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Khatoon A, Hussain SF, Shahid SM, Sidhwani SK, Khan SA, Shaikh OA, Nashwan AJ. Emerging novel sequence types of Staphylococcus aureus in Pakistan. J Infect Public Health 2024; 17:51-59. [PMID: 37992434 DOI: 10.1016/j.jiph.2023.10.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/08/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Despite an increasing incidence of Staphylococcus aureus infection and dissemination in Pakistan, the epidemiology of different Staphylococcus aureus research clones has been the subject of only a small number of investigations. By analyzing the collected data sequence, this study was designed to study the epidemiology of Staphylococcus aureus in the area using multilocus sequence typing (MLST). METHODS A total of 1015 staphylococcus strains collected from the city's tertiary care facilities were biochemically screened, followed by antimicrobial susceptibility testing against a panel of 13 antibiotics. Analyzed methicillin-resistant Staphylococcus aureus (MRSA) was subjected to molecular characterization using multilocus sequence typing (MLST), clonal complex analysis, recombination testing, and phylogenetic analysis. RESULTS Approximately 421 bacteria were verified as Staphylococcus aureus by biochemical analysis. 57% of the isolates exhibited multidrug resistance, of which 89% were found to be methicillin-resistant Staphylococcus aureus (MRSA). MLST results in a total of 39 sequence types (ST) and 5 clonal complexes (CC), out of which twenty-two STs were newly documented worldwide. The most common CC identified was CC8. The direct sequencing data also revealed significant shifts at MLST loci, with point mutations resulting in the aroE-343 and tpi-278 alleles. CONCLUSIONS This study concludes that there is high diversity in the locally circulating clones of Staphylococcus aureus present in nature and that they are defined by their geographic epidemiology. These findings have practical implications for public health, including the need for tailored infection control strategies, antibiotic stewardship, global surveillance, and a deeper understanding of bacterial evolution.
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Affiliation(s)
- Ambrina Khatoon
- The Karachi Institute of Biotechnology & Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan; Ziauddin University, Karachi, Pakistan.
| | - Syed F Hussain
- The Karachi Institute of Biotechnology & Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan; University of Alberta, Edmonton, AB T6G 2J7, Canada.
| | - Syed M Shahid
- The Karachi Institute of Biotechnology & Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan; School of Health Science, Eastern Institute of Technology (EIT), Auckland, New Zealand.
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Segal B, Langham A, Klevansky R, Patel N, Mokoena T, Nassiep M, Ramatlo O, Ahmad A, Duse AG. Analysis of the Trends of Methicillin-Resistant Staphylococcus aureus in Gauteng Public Hospitals from 2009 to 2018. Microbiol Spectr 2023; 11:e0362322. [PMID: 37338400 PMCID: PMC10433859 DOI: 10.1128/spectrum.03623-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/14/2023] [Indexed: 06/21/2023] Open
Abstract
Most investigations into the distribution of methicillin resistant Staphylococcus aureus (MRSA) have focused exclusively on bloodborne infections within individual health care institutions for shorter time periods. This has limited the analysis of a community-spread pathogen to snapshots within the hospital domain. Therefore, in this study we determined the demographic and geographical patterns of MRSA infections and their fluctuation in 10 years within all public hospitals in Gauteng, South Africa. A retrospective analysis of S. aureus samples was done by deduplicating samples in two groups. The sample groups were placed into subsets with respect to demographic and geographical fields and compared across the studied period. Logistic regression was utilized to determine odds ratios for resistant infections in univariate and multivariable configurations. A total of 66,071 unique infectious events were identified from the 148,065 samples received over a 10-year period, out of which 14,356 were identified as bacteremia. MRSA bacteremia rates in Gauteng peaked in 2015 and have since decreased. Within Gauteng, metropolitan areas have the greatest burden of MRSA with children under 5 years of age and males being most affected. Medical wards have the highest S. aureus bacteremia rates, while intensive care units have the highest MRSA bacteremia rates. Patient age, admitting ward, and geographical district are the most important associated factors of resistance. MRSA acquisition rates have shown tremendous growth since 2009 but have since spiked and subsequently decreased. This may be due to the initiation of the National Guidelines on Antimicrobial Stewardship and Infectious Disease Surveillance. Further studies to determine the trajectory of infections are required to support these claims. IMPORTANCE S. aureus is the leading cause of a variety of devastating clinical conditions, including infective endocarditis, bacteremia, and pleuropulmonary infections. It is an important pathogen responsible for substantial morbidity and mortality. MRSA is a variant of interest originally responsible for difficult to treat hospital-acquired infections that has since achieved community spread throughout the world. Most investigations into the distribution of MRSA have focused exclusively on bloodborne infections within individual health care institutions for shorter periods. This has limited the analysis of a community-spread pathogen to snapshots within the hospital domain. This study sought to determine the demographic and geographical patterns of MRSA infections as well as how these have fluctuated over time within all public hospitals. This will also help in understanding the epidemiology and resistance trends of S. aureus, which will help clinicians to understand the clinical prospective and policy makers to design guidelines and strategies for treating such infections.
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Affiliation(s)
- Bradley Segal
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Alice Langham
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Rachel Klevansky
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Namita Patel
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Thabang Mokoena
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Muhammad Nassiep
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Obakeng Ramatlo
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Aijaz Ahmad
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, South Africa
| | - Adriano G. Duse
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, South Africa
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Garrine M, Costa SS, Messa A, Massora S, Vubil D, Ácacio S, Nhampossa T, Bassat Q, Mandomando I, Couto I. Antimicrobial resistance and clonality of Staphylococcus aureus causing bacteraemia in children admitted to the Manhiça District Hospital, Mozambique, over two decades. Front Microbiol 2023; 14:1208131. [PMID: 37555065 PMCID: PMC10406509 DOI: 10.3389/fmicb.2023.1208131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/04/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Staphylococcus aureus is one of the main causes of bacteraemia, associated with high mortality, mainly due to the occurrence of multidrug resistant (MDR) strains. Data on antibiotic susceptibility and genetic lineages of bacteraemic S. aureus are still scarce in Mozambique. The study aims to describe the antibiotic susceptibility and clonality of S. aureus isolated from blood cultures of children admitted to the Manhiça District Hospital over two decades (2001-2019). METHODS A total of 336 S. aureus isolates detected in blood cultures of children aged <5 years were analyzed for antibiotic susceptibility by disk diffusion or minimal inhibitory concentration, and for the presence of resistance determinants by PCR. The clonality was evaluated by SmaI-PFGE, spa typing, and MLST. The SCCmec element was characterized by SCCmec typing. RESULTS Most S. aureus (94%, 317/336) were resistant to at least one class of antibiotics, and one quarter (25%) showed a MDR phenotype. High rates of resistance were detected to penicillin (90%) and tetracycline (48%); followed by erythromycin/clindamycin (25%/23%), and co-trimoxazole (11%), while resistance to methicillin (MRSA strains) or gentamicin was less frequent (≤5%). The phenotypic resistance to distinct antibiotics correlated well with the corresponding resistance determinants (Cohen's κ test: 0.7-1.0). Molecular typing revealed highly diverse clones with predominance of CC5 (17%, 58/336) and CC8 (16%), followed by CC15 (11%) and CC1 (11%). The CC152, initially detected in 2001, re-emerged in 2010 and became predominant throughout the remaining surveillance period, while other CCs (CC1, CC5, CC8, CC15, CC25, CC80, and CC88) decreased over time. The 16 MRSA strains detected belonged to clones t064-ST612/CC8-SCCmecIVd (69%, 11/16), t008-ST8/CC8-SCCmecNT (25%, 4/16) and t5351-ST88/CC88-SCCmecIVa (6%, 1/16). Specific clonal lineages were associated with extended length of stay and high in-hospital mortality. CONCLUSION We document the circulation of diverse MDR S. aureus causing paediatric bacteraemia in Manhiça district, Mozambique, requiring a prompt recognition of S. aureus bacteraemia by drug resistant clones to allow more targeted clinical management of patients.
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Affiliation(s)
- Marcelino Garrine
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Sofia Santos Costa
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Augusto Messa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Sérgio Massora
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Delfino Vubil
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Sozinho Ácacio
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
| | - Tacilta Nhampossa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
| | - Quique Bassat
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ISGlobal, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- ICREA, Barcelona, Spain
- Department of Pediatrics, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Inacio Mandomando
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
- ISGlobal, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Isabel Couto
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
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Lawal OU, Ayobami O, Abouelfetouh A, Mourabit N, Kaba M, Egyir B, Abdulgader SM, Shittu AO. A 6-Year Update on the Diversity of Methicillin-Resistant Staphylococcus aureus Clones in Africa: A Systematic Review. Front Microbiol 2022; 13:860436. [PMID: 35591993 PMCID: PMC9113548 DOI: 10.3389/fmicb.2022.860436] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Background Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of hospital-associated (HA) and community-associated (CA) infections globally. The multi-drug resistant nature of this pathogen and its capacity to cause outbreaks in hospital and community settings highlight the need for effective interventions, including its surveillance for prevention and control. This study provides an update on the clonal distribution of MRSA in Africa. Methods A systematic review was conducted by screening for eligible English, French, and Arabic articles from November 2014 to December 2020, using six electronic databases (PubMed, EBSCOhost, Web of Science, Scopus, African Journals Online, and Google Scholar). Data were retrieved and analyzed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines (registered at PROSPERO: CRD42021277238). Genotyping data was based primarily on multilocus sequence types (STs) and Staphylococcal Cassette Chromosome mec (SCCmec) types. We utilized the Phyloviz algorithm in the cluster analysis and categorization of the MRSA STs into various clonal complexes (CCs). Results We identified 65 studies and 26 publications from 16 of 54 (30%) African countries that provided sufficient genotyping data. MRSA with diverse staphylococcal protein A (spa) and SCCmec types in CC5 and CC8 were reported across the continent. The ST5-IV [2B] and ST8-IV [2B] were dominant clones in Angola and the Democratic Republic of Congo (DRC), respectively. Also, ST88-IV [2B] was widely distributed across the continent, particularly in three Portuguese-speaking countries (Angola, Cape Verde, and São Tomé and Príncipe). The ST80-IV [2B] was described in Algeria and Egypt, while the HA-ST239/ST241-III [3A] was only identified in Egypt, Ghana, Kenya, and South Africa. ST152-MRSA was documented in the DRC, Kenya, Nigeria, and South Africa. Panton-Valentine leukocidin (PVL)-positive MRSA was observed in several CCs across the continent. The median prevalence of PVL-positive MRSA was 33% (ranged from 0 to 77%; n = 15). Conclusion We observed an increase in the distribution of ST1, ST22, and ST152, but a decline of ST239/241 in Africa. Data on MRSA clones in Africa is still limited. There is a need to strengthen genomic surveillance capacity based on a "One-Health" strategy to prevent and control MRSA in Africa.
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Affiliation(s)
- Opeyemi Uwangbaoje Lawal
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Olaniyi Ayobami
- Unit for Healthcare-Associated Infections, Surveillance of Antimicrobial Resistance and Consumption, Robert Koch Institute, Berlin, Germany
| | - Alaa Abouelfetouh
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, AlAlamein International University, Alalamein, Egypt
| | - Nadira Mourabit
- Biotechnology, Environmental Technology and Valorisation of Bio-Resources Team, Department of Biology, Faculty of Sciences and Techniques of Al Hoceima, Abdelmalek Essaadi University, Tetouan, Morocco
| | - Mamadou Kaba
- Division of Medical Microbiology, Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Shima M Abdulgader
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Adebayo Osagie Shittu
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Nigeria.,Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
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Ramaite K, Ekwanzala MD, Dewar JB, Momba MNB. Human-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complex 80 Isolated from Cattle and Aquatic Environments. Antibiotics (Basel) 2021; 10:antibiotics10091038. [PMID: 34572619 PMCID: PMC8468323 DOI: 10.3390/antibiotics10091038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/06/2021] [Accepted: 08/21/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Human-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) has mainly been reported in South African pig and chicken farms. The prevalence of antibiotic-resistant genes (ARGs), virulence factors (VFs), and multilocus sequence types (MLSTs) associated with HA-MRSA in cattle farms has not been reported. Consequently, this study characterised LA-MRSA and its spread from cattle farms into the environment. Method: Husbandry soil (HS), nearby river water (NRW), animal manure (AM) and animal drinking water (ADW) were collected on and around a cattle farm. Presumptive MRSA isolates were identified from these samples using CHROMagar media and genotyped as MRSA sequence types (STs), selected ARGs, and VFs, using polymerase chain reaction. An MLST-based dendrogram was generated to link the farm MRSA strains with those in a nearby river. Results: The prevalence of MRSA was 30.61% for HS, 28.57% for ADW, 22.44% for NRW, and 10.20% for AM. Isolates from HS harboured the highest number of resistant genes, with 100% for mecA, 91.66% for ermA, and 58.33% for blaZ. However, no ermC or tetM genes were detected. MRSA isolates from AM harboured the lowest number of resistant genes. Only sec and seq enterotoxins were found in all the assessed MRSA isolates. MRSA from the farm revealed six STs (ST80, ST728, ST1931, ST2030, ST3247, and ST5440); all of STs belonged to clonal complex 80 (CC80). An MLST-based dendrogram based on the concatenated sequences of MLST genes under the maximum likelihood criterion revealed four clades of amalgamated MRSA isolates from various livestock environmental matrices, including the NRW. Conclusion: The results suggest that livestock environmental matrices might be reservoirs of MRSA that could subsequently disseminate through runoff to pollute water resources. Therefore, continued surveillance of HA-MRSA in livestock environments is warranted.
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Affiliation(s)
- Khuliso Ramaite
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Pretoria 0001, South Africa; (K.R.); (M.D.E.)
| | - Mutshiene Deogratias Ekwanzala
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Pretoria 0001, South Africa; (K.R.); (M.D.E.)
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 41346 Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 41346 Gothenburg, Sweden
| | - John Barr Dewar
- Department of Life and Consumer Sciences, University of South Africa, Florida Campus, Johannesburg 1709, South Africa;
| | - Maggy Ndombo Benteke Momba
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Pretoria 0001, South Africa; (K.R.); (M.D.E.)
- Correspondence: ; Tel.: +27-123826365
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Ward-specific clustering of methicillin-resistant Staphylococcus aureus spa-type t037 and t045 in two hospitals in South Africa: 2013 to 2017. PLoS One 2021; 16:e0253883. [PMID: 34185791 PMCID: PMC8241065 DOI: 10.1371/journal.pone.0253883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/14/2021] [Indexed: 12/02/2022] Open
Abstract
Introduction Methicillin-resistant Staphylococcus aureus (MRSA) is a highly clonal pathogen causing infections in various settings. The aim of this study was to determine if healthcare-associated (HA) MRSA isolates with the same spa-type originating from two geographically distinct hospitals in South Africa were genetically related based on PFGE. Furthermore, a small subset of MRSA isolates were characterised with WGS and then compared to PFGE to determine if PFGE is still a reliable method to define outbreaks and/or transmission chains. Methods Staphylococcus aureus isolated from blood cultures (BC) were submitted to the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM) as part of a laboratory-based surveillance programme (GERMS-SA). The identified HA-MRSA isolates underwent molecular characterisation [Staphylococcal Chromosome Cassette (SCC) mec and spa-typing]. Pulsed-field gel electrophoresis (PFGE) was performed on selected isolates with the same spa-type. Twenty-one MRSA isolates were selected for whole-genome sequencing (WGS) based on spa-type, PFGE clustering, time and place of isolation. Results Eighteen percent (n = 95/529) and 33% (n = 234/710) of isolates collected, from two public tertiary academic hospitals in the Gauteng (GAU) and the Western Cape (WC) provinces, were identified as MRSA, respectively. The most dominant clone in the GAU hospital was t037-III-MRSA (43.2%; n = 41/95). The most dominant clones in the WC hospital was t037-III-MRSA (23.9%, n = 56/234) and t045-I-MRSA (23.5%, n = 55/234). The GAU-t037-III-MRSA cases and WC-t045-I-MRSA cases occurred in the paediatric patient population, whereas the WC-t037-III-MRSA cases occurred in the adult patient population. A novel spa-type (t19935) was detected in the GAU hospital. PFGE showed that the GAU- and WC-t037-III-MRSA isolates were genetically indistinguishable, as well as most of the WC-t045-I-MRSA isolates. The Vienna/Hungarian/Brazilian clone and British EMRSA-3 clone were in circulation and a low frequency of single nucleotide polymorphisms (SNP) (≤20) differences was observed among isolates with the same spa-type. Conclusion The low number of SNP differences is suggestive of uninterrupted strain transmission and the persistence of t037-III-MRSA and t045-I-MRSA from 2013 to 2017 in the two studied hospitals. Alternative infection prevention and control strategies should be considered to supplement control efforts.
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Reddy K, Whitelaw A. Can the Xpert MRSA/SA BC assay be used as an antimicrobial stewardship tool? A prospective assay validation and descriptive impact assessment study in a South African setting. BMC Infect Dis 2021; 21:177. [PMID: 33588782 PMCID: PMC7885373 DOI: 10.1186/s12879-021-05857-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/31/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Positive blood cultures showing Gram positive cocci in clusters signifies either Staphylococcus aureus or the less-virulent coagulase-negative staphylococci. Rapid identification and methicillin susceptibility determination with the Xpert MRSA/SA BC assay can improve management of S. aureus bloodstream infection and reduce inappropriate antibiotic use. METHODS We prospectively evaluated the Xpert MRSA/SA BC assay in comparison with culture, on samples referred to our laboratory in the Western Cape, South Africa. We interviewed attending clinicians upon culture result availability, to assess antibiotic choices and estimate potential impact of the assay. RESULTS Of the 231 samples included, there was 100% concordance between the Xpert MRSA/SA BC assay and culture (methicillin-resistant S. aureus 15/15, methicillin-susceptible S. aureus 42/42, coagulase-negative staphylococci 170/170). Time to final result could be reduced by approximately 30 h with the assay. Of the 178 patients with adequate antibiotic history, optimisation of antistaphylococcal therapy could have occurred more than 1 day sooner in 68.9% with S. aureus bloodstream infection (31/45, 95% CI 53.2-81.4%). Six of the 11 patients with methicillin-resistant S. aureus bloodstream infection (54.5%) could have received anti-MRSA cover sooner. Fifty-four days of antibiotic therapy could have been spared, equating to 0.3 days (95% CI, 0.2-0.4) saved per patient, driven by broad-spectrum beta-lactams (32 days, in 18.0% of the cohort). CONCLUSION This assay has potential as an antimicrobial stewardship tool; costing and impact on clinical outcome in patients with S. aureus bloodstream infection should be assessed.
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Affiliation(s)
- Kessendri Reddy
- Division of Medical Microbiology and Immunology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Services Tygerberg, Cape Town, South Africa.
| | - Andrew Whitelaw
- Division of Medical Microbiology and Immunology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Services Tygerberg, Cape Town, South Africa
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Singh-Moodley A, Lowe M, Mogokotleng R, Perovic O. Diversity of SCCmec elements and spa types in South African Staphylococcus aureus mecA-positive blood culture isolates. BMC Infect Dis 2020; 20:816. [PMID: 33167886 PMCID: PMC7654578 DOI: 10.1186/s12879-020-05547-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The prevalence of Staphylococcus aureus varies depending on the healthcare facility, region and country. To understand its genetic diversity, transmission, dissemination, epidemiology and evolution in a particular geographical location, it is important to understand the similarities and variations in the population being studied. This can be achieved by using various molecular characterisation techniques. This study aimed to provide detailed molecular characterisation of South African mecA-positive S. aureus blood culture isolates by describing the SCCmec types, spa types and to lesser extent, the sequence types obtained from two consecutive national surveillance studies. METHODS S. aureus blood culture isolates from a national laboratory-based and enhanced surveillance programme were identified and antimicrobial susceptibility testing was performed using automated systems. A real-time PCR assay confirmed the presence of the methicillin-resistance determinant, mecA. Conventional PCR assays were used to identify the SCCmec type and spa type, which was subsequently analysed using the Ridom StaphType™ software. Multilocus sequence typing was performed on selected isolates using conventional methods. MRSA clones were defined by their sequence type (ST), SCCmec type and spa type. RESULTS A detailed description of findings is reported in this manuscript. SCCmec type III predominated overall followed by type IV. A total of 71 different spa types and 24 novel spa types were observed. Spa type t037 was the most common and predominated throughout followed by t1257. Isolates were multidrug resistant; isolates belonging to all SCCmec types were resistant to most of the antibiotics with the exception of type I; isolates with spa type t045 showed resistance to all antibiotics except vancomycin. The most diverse SCCmec-spa type complex was composed of the SCCmec type IV element and 53 different spa types. CONCLUSION Although ST data was limited, thereby limiting the number of clones that could be identified, the circulating clones were relatively diverse.
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Affiliation(s)
- Ashika Singh-Moodley
- National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa. .,Faculty of Health Sciences, School of Pathology, Department of Clinical Microbiology and Infectious Diseases, University of the Witwatersrand, Private Bag 3, Wits, Johannesburg, 2050, South Africa.
| | - Michelle Lowe
- National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Ruth Mogokotleng
- National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Olga Perovic
- National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Faculty of Health Sciences, School of Pathology, Department of Clinical Microbiology and Infectious Diseases, University of the Witwatersrand, Private Bag 3, Wits, Johannesburg, 2050, 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] [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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10
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Genovese C, La Fauci V, D'Amato S, Squeri A, Anzalone C, Costa GB, Fedele F, Squeri R. Molecular epidemiology of antimicrobial resistant microorganisms in the 21th century: a review of the literature. ACTA BIO-MEDICA : ATENEI PARMENSIS 2020; 91:256-273. [PMID: 32420962 PMCID: PMC7569612 DOI: 10.23750/abm.v91i2.9176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/10/2020] [Indexed: 12/26/2022]
Abstract
Healthcare-associated infections (HAIs) are the most frequent and severe complication acquired in healthcare settings with high impact in terms of morbidity, mortality and costs. Many bacteria could be implicated in these infections, but, expecially multidrug resistance bacteria could play an important role. Many microbial typing technologies have been developed until to the the bacterial whole-genome sequencing and the choice of a molecular typing method therefore will depend on the skill level and resources of the laboratory and the aim and scale of the investigation. In several studies the molecular investigation of pathogens involved in HAIs was performed with many microorganisms identified as causative agents such as Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Clostridium difficile, Acinetobacter spp., Enterobacter spp., Enterococcus spp., Staphylococcus aureus and several more minor species. Here, we will describe the most and least frequently reported clonal complex, sequence types and ribotypes with their worldwide geographic distribution for the most important species involved in HAIs.
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Affiliation(s)
- Cristina Genovese
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Vincenza La Fauci
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Smeralda D'Amato
- Postgraduate Medical School in Hygiene and Preventive Medicine, University of Messina, Italy.
| | - Andrea Squeri
- Department of Human Pathology of the adult and developmental age Gaetano Barresi, University of Messina, Messina, Italy.
| | - Carmelina Anzalone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Gaetano Bruno Costa
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Francesco Fedele
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
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11
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Osei Sekyere J, Mensah E. Molecular epidemiology and mechanisms of antibiotic resistance in Enterococcus spp., Staphylococcus spp., and Streptococcus spp. in Africa: a systematic review from a One Health perspective. Ann N Y Acad Sci 2020; 1465:29-58. [PMID: 31647583 DOI: 10.1111/nyas.14254] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 08/04/2019] [Accepted: 09/17/2019] [Indexed: 12/19/2022]
Abstract
A systematic review of antibiotic-resistant Gram-positive bacteria in Africa from a One Health perspective is lacking. Here, we report result from a search for English-language articles on the resistance mechanisms and clonality of Gram-positive bacteria in Africa between 2007 and 2019 reported in PubMed, Web of Science, ScienceDirect, and African Journals OnLine; 172 studies from 22 different African countries were identified. Resistance genes, such as mecA, erm(B), erm(C), tet(M), tet(K), tet(L), vanB, vanA, vanC, and tet(O), were found to be common. Staphylococcus spp., Enterococcus spp., and Streptococcus spp. were the main species reported by the studies, with clones such as Staphylococcus aureus ST5 (n = 218 isolates), ST8 (n = 127 isolates), ST80 (n = 133 isolates), and ST88 (n = 117 isolates), and mobile genetic elements such as IS16 (n = 28 isolates), IS256 (n = 96), Tn916 (n = 107 isolates), and SCCmec (n = 4437 isolates) identified. SCCmec IV (n = 747 isolates) was predominant, followed by SCCmec III (n = 305 isolates), SCCmec II (n = 163 isolates), SCCmec V (n = 135 isolates), and SCCmec I (n = 79 isolates). Resistance to penicillin (n = 5926 isolates), tetracycline (n = 5300 isolates), erythromycin (n = 5151 isolates), rifampicin (n = 3823 isolates), gentamycin (n = 3494 isolates), sulfamethoxazole/trimethoprim (n = 3089 isolates), and ciprofloxacin (n = 2746 isolates) was common in most reports from 22 countries. Clonal dissemination of resistance across countries and between humans, animals, and the environment was observed. Resistance rates ranged from 1.4% to 100% for 15 of the studies; 10 were One Health-related studies. Strict infection control measures, antimicrobial stewardship, and periodic One Health epidemiological surveillance studies are needed to monitor and contain the threat of increasing antibiotic resistance in Africa.
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Affiliation(s)
- John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Eric Mensah
- Kumasi Centre for Collaborative Research in Tropical Medicine, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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12
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Kalayu AA, Woldetsadik DA, Woldeamanuel Y, Wang SH, Gebreyes WA, Teferi T. Burden and antimicrobial resistance of S. aureus in dairy farms in Mekelle, Northern Ethiopia. BMC Vet Res 2020; 16:20. [PMID: 31969151 PMCID: PMC6977269 DOI: 10.1186/s12917-020-2235-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/07/2020] [Indexed: 12/23/2022] Open
Abstract
Background Staphylococcus aureus is a frequent colonizer of human and several animal species, including dairy cows. It is the most common cause of intramammary infections in dairy cows. Its public health importance increases inline to the continuous emergence of drug-resistant strains; such as Methicillin-resistant S. aureus (MRSA). Indeed, the recent emergence of human and veterinary adapted MRSA demands serious attention. The aim of this study was to determine the burden and drug resistance pattern of S. aureus in dairy farms in Mekelle and determine the molecular characteristics of MRSA. Results This study was done on 385 lactating dairy cows and 71 dairy farmers. The ages of the cows and farmworkers were between 3 and 14 and 17–63 years respectively. S. aureus was isolated from 12.5% of cows and 31% of farmworkers. Highest resistance was observed for penicillin (> 90%) followed by tetracycline (32–35%) and trimethoprim-sulphamethoxazole (10–27%). But no resistance was observed for vancomycin, daptomycin, and rifampin. Only one isolate was MRSA both phenotypically and harboring mecA. This isolate was from nasal of a farmworker and was MRSA SCCmec Iva, spa type t064 of CC8. Multi-drug resistance was observed in 6.2% of cow isolates and 13.6% of nasal isolates. Conclusions In this study, S. aureus infected 12.5% of dairy cows and colonized 31% of farmworkers. Except for penicillin, resistance to other drugs was rare. Although no MRSA was found from dairy cows the existence of the human and animal adapted and globally spread strain, MRSA SCCmec IVa spa t064, warrants for a coordinated action to tackle AMR in both human and veterinary in the country.
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Affiliation(s)
- Alem Abrha Kalayu
- Department of Microbiology, Yekatit 12 Hospital Medical College, MCH building, 3rd floor, Room number 321, Addis Ababa, Ethiopia.
| | - Daniel Asrat Woldetsadik
- Department of Microbiology, Immunology and Parasitology; College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Yimtubezinash Woldeamanuel
- Department of Microbiology, Immunology and Parasitology; College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Shu-Hua Wang
- Infectious Disease Division, Internal Medicine Department, College of Medicine, the Ohio State University, Columbus, USA
| | - Wondwossen A Gebreyes
- Molecular Epidemiology, College of Veterinary Medicine, the Ohio State University, Columbus, USA
| | - Tadesse Teferi
- Tropical Veterinary Medicine, College of Veterinary Medicine, Mekelle University, Mekelle, Ethiopia
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13
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The association between pathogen factors and clinical outcomes in patients with Staphylococcus aureus bacteraemia in a tertiary hospital, Cape Town. Int J Infect Dis 2019; 91:111-118. [PMID: 31790814 DOI: 10.1016/j.ijid.2019.11.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Staphylococcus aureus is a serious pathogen, able to cause life-threatening infections such as bacteraemia. The association between S. aureus microbial characteristics and clinical outcomes is under-investigated in African settings. This study aimed to determine the molecular epidemiology and virulence characteristics of S. aureus isolates from bacteraemic patients at Tygerberg Hospital, South Africa, and to investigate the associations between pathogen characteristics and clinical outcomes. METHODS This study included 199 S. aureus isolates collected from blood cultures between February 2015 and March 2017. Methicillin resistance was determined using disc diffusion and all resistant isolates were further characterized by staphylococcal cassette chromosome mec (SCCmec) typing. Genotyping was done using spa and agr typing, and agr functionality was assessed using the phenotypic δ-haemolysin assay. Logistic regression models were performed to describe the associations between strain characteristics and the clinical outcomes methicillin resistance, in-hospital mortality, and length of stay (LOS). RESULTS Of the 199 S. aureus isolates collected, 27% were MRSA, and the overall crude in-hospital mortality rate was 29%. Seventy-three different spa types were identified, including seven new types. Agr I was the most common type, in 99 (49.7%) isolates, followed by agr II, III, and IV in 57 (28.6%), 37 (18.6%), and six (3%) isolates, respectively. Agr dysfunctionality was observed in 25 (13%) isolates, mostly belonging to spa-clonal complex (CC) 012. Methicillin resistance was significantly associated with hospital-acquired infection (odds ratio (OR) 4.77, 95% confidence interval (CI) 2.09-10.87). A significant increase in mortality was observed with increasing age (OR 7.48, 95% CI 2.82-19.8) and having a hospital-acquired infection (OR 2.26, 95% CI 1.12-4.55). S. aureus strains with a functional agr system showed an association with longer duration of stay (OR 1.66, 95% CI 0.93-2.99). CONCLUSIONS We report the lowest MRSA prevalence at Tygerberg Hospital for the past 10 years, and agr dysfunctionality was shown to be driven by a certain genotype, spa-CC012. Despite the limited available clinical data, the study provided insights into associations between S. aureus epidemiology and agr-related virulence characteristics, and clinical outcomes.
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14
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Singh-Moodley A, Strasheim W, Mogokotleng R, Ismail H, Perovic O. Unconventional SCCmec types and low prevalence of the Panton-Valentine Leukocidin exotoxin in South African blood culture Staphylococcus aureus surveillance isolates, 2013-2016. PLoS One 2019; 14:e0225726. [PMID: 31774877 PMCID: PMC6881059 DOI: 10.1371/journal.pone.0225726] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/11/2019] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus aureus is a healthcare-associated pathogen that can harbour multiple antimicrobial resistance determinants and express multiple virulence factors e.g. Panton-Valentine Leukocidin (PVL). Unknown staphylococcal cassette chromosome mec (SCCmec) typing patterns were previously observed among 11% (n = 52) of methicillin-resistant S. aureus (MRSA) isolates; we further investigated these as well as the proportion of PVL, encoded by lukS/F-PV, in 761 S. aureus isolates from patients with a diagnosis of pneumonia/lower respiratory tract, skin/soft tissue, bone and joint infection. S. aureus isolates from blood culture were identified and antimicrobial susceptibility testing was performed using automated systems. Conventional PCR assays were used to identify the ccr and mec gene complexes in mecA-positive isolates with an unknown SCCmec type and screen for lukS/F-PV. Epidemiological data was used to classify isolates as healthcare- or community-associated infections. Antimicrobial susceptibility profiles according to SCCmec type and PVL were reported. Of the unknown SCCmec types, isolates were interpreted as type I-like (86%, 38/44), type II-like (9%, 4/44) and type III-like (5%, 2/44). Eight isolates did not produce definitive results. Of all MRSA isolates, majority were multidrug-resistant as indicated by their non-susceptibility to most antimicrobial agents; 92% were healthcare-associated. PVL was seen in 14% of the isolates (MRSA: 25%, MSSA: 75%); 56% were classified as healthcare-associated infection. The SCCmec typing method did not definitively classify all unknown isolates into clearly defined types. It showed that majority of these isolates were not the conventional types; untypeable elements appeared to be composite SCCmec elements, consisting of multiple ccr gene complexes. Majority of the MRSA isolates were non-susceptible to most antibiotics indicating that multiple resistance genes are present in our population. Furthermore, the proportion of PVL was low and more prevalent in MSSA.
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Affiliation(s)
- 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, Johannesburg, South Africa
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Wilhelmina Strasheim
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, 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, Johannesburg, South Africa
| | - Husna Ismail
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, 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, Johannesburg, South Africa
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
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15
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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] [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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16
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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. THE SCIENCE OF THE TOTAL ENVIRONMENT 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] [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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