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Patel S, Jooste E, Glynos C, Mbajiorgu O, Sipahlanga A, Ngubane W, Maharaj G, Moeng MS, Luvhengo TE. Microbiology and Antimicrobial Resistance Profile in Patients with Diabetic Foot Sepsis at a Central Hospital in Johannesburg, South Africa. Diagnostics (Basel) 2024; 15:32. [PMID: 39795560 PMCID: PMC11720570 DOI: 10.3390/diagnostics15010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 12/16/2024] [Accepted: 12/23/2024] [Indexed: 01/13/2025] Open
Abstract
Background: Diabetic foot sepsis (DFS) is the leading cause of lower extremity amputations and timely initiation of effective antimicrobial therapy is paramount during its management. This study investigated causative microorganisms and their antimicrobial susceptibility profile in patients with DFS. Materials and Methods: A retrospective review was conducted on patients who were 18-years and older admitted with DFS. Data collected included demographic information, comorbidities, clinical findings, types of specimens collected and results of microscopy, culture, and sensitivity (MC&S), treatment, and outcomes. Results: One hundred and sixty-eight records were found, of which 64.3% were of male patients. The median (IQR) age of males was 58 years (IQR 54-65) compared to 61 years (IQR 54-67) for females. Results of MC&S were available in 63.1% of the records, and E. faecalis was cultured in 16%, P. mirabilis in 10%, and S. aureus in 8% of cases. Amoxicillin/Clavulanic acid was prescribed in 69% of the cases. Resistance to at least one antimicrobial was shown in 88% of S. aureus and 80% of P. mirabilis species. Conclusions: The commonly cultured organisms in patients with DFS were E. faecalis 16%, P. mirabilis 10%, and S. aureus. Amoxicillin/Clavulanic was prescribed empirically in 69% of the cases despite high rates of resistance, and in 37% treatment was not preceded by collection of specimens for MC&S. We therefore recommend collection of specimens for MC&S before initiation of antimicrobial therapy in all patients with DFS.
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Affiliation(s)
- Simran Patel
- Unit of Undergraduate Medical Education, University of the Witwatersrand, Johannesburg 2017, South Africa; (S.P.); (E.J.); (C.G.); (O.M.); (A.S.); (W.N.); (G.M.)
| | - Emeline Jooste
- Unit of Undergraduate Medical Education, University of the Witwatersrand, Johannesburg 2017, South Africa; (S.P.); (E.J.); (C.G.); (O.M.); (A.S.); (W.N.); (G.M.)
| | - Charalambia Glynos
- Unit of Undergraduate Medical Education, University of the Witwatersrand, Johannesburg 2017, South Africa; (S.P.); (E.J.); (C.G.); (O.M.); (A.S.); (W.N.); (G.M.)
| | - Onyiyechukwu Mbajiorgu
- Unit of Undergraduate Medical Education, University of the Witwatersrand, Johannesburg 2017, South Africa; (S.P.); (E.J.); (C.G.); (O.M.); (A.S.); (W.N.); (G.M.)
| | - Anelisa Sipahlanga
- Unit of Undergraduate Medical Education, University of the Witwatersrand, Johannesburg 2017, South Africa; (S.P.); (E.J.); (C.G.); (O.M.); (A.S.); (W.N.); (G.M.)
| | - Wandile Ngubane
- Unit of Undergraduate Medical Education, University of the Witwatersrand, Johannesburg 2017, South Africa; (S.P.); (E.J.); (C.G.); (O.M.); (A.S.); (W.N.); (G.M.)
| | - Gopala Maharaj
- Unit of Undergraduate Medical Education, University of the Witwatersrand, Johannesburg 2017, South Africa; (S.P.); (E.J.); (C.G.); (O.M.); (A.S.); (W.N.); (G.M.)
| | - Maeyane Stephens Moeng
- Department of Surgery, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2193, South Africa;
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Shobo CO, Amoako DG, Allam M, Ismail A, Essack SY, Bester LA. A Genomic Snapshot of Antibiotic-Resistant Enterococcus faecalis within Public Hospital Environments in South Africa. Glob Health Epidemiol Genom 2023; 2023:6639983. [PMID: 37342729 PMCID: PMC10279497 DOI: 10.1155/2023/6639983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
Abstract
Enterococci are among the most common opportunistic hospital pathogens. This study used whole-genome sequencing (WGS) and bioinformatics to determine the antibiotic resistome, mobile genetic elements, clone and phylogenetic relationship of Enterococcus faecalis isolated from hospital environments in South Africa. This study was carried out from September to November 2017. Isolates were recovered from 11 frequently touched sites by patients and healthcare workers in different wards at 4 levels of healthcare (A, B, C, and D) in Durban, South Africa. Out of the 245 identified E. faecalis isolates, 38 isolates underwent whole-genome sequencing (WGS) on the Illumina MiSeq platform, following microbial identification and antibiotic susceptibility tests. The tet(M) (31/38, 82%) and erm(C) (16/38, 42%) genes were the most common antibiotic-resistant genes found in isolates originating from different hospital environments which corroborated with their antibiotic resistance phenotypes. The isolates harboured mobile genetic elements consisting of plasmids (n = 11) and prophages (n = 14) that were mostly clone-specific. Of note, a large number of insertion sequence (IS) families were found on the IS3 (55%), IS5 (42%), IS1595 (40%), and Tn3 transposons the most predominant. Microbial typing using WGS data revealed 15 clones with 6 major sequence types (ST) belonging to ST16 (n = 7), ST40 (n = 6), ST21 (n = 5), ST126 (n = 3), ST23 (n = 3), and ST386 (n = 3). Phylogenomic analysis showed that the major clones were mostly conserved within specific hospital environments. However, further metadata insights revealed the complex intraclonal spread of these E. faecalis major clones between the sampling sites within each specific hospital setting. The results of these genomic analyses will offer insights into antibiotic-resistantE. faecalis in hospital environments relevant to the design of optimal infection prevention strategies in hospital settings.
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Affiliation(s)
- Christiana O. Shobo
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- School of Laboratory Medicine and Medical Science, Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4000, South Africa
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Daniel G. Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, UAE
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Linda A. Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
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