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Khasapane NG, Nkhebenyane J, Mnisi Z, Kwenda S, Thekisoe O. Comprehensive whole genome analysis of Staphylococcus aureus isolates from dairy cows with subclinical mastitis. Front Microbiol 2024; 15:1376620. [PMID: 38650877 PMCID: PMC11033518 DOI: 10.3389/fmicb.2024.1376620] [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: 01/26/2024] [Accepted: 03/19/2024] [Indexed: 04/25/2024] Open
Abstract
Staphylococcus species are the primary cause of mastitis in dairy cows across the world. Staphylococcus aureus has recently become a pathogen that is zoonotic and multidrug resistant. This study aimed to sequence whole genomes of 38 S. aureus isolates from 55 subclinical mastitis dairy cows of 7 small-scale farmers in the Free State Province, South Africa and document and their antimicrobial and virulence genes. The 38 isolates were grouped by the in silico multi-locus sequencing types (MLST) into seven sequence types (STs), that is (ST 97, 352, 152, 243) and three new STs (ST8495, ST8500, and ST8501). Thirty-three S. aureus isolates were divided into 7 core single-nucleotide polymorphism (SNP) clusters. Among the 9 distinct spa-types that were detected, Spa-types t2883 accounted for the majority of isolates at 12 (31.57%), followed by t416 with 11 (28.94%) and t2844 with 5 (13.15%). The data also revealed the identification of four (4) plasmids, with Rep_N (rep20) accounting for the majority of isolates with 17 (44.73%), followed by Inc18 (repUS5) with 2 (5.26%). These isolates included 11 distinct antimicrobial resistance genes and 23 genes linked to bacterial virulence. Surprisingly, no methicillin resistance associated genes were detected in these isolates. Genome data of the current study will contribute to understanding epidemiology S. aureus genotypes and ultimately aid in developing treatment and control plans to stop the spread of mastitis in the Free State province and South Africa as a whole.
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Affiliation(s)
- Ntelekwane George Khasapane
- Department of Life Sciences, Centre for Applied Food Safety and Biotechnology, Central University of Technology, Bloemfontein, South Africa
| | - Jane Nkhebenyane
- Department of Life Sciences, Centre for Applied Food Safety and Biotechnology, Central University of Technology, Bloemfontein, South Africa
| | - Zamantungwa Mnisi
- Clinvet International, Study Operations, Bloemfontein, South Africa
- Vectors and Vector-Borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Stanford Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Oriel Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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Ajibade OA, Oladipo EK, Kwenda S, Khumalo Z, Ismail A, Oloke JK, Oyawoye OM, Onyeaka H. Whole genomic sequence of Enterobacter sichuanensis AJI 2411 - A plant growth promoting rhizobacteria. Gene 2023; 887:147725. [PMID: 37625562 DOI: 10.1016/j.gene.2023.147725] [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: 05/03/2023] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Abstract
Enterobacter sichuanensis AJI 2411 is a rhizobacteria displaying plant growth promoting potentials, which was isolated from the rhizosphere of soybeans in Ede, Osun State, Nigeria. The full genome of Enterobacter sichuanensis AJI 2411 was sequenced and reported in this study to shed light on the molecular mechanisms that aids the bacteria's plant growth-promoting abilities.
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Affiliation(s)
- Oluwatosin Akinola Ajibade
- Department of Microbiology, Laboratory of Industrial Microbiology, Adeleke University, Ede, Osun State, Nigeria; Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria.
| | - Elijah Kolawole Oladipo
- Department of Microbiology, Laboratory of Industrial Microbiology, Adeleke University, Ede, Osun State, Nigeria; Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria.
| | - Stanford Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, Gauteng, South Africa
| | - Zamantungwa Khumalo
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, Gauteng, South Africa; Veterinary Tropical Diseases Department, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, Gauteng, South Africa
| | - Julius Kola Oloke
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Precious Cornerstone University, Off Old Ife Road, Agodi, Ibadan, Oyo State, Nigeria.
| | - Olubukola Monisola Oyawoye
- Department of Microbiology, Laboratory of Industrial Microbiology, Adeleke University, Ede, Osun State, Nigeria; Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria.
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Khasapane NG, Kwenda S, Khumalo ZTH, Nkhebenyane SJ, Thekisoe O. Three novel sequencing types from seventeen Staphylococcus aureus genomes isolated from dairy cows milk in the Free State Province of South Africa. Microbiol Resour Announc 2023; 12:e0073923. [PMID: 37966235 PMCID: PMC10720483 DOI: 10.1128/mra.00739-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/07/2023] [Indexed: 11/16/2023] Open
Abstract
Staphylococcus aureus is one of the major pathogens causing bovine mastitis, which results in huge economic losses in the dairy industry worldwide. Here, we report genome sequences of 17 S. aureus strains, with three novel sequencing types (ST8495, ST8500, and ST8501) isolated from the milk of dairy cows with subclinical mastitis.
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Affiliation(s)
- Ntelekwane George Khasapane
- Department of Life Sciences, Centre for Applied Food Sustainability and Biotechnology, Central University of Technology, Bloemfontein, South Africa
| | - Stanford Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Zamantungwa Thobeka Happiness Khumalo
- Clinvet International, Study Operations, Uitsig Road, Universitas, Bloemfontein, South Africa
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Sebolelo Jane Nkhebenyane
- Department of Life Sciences, Centre for Applied Food Sustainability and Biotechnology, Central University of Technology, Bloemfontein, South Africa
| | - Oriel Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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Khasapane NG, Khumalo ZTH, Kwenda S, Nkhebenyane SJ, Thekisoe O. Characterisation of Milk Microbiota from Subclinical Mastitis and Apparently Healthy Dairy Cattle in Free State Province, South Africa. Vet Sci 2023; 10:616. [PMID: 37888568 PMCID: PMC10610705 DOI: 10.3390/vetsci10100616] [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: 08/13/2023] [Revised: 10/04/2023] [Accepted: 10/08/2023] [Indexed: 10/28/2023] Open
Abstract
Bovine mastitis is an inflammation of the udder tissue of the mammary gland brought on by microbial infections or physical damage. It is characterised by physical, chemical, and biological changes in the udder and milk. While several different bacterial species have been identified as causative agents of mastitis, many subclinical mastitis (SCM) cases remain culture-negative. The aim of this study was to characterise milk microbiota from SCM and apparently healthy dairy cows (non-SCM) by 16S rRNA sequencing. Alpha-diversity metrics showed significant differences between SCM cows and non-SCM counterparts. The beta-diversity metrics in the principal coordinate analysis significantly clustered samples by type (PERMANOVA test, p < 0.05), while non-metric dimensional scaling did not (PERMANOVA test, p = 0.07). The overall analysis indicated a total of 95 phyla, 33 classes, 82 orders, 124 families, 202 genera, and 119 bacterial species. Four phyla, namely Actinobacteriota, Bacteroidota, Firmicutes, and Proteobacteria collectively accounted for more than 97% of all sequencing reads from SCM and non-SCM cow samples. The most abundant bacterial classes were Actinobacteria, Bacilli, Bacteroidia, Clostridia, and Gammaproteobacteria in non-SCM cow samples, whilst SCM cow samples were mainly composed of Actinobacteria, Alphaproteobacteria, Bacilli, Clostridia, and Gammaproteobacteria. Dominant bacterial species in non-SCM cow samples were Anthropi spp., Pseudomonas azotoformans, P. fragi, Acinetobacter guillouiae, Enterococcus italicus, Lactococcus lactis, whilst P. azotoformans, Mycobacterium bovis, P. fragi, Acinetobacter guillouiae, and P. koreensis were dominant in the SCM cow samples. The current study found differences in bacterial species between SCM and non-SCM cow milk; hence, the need for detailed epidemiological studies.
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Affiliation(s)
- N. G. Khasapane
- Centre for Applied Food Safety and Biotechnology, Department of Life Sciences, Central University of Technology, 1 Park Road, Bloemfontein 9300, South Africa;
| | - Z. T. H. Khumalo
- ClinVet International, Study Management, Bainsvlei, Bloemfontein 9300, South Africa;
- Vectors and Vector-Borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, Pretoria 0110, South Africa
| | - S. Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa;
| | - S. J. Nkhebenyane
- Centre for Applied Food Safety and Biotechnology, Department of Life Sciences, Central University of Technology, 1 Park Road, Bloemfontein 9300, South Africa;
| | - O. Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa;
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Magobo RE, Ismail H, Lowe M, Strasheim W, Mogokotleng R, Perovic O, Kwenda S, Ismail A, Makua M, Bore A, Phayane R, Naidoo H, Dennis T, Ngobese M, Wijnant W, Govender NP. Outbreak of NDM-1- and OXA-181-Producing Klebsiella pneumoniae Bloodstream Infections in a Neonatal Unit, South Africa. Emerg Infect Dis 2023; 29:1531-1539. [PMID: 37486166 PMCID: PMC10370860 DOI: 10.3201/eid2908.230484] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
After an increase in carbapenem-resistant Klebsiella pneumoniae (CRKP) bloodstream infections and associated deaths in the neonatal unit of a South Africa hospital, we conducted an outbreak investigation during October 2019-February 2020 and cross-sectional follow-up during March 2020-May 2021. We used genomic and epidemiologic data to reconstruct transmission networks of outbreak-related clones. We documented 31 cases of culture-confirmed CRKP infection and 14 deaths. Two outbreak-related clones (blaNDM-1 sequence type [ST] 152 [n = 16] and blaOXA-181 ST307 [n = 6]) cocirculated. The major clone blaNDM-1 ST152 accounted for 9/14 (64%) deaths. Transmission network analysis identified possible index cases of blaOXA-181 ST307 in October 2019 and blaNDM-1 ST152 in November 2019. During the follow-up period, 11 new cases of CRKP infection were diagnosed; we did not perform genomic analysis. Sustained infection prevention and control measures, adequate staffing, adhering to bed occupancy limits, and antimicrobial stewardship are key interventions to control such outbreaks.
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Mtshali K, Khumalo ZTH, Kwenda S, Arshad I, Thekisoe OMM. Exploration and comparison of bacterial communities present in bovine faeces, milk and blood using 16S rRNA metagenomic sequencing. PLoS One 2022; 17:e0273799. [PMID: 36044481 PMCID: PMC9432762 DOI: 10.1371/journal.pone.0273799] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 12/22/2021] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to facilitate everyday household activities and occasional rituals. Ecologically, the body sites from which they are derived consist of distinct microbial communities forming a complex ecosystem of niches. We aimed to explore and compare the faecal, milk and blood microbiota of cows through 16S rRNA sequencing. All downstream analyses were performed using applications in R Studio (v3.6.1). Alpha-diversity metrics showed significant differences between faeces and blood; faeces and milk; but non-significant between blood and milk using Kruskal-Wallis test, P < 0,05. The beta-diversity metrics on Principal Coordinate Analysis and Non-Metric Dimensional Scaling significantly clustered samples by type (PERMANOVA test, P < 0,05). The overall analysis revealed a total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera. Firmicutes, Bacteroidota and Proteobacteria were the most abundant phyla overall. A total of 58 genus-level taxa occurred concurrently between the body sites. The important taxa could be categorized into four potentially pathogenic clusters i.e. arthropod-borne; food-borne and zoonotic; mastitogenic; and metritic and abortigenic. A number of taxa were significantly differentially abundant (DA) between sites based on the Wald test implemented in DESeq2 package. Majority of the DA taxa (i.e. Romboutsia, Paeniclostridium, Monoglobus, Akkermansia, Turicibacter, Bacteroides, Candidatus_Saccharimonas, UCG-005 and Prevotellaceae_UCG-004) were significantly enriched in faeces in comparison to milk and blood, except for Anaplasma which was greatly enriched in blood and was in turn the largest microbial genus in the entire analysis. This study provides insights into the microbial community composition of the sampled body sites and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the community of Waaihoek in KwaZulu-Natal, Republic of South Africa pertaining to their unsanitary practices associated with the use of cattle by-products.
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Affiliation(s)
- Khethiwe Mtshali
- Biomedical Sciences Department, Tshwane University of Technology, Pretoria, South Africa
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
- * E-mail: ,
| | - Zamantungwa Thobeka Happiness Khumalo
- Faculty of Veterinary Science, Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, South Africa
- Study Management, ClinVet International, Bainsvlei, Bloemfontein, South Africa
| | - Stanford Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Ismail Arshad
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Science, Department of Biochemistry and Microbiology, Engineering and Agriculture, University of Venda, Thohoyandou, 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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Poopedi E, Kwenda S, Singh T, Gomba A. Potential occupational exposure to respiratory and gastrointestinal bacterial pathogens at wastewater treatment plants, South Africa. Saf Health Work 2022. [DOI: 10.1016/j.shaw.2021.12.1377] [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: 11/28/2022] Open
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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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Mathew JM, Mpangase PT, Sengupta D, Kwenda S, Mavri-Damelin D, Ramsay M. UGT1A1 regulatory variant with potential effect on efficacy of HIV and cancer drugs commonly prescribed in South Africa. Pharmacogenomics 2021; 22:963-972. [PMID: 34528449 DOI: 10.2217/pgs-2021-0062] [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] [Indexed: 11/21/2022] Open
Abstract
Aim: Despite the high disease burden of human immunodeficiency virus (HIV) infection and colorectal cancer (CRC) in South Africa (SA), treatment-relevant pharmacogenetic variants are understudied. Materials & methods: Using publicly available genotype and gene expression data, a bioinformatic pipeline was developed to identify liver expression quantitative trait loci (eQTLs). Results: A novel cis-eQTL, rs28967009, was identified for UGT1A1, which is predicted to upregulate UGT1A1 expression thereby potentially affecting the metabolism of dolutegravir and irinotecan, which are extensively prescribed in SA for HIV and colorectal cancer treatment, respectively. Conclusion: As increased UGT1A1 expression could affect the clinical outcome of dolutegravir and irinotecan treatment by increasing drug clearance, patients with the rs28967009A variant may require increased drug doses to reach therapeutic levels or should be prescribed alternative drugs.
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Affiliation(s)
- Jenny Mary Mathew
- Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa.,Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Phelelani Thokozani Mpangase
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Stanford Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, 2192, South Africa
| | - Demetra Mavri-Damelin
- School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Michèle Ramsay
- Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa.,Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2050, South Africa
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11
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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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12
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Khasapane NG, Nkhebenyane JS, Kwenda S, Khumalo ZTH, Mtshali PS, Taioe MO, Thekisoe OMM. Application of culture, PCR, and PacBio sequencing for determination of microbial composition of milk from subclinical mastitis dairy cows of smallholder farms. Open Life Sci 2021; 16:800-808. [PMID: 34458582 PMCID: PMC8374232 DOI: 10.1515/biol-2021-0080] [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: 04/20/2021] [Revised: 05/31/2021] [Accepted: 06/21/2021] [Indexed: 01/04/2023] Open
Abstract
Mastitis is a cow disease usually signalized by irritation, swelling, and soreness of the udder. It is characterized by physical, chemical, and biological changes in the udder and milk. The aim of this study was to detect and characterize pathogens causing subclinical mastitis (SCM) from the milk of dairy cows of small-scale farmers through culture and molecular techniques. Milk was collected from 32 cows belonging to 8 small-scale farmers around Harrismith District, South Africa. The results showed that screening of SCM by California mastitis test and somatic cell counts (SCC) was 21.87 and 25%, respectively. Culture methods revealed the presence of Staphylococcus aureus at 93% followed by Streptococci spp. and Escherichia coli at 36.4 and 13.3%, respectively. The PCR could only detect E. coli, while single-molecule real-time sequencing showed a total of 2 phyla, 5 families, 7 genera, and 131 species. Clostridiaceae was the most abundant family, while Romboutsia was the most abundant genus followed by Turicibacter spp. The present study has documented the occurrence of SCM causing pathogens in milk collected from cows of small-scale farmers in Harrismith, indicating that SCM may be present at higher levels than expected.
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Affiliation(s)
- Ntelekwane G Khasapane
- Department of Life Sciences, Centre for Applied Food Sustainability and Biotechnology, Central University of Technology, Bloemfontein, 9300, South Africa
| | - Jane S Nkhebenyane
- Department of Life Sciences, Centre for Applied Food Sustainability and Biotechnology, Central University of Technology, Bloemfontein, 9300, South Africa
| | - Stanford Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Zamantungwa T H Khumalo
- Sequencing Core Facility, National Institute for Communicable Diseases, 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
| | - Phillip S Mtshali
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Moeti O Taioe
- Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research (ARC-OVR), Onderstepoort 0110, South Africa
| | - Oriel M M Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2531, South Africa
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13
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Maphanga TG, Naicker SD, Kwenda S, Muñoz JF, van Schalkwyk E, Wadula J, Nana T, Ismail A, Coetzee J, Govind C, Mtshali PS, Mpembe RS, Govender NP. In Vitro Antifungal Resistance of Candida auris Isolates from Bloodstream Infections, South Africa. Antimicrob Agents Chemother 2021; 65:e0051721. [PMID: 34228535 PMCID: PMC8370198 DOI: 10.1128/aac.00517-21] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 03/12/2021] [Accepted: 06/24/2021] [Indexed: 11/20/2022] Open
Abstract
Candida auris is a multidrug-resistant fungal pathogen that is endemic in South African hospitals. We tested bloodstream C. auris isolates that were submitted to a reference laboratory for national laboratory-based surveillance for candidemia in 2016 and 2017. We confirmed the species identification by phenotypic/molecular methods. We tested susceptibility to amphotericin B, anidulafungin, caspofungin, micafungin, itraconazole, posaconazole, voriconazole, fluconazole, and flucytosine using broth microdilution and Etest methods. We interpreted MICs using tentative breakpoints. We sequenced the genomes of a subset of isolates and compared them to the C. auris B8441 reference strain. Of 400 C. auris isolates, 361 (90%) were resistant to at least one antifungal agent, 339 (94%) to fluconazole alone (MICs of ≥32 µg/ml), 19 (6%) to fluconazole and amphotericin B (MICs of ≥2 µg/ml), and 1 (0.3%) to amphotericin B alone. Two (0.5%) isolates from a single patient were pan-resistant (resistant to fluconazole, amphotericin B, and echinocandins). Of 92 isolates selected for whole-genome sequencing, 77 clustered in clade III, including the pan-resistant isolates, 13 in clade I, and 2 in clade IV. Eighty-four of the isolates (91%) were resistant to at least one antifungal agent; both resistant and susceptible isolates had mutations. The common substitutions identified across the different clades were VF125AL, Y132F, K177R, N335S, and E343D in ERG11; N647T in MRR1; A651P, A657V, and S195G in TAC1b; S639P in FKS1HP1; and S58T in ERG3. Most South African C. auris isolates were resistant to azoles, although resistance to polyenes and echinocandins was less common. We observed mutations in resistance genes even in phenotypically susceptible isolates.
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Affiliation(s)
- Tsidiso G. Maphanga
- National Institute for Communicable Diseases, Centre for Healthcare-Associated Infections, Antimicrobial Resistance, and Mycoses, National Health Laboratory Service, Johannesburg, South Africa
| | - Serisha D. Naicker
- National Institute for Communicable Diseases, Centre for Healthcare-Associated Infections, Antimicrobial Resistance, and Mycoses, National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stanford Kwenda
- National Institute for Communicable Diseases, Sequencing Core Facility, National Health Laboratory Service, Johannesburg, South Africa
| | - Jose F. Muñoz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Erika van Schalkwyk
- National Institute for Communicable Diseases, Centre for Healthcare-Associated Infections, Antimicrobial Resistance, and Mycoses, National Health Laboratory Service, Johannesburg, South Africa
| | - Jeannette Wadula
- National Health Laboratory Service, Chris Hani Baragwaneth Academic Hospital, Soweto, South Africa
| | - Trusha Nana
- National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Arshad Ismail
- National Institute for Communicable Diseases, Sequencing Core Facility, National Health Laboratory Service, Johannesburg, South Africa
| | | | | | - Phillip S. Mtshali
- National Institute for Communicable Diseases, Sequencing Core Facility, National Health Laboratory Service, Johannesburg, South Africa
| | - Ruth S. Mpembe
- National Institute for Communicable Diseases, Centre for Healthcare-Associated Infections, Antimicrobial Resistance, and Mycoses, National Health Laboratory Service, Johannesburg, South Africa
| | - Nelesh P. Govender
- National Institute for Communicable Diseases, Centre for Healthcare-Associated Infections, Antimicrobial Resistance, and Mycoses, 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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14
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Loubser S, Kwenda S, Sengupta D, Tiemessen CT. Identification of a novel allele, HLA-DPB1*34:01:01:03, in Black South African individuals. HLA 2019; 94:547-549. [PMID: 31464043 DOI: 10.1111/tan.13681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 08/23/2019] [Accepted: 08/23/2019] [Indexed: 12/01/2022]
Abstract
Genetic characterisation of a non-coding region allelic variant, HLA-DPB1*34:01:01:03, in Black South African individuals.
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Affiliation(s)
- Shayne Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa
| | - Stanford Kwenda
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa.,Sequencing Core Facility, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, Republic of South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa
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15
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Loubser S, Kwenda S, Sengupta D, Tiemessen CT. Identification of a novel recombinant allele, HLA-DPB1*835:01:01:02, in Black South African individuals. HLA 2019; 94:549-551. [PMID: 31478356 DOI: 10.1111/tan.13680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 08/23/2019] [Accepted: 08/23/2019] [Indexed: 11/27/2022]
Abstract
Genetic characterisation of a novel intra-locus recombinant allele, HLA-DPB1*835:01:01:02, in Black South African individuals.
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Affiliation(s)
- Shayne Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, Republic of South Africa.,National Health Laboratory Service (NHLS), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa
| | - Stanford Kwenda
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, Republic of South Africa.,Sequencing Core Facility, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, Republic of South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, Republic of South Africa.,National Health Laboratory Service (NHLS), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa
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16
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Sibanda S, Kwenda S, Tanui CK, Shyntum DY, Coutinho TA, Moleleki LN. Transcriptome Profiling Reveals the EanI/R Quorum Sensing Regulon in Pantoea Ananatis LMG 2665 T. Genes (Basel) 2018; 9:E148. [PMID: 29518982 PMCID: PMC5867869 DOI: 10.3390/genes9030148] [Citation(s) in RCA: 6] [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: 01/30/2018] [Revised: 02/26/2018] [Accepted: 03/01/2018] [Indexed: 11/23/2022] Open
Abstract
Pantoea ananatis LMG 2665T synthesizes and utilizes acyl homoserine lactones (AHLs) for signalling. The complete set of genes regulated by the EanI/R quorum sensing (QS) system in this strain is still not fully known. In this study, RNA-sequencing (RNA-seq) was used to identify the EanI/R regulon in LMG 2665T. Pairwise comparisons of LMG 2665T in the absence of AHLs (Optical density (OD)600 = 0.2) and in the presence of AHLs (OD600 = 0.5) were performed. Additionally, pairwise comparisons of LMG 2665T and its QS mutant at OD600 = 0.5 were undertaken. In total, 608 genes were differentially expressed between LMG 2665T at OD600 = 0.5 versus the same strain at OD600 = 0.2 and 701 genes were differentially expressed between LMG 2665T versus its QS mutant at OD600 = 0.5. A total of 196 genes were commonly differentially expressed between the two approaches. These constituted approximately 4.5% of the whole transcriptome under the experimental conditions used in this study. The RNA-seq data was validated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). Genes found to be regulated by EanI/R QS were those coding for redox sensing, metabolism, flagella formation, flagella dependent motility, cell adhesion, biofilm formation, regulators, transport, chemotaxis, methyl accepting proteins, membrane proteins, cell wall synthesis, stress response and a large number of hypothetical proteins. The results of this study give insight into the genes that are regulated by the EanI/R system in LMG 2665T. Functional characterization of the QS regulated genes in LMG 2665T could assist in the formulation of control strategies for this plant pathogen.
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Affiliation(s)
- Siphathele Sibanda
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa.
- Centre for Microbial Ecology and Genomics (CMEG), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa.
| | - Stanford Kwenda
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa.
| | - Collins K Tanui
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa.
| | - Divine Y Shyntum
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa.
| | - Teresa A Coutinho
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa.
- Centre for Microbial Ecology and Genomics (CMEG), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa.
| | - Lucy N Moleleki
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa.
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Gorshkov V, Kwenda S, Petrova O, Osipova E, Gogolev Y, Moleleki LN. Global Gene Expression Analysis of Cross-Protected Phenotype of Pectobacterium atrosepticum. PLoS One 2017; 12:e0169536. [PMID: 28081189 PMCID: PMC5230779 DOI: 10.1371/journal.pone.0169536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 10/16/2016] [Accepted: 12/19/2016] [Indexed: 12/25/2022] Open
Abstract
The ability to adapt to adverse conditions permits many bacterial species to be virtually ubiquitous and survive in a variety of ecological niches. This ability is of particular importance for many plant pathogenic bacteria that should be able to exist, except for their host plants, in different environments e.g. soil, water, insect-vectors etc. Under some of these conditions, bacteria encounter absence of nutrients and persist, acquiring new properties related to resistance to a variety of stress factors (cross-protection). Although many studies describe the phenomenon of cross-protection and several regulatory components that induce the formation of resistant cells were elucidated, the global comparison of the physiology of cross-protected phenotype and growing cells has not been performed. In our study, we took advantage of RNA-Seq technology to gain better insights into the physiology of cross-protected cells on the example of a harmful phytopathogen, Pectobacterium atrosepticum (Pba) that causes crop losses all over the world. The success of this bacterium in plant colonization is related to both its virulence potential and ability to persist effectively under various stress conditions (including nutrient deprivation) retaining the ability to infect plants afterwards. In our previous studies, we showed Pba to be advanced in applying different adaptive strategies that led to manifestation of cell resistance to multiple stress factors. In the present study, we determined the period necessary for the formation of cross-protected Pba phenotype under starvation conditions, and compare the transcriptome profiles of non-adapted growing cells and of adapted cells after the cross-protective effect has reached the maximal level. The obtained data were verified using qRT-PCR. Genes that were expressed differentially (DEGs) in two cell types were classified into functional groups and categories using different approaches. As a result, we portrayed physiological features that distinguish cross-protected phenotype from the growing cells.
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Affiliation(s)
- Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics of Kazan Science Centre of Russian Academy of Sciences, Kazan, Russia
- Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan, Russia
| | - Stanford Kwenda
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Olga Petrova
- Kazan Institute of Biochemistry and Biophysics of Kazan Science Centre of Russian Academy of Sciences, Kazan, Russia
| | - Elena Osipova
- Kazan Institute of Biochemistry and Biophysics of Kazan Science Centre of Russian Academy of Sciences, Kazan, Russia
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics of Kazan Science Centre of Russian Academy of Sciences, Kazan, Russia
- Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan, Russia
| | - Lucy N. Moleleki
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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18
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Kwenda S, Motlolometsi TV, Birch PRJ, Moleleki LN. RNA-seq Profiling Reveals Defense Responses in a Tolerant Potato Cultivar to Stem Infection by Pectobacterium carotovorum ssp. brasiliense. Front Plant Sci 2016; 7:1905. [PMID: 28066465 PMCID: PMC5167753 DOI: 10.3389/fpls.2016.01905] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 12/01/2016] [Indexed: 05/28/2023]
Abstract
Pectobacterium carotovorum subsp. brasiliense is a member of the soft rot Enterobacteriaceae (SRE) family that causes tuber soft rot and blackleg diseases of stems in potato plants. Currently, there are no effective chemical strategies for the control of members of the SRE. Thus, an understanding of the inducible defense responses in stems of potato plants is important, particularly during colonization of the vascular system. Here, time-course RNA-sequencing analysis was used to compare expressed genes between a susceptible potato cultivar (Solanum tuberosum cv Valor) and a tolerant cultivar (S. tuberosum cv BP1) at 0, 6, 12, 24, and 72 h post-inoculation with P. c. brasiliense. In total, we identified 6139 and 8214 differentially expressed genes (DEGs) in the tolerant and susceptible cultivars, compared to mock-inoculated controls, respectively. Key DEGs distinguishing between tolerance and susceptibility were associated with negative regulation of cell death and plant-type cell wall organization/biogenesis biological processes in the tolerant and susceptible cultivars, respectively. Among these were DEGs involved in signaling (mainly MAPK cascade and ethylene pathway), defense-related transcription regulation including WRKY transcription factors, and downstream secondary cell biosynthesis. Together, our results suggest that S. tuberosum cv BP1 likely employs quantitative defense response against P. c. brasiliense. Overall, our study provides the first transcriptome-wide insight into the molecular basis of tolerance and/or resistance of potato stems to SRE infection.
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Affiliation(s)
- Stanford Kwenda
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Tshepiso V. Motlolometsi
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Paul R. J. Birch
- Division of Plant Sciences, James Hutton Institute, College of Life Sciences, University of DundeeDundee, UK
| | - Lucy N. Moleleki
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
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19
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Kwenda S, Birch PRJ, Moleleki LN. Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection. BMC Genomics 2016; 17:614. [PMID: 27515663 PMCID: PMC4982125 DOI: 10.1186/s12864-016-2967-9] [Citation(s) in RCA: 40] [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: 03/29/2016] [Accepted: 07/25/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored. RESULTS In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum tuberosum) from stem tissues. The lincRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lincRNAs possess single exons. A time-course RNA-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincRNAs are responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover, coexpression analysis revealed that 17 of these lincRNAs are highly associated with 12 potato defence-related genes. CONCLUSIONS Together, these results suggest that lincRNAs have potential functional roles in potato defence responses. Furthermore, this work provides the first library of potato lincRNAs and a set of novel lincRNAs implicated in potato defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens.
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Affiliation(s)
- Stanford Kwenda
- Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, 0028, South Africa
| | - Paul R J Birch
- The Division of Plant Sciences, College of Life Sciences, University of Dundee (at The James Hutton Institute), Dundee, DD25DA, Scotland, UK
| | - Lucy N Moleleki
- Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, 0028, South Africa.
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20
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Kwenda S, Gorshkov V, Ramesh AM, Naidoo S, Rubagotti E, Birch PRJ, Moleleki LN. Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum. BMC Genomics 2016; 17:47. [PMID: 26753530 PMCID: PMC4710047 DOI: 10.1186/s12864-016-2376-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 09/03/2015] [Accepted: 01/06/2016] [Indexed: 12/15/2022] Open
Abstract
Background Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood. Results In the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress responses. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 68 sRNAs were differentially expressed with 47 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome. Conclusions Since many of the identified sRNAs are starvation-induced, the results of our study suggests that sRNAs play key roles in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2376-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stanford Kwenda
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia. .,Department of Botany and Plant Physiology, Kazan Federal University, Kazan, Russia.
| | - Aadi Moolam Ramesh
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Sanushka Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology (FABI), University of Pretoria, Pretoria, South Africa.
| | - Enrico Rubagotti
- Genomics Research Institute, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa.
| | - Paul R J Birch
- Division of Plant Sciences, College of Life Sciences, University of Dundee (at The James Hutton Institute), Errol Road, Invergowrie, Dundee, DD25DA, Scotland, UK.
| | - Lucy N Moleleki
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
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21
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Onkendi EM, Ramesh AM, Kwenda S, Naidoo S, Moleleki L. Draft Genome Sequence of a Virulent Pectobacterium carotovorum subsp. brasiliense Isolate Causing Soft Rot of Cucumber. Genome Announc 2016; 4:e01530-15. [PMID: 26744374 PMCID: PMC4706333 DOI: 10.1128/genomea.01530-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 11/20/2022]
Abstract
Pectobacterium carotovorum subsp. brasiliense causes soft rot and blackleg diseases on potatoes, ornamentals, and other crops of economic importance. Here, we report a draft genome sequence of a highly virulent P. carotovorum subsp. brasiliense strain, PcbHPI01, isolated from a cucumber in South Africa.
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Affiliation(s)
- Edward M Onkendi
- Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), Pretoria, South Africa Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
| | - Aadi Moolam Ramesh
- Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), Pretoria, South Africa Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
| | - Stanford Kwenda
- Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), Pretoria, South Africa Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
| | - Sanushka Naidoo
- Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), Pretoria, South Africa Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Lucy Moleleki
- Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), Pretoria, South Africa Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
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