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Nyasinga J, Munshi Z, Kigen C, Nyerere A, Musila L, Whitelaw A, Ziebuhr W, Revathi G. Displacement of Hospital-Acquired, Methicillin-Resistant Staphylococcus aureus Clones by Heterogeneous Community Strains in Kenya over a 13-Year Period. Microorganisms 2024; 12:1171. [PMID: 38930553 PMCID: PMC11205442 DOI: 10.3390/microorganisms12061171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 06/28/2024] Open
Abstract
We determined antibiotic susceptibility and employed Oxford Nanopore whole-genome sequencing to explore strain diversity, resistance, and virulence gene carriage among methicillin-resistant Staphylococcus aureus (MRSA) strains from different infection sites and timepoints in a tertiary Kenyan hospital. Ninety-six nonduplicate clinical isolates recovered between 2010 and 2023, identified and tested for antibiotic susceptibility on the VITEK ID/AST platform, were sequenced. Molecular typing, antibiotic resistance, and virulence determinant screening were performed using the relevant bioinformatics tools. The strains, alongside those from previous studies, were stratified into two periods covering 2010-2017 and 2018-2023 and comparisons were made. Mirroring phenotypic profiles, aac(6')-aph(2″) [aminoglycosides]; gyrA (S84L) and grlA (S80Y) [fluoroquinolones]; dfrG [anti-folates]; and tet(K) [tetracycline] resistance determinants dominated the collection. While the proportion of ST239/241-t037-SCCmec III among MRSA reduced from 37.7% to 0% over the investigated period, ST4803-t1476-SCCmec IV and ST152-t355-SCCmec IV were pre-eminent. The prevalence of Panton-Valentine leucocidin (PVL) and arginine catabolic mobile element (ACME) genes was 38% (33/87) and 6.8% (6/87), respectively. We observed the displacement of HA-MRSA ST239/241-t037-SCCmec III with the emergence of ST152-t355-SCCmec IV and a greater clonal heterogeneity. The occurrence of PVL+/ACME+ CA-MRSA in recent years warrants further investigations into their role in the CA-MRSA virulence landscape, in a setting of high PVL prevalence.
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Affiliation(s)
- Justin Nyasinga
- Department of Pathology, Aga Khan University, Nairobi P.O. Box 30270-00100, Kenya; (J.N.); (Z.M.)
- Department of Biomedical Sciences and Technology, Technical University of Kenya, Nairobi P.O. Box 52428-00200, Kenya
- Institute of Science, Technology & Innovation, Pan-African University, Nairobi P.O. Box 62000-00200, Kenya;
| | - Zubair Munshi
- Department of Pathology, Aga Khan University, Nairobi P.O. Box 30270-00100, Kenya; (J.N.); (Z.M.)
| | - Collins Kigen
- Walter Reed Army Institute of Research—Africa, Kericho P.O. Box 1357-20200, Kenya; (C.K.); (L.M.)
| | - Andrew Nyerere
- Institute of Science, Technology & Innovation, Pan-African University, Nairobi P.O. Box 62000-00200, Kenya;
| | - Lillian Musila
- Walter Reed Army Institute of Research—Africa, Kericho P.O. Box 1357-20200, Kenya; (C.K.); (L.M.)
| | - Andrew Whitelaw
- Division of Medical Microbiology and Immunology, Stellenbosch University, Matieland, Stellenbosch 7602, South Africa;
| | - Wilma Ziebuhr
- Institute of Molecular Infection Biology, Josef-Schneider Str. 2D/15, D-97080 Wurzburg, Germany;
| | - Gunturu Revathi
- Department of Pathology, Aga Khan University, Nairobi P.O. Box 30270-00100, Kenya; (J.N.); (Z.M.)
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Ibrahim RA, Berhe N, Mekuria Z, Seyoum ET, Balada-Llasat JM, Abebe T, Mariam SH, Tsige E, Fentaw Dinku S, Wang SH. Antimicrobial Resistance and Virulence Gene Profile of Clinical Staphylococcus aureus: A Multi-Center Study from Ethiopia. Infect Drug Resist 2023; 16:4835-4844. [PMID: 37520455 PMCID: PMC10386829 DOI: 10.2147/idr.s419577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
Background Staphylococcus aureus causes a wide range of infections from mild skin and soft tissue to severe life-threatening bacteremia. The pathogenicity of S. aureus infections is related to various bacterial surface components and extracellular proteins such as toxic-shock syndrome (TSS) toxin and Panton-Valentine leukocidin (PVL). In this study we determine the antimicrobial resistance of isolated strains and their virulence genes in Ethiopia. Methods A total of 190 archived S. aureus isolates from four Ethiopia Antimicrobial Resistance (AMR) Surveillance sites were analyzed. The identification of S. aureus was done by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF Biotyper) and antimicrobial susceptibility test (AST) was done using VITEK® 2. Multiplex PCR was used to detect mecA, mecC, pvl and spa genes and super-antigens (sea, seb, sec, seh and sej staphylococcal enterotoxins). Results A total of 172 isolates were confirmed as S. aureus, 9 (5.23%) were methicillin-resistant S. aureus (MRSA) and 163 (94.76%) were methicillin-susceptible S. aureus (MSSA). AST showed that 152 (88.4%) isolates were resistant to penicillin; 90 (52.32%) resistant to trimethoprim-sulfamethoxazole; and 45 (26.16%) resistant to tetracycline. A total of 66 (38.37%) isolates harbored at least one staphylococcal enterotoxin gene and 31 (46.96%) isolates had more than one. The most frequent enterotoxin gene encountered was seb 28 (16.28%). The TSST-1 gene was detected in 23 (13.37%). Presence of staphylococcal enterotoxin gene showed significant association with antibiotic resistance to cefoxitin, benzylpenicillin, oxacillin, erythromycin, clindamycin, tetracycline and SXT. The pvl gene was detected in 102 (59.3%) of isolates. Isolates from patients below 15 years of age showed significantly high numbers of pvl gene (P = 0.02). Presence of sej (P = 0.011) and TSST-1 (P <0.001) genes were associated with the presence of pvl gene. Conclusion In this study, isolates were highly resistant to oral antibiotics and the pvl, seb, sea and TSST-1 genes were prevalent.
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Affiliation(s)
- Rajiha A Ibrahim
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Bacterial, Parasitic and Zoonotic Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
| | - Nega Berhe
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Zelalem Mekuria
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Veterinary Preventive Medicine, Colleges of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Eyasu T Seyoum
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
| | - Joan-Miquel Balada-Llasat
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Tamrat Abebe
- Department of Microbiology, Immunology, and Parasitology, Schools of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon H Mariam
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Estifanos Tsige
- Bacterial, Parasitic and Zoonotic Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Surafel Fentaw Dinku
- Bacterial, Parasitic and Zoonotic Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Shu-Hua Wang
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
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Ibrahim RA, Mekuria Z, Wang SH, Mediavilla JR, Kreiswirth B, Seyoum ET, Mariam SH, Gebreyes WA, Kefale TA, Guma GT, Berhe N. Clonal diversity of Staphylococcus aureus isolates in clinical specimens from selected health facilities in Ethiopia. BMC Infect Dis 2023; 23:399. [PMID: 37308817 DOI: 10.1186/s12879-023-08380-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 06/07/2023] [Indexed: 06/14/2023] Open
Abstract
Staphylococcus aureus is among the top three causative agents of nosocomial infection in Ethiopia. The majority of studies in Ethiopia have focused on the epidemiology of S. aureus in hospital settings, with limited molecular genotyping results. Molecular characterization of S. aureus is essential for identification of strains, and contributes to the control and prevention of S. aureus infection. The aim of the current study was to determine the molecular epidemiology of methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) isolates recovered from clinical specimens in Ethiopia. A total of 161 MSSA and 9 MRSA isolates were characterized using pulsed-field gel electrophoresis (PFGE) and staphylococcal protein A (spa) typing. Based on the PFGE analysis, MSSA isolates were grouped into eight pulso-types groups (from A to I), while MRSA isolates clustered into three (A, B and C) pulso-types with more than 80% similarity. The spa typing analysis showed diversity of S. aureus with 56 distinct spa types. Spa type t355 was most prevalent (56/170, 32.9%), while eleven new spa types were detected including t20038, t20039, and t20042. The identified spa types were clustered into 15 spa-clonal complexes (spa-CCs) using BURP analysis; novel/unknown spa types were further subjected to MLST analysis. The majority of isolates belonged to spa-CC 152 (62/170, 36.4%), followed by spa-CC 121 (19/170, 11.2%), and spa-CC 005 (18 /170, 10.6%). Of the nine MRSA isolates, 2 (22.2%) were spa-CC 239 with staphylococcal cassette chromosome (SCC)mec III. These findings highlight the diversity of S. aureus strains in Ethiopia, as well as the presence of potentially epidemic strains circulating in the country necessitating further characterization of S. aureus for antimicrobial resistance detection and infection prevention purposes.
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Affiliation(s)
- Rajiha Abubeker Ibrahim
- Akililu Lemma Institute of Pathobiology, Addis Ababa University, Ababa, Ethiopia.
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
- Ohio State Global One Health (GOH) LLC, Addis Ababa, Ethiopia.
| | - Zelalem Mekuria
- Colleges of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
- Global One Health initiative (GOHi), The Ohio State University, Columbus, OH, USA
| | - Shu-Hua Wang
- Global One Health initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Infectious Disease Division, Internal Medicine Department, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Jose R Mediavilla
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Barry Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Eyasu T Seyoum
- Ohio State Global One Health (GOH) LLC, Addis Ababa, Ethiopia
| | - Solomon H Mariam
- Akililu Lemma Institute of Pathobiology, Addis Ababa University, Ababa, Ethiopia
| | - Wondwossen A Gebreyes
- Colleges of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
- Global One Health initiative (GOHi), The Ohio State University, Columbus, OH, USA
| | | | | | - Nega Berhe
- Akililu Lemma Institute of Pathobiology, Addis Ababa University, Ababa, Ethiopia
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Tsai SH, Chang PY, Wen YH, Lin WT, Hsu FP, Chen DP. Screening of single nucleotide polymorphisms within HLA region related to hematopoietic stem cell transplantation using MassARRAY technology. Sci Rep 2023; 13:5913. [PMID: 37041193 PMCID: PMC10090154 DOI: 10.1038/s41598-023-33149-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 04/07/2023] [Indexed: 04/13/2023] Open
Abstract
A growing number of studies showed that single nucleotide polymorphisms (SNPs) in the human leukocyte antigen (HLA)-related genes were associated with the outcome of hematopoietic stem cell transplantation (HSCT). Thus, other SNPs located nearby the classical HLA genes must be considered in HSCT. We evaluated the clinical feasibility of MassARRAY by comparing to Sanger sequencing. The PCR amplicons with each one of the 17 loci that were related to the outcomes of HSCT published by our previous study were transferred onto a SpectroCHIP Array for genotyping by mass spectrometry. The sensitivity of MassARRAY was 97.9% (614/627) and the specificity was 100% (1281/1281), where the positive predictive value (PPV) was 100% (614/614) and the negative predictive value (NPV) was 99.0% (1281/1294). MassARRAY is high-throughput, which can accurately analyze multiple SNPs at the same time. Based on these properties, we proposed that it could be an efficient method to match the genotype between the graft and the recipient before transplantation.
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Affiliation(s)
- Shu-Hui Tsai
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 333, Taiwan
| | - Pi-Yueh Chang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 333, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ying-Hao Wen
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 333, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Tzu Lin
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 333, Taiwan
| | - Fang-Ping Hsu
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 333, Taiwan
| | - Ding-Ping Chen
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 333, Taiwan.
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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Obanda BA, Gibbons CL, Fèvre EM, Bebora L, Gitao G, Ogara W, Wang SH, Gebreyes W, Ngetich R, Blane B, Coll F, Harrison EM, Kariuki S, Peacock SJ, Cook EAJ. Multi-Drug Resistant Staphylococcus aureus Carriage in Abattoir Workers in Busia, Kenya. Antibiotics (Basel) 2022; 11:antibiotics11121726. [PMID: 36551383 PMCID: PMC9774130 DOI: 10.3390/antibiotics11121726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Abattoir workers have been identified as high-risk for livestock-associated Staphylococcus aureus carriage. This study investigated S. aureus carriage in abattoir workers in Western Kenya. Nasal swabs were collected once from participants between February-November 2012. S. aureus was isolated using bacterial culture and antibiotic susceptibility testing performed using the VITEK 2 instrument and disc diffusion methods. Isolates underwent whole genome sequencing and Multi Locus Sequence Types were derived from these data. S. aureus (n = 126) was isolated from 118/737 (16.0%) participants. Carriage was higher in HIV-positive (24/89, 27.0%) than HIV−negative participants (94/648, 14.5%; p = 0.003). There were 23 sequence types (STs) identified, and half of the isolates were ST152 (34.1%) or ST8 (15.1%). Many isolates carried the Panton-Valentine leucocidin toxin gene (42.9%). Only three isolates were methicillin resistant S. aureus (MRSA) (3/126, 2.4%) and the prevalence of MRSA carriage was 0.4% (3/737). All MRSA were ST88. Isolates from HIV-positive participants (37.0%) were more frequently resistant to sulfamethoxazole/trimethoprim compared to isolates from HIV-negative participants (6.1%; p < 0.001). Similarly, trimethoprim resistance genes were more frequently detected in isolates from HIV-positive (81.5%) compared to HIV-negative participants (60.6%; p = 0.044). S. aureus in abattoir workers were representative of major sequence types in Africa, with a high proportion being toxigenic isolates. HIV-positive individuals were more frequently colonized by antimicrobial resistant S. aureus which may be explained by prophylactic antimicrobial use.
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Affiliation(s)
- Benear Apollo Obanda
- Department of Veterinary Pathology, Microbiology and Parasitology, University of Nairobi, Nairobi P.O. Box 29053-00625, Kenya
- Global One Health Initiative, The Ohio State University, Columbus, OH 43210, USA
- Centre for Microbiology Research Nairobi, Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya
| | | | - Eric M. Fèvre
- Institute of Infection, Veterinary & Ecological Sciences, Leahurst Campus, University of Liverpool, Chester High Road, Neston CH64 7TE, UK
- International Livestock Research Institute, Nairobi P.O. Box 30709-00100, Kenya
- Correspondence: (E.M.F.); (E.A.J.C.)
| | - Lilly Bebora
- Department of Veterinary Pathology, Microbiology and Parasitology, University of Nairobi, Nairobi P.O. Box 29053-00625, Kenya
| | - George Gitao
- Department of Veterinary Pathology, Microbiology and Parasitology, University of Nairobi, Nairobi P.O. Box 29053-00625, Kenya
| | - William Ogara
- Department of Public Health Pharmacology and Toxicology, University of Nairobi, Nairobi P.O. Box 29053-00625, Kenya
| | - Shu-Hua Wang
- Global One Health Initiative, The Ohio State University, Columbus, OH 43210, USA
- Division of Infectious Disease, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Wondwossen Gebreyes
- Global One Health Initiative, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Ronald Ngetich
- Centre for Microbiology Research Nairobi, Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Francesc Coll
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Ewan M. Harrison
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Samuel Kariuki
- Centre for Microbiology Research Nairobi, Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Elizabeth A. J. Cook
- International Livestock Research Institute, Nairobi P.O. Box 30709-00100, Kenya
- Correspondence: (E.M.F.); (E.A.J.C.)
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“Omic” Approaches to Bacteria and Antibiotic Resistance Identification. Int J Mol Sci 2022; 23:ijms23179601. [PMID: 36077000 PMCID: PMC9455953 DOI: 10.3390/ijms23179601] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/28/2022] Open
Abstract
The quick and accurate identification of microorganisms and the study of resistance to antibiotics is crucial in the economic and industrial fields along with medicine. One of the fastest-growing identification methods is the spectrometric approach consisting in the matrix-assisted laser ionization/desorption using a time-of-flight analyzer (MALDI-TOF MS), which has many advantages over conventional methods for the determination of microorganisms presented. Thanks to the use of a multiomic approach in the MALDI-TOF MS analysis, it is possible to obtain a broad spectrum of data allowing the identification of microorganisms, understanding their interactions and the analysis of antibiotic resistance mechanisms. In addition, the literature data indicate the possibility of a significant reduction in the time of the sample preparation and analysis time, which will enable a faster initiation of the treatment of patients. However, it is still necessary to improve the process of identifying and supplementing the existing databases along with creating new ones. This review summarizes the use of “-omics” approaches in the MALDI TOF MS analysis, including in bacterial identification and antibiotic resistance mechanisms analysis.
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