome single nucleotide analysis was undertaken to assess clonal relatedness among isolates. A lower MRSA prevalence was observed in pigs in Cameroon (n = 1/13; 0.07%) compared with South Africa (n = 4/22; 18.18%), and none of the workers were colonized by MRSA. Genome analysis identified various antibiotic resistance genes along with six virulence factors in all isolates. All MRSA isolates belonged to the clonal lineage ST398 (spa-type t011) and harboured the type Vc SCCmec and several plasmids. Our study shows that the livestock-associated MRSA clonal lineage ST398 is already present in both Cameroon and South Africa and is probably underestimated in the absence of molecular epidemiological studies. It reveals the serious food safety and public health threat associated with this animal strain and underscores the need for interventions to contain this resistant clone.
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Affiliation(s)
- Luria Leslie Founou
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Department of Food Safety and Environmental Microbiology, Centre of Expertise and Biological Diagnostic of Cameroon, Yaoundé, Cameroon
| | - Raspail Carrel Founou
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Department of Clinical Microbiology, Centre of Expertise and Biological Diagnostic of Cameroon, Yaoundé, Cameroon
| | - Mushal Allam
- Sequencing Core Facility, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Health Laboratory Service, Johannesburg, South Africa
| | - Cyrille Finyom Djoko
- Metabiota Inc., Yaoundé, Cameroon.,Centre for Research and Doctoral Training in Life Science, Health and Environment, The Biotechnology Centre, University of Yaoundé I, Yaoundé, Cameroon
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Smith AM, Tau NP, Smouse SL, Allam M, Ismail A, Ramalwa NR, Disenyeng B, Ngomane M, Thomas J. Outbreak of Listeria monocytogenes in South Africa, 2017-2018: Laboratory Activities and Experiences Associated with Whole-Genome Sequencing Analysis of Isolates. Foodborne Pathog Dis 2019; 16:524-530. [PMID: 31062992 PMCID: PMC6653791 DOI: 10.1089/fpd.2018.2586] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In South Africa, a progressive increase in listeriosis cases was noted from mid-June 2017, heralding what was to become the world's largest listeriosis outbreak. A total of 1060 cases were reported for the period January 1, 2017 to July 17, 2018. We describe laboratory activities, experiences, and results of whole-genome sequencing (WGS) analysis of Listeria monocytogenes isolates associated with this outbreak. Bacteria were identified using the VITEK-2 COMPACT 15 microbial identification system. WGS was performed using Illumina MiSeq technology. WGS data were analyzed using CLC Genomics Workbench Software and free-to-use on-line analysis tools/pipelines. Multilocus sequence typing (MLST) showed that 91% of clinical isolates were sequence type 6 (ST6), determining that the outbreak was largely associated with L. monocytogenes ST6. Epidemiological and laboratory findings led to investigation of a large ready-to-eat processed meat production facility in South Africa, named Enterprise Foods. L. monocytogenes ST6 was found in environmental sampling swabs of the production facility and in ready-to-eat processed meat products (including polony, a product similar to bologna sausage) manufactured at the facility. ST6 isolates, sourced at the Enterprise Foods production facility and from Enterprise food products, were shown by single nucleotide polymorphism (SNP) analysis to be highly related to clinical isolates; these nonclinical ST6 isolates showed <10 SNP differences when compared to clinical ST6 isolates. Core-genome MLST showed that clinical ST6 isolates and Enterprise-related ST6 isolates had no more than 4 allele differences between each other, suggestive of a high probability of epidemiological relatedness. WGS data interpreted together with epidemiological data concluded that the source of the listeriosis outbreak was ready-to-eat processed meat products manufactured by Enterprise Foods. Listeriosis has now been added to the South African list of mandatory notifiable medical conditions. Surveillance systems have been strengthened to facilitate prevention and early detection of listeriosis outbreaks.
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Affiliation(s)
- Anthony M Smith
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa.,2 Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nomsa P Tau
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Shannon L Smouse
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- 3 Sequencing Core Facility, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- 3 Sequencing Core Facility, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ntsieni R Ramalwa
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Bolele Disenyeng
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mimmy Ngomane
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Juno Thomas
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa.,2 Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Founou LL, Founou RC, Allam M, Ismail A, Essack SY. Draft genome sequence of a methicillin-resistant Staphylococcus epidermidis isolate from swine. J Glob Antimicrob Resist 2018; 15:250-251. [PMID: 30366149 DOI: 10.1016/j.jgar.2018.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/04/2018] [Accepted: 10/14/2018] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES Here we report the draft genome sequence of a methicillin-resistant Staphylococcus epidermidis strain (sequence type 59) isolated from a pooled rectal sample from pigs collected in an abattoir in South Africa. METHODS Genomic DNA of S. epidermidis PR246B0 was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using CLC Genomics Workbench (QIAGEN). The assembled contigs were annotated and antimicrobial resistance genes, plasmids and the sequence type were identified. RESULTS The genome comprised a circular chromosome of 2537769bp, with a G-C content of 32.32% and various antimicrobial resistance genes associated with resistance to β-lactams, fluoroquinolones, aminoglycosides, fosfomycin, macrolides, lincosamides and tetracycline. Genome analysis also revealed the presence of seven plasmid replicon types. CONCLUSION The genome sequence reported herein will provide useful information for a better understanding of the genetic structure of the S. epidermidis genome in Africa.
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Affiliation(s)
- Luria Leslie Founou
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Food Safety and Environmental Microbiology, Centre of Expertise and Biological Diagnostic of Cameroon (CEDBCAM), Yaoundé, Cameroon.
| | - Raspail Carrel Founou
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Clinical Microbiology, Centre of Expertise and Biological Diagnostic of Cameroon (CEDBCAM), Yaoundé, Cameroon
| | - Mushal Allam
- Sequencing Core Facility, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Health Laboratory Service, Johannesburg, South Africa
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Jansen van Vuren P, Allam M, Wiley MR, Ismail A, Storm N, Birkhead M, Markotter W, Palacios G, Paweska JT. A novel adenovirus isolated from the Egyptian fruit bat in South Africa is closely related to recent isolates from China. Sci Rep 2018; 8:9584. [PMID: 29942032 PMCID: PMC6018157 DOI: 10.1038/s41598-018-27836-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/18/2018] [Indexed: 01/20/2023] Open
Abstract
Recently a number of novel adenoviruses have been isolated from diverse bat species and from diverse geographical locations. We describe the isolation of a novel adenovirus (Family Adenoviridae, genus Mastadenovirus) from a pool of liver and spleen tissue of an apparently healthy wild-caught Egyptian fruit bat (Rousettus aegyptiacus) in South Africa. Genetically the virus is most closely related to four mastadenoviruses recently isolated in China, from Miniopterus schreibersi and Rousettus leschenaultii bats, which are highly divergent from previously identified bat adenoviruses. The length of the Rousettus aegyptiacus adenovirus-3085 (RaegAdV-3085) genome, at 29,342 bp is similar to its closest relatives, and contains 27 open reading frames. The RaegAdV-3085 genome has a low G + C content (36.4%) relative to other viruses in the genus (between 43.6 and 63.9%) but similar to its closest relatives. The inverted terminal repeat (ITR) of RaegAdV-3085 is only 40 bp compared to between 61 and 178 bp of its closest relatives. The discovery of RaegAdV-3085 expands the diversity of known adenoviruses in bats and might represent a member of a new mastadenovirus species in bats.
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Affiliation(s)
- Petrus Jansen van Vuren
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, South Africa
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Mushal Allam
- Core Sequencing Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Michael R Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, USA
| | - Arshad Ismail
- Core Sequencing Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Nadia Storm
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Monica Birkhead
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, USA
| | - Janusz T Paweska
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, South Africa.
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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