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Kiros T, Belete D, Andualem T, Workineh L, Tilahun M, Eyayu T, Getie B, Tiruneh T, Kiflom S, Damtie S, Gebreyesus T. Carriage of β-lactamase and carbapenemase-producing Enterobacteriaceae in hospitalized patients at debre tabor comprehensive specialized hospital. Heliyon 2023; 9:e20072. [PMID: 37809731 PMCID: PMC10559802 DOI: 10.1016/j.heliyon.2023.e20072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
Background Antimicrobial resistance has remained global public health threat. Carriage with drug-resistant bacterial pathogens, particularly beta-lactamase and carbapenemase-producing Enterobacteriaceae is among the most concerning. The purpose of this study was to look into the magnitude, antimicrobial resistance patterns, and associated risk factors among hospitalized patients. Methods A facility-based cross-sectional study was conducted on 383 hospitalized patients at Debre Tabor Comprehensive Specialized Hospital between September 2022 and May 2023. A pre-tested structured questionnaire was used to collect sociodemographic and clinical data. The data on the etiologic agent was collected using standard bacteriological techniques. Briefly, stool specimens were collected aseptically into sterile, leak-proof stool cups. The stool sample was inoculated onto MacConkey agar and incubated aerobically at 37 °C for 24 h. The species isolation and antimicrobial resistance patterns were then performed adhering to bacteriological procedures. In the analysis, a p-value of <0.05 was considered statistically significant. Results There were 383 study participants, and men made up the majority (55.6%). The study participants' mean age was 33 ± 18 years. Three hundred and seventy-seven (88%) of the study's participants had no previous history of antibiotic use. There were 102 (26.6%) and 21 (5.5%) cases of gastrointestinal carriage caused by Enterobacteriaceae that produce beta-lactamase and carbapenemase, respectively. In total, 175 isolates of Enterobacteriaceae were detected. E. coli (n = 89) and K. pneumoniae (n = 51) were the most frequently recovered. In this study, 46 (79.3%) and 8 (13.8%) isolates of E. coli that produce beta-lactamase were resistant to ampicillin and amoxicillin/clavulanic acid, respectively. Furthermore, participants who had previously used antibiotics experienced a two-fold increase in exposure to gastrointestinal tract carriage by carbapenemase-producing Enterobacteriaceae [AOR, 95% CI (2.01, 1.06-2.98), p = 0.001]. Conclusions The emergence of drug-resistant pathogens is a growing concern. An increase in the prevalence of drug-resistant infections in hospitalized patients is warranting further investigation.
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Affiliation(s)
- Teklehaimanot Kiros
- Department of Medical Laboratory Sciences, College of Health Sciences and School of Medicine, Debre Tabor University, Debre Tabor, Ethiopia
| | - Debaka Belete
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Tesfaye Andualem
- Department of Medical Laboratory Sciences, College of Health Sciences and School of Medicine, Debre Tabor University, Debre Tabor, Ethiopia
| | - Lemma Workineh
- Department of Medical Laboratory Sciences, College of Health Sciences and School of Medicine, Debre Tabor University, Debre Tabor, Ethiopia
| | - Mekdes Tilahun
- Department of Medical Laboratory Sciences, College of Health Sciences and School of Medicine, Debre Tabor University, Debre Tabor, Ethiopia
| | - Tahir Eyayu
- Department of Medical Laboratory Sciences, College of Health Sciences and School of Medicine, Debre Tabor University, Debre Tabor, Ethiopia
| | - Birhanu Getie
- Department of Medical Laboratory Sciences, College of Health Sciences and School of Medicine, Debre Tabor University, Debre Tabor, Ethiopia
| | - Tegenaw Tiruneh
- Department of Medical Laboratory Sciences, College of Health Sciences and School of Medicine, Debre Tabor University, Debre Tabor, Ethiopia
| | - Saymon Kiflom
- College of Natural and Computational Sciences, Mekelle University, Mekelle, Ethiopia
| | - Shewaneh Damtie
- Department of Medical Laboratory Sciences, College of Health Sciences and School of Medicine, Debre Tabor University, Debre Tabor, Ethiopia
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Owusu FA, Obeng-Nkrumah N, Gyinae E, Kodom S, Tagoe R, Tabi BKA, Dayie NTKD, Opintan JA, Egyir B. Occurrence of Carbapenemases, Extended-Spectrum Beta-Lactamases and AmpCs among Beta-Lactamase-Producing Gram-Negative Bacteria from Clinical Sources in Accra, Ghana. Antibiotics (Basel) 2023; 12:1016. [PMID: 37370334 DOI: 10.3390/antibiotics12061016] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Beta-lactamase (β-lactamase)-producing Gram-negative bacteria (GNB) are of public health concern due to their resistance to routine antimicrobials. We investigated the antimicrobial resistance and occurrence of carbapenemases, extended-spectrum β-lactamases (ESBLs) and AmpCs among GNB from clinical sources. GNB were identified using matrix-assisted laser desorption/ionization time of flight-mass spectrometry (MALDITOF-MS). Antimicrobial susceptibility testing was performed via Kirby-Bauer disk diffusion and a microscan autoSCAN system. β-lactamase genes were determined via multiplex polymerase chain reactions. Of the 181 archived GNB analyzed, Escherichia coli and Klebsiella pneumoniae constituted 46% (n = 83) and 17% (n = 30), respectively. Resistance to ampicillin (51%), third-generation cephalosporins (21%), and ertapenem (21%) was observed among the isolates, with 44% being multi-drug resistant (MDR). β-lactamase genes such as AmpCs ((blaFOX-M (64%) and blaDHA-M and blaEDC-M (27%)), ESBLs ((blaCTX-M (81%), other β-lactamase genes blaTEM (73%) and blaSHV (27%)) and carbapenemase ((blaOXA-48 (60%) and blaNDM and blaKPC (40%)) were also detected. One K. pneumoniae co-harbored AmpC (blaFOX-M and blaEBC-M) and carbapenemase (blaKPC and blaOXA-48) genes. blaOXA-48 gene was detected in one carbapenem-resistant Acinetobacter baumannii. Overall, isolates were resistant to a wide range of antimicrobials including last-line treatment options. This underpins the need for continuous surveillance for effective management of infections caused by these pathogens in our settings.
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Affiliation(s)
- Felicia A Owusu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra 00233, Ghana
| | - Noah Obeng-Nkrumah
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra 00233, Ghana
| | - Esther Gyinae
- Department of Microbiology, Korle-Bu Teaching Hospital, Accra 00233, Ghana
| | | | - Rhodalyn Tagoe
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra 00233, Ghana
| | - Blessing Kofi Adu Tabi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra 00233, Ghana
| | - Nicholas T K D Dayie
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra 00233, Ghana
| | - Japheth A Opintan
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra 00233, Ghana
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra 00233, Ghana
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3
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Ramatla T, Tawana M, Lekota KE, Thekisoe O. Antimicrobial resistance genes of Escherichia coli, a bacterium of "One Health" importance in South Africa: Systematic review and meta-analysis. AIMS Microbiol 2023; 9:75-89. [PMID: 36891533 PMCID: PMC9988412 DOI: 10.3934/microbiol.2023005] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
This is a systematic review and meta-analysis that evaluated the prevalence of Escherichia coli antibiotic-resistant genes (ARGs) in animals, humans, and the environment in South Africa. This study followed Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines to search and use literature published between 1 January 2000 to 12 December 2021, on the prevalence of South African E. coli isolates' ARGs. Articles were downloaded from African Journals Online, PubMed, ScienceDirect, Scopus, and Google Scholar search engines. A random effects meta-analysis was used to estimate the antibiotic-resistant genes of E. coli in animals, humans, and the environment. Out of 10764 published articles, only 23 studies met the inclusion criteria. The obtained results indicated that the pooled prevalence estimates (PPE) of E. coli ARGs was 36.3%, 34.4%, 32.9%, and 28.8% for blaTEM-M-1 , ampC, tetA, and bla TEM, respectively. Eight ARGs (blaCTX-M , blaCTX-M-1 , blaTEM , tetA, tetB, sul1, sulII, and aadA) were detected in humans, animals and the environmental samples. Human E. coli isolate samples harboured 38% of the ARGs. Analyzed data from this study highlights the occurrence of ARGs in E. coli isolates from animals, humans, and environmental samples in South Africa. Therefore, there is a necessity to develop a comprehensive "One Health" strategy to assess antibiotics use in order to understand the causes and dynamics of antibiotic resistance development, as such information will enable the formulation of intervention strategies to stop the spread of ARGs in the future.
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Affiliation(s)
- Tsepo Ramatla
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2531, South Africa
| | - Mpho Tawana
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2531, South Africa
| | - Kgaugelo E Lekota
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2531, South Africa
| | - Oriel Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2531, South Africa
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Prevalence and Molecular Characterisation of Extended-Spectrum Beta-Lactamase-Producing Shiga Toxin-Producing Escherichia coli, from Cattle Farm to Aquatic Environments. Pathogens 2022; 11:pathogens11060674. [PMID: 35745529 PMCID: PMC9230396 DOI: 10.3390/pathogens11060674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 01/23/2023] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing bacteria are a major problem for public health worldwide because of limited treatment options. Currently, only limited information is available on ESBL-producing Shiga toxin-producing Escherichia coli (STEC) in cattle farms and the surrounding aquatic environment. This study sought to track and characterise ESBL-producing STEC disseminating from a cattle farm into the water environment. Animal husbandry soil (HS), animal manure (AM), animal drinking water (ADW), and nearby river water (NRW) samples were collected from the cattle farm. Presumptive ESBL-producing STEC were isolated and identified using chromogenic media and mass spectrophotometry methods (MALDI-TOF-MS), respectively. The isolates were subjected to molecular analysis, and all confirmed ESBL-producing STEC isolates were serotyped for their O serogroups and assessed for antibiotic resistance genes (ARGs) and for the presence of selected virulence factors (VFs). A phylogenetic tree based on the multilocus sequences was constructed to determine the relatedness among isolates of ESBL-producing STEC. The highest prevalence of ESBL-producing STEC of 83.33% was observed in HS, followed by ADW with 75%, NRW with 68.75%, and the lowest was observed in AM with 64.58%. Out of 40 randomly selected isolates, 88% (n = 35) belonged to the serogroup O45 and 13% (n = 5) to the serogroup O145. The multilocus sequence typing (MLST) analysis revealed four different sequence types (STs), namely ST10, ST23, ST165, and ST117, and the predominant ST was found to be ST10. All 40 isolates carried sul1 (100%), while blaOXA, blaCTX-M, sul2, blaTEM, and qnrS genes were found in 98%, 93%, 90%, 83%, and 23% of the 40 isolates, respectively. For VFs, only stx2 was detected in ESBL-producing STEC isolates. The results of the present study indicated that a cattle environment is a potential reservoir of ESBL-producing STEC, which may disseminate into the aquatic environment through agricultural runoff, thus polluting water sources. Therefore, continual surveillance of ESBL-producing STEC non-O157 would be beneficial for controlling and preventing STEC-related illnesses originating from livestock environments.
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Verma J, Jain D, Mallik D, Ghosh AS. Comparative insight into the roles of the non active-site residues E169 and N173 in imparting the beta-lactamase activity of CTX-M-15. FEMS Microbiol Lett 2022; 369:6530193. [PMID: 35175332 DOI: 10.1093/femsle/fnac018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/03/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
CTX-M-15 is a major extended-spectrum beta-lactamase disseminated throughout the globe. The roles of amino acids present in the active-site are widely studied though little is known about the role of the amino acids lying at the close proximity of the CTX-M-15 active-site. Here, by using site-directed mutagenesis we attempted to decipher the role of individual amino acids lying outside the active-site in imparting the beta-lactamase activity of CTX-M-15. Based on the earlier evidence, three amino acid residues namely, Glu169, Asp173 and Arg277 were substituted with alanine. The antibiotic susceptibility of E. coli cells harboring E169A and N173A substituted CTX-M-15 were enhanced by ∼ >32 fold for penicillins and ∼ 4-32 fold for cephalosporins, in comparison to CTX-M-15. However, cells carrying CTX-M-15_R277A did not show a significant difference in antibiotic susceptibility as compared to the wild-type. Further, the catalytic efficiency of the purified CTX-M-15_E169A and CTX-M-15_N173A were compromised when compared with the efficient beta-lactam hydrolysis of purified CTX-M-15. Moreover, the thermal stability of the mutated proteins CTX-M-15_E169A and CTX-M-15_N173A were reduced as compared to the wild type CTX-M-15. Therefore, we conclude that E169 and N173 are crucial non-active-site amino acids that are able to govern the CTX-M-15 activity.
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Affiliation(s)
- Jyoti Verma
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Diamond Jain
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Dhriti Mallik
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Anindya S Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
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6
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Takawira FT, Pitout JD, Thilliez G, Mashe T, Gutierrez AV, Kingsley RA, Peirano G, Matheu J, Midzi SM, Mwamakamba LW, Gally DL, Tarupiwa A, Mukavhi L, Ehlers MM, Mtapuri-Zinyowera S, Kock MM. Molecular epidemiology of extended-spectrum beta-lactamase-producing extra-intestinal pathogenic Escherichia coli strains over a 2-year period (2017-2019) from Zimbabwe. Eur J Clin Microbiol Infect Dis 2021:10.1007/s10096-021-04379-z. [PMID: 34779943 DOI: 10.1007/s10096-021-04379-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/20/2021] [Indexed: 10/19/2022]
Abstract
This study was designed to characterize extended-spectrum beta-lactamase (ESBL)-producing extra-intestinal pathogenic Escherichia coli (E.coli) (ExPEC) associated with urinary tract infections in nine different geographic regions of Zimbabwe over a 2-year period (2017-2019). A total of 48 ESBL-positive isolates from urine specimen were selected for whole-genome sequencing from 1246 Escherichia coli isolates biobanked at the National Microbiology Reference laboratory using phenotypic susceptibility testing results from the National Escherichia coli Surveillance Programme to provide representation of different geographical regions and year of isolation. The majority of ESBL E. coli isolates produced cefotaximase-Munich (CTX-M)-15, CTX-M-27, and CTX-M-14. In this study, sequence types (ST) 131 and ST410 were the most predominant antimicrobial-resistant clones and responsible for the increase in ESBL-producing E. coli strains since 2017. Novel ST131 complex strains were recorded during the period 2017 to 2018, thus showing the establishment and evolution of this antimicrobial-resistant ESBL clone in Zimbabwe posing an important public health threat. Incompatibility group F plasmids were predominant among ST131 and ST410 isolates with the following replicons recorded most frequently: F1:A2:B20 (9/19, 47%), F2:A1: B (5/19, 26%), and F1:A1:B49 (8/13, 62%). The results indicate the need for continuous tracking of different ESBL ExPEC clones on a global scale, while targeting specific STs (e.g. ST131 and ST410) through control programs will substantially decrease the spread of ESBLs among ExPEC.
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Affiliation(s)
- Faustinos Tatenda Takawira
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Johann Dd Pitout
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Microbiology, Alberta Precision Laboratories, Department Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Tapfumanei Mashe
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | | | | | - Gisele Peirano
- Department of Microbiology, Alberta Precision Laboratories, Department Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jorge Matheu
- World Health Organization (WHO), Geneva, Switzerland
| | | | | | - David L Gally
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Edinburgh, Scotland
| | - Andrew Tarupiwa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Leckson Mukavhi
- University of Zimbabwe College of Health Sciences, Health Professions Education, Harare, Zimbabwe
| | - Marthie M Ehlers
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- National Health Laboratory Service, Academic Division, Pretoria, South Africa
| | | | - Marleen M Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.
- National Health Laboratory Service, Academic Division, Pretoria, South Africa.
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Richter L, du Plessis EM, Duvenage S, Allam M, Ismail A, Korsten L. Whole Genome Sequencing of Extended-Spectrum- and AmpC- β-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa. Front Microbiol 2021; 12:734649. [PMID: 34659162 PMCID: PMC8517129 DOI: 10.3389/fmicb.2021.734649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase- (AmpC) producing Enterobacterales in irrigation water and associated irrigated fresh produce represents risks related to the environment, food safety, and public health. In South Africa, information about the presence of ESBL/AmpC-producing Enterobacterales from non-clinical sources is limited, particularly in the water-plant-food interface. This study aimed to characterize 19 selected MDR ESBL/AmpC-producing Escherichia coli (n=3), Klebsiella pneumoniae (n=5), Serratia fonticola (n=10), and Salmonella enterica (n=1) isolates from spinach and associated irrigation water samples from two commercial spinach production systems within South Africa, using whole genome sequencing (WGS). Antibiotic resistance genes potentially encoding resistance to eight different classes were present, with bla CTX-M-15 being the dominant ESBL encoding gene and bla ACT-types being the dominant AmpC encoding gene detected. A greater number of resistance genes across more antibiotic classes were seen in all the K. pneumoniae strains, compared to the other genera tested. From one farm, bla CTX-M-15-positive K. pneumoniae strains of the same sequence type 985 (ST 985) were present in spinach at harvest and retail samples after processing, suggesting successful persistence of these MDR strains. In addition, ESBL-producing K. pneumoniae ST15, an emerging high-risk clone causing nosocomical outbreaks worldwide, was isolated from irrigation water. Known resistance plasmid replicon types of Enterobacterales including IncFIB, IncFIA, IncFII, IncB/O, and IncHI1B were observed in all strains following analysis with PlasmidFinder. However, bla CTX-M-15 was the only β-lactamase resistance gene associated with plasmids (IncFII and IncFIB) in K. pneumoniae (n=4) strains. In one E. coli and five K. pneumoniae strains, integron In191 was observed. Relevant similarities to human pathogens were predicted with PathogenFinder for all 19 strains, with a confidence of 0.635-0.721 in S. fonticola, 0.852-0.931 in E. coli, 0.796-0.899 in K. pneumoniae, and 0.939 in the S. enterica strain. The presence of MDR ESBL/AmpC-producing E. coli, K. pneumoniae, S. fonticola, and S. enterica with similarities to human pathogens in the agricultural production systems reflects environmental and food contamination mediated by anthropogenic activities, contributing to the spread of antibiotic resistance genes.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Erika M. du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
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Zwane T, Shuping L, Perovic O. Etiology and Antimicrobial Susceptibility of Pathogens Associated with Urinary Tract Infections among Women Attending Antenatal Care in Four South African Tertiary-Level Facilities, 2015-2019. Antibiotics (Basel) 2021; 10:669. [PMID: 34199691 PMCID: PMC8229093 DOI: 10.3390/antibiotics10060669] [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: 05/04/2021] [Revised: 05/23/2021] [Accepted: 05/31/2021] [Indexed: 12/29/2022] Open
Abstract
In South Africa, uncomplicated community-acquired UTIs (CA-UTIs) are treated empirically; however, the extent of antibiotic resistance among these pathogens is not well known. We conducted a descriptive cross-sectional study of women attending ANCs at four tertiary public-sector hospitals in Gauteng. Female patients aged 15-49 years, with urine cultures performed between January 2015 and December 2019, were included. A case of culture-confirmed UTI was defined as any woman with ≤2 uropathogens with a bacterial count of ≥105 colony-forming units per ml for at least one pathogen. We identified 3558 cases of culture-confirmed UTIs in women with a median age of 30 years (interquartile range; 25-35). E. coli accounted for most infections (56% (1994/3558)), followed by E. faecalis, with a prevalence of 17% (609/3558). The prevalence of K. pneumoniae was 5% (193/3558), 5% (186/3558) for S. agalactiae, and 5% (179/3558) for P. mirabilis. Ninety-five percent (1827/1927) of the E. coli and 99% of the E. faecalis (301/305) isolates were susceptible to nitrofurantoin. Common uropathogens showed high susceptibility to first-line antibiotics, gentamicin and nitrofurantoin, as recommended for use in primary healthcare settings. Overall, our study provided an indication of the level of antimicrobial resistance in the four facilities.
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Affiliation(s)
- Thembekile Zwane
- Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Private Bag 3 Wits, Johannesburg 2050, South Africa
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Private Bag X4 Sandringham, Johannesburg 2131, South Africa;
- South African Field Epidemiology Training Program, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Private Bag X4 Sandringham, Johannesburg 2131, South Africa
| | - Liliwe Shuping
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Private Bag X4 Sandringham, Johannesburg 2131, South Africa;
| | - Olga Perovic
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Private Bag X4 Sandringham, Johannesburg 2131, South Africa;
- Department of Clinical Microbiology and Infectious Disease, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Private Bag 3 Wits, Johannesburg 2050, South Africa
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Genetic Determinants of Resistance among ESBL-Producing Enterobacteriaceae in Community and Hospital Settings in East, Central, and Southern Africa: A Systematic Review and Meta-Analysis of Prevalence. ACTA ACUST UNITED AC 2021; 2021:5153237. [PMID: 34122680 PMCID: PMC8192179 DOI: 10.1155/2021/5153237] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/17/2020] [Accepted: 05/29/2021] [Indexed: 12/25/2022]
Abstract
Background The world prevalence of community and hospital-acquired extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is increasing tremendously. Bacteria harboring ESBLs are currently the number one critical pathogens posing a major threat to human health. Objective To provide a summary of molecular evidence on the prevalence of ESBL-producing Enterobacteriaceae (ESBL-E) and associated genes at community and hospital settings in East, Central, and Southern African countries. Methods We conducted a systematic literature search on PubMed and Google Scholar databases for the available molecular studies on ESBL-E in hospitals and community settings in East, Central, and Sothern Africa (ECSA). Published studies in English language involving gene characterization of ESBLs from human samples in hospital and community settings were included in the review, inception to November 2019. A random effect meta-analysis was performed to estimate the prevalence of ESBL-E. Results A total of 27 studies involving molecular characterization of resistance genes from 20,225 ESBL-E isolates were included in the analysis. Seventy-four percent of all studies were hospital based, 15% were based in community settings, and others were done in both hospital and community settings. Of all the studies, 63% reported E. coli as the dominant isolate among ESBL-E recovered from clinical samples and Klebsiella pneumoniae was reported dominant isolates in 33% of all studies. A random pooled prevalence of ESBL-E was 38% (95% CI = 24–53%), highest in Congo, 92% (95% CI = 90–94%), and lowest in Zimbabwe, 14% (95% CI = 9–20%). Prevalence was higher in hospital settings 41% (95% CI = 23–58%) compared to community settings 34% (95% CI = 8–60%). ESBL genes detected from clinical isolates with ESBL-E phenotypes in ECSA were those of Ambler molecular class A [1] that belongs to both functional groups 2be and 2d of Bush and Jacob classification of 2010 [2]. Majority of studies (n = 22, 81.5%) reported predominance of blaCTX-M gene among isolates, particularly CTX-M-15. Predictors of ESBL-E included increased age, hospital admissions, previous use of antibiotics, and paramedical use of herbs. Conclusion Few studies have been conducted at a molecular level to understand the genetic basis of increased resistance among members of ESBL-E in ECSA. Limited molecular studies in the ECSA region leave a gap in estimating the burden and risk posed by the carriage of ESBL genes in these countries. We found a high prevalence of ESBL-E most carrying CTX-M enzyme in ECSA with a greater variation between countries. This could be an important call for combined (regional or global) efforts to combat the problem of antimicrobial resistance (AMR) in the region. Antibiotic use and hospital admission increased the carriage of ESBL-E, while poor people contributed little to the increase of AMR due to lack of access and failure to meet the cost of healthcare compared to high income individuals.
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Seni J, Peirano G, Mshana SE, Pitout JDD, DeVinney R. The importance of Escherichia coli clonal complex 10 and ST131 among Tanzanian patients on antimicrobial resistance surveillance programs. Eur J Clin Microbiol Infect Dis 2021:10.1007/s10096-021-04271-w. [PMID: 34009529 DOI: 10.1007/s10096-021-04271-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/04/2021] [Indexed: 11/29/2022]
Abstract
The objective of this study was to characterize antimicrobial resistance (AMR) of WHO priority 1 critical pathogen (extrapathogenic Escherichia coli (ExPEC), sequence types (STs), and ST131 clades from patients in Tanzania so as to guide specific antimicrobial therapies and preventive measures. A total of 143 ExPEC strains (128 from pregnant women with urinary tract infections and 15 from children with blood stream infections) were collected between March 2016 and October 2017. These were characterized into ST-fimH clones by a 7-single nucleotide polymorphism quantitative polymerase chain reaction (7-SNP qPCR) and gene sequencing, and to ST131 clades by multiplex PCR. The extended-spectrum beta-lactamases (ESBL) production was 16.1% (23/143), and was predominantly due to the blaCTX-M-15 (91.3%, n=21). ESBL production was significantly more among strains from children (53.3%) than pregnant women (11.7%) (OR (95%CI): 8.61 (2.73-27.15); p-value <0.001)). Approximately 61.5% (n=88) ExPEC were typed into their respective STs/CCs (87 by the 7-SNP qPCR and by an additional of one or two genes sequencing). The commonest STs/CCs among typeable strains were CC10 (28.4%, n=25), ST131 (18.2%, n=16), and ST38 (10.2%, n=9). The ST131 clades (C1 (4, 25.0%) and C2 (6, 37.5%)) were predominantly associated with fluoroquinolone resistance and ESBL production, respectively. Approximately 60.8% of ExPEC strains and all dominant clones were typed by the 7-SNP qPCR by additional sequencing. The multiplex clade PCR allowed linkage of the global clone ST131 with AMR phenotypes. These feasible and user-friendly molecular tools can be routinely used for surveillance programs in resource-limited settings.
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Affiliation(s)
- Jeremiah Seni
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Microbiology and Immunology, Weill-Bugando School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania.
| | - Gisele Peirano
- Division of Microbiology, Calgary Laboratory Services, Calgary, AB, Canada
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Weill-Bugando School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
| | - Johann D D Pitout
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Division of Microbiology, Calgary Laboratory Services, Calgary, AB, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
| | - Rebekah DeVinney
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Prevalence of Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae in Ethiopia: A Systematic Review and Meta-Analysis. Int J Microbiol 2021; 2021:6669778. [PMID: 33859697 PMCID: PMC8026286 DOI: 10.1155/2021/6669778] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/19/2021] [Accepted: 03/21/2021] [Indexed: 11/25/2022] Open
Abstract
Background Antimicrobial resistance especially caused by extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) has become a global public health concern. Globally, these isolates have remained the most important causes of several infections and associated mortality. Their rapid spread in Ethiopia is associated with a lack of regular surveillance and antibiotic stewardship programs. Isolates of ESBL-PE from different regions of Ethiopia were searched exhaustively. However, published data regarding the pooled estimate of ESBL-PE are not conducted in Ethiopia. For this reason, we systematically reviewed laboratory-based studies to summarize the overall pooled prevalence of the isolates recovered from various human specimens. Methods An exhaustive literature search was carried out using the major electronic databases including PubMed, Web of Science, MEDLINE, EMBASE, CINAHL, Google Scholar, Cochrane Library, Scopus, and Wiley Online Library to identify potentially relevant studies without date restriction. Original articles which address the research question were identified, screened, and included using the PRISMA follow diagram. Data extraction form was prepared in Microsoft Excel, and data quality was assessed by using 9-point Joanna Briggs Institute critical appraisal tools. Then, data were exported to STATA 16.0 software for analyses of pooled estimation of outcome measures. Estimation of outcome measures at 95% confidence interval was performed using Der-Simonian-Laird's random-effects model. Finally, results were presented via text, figures, and tables. Results A comprehensive electronic database literature search has yielded a total of 86 articles. Among the total, 68 original articles were excluded after the review process. A total of 18 studies with 1191 bacterial isolates recovered from 7919 various clinical samples sizes were included for systematic review and meta-analysis. In this study, the pooled prevalence of ESBL-PE was 18% (95% CI: 9–26). Nine out of the total (50%) reviewed articles were studied using the combination disk test. Likewise, E. coli and K. pneumoniae (50% both) were the predominant isolates of ESBL-PE in addition to other isolates such as Salmonella spp. and Shigella spp. Conclusion This meta-analysis has shown a low pooled estimate of ESBL-PE in Ethiopia.
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Mbanga J, Amoako DG, Abia ALK, Allam M, Ismail A, Essack SY. Genomic Insights of Multidrug-Resistant Escherichia coli From Wastewater Sources and Their Association With Clinical Pathogens in South Africa. Front Vet Sci 2021; 8:636715. [PMID: 33718473 PMCID: PMC7952442 DOI: 10.3389/fvets.2021.636715] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/01/2021] [Indexed: 01/09/2023] Open
Abstract
There is limited information on the comparative genomic diversity of antibiotic-resistant Escherichia coli from wastewater. We sought to characterize environmental E. coli isolates belonging to various pathotypes obtained from a wastewater treatment plant (WWTP) and its receiving waters using whole-genome sequencing (WGS) and an array of bioinformatics tools to elucidate the resistomes, virulomes, mobilomes, clonality, and phylogenies. Twelve multidrug-resistant (MDR) diarrheagenic E. coli isolates were obtained from the final effluent of a WWTP, and the receiving river upstream and downstream of the WWTP were sequenced on an Illumina MiSeq machine. The multilocus sequence typing (MLST) analysis revealed that multiple sequence types (STs), the most common of which was ST69 (n = 4) and ST10 (n = 2), followed by singletons belonging to ST372, ST101, ST569, ST218, and ST200. One isolate was assigned to a novel ST ST11351. A total of 66.7% isolates were positive for β-lactamase genes with 58.3% harboring the bla TEM1B gene and a single isolate the blaCTX-M-14 and blaCTX-M-55 extended-spectrum β-lactamase (ESBL) genes. One isolate was positive for the mcr-9 mobilized colistin resistance gene. Most antibiotic resistance genes (ARGs) were associated with mobile genetic support: class 1 integrons (In22, In54, In191, and In369), insertion sequences (ISs), and/or transposons (Tn402 or Tn21). A total of 31 virulence genes were identified across the study isolates, including those responsible for adhesion (lpfA, iha, and aggR), immunity (air, gad, and iss), and toxins (senB, vat, astA, and sat). The virulence genes were mostly associated with IS (IS1, IS3, IS91, IS66, IS630, and IS481) or prophages. Co-resistance to heavy metal/biocide, antibiotics were evident in several isolates. The phylogenomic analysis with South African E. coli isolates from different sources (animals, birds, and humans) revealed that isolates from this study mostly clustered with clinical isolates. Phylogenetics linked with metadata revealed that isolates did not cluster according to source but according to ST. The occurrence of pathogenic and MDR isolates in the WWTP effluent and the associated river is a public health concern.
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Affiliation(s)
- Joshua Mbanga
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Daniel G. Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Akebe L. K. Abia
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
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Annear D, Gaida R, Myburg K, Black J, Truter I, Bamford C, Govender S. Spectrum of Bacterial Colonization in Patients Hospitalized for Treatment of Multidrug-Resistant Tuberculosis. Microb Drug Resist 2020; 27:691-697. [PMID: 33074767 DOI: 10.1089/mdr.2020.0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study investigated the bacterial colonization in patients admitted for treatment of drug-resistant tuberculosis in a specialized TB hospital. Identification and antimicrobial susceptibility testing of bacterial isolates (n = 62) from nasal, groin, and rectal swabs [patient cohort (n = 37)] were determined by the VITEK-MS system. Resistance gene analysis was by PCR and DNA sequencing. Molecular typing of Klebsiella pneumoniae isolates was by Multilocus Sequencing Typing (MLST). Patients (n = 13/37; 35%) were colonized by multidrug-resistant (MDR) bacteria (ESBL and MRSA) on admission. Of the 24 patients who were not colonized by MDR bacteria on admission, 46% (17/37) became colonized by MDR bacteria within 1 month of admission, mostly with ESBL-producing Enterobacteriales and resistance to aminoglycosides and fluoroquinolones. ESBL Escherichia coli (41/62; 66%) and K. pneumoniae (14/62; 23%) predominated. Genes encoding for ESBLs (blaCTX-M-14, blaCTX-M-15, blaSHV-28, blaOXA-1, and blaOXY-2) and plasmid-mediated quinolone resistant genes (qnrB1, qnrB4, and qnrB10) were detected. MLST revealed genetic diversity among the K. pneumoniae isolates from hospitalized patients. This study provides insight into bacterial pathogen colonization in hospitalized TB patients with the first occurrence of the qnrB4 and qnrB10 genes and co-expression of genes: qnrB4+aac(6')-lb-cr, qnrB10+aac(6')-lb-cr, qnrB4+qnrS1, and qnrB10+qnrS1 in fluoroquinolone-resistant E. coli isolates within South Africa. However, the source and colonization routes of these isolates could not be determined.
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Affiliation(s)
- Dale Annear
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
| | - Razia Gaida
- Drug Utilization Research Unit (DURU), Department of Pharmacy, Nelson Mandela University, Port Elizabeth, South Africa
| | - Kierra Myburg
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
| | - John Black
- Drug Utilization Research Unit (DURU), Department of Pharmacy, Nelson Mandela University, Port Elizabeth, South Africa.,Department of Medicine, Livingstone Hospital, Eastern Cape Department of Health, Port Elizabeth, South Africa
| | - Ilse Truter
- Drug Utilization Research Unit (DURU), Department of Pharmacy, Nelson Mandela University, Port Elizabeth, South Africa
| | - Colleen Bamford
- National Health Laboratory Service, Groote Schuur Hospital Microbiology Laboratory, Cape Town, South Africa.,Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Sharlene Govender
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
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Dantas Palmeira J, Ferreira HMN. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in cattle production - a threat around the world. Heliyon 2020; 6:e03206. [PMID: 32042963 PMCID: PMC7002838 DOI: 10.1016/j.heliyon.2020.e03206] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/01/2019] [Accepted: 01/09/2020] [Indexed: 01/19/2023] Open
Abstract
Food producing animal is a global challenge in terms of antimicrobial resistance spread. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae are relevant opportunistic pathogens that may spread in many ecological niches of the One Health approach as human, animal and environment due to intestinal selection of antimicrobial resistant commensals in food production animals. Cattle production is a relevant ecological niche for selection of commensal bacteria with antimicrobial resistance from microbiota. Enterobacteriaceae show importance in terms of circulation of resistant-bacteria and antimicrobial resistance genes via food chain creating a resistance reservoir, setting up a threat for colonization of humans and consequent health risk. ESBL-producing Enterobacteriaceae are a threat in terms of human health responsible for life threatening outbreaks and silent enteric colonization of community populations namely the elder population. Food associated colonization is a risk difficult to handle and control. In a time of globalization of food trading, population intestinal colonization is a mirror of food production and in that sense this work aims to make a picture of ESBL-producing Enterobacteriaceae in animal production for food over the world in order to make some light in this reality of selection of resistant threats in food producing animal.
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Affiliation(s)
- Josman Dantas Palmeira
- Microbiology - Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal.,UCIBIO - Research Unit on Applied Molecular Biosciences, REQUIMTE, Portugal
| | - Helena Maria Neto Ferreira
- Microbiology - Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal.,UCIBIO - Research Unit on Applied Molecular Biosciences, REQUIMTE, Portugal
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Mbelle NM, Feldman C, Sekyere JO, Maningi NE, Modipane L, Essack SY. Pathogenomics and Evolutionary Epidemiology of Multi-Drug Resistant Clinical Klebsiella pneumoniae Isolated from Pretoria, South Africa. Sci Rep 2020; 10:1232. [PMID: 31988374 PMCID: PMC6985128 DOI: 10.1038/s41598-020-58012-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/09/2020] [Indexed: 11/14/2022] Open
Abstract
Antibiotic-resistant Klebsiella pneumoniae is increasingly being implicated in invasive infections worldwide with high mortalities. Forty-two multidrug resistant (MDR) K. pneumoniae isolates were collected over a 4-month period. Antimicrobial susceptibility was determined using Microscan. The evolutionary epidemiology, resistome, virulome and mobilome of the isolates were characterised using whole-genome sequencing and bioinformatics analysis. All isolates contained the blaCTX-M gene, whilst 41/42(97%) contained blaTEM, 36/42(86%) contained blaOXA and 35/42(83%) harboured blaSHV genes. Other resistance genes found included blaLEN, aac(6′)-lb-cr, qnrA, qnrB, qnrS, oqxAB, aad, aph, dfr, sul1, sul2, fosA, and cat genes. Fluoroquinolone and colistin resistance-conferring mutations in parC, gyrAB, pmrAB, phoPQ and kpnEF were identified. The blaLEN gene, rarely described worldwide, was identified in four isolates. The isolates comprised diverse sequence types, the most common being ST152 in 7/42(17%) isolates; clone-specific O and K capsule types were identified. Diverse virulence genes that were not clone-specific were identified in all but one isolate. IncF, IncH and IncI plasmid replicons and two novel integrons were present. The blaCTX-M-15 and blaTEM-1 genes were bracketed by Tn3 transposons, ISEc9, a resolvase and IS91 insertion sequence. There were 20 gene cassettes in 14 different cassette arrays, with the dfrA and aadA gene cassettes being the most frequent. Phylogenetic analysis demonstrated that the isolates were evolutionarily associated with strains from both South Africa and abroad. These findings depict the rich resistome, mobilome and virulome repertoire in clinical K. pneumoniae strains, which are mainly transmitted by clonal, multiclonal and horizontal means in South Africa.
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Affiliation(s)
- Nontombi Marylucy Mbelle
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.,National Health Laboratory Service, Johannesburg, South Africa
| | - Charles Feldman
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
| | | | - Lesedi Modipane
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu/Natal, Durban, South Africa
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The Resistome, Mobilome, Virulome and Phylogenomics of Multidrug-Resistant Escherichia coli Clinical Isolates from Pretoria, South Africa. Sci Rep 2019; 9:16457. [PMID: 31712587 PMCID: PMC6848087 DOI: 10.1038/s41598-019-52859-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022] Open
Abstract
Antibiotic-resistant Escherichia coli is a common occurrence in food, clinical, community and environmental settings worldwide. The resistome, mobilome, virulome and phylogenomics of 20 multidrug resistant (MDR) clinical E. coli isolates collected in 2013 from Pretoria, South Africa, were characterised. The isolates were all extended-spectrum β-lactamase producers, harbouring CTX-M (n = 16; 80%), TEM-1B (n = 10; 50%) and OXA (n = 12, 60%) β-lactamases alongside genes mediating resistance to fluoroquinolones, aminoglycosides, tetracyclines etc. Most resistance determinants were found on contigs containing IncF plasmid replicons and bracketed by composite transposons (Tn3), diverse ISs and class 1 integrons (In13, In54, In369, and In467). Gene cassettes such as blaOXA,dfrA5-psp-aadA2-cmlA1a-aadA1-qac and estX3-psp-aadA2-cmlA1a-aadA1a-qac were encompassed by Tn3 and ISs; several isolates had same or highly similar genomic antibiotic resistance islands. ST131 (n = 10), ST617 (n = 2) and singletons of ST10, ST73, ST95, ST410, ST648, ST665, ST744 and ST998 clones were phylogenetically related to clinical (human and animal) strains from Egypt, Kenya, Niger, Nigeria, Tanzania, and UK. A rich repertoire of virulence genes, including iss, gad and iha were identified. MDR E. coli harbouring chromosomal and plasmid-borne resistance genes in same and multiple clones exist in South Africa, which is very worrying for clinical epidemiology and infectious diseases management.
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Malande OO, Nuttall J, Pillay V, Bamford C, Eley B. A ten-year review of ESBL and non-ESBL Escherichia coli bloodstream infections among children at a tertiary referral hospital in South Africa. PLoS One 2019; 14:e0222675. [PMID: 31550295 PMCID: PMC6759190 DOI: 10.1371/journal.pone.0222675] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/03/2019] [Indexed: 12/04/2022] Open
Abstract
Introduction There are few studies describing Escherichia coli (E. coli) bloodstream infection (BSI) among children in Africa, yet E.coli is increasing in importance as a cause of antibiotic resistant infection in paediatric settings. Methods In this retrospective, descriptive study aspects of E. coli BSI epidemiology are described over a 10-year period including incidence risk, risk factors for extended-spectrum β-lactamase (ESBL)-producing E. coli BSI, antibiotic susceptibility of the bacterial isolates and outcome including risk factors for severe disease. Results There were 583 new E. coli BSI episodes among 217,483 admissions, an overall incidence risk of 2.7 events/1,000 hospital admissions. Of 455 of these E. coli BSI episodes that were analysed, 136 (29.9%) were caused by ESBL-producing isolates. Risk factors for ESBL-producing E. coli BSI included hospitalization in the 28-day period preceding E. coli BSI episodes, having an underlying chronic illness other than HIV infection at the time of the E. coli BSI and having a temperature of 38° Celsius or higher at the time of the E. coli BSI. None of the E. coli isolates were resistant to carbapenems or colistin. The mortality rate was 5.9% and admission to the intensive care unit was required in 12.3% of BSI episodes. Predictors of severe disease included age less than 1 month, hospitalization in the 28-day period preceding E. coli BSI and BSI without a definable focus. Conclusions These findings extend our understanding of E. coli BSI in a sub-Saharan African setting, provide useful information that can guide empiric treatment choices for community- and hospital-acquired BSI and help inform prevention strategies.
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Affiliation(s)
- Oliver Ombeva Malande
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | - James Nuttall
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Vashini Pillay
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Colleen Bamford
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
- Division of Microbiology, University of Cape Town, Cape Town, South Africa
| | - Brian Eley
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
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Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a majority of human extraintestinal infections globally, resulting in enormous direct medical and social costs. ExPEC strains are comprised of many lineages, but only a subset is responsible for the vast majority of infections. Few systematic surveillance systems exist for ExPEC. To address this gap, we systematically reviewed and meta-analyzed 217 studies (1995 to 2018) that performed multilocus sequence typing or whole-genome sequencing to genotype E. coli recovered from extraintestinal infections or the gut. Twenty major ExPEC sequence types (STs) accounted for 85% of E. coli isolates from the included studies. ST131 was the most common ST from 2000 onwards, covering all geographic regions. Antimicrobial resistance-based isolate study inclusion criteria likely led to an overestimation and underestimation of some lineages. European and North American studies showed similar distributions of ExPEC STs, but Asian and African studies diverged. Epidemiology and population dynamics of ExPEC are complex; summary proportion for some STs varied over time (e.g., ST95), while other STs were constant (e.g., ST10). Persistence, adaptation, and predominance in the intestinal reservoir may drive ExPEC success. Systematic, unbiased tracking of predominant ExPEC lineages will direct research toward better treatment and prevention strategies for extraintestinal infections.
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Richter L, Du Plessis EM, Duvenage S, Korsten L. Occurrence, Identification, and Antimicrobial Resistance Profiles of Extended-Spectrum and AmpC β-Lactamase-Producing Enterobacteriaceae from Fresh Vegetables Retailed in Gauteng Province, South Africa. Foodborne Pathog Dis 2019; 16:421-427. [PMID: 30785775 DOI: 10.1089/fpd.2018.2558] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase-producing Enterobacteriaceae are no longer restricted to the health care system, but represent increased risks related to environmental integrity and food safety. Fresh produce has been increasingly reported to constitute a reservoir of multidrug-resistant (MDR) potential human pathogenic Enterobacteriaceae. This study aimed to detect, identify, and characterize the antimicrobial resistance of ESBL/AmpC-producing Enterobacteriaceae isolates from fresh vegetables at point of sale. Vegetable samples (spinach, tomatoes, lettuce, cucumber, and green beans; n = 545) were purchased from retailers in Gauteng, the most densely populated province in South Africa. These included street vendors, trolley vendors, farmers' market stalls, and supermarket chain stores. Selective enrichment, plating onto chromogenic media, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) confirmation of isolate identities showed that 17.4% (95/545) vegetable samples analyzed were contaminated with presumptive ESBL/AmpC-producing Enterobacteriaceae. Dominant species identified included Escherichia coli, Enterobacter cloacae, Enterobacter asburiae, and Klebsiella pneumoniae. Phenotypic antibiotic resistance analysis showed that 96.1% of 77 selected isolates were MDR, while resistance to aminoglycoside (94.8%), chloramphenicol (85.7%), and tetracycline (53.2%) antibiotic classes was most prevalent. Positive phenotypic analysis for ESBL production was shown in 61 (79.2%) of the 77 isolates, and AmpC production in 41.6% of the isolates. PCR and sequencing confirmed the presence of β-lactamase genes in 75.3% isolates from all vegetable types analyzed, mainly in E. coli, Enterobacter spp., and Serratia spp. isolates. CTX-M group 9 (32.8%) was the dominant ESBL type, while EBC (24.1%) was the most prevalent plasmidic type AmpC β-lactamase. Our findings document for the first time the presence of MDR ESBL/AmpC-producing Enterobacteriaceae in raw vegetables sold at selected retailers in Gauteng Province, South Africa.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Erika M Du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
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20
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Diwan V, Hanna N, Purohit M, Chandran S, Riggi E, Parashar V, Tamhankar AJ, Stålsby Lundborg C. Seasonal Variations in Water-Quality, Antibiotic Residues, Resistant Bacteria and Antibiotic Resistance Genes of Escherichia coli Isolates from Water and Sediments of the Kshipra River in Central India. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:E1281. [PMID: 29914198 PMCID: PMC6024939 DOI: 10.3390/ijerph15061281] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/14/2018] [Accepted: 06/14/2018] [Indexed: 12/23/2022]
Abstract
OBJECTIVES To characterize the seasonal variation, over one year, in water-quality, antibiotic residue levels, antibiotic resistance genes and antibiotic resistance in Escherichia coli isolates from water and sediment of the Kshipra River in Central India. METHODS Water and sediment samples were collected from seven selected points from the Kshipra River in the Indian city of Ujjain in the summer, rainy season, autumn and winter seasons in 2014. Water quality parameters (physical, chemical and microbiological) were analyzed using standard methods. High-performance liquid chromatography⁻tandem mass spectrometry was used to determine the concentrations of antibiotic residues. In river water and sediment samples, antibiotic resistance and multidrug resistance patterns of isolated E. coli to 17 antibiotics were tested and genes coding for resistance and phylogenetic groups were detected using multiplex polymerase chain reaction. One-way analysis of variance (ANOVA) and Fisher tests were applied to determine seasonal variation. RESULTS In river water, seasonal variation was significantly associated with various water quality parameters, presence of sulfamethoxazole residues, bacteria resistant to ampicillin, cefepime, meropenem, amikacin, gentamicin, tigecycline, multidrug resistance and CTX-M-1 gene. The majority of the Extended Spectrum Beta-Lactamase (ESBL)-producing E. coli isolates from river water and sediment in all different seasons belonged to phylogenetic group A or B1. CONCLUSIONS Antibiotic pollution, resistance and resistance genes in the Kshipra River showed significant seasonal variation. Guidelines and regulatory standards are needed to control environmental dissemination of these “pollutants” in this holy river.
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Affiliation(s)
- Vishal Diwan
- Department of Public Health and Environment, R.D. Gardi Medical College, Ujjain 456006, India.
- Department of Public Health Sciences, Global Health, Health Systems and Policy (HSP): Medicines Focusing Antibiotics, Karolinska Institutet, Stockholm 171 77, Sweden.
- International Centre for Health Research, Ujjain Charitable Trust Hospital and Research Centre, Ujjain 456001, India.
| | - Nada Hanna
- Department of Public Health Sciences, Global Health, Health Systems and Policy (HSP): Medicines Focusing Antibiotics, Karolinska Institutet, Stockholm 171 77, Sweden.
| | - Manju Purohit
- Department of Public Health Sciences, Global Health, Health Systems and Policy (HSP): Medicines Focusing Antibiotics, Karolinska Institutet, Stockholm 171 77, Sweden.
- Department of Pathology, R.D. Gardi Medical College, Ujjain 456006, India.
| | - Salesh Chandran
- HLL Biotech Ltd., Integrated Vaccines Complex, Melaripakkam (Post), Thirukalukundram Taluk, Chengalpattu 603001, India.
| | - Emilia Riggi
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia 27100, Italy.
- Research Center in Epidemiology and Preventive Medicine (EPIMED), University of Insubria, Varese 21100, Italy.
| | - Vivek Parashar
- Department of Public Health and Environment, R.D. Gardi Medical College, Ujjain 456006, India.
| | - Ashok J Tamhankar
- Department of Public Health Sciences, Global Health, Health Systems and Policy (HSP): Medicines Focusing Antibiotics, Karolinska Institutet, Stockholm 171 77, Sweden.
- Indian Initiative for Management of Antibiotic Resistance, Department of Environmental Medicine, R.D. Gardi Medical College, Ujjain 456006, India.
| | - Cecilia Stålsby Lundborg
- Department of Public Health Sciences, Global Health, Health Systems and Policy (HSP): Medicines Focusing Antibiotics, Karolinska Institutet, Stockholm 171 77, Sweden.
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21
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Seni J, Peirano G, Okon KO, Jibrin YB, Mohammed A, Mshana SE, DeVinney R, Pitout JDD. The population structure of clinical extra-intestinal Escherichia coli in a teaching hospital from Nigeria. Diagn Microbiol Infect Dis 2018; 92:46-49. [PMID: 29859643 DOI: 10.1016/j.diagmicrobio.2018.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/01/2018] [Accepted: 04/05/2018] [Indexed: 10/17/2022]
Abstract
Limited information is available regarding the population structure of extra-intestinal pathogenic Escherichia coli (ExPEC) in Africa. Antimicrobial resistance profiles, sequence types (STs) and fimH types were determined on 60 clinical ExPEC from Nigeria using a 7-single nucleotide polymorphism quantitative PCR and sequencing of certain genes. Different ST131 clades were identified with a multiplex PCR. The isolates were mostly obtained from urines (58.3%). Not-susceptibility rates were as follows: trimethoprim-sulfamethoxazole (98%), cefotaxime (68%), gentamicin (55%), ciprofloxacin (62%) and piperacillin-tazobactam (2%). Dominant STs were associated with CTX-M-15 and included ST131-fimH30 (23%), ST457-fimH145 (20%), ST405-fimH27 (13%) and ST95-fimH41 (10%). We found the 7-SNP qPCR to be simple and cost-effective that can be utilized to tract different ExPEC clones on a global scale. This study provided insight into the population structure of ExPEC from Nigeria showing high prevalence of the rarely reported ST457 and the presence of multidrug resistant ST95.
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Affiliation(s)
- Jeremiah Seni
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary,Calgary, Alberta, Canada
| | - Giselle Peirano
- Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary,Calgary, Alberta, Canada; Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada
| | | | - Yusuf Bara Jibrin
- Department of Internal Medicine, Abubakar Tafawa Balewa University teaching hospital Bauchi
| | - Alkali Mohammed
- Department of Internal Medicine, Abubakar Tafawa Balewa University teaching hospital Bauchi
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Rebekah DeVinney
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary,Calgary, Alberta, Canada
| | - Johann D D Pitout
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary,Calgary, Alberta, Canada; Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary,Calgary, Alberta, Canada; Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.
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22
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Musicha P, Feasey NA, Cain AK, Kallonen T, Chaguza C, Peno C, Khonga M, Thompson S, Gray KJ, Mather AE, Heyderman RS, Everett DB, Thomson NR, Msefula CL. Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting. J Antimicrob Chemother 2017; 72:1602-1609. [PMID: 28333330 PMCID: PMC5437524 DOI: 10.1093/jac/dkx058] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/01/2017] [Indexed: 12/24/2022] Open
Abstract
Objectives Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi. Methods Ninety-four E. coli isolates from patients admitted to Queen's Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics. Results Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was bla CTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates]. Conclusions This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance.
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Affiliation(s)
| | - Nicholas A Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Amy K Cain
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Teemu Kallonen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Chrispin Chaguza
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Margaret Khonga
- Microbiology Unit, Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Sarah Thompson
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Katherine J Gray
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Alison E Mather
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Division of Infection and Immunity, University College London, London, UK
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Chisomo L Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Microbiology Unit, Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
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23
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Tsai WL, Hung CH, Chen HA, Wang JL, Huang IF, Chiou YH, Chen YS, Lee SSJ, Hung WY, Cheng MF. Extended-spectrum β-lactamase-producing Escherichia coli bacteremia: Comparison of pediatric and adult populations. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 51:723-731. [PMID: 28927684 DOI: 10.1016/j.jmii.2017.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 07/05/2017] [Accepted: 08/17/2017] [Indexed: 11/17/2022]
Abstract
BACKGROUND/PURPOSE The prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is increasing worldwide. This study investigated the clinical features and bacteriology of pediatric patients with ESBL-producing E. coli bacteremia and compared their characteristics with those of adult patients. METHODS Clinical and laboratory data from all of the 41 patients aged ≤18 years diagnosed with E. coli bacteremia were collected over 5 years. Patients aged >18 years diagnosed with E. coli bacteremia, matched 1:1 for calendar time, were enrolled as the adult group. All E. coli isolates were tested for their blaCTX-M group and sequence type 131 (ST131). A novel seven-single nucleotide polymorphism-based clonotyping test was applied to detect the septatypes of each isolate. RESULTS In the adult group, patients with ESBL-producing E. coli bacteremia had more previous hospitalizations and antimicrobial agent use than did those with non-ESBL-producing E. coli bacteremia, but these differences were not found in pediatric group. In the pediatric group, the proportion of isolates producing CTX-M group 9 was higher than that in the adult group (85.7% vs. 42.9%; p < 0.05). Among both groups, there were more E. coli ST131 in ESBL isolates in than there were non-ESBL isolates. The distribution of septatypes was more homogenous in ESBL-producing E. coli among the pediatric patients than among the adult patients. CONCLUSION ST131 was the major clone causing E. coli bacteremia in both pediatric and adult populations. The pediatric population demonstrated a higher number of isolates producing CTX-M group 9 with more homogenous septatypes compared with the adult population.
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Affiliation(s)
- Wan-Lin Tsai
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC
| | - Chih-Hsin Hung
- Department of Chemical Engineering, Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan, ROC
| | - Hui-An Chen
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC; School of Medicine, National Yang-Ming University, Taipei, Taiwan, ROC
| | - Jiun-Ling Wang
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan, ROC
| | - I-Fei Huang
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC; School of Medicine, National Yang-Ming University, Taipei, Taiwan, ROC
| | - Yee-Hsuan Chiou
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC; School of Medicine, National Yang-Ming University, Taipei, Taiwan, ROC; Fooyin University, Kaohsiung, Taiwan, ROC
| | - Yao-Shen Chen
- School of Medicine, National Yang-Ming University, Taipei, Taiwan, ROC; Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC
| | - Susan Shin-Jung Lee
- School of Medicine, National Yang-Ming University, Taipei, Taiwan, ROC; Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC
| | - Wan-Yu Hung
- Department of Chemical Engineering, Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan, ROC
| | - Ming-Fang Cheng
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC; School of Medicine, National Yang-Ming University, Taipei, Taiwan, ROC; Fooyin University, Kaohsiung, Taiwan, ROC.
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24
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Sangare SA, Maiga AI, Guindo I, Maiga A, Camara N, Savadogo S, Diallo S, Bougoudogo F, Armand-Lefevre L, Andremont A, Maiga II. Prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae isolated from blood cultures in Africa. Med Mal Infect 2016; 45:374-82. [PMID: 26433872 DOI: 10.1016/j.medmal.2015.08.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 06/09/2015] [Accepted: 08/31/2015] [Indexed: 11/15/2022]
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae have been isolated from many regions of the world. Epidemiological studies are being conducted in Europe, North America, and Asia. No study has however been conducted in Africa to determine the prevalence and distribution of ESBLs on the continent. This literature review aimed at describing the prevalence of ESBL-producing Enterobacteriaceae isolated from blood cultures, as well as the ESBL genes involved at the international level. Our focus was mainly on Africa. We conducted a literature review on PubMed. Articles related to our study field and published between 1996 and 2014 were reviewed and entirely read for most of them, while we only focused on the abstracts of some other articles. Relevant articles to our study were then carefully reviewed and included in the review. The prevalence of ESBL-producing Enterobacteriaceae differs from one country to another. The results of our literature review however indicate that class A ESBLs prevail over the other types. We took into consideration articles focusing on various types of samples to assess the prevalence of ESBL-producing Enterobacteriaceae, but information on isolates from blood cultures is limited. The worldwide prevalence of ESBL-producing Enterobacteriaceae has increased over time. Evidence of ESBL-producing Enterobacteriaceae can be found in all regions of the world. Studies conducted in Africa mainly focused on the Northern and Eastern parts of the continent, while only rare studies were carried out in the rest of the continent.
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Affiliation(s)
- S A Sangare
- Laboratory of bacteriology, university hospital Gabriel-Touré, Bamako, Mali; Laboratory of bacteriology, university hospital Bichat-Claude Bernard and UMR Inserm 1137 Iame, 46, rue Henri-Huchard, 75018 Paris, France; Faculty of pharmacy, university of sciences, techniques, and technologies of Bamako (USTTB), Bamako, Mali.
| | - A I Maiga
- Laboratory of bacteriology, university hospital Gabriel-Touré, Bamako, Mali; Faculty of pharmacy, university of sciences, techniques, and technologies of Bamako (USTTB), Bamako, Mali
| | - I Guindo
- Faculty of pharmacy, university of sciences, techniques, and technologies of Bamako (USTTB), Bamako, Mali; National institute for research in public health, Bamako, Mali
| | - A Maiga
- Laboratory of bacteriology, university hospital Point G, Bamako, Mali
| | - N Camara
- Laboratory of bacteriology, university hospital Gabriel-Touré, Bamako, Mali
| | - S Savadogo
- Laboratory of bacteriology, university hospital Point G, Bamako, Mali
| | - S Diallo
- Faculty of pharmacy, university of sciences, techniques, and technologies of Bamako (USTTB), Bamako, Mali; Infectious diseases center "Charles Mérieux", Bamako, Mali
| | - F Bougoudogo
- Faculty of pharmacy, university of sciences, techniques, and technologies of Bamako (USTTB), Bamako, Mali; National institute for research in public health, Bamako, Mali
| | - L Armand-Lefevre
- Laboratory of bacteriology, university hospital Bichat-Claude Bernard and UMR Inserm 1137 Iame, 46, rue Henri-Huchard, 75018 Paris, France
| | - A Andremont
- Laboratory of bacteriology, university hospital Bichat-Claude Bernard and UMR Inserm 1137 Iame, 46, rue Henri-Huchard, 75018 Paris, France
| | - I I Maiga
- Laboratory of bacteriology, university hospital Point G, Bamako, Mali; Faculty of medicine and odonto-stomatology, university of sciences, techniques, and technologies of Bamako (USTTB), Bamako, Mali
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25
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Ouedraogo AS, Sanou M, Kissou A, Sanou S, Solaré H, Kaboré F, Poda A, Aberkane S, Bouzinbi N, Sano I, Nacro B, Sangaré L, Carrière C, Decré D, Ouégraogo R, Jean-Pierre H, Godreuil S. High prevalence of extended-spectrum ß-lactamase producing enterobacteriaceae among clinical isolates in Burkina Faso. BMC Infect Dis 2016; 16:326. [PMID: 27400864 PMCID: PMC4939587 DOI: 10.1186/s12879-016-1655-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 06/08/2016] [Indexed: 11/10/2022] Open
Abstract
Background Nothing is known about the epidemiology and resistance mechanisms of extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-PE) in Burkina Faso. The objective of this study was to determine ESBL-PE prevalence and to characterize ESBL genes in Burkina Faso. Methods During 2 months (June-July 2014), 1602 clinical samples were sent for bacteriologic investigations to the microbiology laboratories of the tree main hospitals of Burkina Faso. Isolates were identified by mass spectrometry using a matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) BioTyper. Antibiotic susceptibility was tested using the disk diffusion method on Müller-Hinton agar. The different ESBL genes in potential ESBL-producing isolates were detected by PCR and double stranded DNA sequencing. Escherichia coli phylogenetic groups were determined using a PCR-based method. Results ESBL-PE frequency was 58 % (179 strains among the 308 Enterobacteriaceae isolates identified in the collected samples; 45 % in outpatients and 70 % in hospitalized patients). The CTX-M-1 group was dominant (94 %, CTX-M-15 enzyme), followed by the CTX-M-9 group (4 %). ESBL producers were more often found in E. coli (67.5 %) and Klebsiella pneumoniae (26 %) isolates. E. coli isolates (n = 202; 60 % of all Enterobacteriaceae samples) were distributed in eight phylogenetic groups (A = 49, B1 = 15, B2 = 43, C = 22, Clade I = 7, D = 37, F = 13 and 16 unknown); 22 strains belonged to the sequence type ST131. No association between a specific strain and ESBL production was detected. Conclusions This report shows the alarming spread of ESBL genes in Burkina Faso. Public health efforts should focus on education (population and healthcare professionals), surveillance and promotion of correct and restricted antibiotic use to limit their dissemination.
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Affiliation(s)
- Abdoul-Salam Ouedraogo
- Centre Hospitalier Universitaire Souro Sanou, BP 676, Bobo Dioulasso, Burkina Faso. .,Centre Hospitalier Régional Universitaire (CHRU) de Montpellier, Département de Bactériologie-Virologie, Montpellier, France. .,Université Montpellier 1, Montpellier, France. .,INSERM U1058 "Infection by HIV and by agents with mucocutaneous tropism: from pathogenesis to prevention" and Department of Bacteriology-Virology, CHU Arnaud de Villeneuve, 371 avenue du doyen Gaston Giraud, 34295, Montpellier Cedex 5, France.
| | - Mahamadou Sanou
- Centre Hospitalier Universitaire Pédiatrique Charles de Gaulle, Ouagadougou, Burkina Faso
| | - Aimée Kissou
- Centre Hospitalier Universitaire Souro Sanou, BP 676, Bobo Dioulasso, Burkina Faso
| | - Soufiane Sanou
- Centre Hospitalier Universitaire Souro Sanou, BP 676, Bobo Dioulasso, Burkina Faso
| | - Hermann Solaré
- Centre Hospiatlier Universitaire Yalgado Ouédraogo, Ouagadougou, Burkina Faso
| | - Firmin Kaboré
- Centre Hospitalier Universitaire Souro Sanou, BP 676, Bobo Dioulasso, Burkina Faso
| | - Armel Poda
- Centre Hospitalier Universitaire Souro Sanou, BP 676, Bobo Dioulasso, Burkina Faso
| | - Salim Aberkane
- Centre Hospitalier Régional Universitaire (CHRU) de Montpellier, Département de Bactériologie-Virologie, Montpellier, France.,Université Montpellier 1, Montpellier, France.,INSERM U1058 "Infection by HIV and by agents with mucocutaneous tropism: from pathogenesis to prevention" and Department of Bacteriology-Virology, CHU Arnaud de Villeneuve, 371 avenue du doyen Gaston Giraud, 34295, Montpellier Cedex 5, France
| | - Nicolas Bouzinbi
- Centre Hospitalier Régional Universitaire (CHRU) de Montpellier, Département de Bactériologie-Virologie, Montpellier, France.,Université Montpellier 1, Montpellier, France.,INSERM U1058 "Infection by HIV and by agents with mucocutaneous tropism: from pathogenesis to prevention" and Department of Bacteriology-Virology, CHU Arnaud de Villeneuve, 371 avenue du doyen Gaston Giraud, 34295, Montpellier Cedex 5, France
| | - Idrissa Sano
- Centre Hospiatlier Universitaire Yalgado Ouédraogo, Ouagadougou, Burkina Faso
| | - Boubacar Nacro
- Centre Hospitalier Universitaire Souro Sanou, BP 676, Bobo Dioulasso, Burkina Faso
| | - Lassana Sangaré
- Centre Hospiatlier Universitaire Yalgado Ouédraogo, Ouagadougou, Burkina Faso
| | - Christian Carrière
- Centre Hospitalier Régional Universitaire (CHRU) de Montpellier, Département de Bactériologie-Virologie, Montpellier, France.,Université Montpellier 1, Montpellier, France.,INSERM U1058 "Infection by HIV and by agents with mucocutaneous tropism: from pathogenesis to prevention" and Department of Bacteriology-Virology, CHU Arnaud de Villeneuve, 371 avenue du doyen Gaston Giraud, 34295, Montpellier Cedex 5, France
| | - Dominique Decré
- CIMI, team E13 (bacteriology), Sorbonne University, UPMC Université Paris 06 CR7, F-75013, Paris, France.,INSERM U1135, CIMI, team E13, Paris, France.,AP-HP, Microbiology, St-Antoine Hospital, Paris, France
| | - Rasmata Ouégraogo
- Centre Hospitalier Universitaire Pédiatrique Charles de Gaulle, Ouagadougou, Burkina Faso
| | - Hélène Jean-Pierre
- Centre Hospitalier Régional Universitaire (CHRU) de Montpellier, Département de Bactériologie-Virologie, Montpellier, France
| | - Sylvain Godreuil
- Centre Hospitalier Régional Universitaire (CHRU) de Montpellier, Département de Bactériologie-Virologie, Montpellier, France.,Université Montpellier 1, Montpellier, France.,INSERM U1058 "Infection by HIV and by agents with mucocutaneous tropism: from pathogenesis to prevention" and Department of Bacteriology-Virology, CHU Arnaud de Villeneuve, 371 avenue du doyen Gaston Giraud, 34295, Montpellier Cedex 5, France
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26
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Yanat B, Machuca J, Díaz-De-Alba P, Mezhoud H, Touati A, Pascual Á, Rodríguez-Martínez JM. Characterization of Plasmid-Mediated Quinolone Resistance Determinants in High-Level Quinolone-Resistant Enterobacteriaceae Isolates from the Community: First Report of qnrD Gene in Algeria. Microb Drug Resist 2016; 23:90-97. [PMID: 27115732 DOI: 10.1089/mdr.2016.0031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE The objective was to assess the prevalence of plasmid-mediated quinolone resistance (PMQR)-producing isolates in a collection of quinolone-resistant Enterobacteriaceae of community origin isolated in Bejaia, Algeria. METHODS A total of 141 nalidixic acid-resistant Enterobacteriaceae community isolates were collected in Bejaia (Northern Algeria) and screened for PMQR genes using polymerase chain reaction (PCR). For PMQR-positive strains, antimicrobial susceptibility testing was performed by broth microdilution and disk diffusion. Mutations in the quinolone resistance-determining regions of the target genes, gyrA and parC, were detected with a PCR-based method and sequencing. Southern blotting, conjugation and transformation assays and molecular typing by pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing were also performed. RESULTS The prevalence of PMQR-producing Enterobacteriaceae isolates was 13.5% (19/141); 11 of these isolates produced Aac(6')-Ib-cr and 8 were qnr-positive (4 qnrB1-like, 2 qnrS1-like, and 2 qnrD1-like), including the association with aac(6')-Ib-cr gene in three cases. PMQR gene transfer by conjugation was successful in 6 of 19 isolates tested. PFGE revealed that most of the PMQR-positive Escherichia coli isolates were unrelated, except for two groups comprising two and four isolates, respectively, including the virulent multidrug-resistant clone E. coli ST131 that were clonally related. CONCLUSION Our findings indicate that PMQR determinants are prevalent in Enterobacteriaceae isolates from the community studied. We describe the first report of the qnrD gene in Algeria.
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Affiliation(s)
- Betitera Yanat
- 1 Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia , Bejaia, Algeria .,2 Department of Microbiology, University of Seville , Seville, Spain
| | - Jesús Machuca
- 2 Department of Microbiology, University of Seville , Seville, Spain .,3 Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III , Madrid, Spain .,4 Unidad Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena , Sevilla, Spain
| | - Paula Díaz-De-Alba
- 4 Unidad Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena , Sevilla, Spain
| | - Halima Mezhoud
- 1 Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia , Bejaia, Algeria
| | - Abdelaziz Touati
- 1 Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia , Bejaia, Algeria
| | - Álvaro Pascual
- 2 Department of Microbiology, University of Seville , Seville, Spain .,3 Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III , Madrid, Spain .,4 Unidad Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena , Sevilla, Spain
| | - José-Manuel Rodríguez-Martínez
- 2 Department of Microbiology, University of Seville , Seville, Spain .,3 Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III , Madrid, Spain
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Chattaway MA, Aboderin AO, Fashae K, Okoro CK, Opintan JA, Okeke IN. Fluoroquinolone-Resistant Enteric Bacteria in Sub-Saharan Africa: Clones, Implications and Research Needs. Front Microbiol 2016; 7:558. [PMID: 27148238 PMCID: PMC4841292 DOI: 10.3389/fmicb.2016.00558] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/04/2016] [Indexed: 11/13/2022] Open
Abstract
Fluoroquinolones came into widespread use in African countries in the early 2000s, after patents for the first generation of these drugs expired. By that time, quinolone antibacterial agents had been used intensively worldwide and resistant lineages of many bacterial species had evolved. We sought to understand which Gram negative enteric pandemic lineages have been reported from Africa, as well as the nature and transmission of any indigenous resistant clones. A systematic review of articles indexed in the Medline and AJOL literature databases was conducted. We report on the findings of 43 eligible studies documenting local or pandemic fluoroquinolone-resistant enteric clones in sub-Sahara African countries. Most reports are of invasive non-typhoidal Salmonella and Escherichia coli lineages and there have been three reports of cholera outbreaks caused by fluoroquinolone-resistant Vibrio cholerae O1. Fluoroquinolone-resistant clones have also been reported from commensals and animal isolates but there are few data for non-Enterobacteriaceae and almost none for difficult-to-culture Campylobacter spp. Fluoroquinolone-resistant lineages identified in African countries were universally resistant to multiple other classes of antibacterial agents. Although as many as 972 non-duplicate articles refer to fluoroquinolone resistance in enteric bacteria from Africa, most do not report on subtypes and therefore information on the epidemiology of fluoroquinolone-resistant clones is available from only a handful of countries in the subcontinent. When resistance is reported, resistance mechanisms and lineage information is rarely investigated. Insufficient attention has been given to molecular and sequence-based methods necessary for identifying and tracking resistant clones in Africa and more research is needed in this area.
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Affiliation(s)
- Marie A Chattaway
- Gastrointestinal Bacteria Reference Unit, Public Health England London, UK
| | - Aaron O Aboderin
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Obafemi Awolowo University Ile-Ife, Nigeria
| | - Kayode Fashae
- Department of Microbiology, University of Ibadan Ibadan, Nigeria
| | | | - Japheth A Opintan
- Department of Medical Microbiology, School of Biomedical and Allied Health Sciences, University of Ghana Accra, Ghana
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan Ibadan, Nigeria
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Dautzenberg MJD, Haverkate MR, Bonten MJM, Bootsma MCJ. Epidemic potential of Escherichia coli ST131 and Klebsiella pneumoniae ST258: a systematic review and meta-analysis. BMJ Open 2016; 6:e009971. [PMID: 26988349 PMCID: PMC4800154 DOI: 10.1136/bmjopen-2015-009971] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES Observational studies have suggested that Escherichia coli sequence type (ST) 131 and Klebsiella pneumoniae ST258 have hyperendemic properties. This would be obvious from continuously high incidence and/or prevalence of carriage or infection with these bacteria in specific patient populations. Hyperendemicity could result from increased transmissibility, longer duration of infectiousness, and/or higher pathogenic potential as compared with other lineages of the same species. The aim of our research is to quantitatively estimate these critical parameters for E. coli ST131 and K. pneumoniae ST258, in order to investigate whether E. coli ST131 and K. pneumoniae ST258 are truly hyperendemic clones. PRIMARY OUTCOME MEASURES A systematic literature search was performed to assess the evidence of transmissibility, duration of infectiousness, and pathogenicity for E. coli ST131 and K. pneumoniae ST258. Meta-regression was performed to quantify these characteristics. RESULTS The systematic literature search yielded 639 articles, of which 19 data sources provided information on transmissibility (E. coli ST131 n=9; K. pneumoniae ST258 n=10)), 2 on duration of infectiousness (E. coli ST131 n=2), and 324 on pathogenicity (E. coli ST131 n=285; K. pneumoniae ST258 n=39). Available data on duration of carriage and on transmissibility were insufficient for quantitative assessment. In multivariable meta-regression E. coli isolates causing infection were associated with ST131, compared to isolates only causing colonisation, suggesting that E. coli ST131 can be considered more pathogenic than non-ST131 isolates. Date of isolation, location and resistance mechanism also influenced the prevalence of ST131. E. coli ST131 was 3.2 (95% CI 2.0 to 5.0) times more pathogenic than non-ST131. For K. pneumoniae ST258 there were not enough data for meta-regression assessing the influence of colonisation versus infection on ST258 prevalence. CONCLUSIONS With the currently available data, it cannot be confirmed nor rejected, that E. coli ST131 or K. pneumoniae ST258 are hyperendemic clones.
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Affiliation(s)
- M J D Dautzenberg
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M R Haverkate
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M C J Bootsma
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands Faculty of Sciences, Department of Mathematics, Utrecht University, Utrecht, The Netherlands
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The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin Microbiol Rev 2015; 28:565-91. [PMID: 25926236 DOI: 10.1128/cmr.00116-14] [Citation(s) in RCA: 595] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Escherichia coli sequence type 131 (ST131) and Klebsiella pneumoniae ST258 emerged in the 2000s as important human pathogens, have spread extensively throughout the world, and are responsible for the rapid increase in antimicrobial resistance among E. coli and K. pneumoniae strains, respectively. E. coli ST131 causes extraintestinal infections and is often fluoroquinolone resistant and associated with extended-spectrum β-lactamase production, especially CTX-M-15. K. pneumoniae ST258 causes urinary and respiratory tract infections and is associated with carbapenemases, most often KPC-2 and KPC-3. The most prevalent lineage within ST131 is named fimH30 because it contains the H30 variant of the type 1 fimbrial adhesin gene, and recent molecular studies have demonstrated that this lineage emerged in the early 2000s and was then followed by the rapid expansion of its sublineages H30-R and H30-Rx. K. pneumoniae ST258 comprises 2 distinct lineages, namely clade I and clade II. Moreover, it seems that ST258 is a hybrid clone that was created by a large recombination event between ST11 and ST442. Epidemic plasmids with blaCTX-M and blaKPC belonging to incompatibility group F have contributed significantly to the success of these clones. E. coli ST131 and K. pneumoniae ST258 are the quintessential examples of international multidrug-resistant high-risk clones.
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Abstract
In 2008, a previously unknown Escherichia coli clonal group, sequence type 131 (ST131), was identified on three continents. Today, ST131 is the predominant E. coli lineage among extraintestinal pathogenic E. coli (ExPEC) isolates worldwide. Retrospective studies have suggested that it may originally have risen to prominence as early as 2003. Unlike other classical group B2 ExPEC isolates, ST131 isolates are commonly reported to produce extended-spectrum β-lactamases, such as CTX-M-15, and almost all are resistant to fluoroquinolones. Moreover, ST131 E. coli isolates are considered to be truly pathogenic, due to the spectrum of infections they cause in both community and hospital settings and the large number of virulence-associated genes they contain. ST131 isolates therefore seem to contradict the widely held view that high levels of antimicrobial resistance are necessarily associated with a fitness cost leading to a decrease in pathogenesis. Six years after the first description of E. coli ST131, this review outlines the principal traits of ST131 clonal group isolates, based on the growing body of published data, and highlights what is currently known and what we need to find out to provide public health authorities with better information to help combat ST131.
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Rafaï C, Frank T, Manirakiza A, Gaudeuille A, Mbecko JR, Nghario L, Serdouma E, Tekpa B, Garin B, Breurec S. Dissemination of IncF-type plasmids in multiresistant CTX-M-15-producing Enterobacteriaceae isolates from surgical-site infections in Bangui, Central African Republic. BMC Microbiol 2015; 15:15. [PMID: 25648151 PMCID: PMC4326526 DOI: 10.1186/s12866-015-0348-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/14/2015] [Indexed: 11/19/2022] Open
Abstract
Background Surgical-site infection is the most frequent health care-associated infection in the developing world, with a strikingly higher prevalence than in developed countries We studied the prevalence of resistance to antibiotics in Enterobacteriaceae isolates from surgical-site infections collected in three major tertiary care centres in Bangui, Central African Republic. We also studied the genetic basis for antibiotic resistance and the genetic background of third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae. Results Between April 2011 and April 2012, 195 patients with nosocomial surgical-site infections were consecutively recruited into the study at five surgical departments in three major tertiary care centres. Of the 165 bacterial isolates collected, most were Enterobacteriaceae (102/165, 61.8%). Of these, 65/102 (63.7%) were 3GC-R, which were characterized for resistance gene determinants and genetic background. The blaCTX-M-15 and aac(6′)-Ib-cr genes were detected in all strains, usually associated with qnr genes (98.5%). Escherichia coli, the most commonly recovered species (33/65, 50.8%), occurred in six different sequence types, including the pandemic B2-O25b-ST131 group (12/33, 36.4%). Resistance transfer was studied in one representative strain of the resistance gene content in each repetitive extragenic palindromic and enterobacterial repetitive intergenic consensus sequence-PCR banding pattern. Plasmids were characterized by PCR-based replicon typing and sub-typing schemes. In most isolates (18/27, 66.7%), blaCTX-M-15 genes were found in incompatibility groups F/F31:A4:B1 and F/F36:A4:B1 conjugative plasmids. Horizontal transfer of both plasmids is probably an important mechanism for the spread of blaCTX-M-15 among Enterobacteriaceae species and hospitals. The presence of sets of antibiotic resistance genes in these two plasmids indicates their capacity for gene rearrangement and their evolution into new variants. Conclusions Diverse modes are involved in transmission of resistance, plasmid dissemination probably playing a major role.
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Affiliation(s)
- Clotaire Rafaï
- Institut Pasteur, Laboratory of Bacteriology, Avenue de l'Independance, BP 923, Bangui, Central African Republic.
| | - Thierry Frank
- Institut Pasteur, Laboratory of Bacteriology, Avenue de l'Independance, BP 923, Bangui, Central African Republic.
| | - Alexandre Manirakiza
- Institut Pasteur, Unit of Epidemiology, Avenue de l'Independance, BP 923, Bangui, Central African Republic.
| | - Alfred Gaudeuille
- Complexe Pédiatrique, Department of Paediatric Surgery, Avenue de l'Independance, Bangui, Central African Republic.
| | - Jean-Robert Mbecko
- Institut Pasteur, Laboratory of Bacteriology, Avenue de l'Independance, BP 923, Bangui, Central African Republic.
| | - Luc Nghario
- Hôpital de l'Amitié, Department of General Surgery, Avenue de l'Independance, Bangui, Central African Republic.
| | - Eugene Serdouma
- Hôpital de l'Amitié, Department of Gynaecology and Obstetrics, Avenue de l'Independance, Bangui, Central African Republic.
| | - Bertrand Tekpa
- Hôpital Communautaire, Department of Orthopaedic Surgery, Avenue des Martyrs, Bangui, Central African Republic.
| | - Benoit Garin
- Institut Pasteur, Laboratory of Bacteriology, BP 1274, Antananarivo, Madagascar.
| | - Sebastien Breurec
- Institut Pasteur, Laboratory of Bacteriology, Avenue de l'Independance, BP 923, Bangui, Central African Republic. .,University of Antilles, Faculty of Medecine, Pointe-à-Pitre, French West Indies.
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Gqunta K, Govender S. Characterization of ESBL-producing Escherichia coli ST131 isolates from Port Elizabeth. Diagn Microbiol Infect Dis 2014; 81:44-6. [PMID: 25456044 DOI: 10.1016/j.diagmicrobio.2014.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 10/04/2014] [Accepted: 10/15/2014] [Indexed: 11/16/2022]
Abstract
This study investigated resistance determinants and genetic relatedness in extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates. PCR and DNA sequencing were used for screening isolates for blaCTX-M, blaTEM, and blaSHV (qnrA, qnrB, qnrC, qnrD, qnrS, aac(6)-lb-cr, and qepA) resistance genes and the sequence type 131 (ST131) clone. Genetic relatedness of E. coli ST131 isolates was determined by pulsed-field gel electrophoresis. Twelve isolates belonged to the ST131 clonal complex, while 8 were positive for aac(6')-lb-cr with qnrB1 also detected in 1 isolate. This study describes the first occurrence of CTX-M-9, qnrB1+aac(6')-lb-cr and CTX-M-3+qnrS1 among E. coli ST131 isolates from South Africa and illustrates their genetic diversity.
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Affiliation(s)
- Kwanele Gqunta
- Department of Biochemistry and Microbiology, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa
| | - Sharlene Govender
- Department of Biochemistry and Microbiology, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa.
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Characteristics of Escherichia coli sequence type 131 isolates that produce extended-spectrum β-lactamases: global distribution of the H30-Rx sublineage. Antimicrob Agents Chemother 2014; 58:3762-7. [PMID: 24752265 DOI: 10.1128/aac.02428-14] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We designed a study to describe the characteristics of sequence type 131 (ST131) lineages, including the H30-Rx sublineage, among a global collection of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates from 9 countries collected from 2000 to 2011. A total of 240 nonrepeat isolates from Canada, the United States, Brazil, the Netherlands, France, the United Arab Emirates (UAE), India, South Africa, and New Zealand were included. Established PCR, sequencing, and typing methods were used to define ST131 lineages, H30 and H30-Rx phylogenetic groups, gyrA and parC mutations, virotypes, and plasmid-mediated quinolone resistance determinants. The majority of the isolates produced CTX-M-15 with aac(6')-lb-cr, belonged to phylogenetic group B2, and were positive for the H30 lineage with the gyrA1AB and parC1aAB mutations. ST131 showed 15 distinct pulsotypes; 43% of the isolates belonged to four pulsotypes, with a global distribution. Seventy-five percent of the ST131 isolates belonged to H30-Rx; this sublineage was present in all the countries and was associated with multidrug resistance, blaCTX-M-15, aac(6')-lb-cr, and virotypes A and C. The H41 lineage was negative for the ST131 pabB allele-specific PCR. The multidrug-resistant H30-Rx sublineage poses an important public health threat due to its global distribution, association with virotype C, and high prevalence among ST131 isolates that produce CTX-M-15.
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Storberg V. ESBL-producing Enterobacteriaceae in Africa - a non-systematic literature review of research published 2008-2012. Infect Ecol Epidemiol 2014; 4:20342. [PMID: 24765249 PMCID: PMC3955770 DOI: 10.3402/iee.v4.20342] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 01/21/2014] [Accepted: 02/12/2014] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION Enterobacteriaceae producing extended-spectrum beta-lactamases (ESBL) has been found all over the world, and risk factors for acquiring these bacteria involve hospital care and antibiotic treatment. Surveillance studies are present in Europe, North America, and Asia, but there is no summarizing research published on the situation in Africa. AIM This review aims to describe the prevalence of ESBL-producing Enterobacteriaceae in hospital and community settings in Africa and the ESBL genes involved. METHOD A non-systematic literature search was performed in PubMed. All articles published between 2008 and 2012 were screened and read in full text. Relevant articles were assessed for quality of evidence and included in the review. Articles were divided into regional areas in Africa and tabulated. RESULTS ESBL-producing Enterobacteriaceae in hospitalized patients and in communities varies largely between countries and specimens but is common in Africa. ESBLs (class A and D) and plasmid-encoded AmpC (pAmpC) were regularly found, but carbapenemases were also present. CONCLUSION ESBL-producing Enterobacteriaceae in hospital and community settings in Africa is common. Surveillance of antimicrobial resistance needs to be implemented in Africa to tailor interventions targeted at stopping the dissemination of ESBL-producing Enterobacteriaceae.
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Affiliation(s)
- Viktor Storberg
- Department of Women's and Children's Health, International Maternal and Child Health, Uppsala University, Uppsala, Sweden
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Extended-spectrum cephalosporin-resistant Gram-negative organisms in livestock: an emerging problem for human health? Drug Resist Updat 2013; 16:22-45. [PMID: 23395305 DOI: 10.1016/j.drup.2012.12.001] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 12/22/2012] [Indexed: 12/18/2022]
Abstract
Escherichia coli, Salmonella spp. and Acinetobacter spp. are important human pathogens. Serious infections due to these organisms are usually treated with extended-spectrum cephalosporins (ESCs). However, in the past two decades we have faced a rapid increasing of infections and colonization caused by ESC-resistant (ESC-R) isolates due to production of extended-spectrum-β-lactamases (ESBLs), plasmid-mediated AmpCs (pAmpCs) and/or carbapenemase enzymes. This situation limits drastically our therapeutic armamentarium and puts under peril the human health. Animals are considered as potential reservoirs of multidrug-resistant (MDR) Gram-negative organisms. The massive and indiscriminate use of antibiotics in veterinary medicine has contributed to the selection of ESC-R E. coli, ESC-R Salmonella spp. and, to less extent, MDR Acinetobacter spp. among animals, food, and environment. This complex scenario is responsible for the expansion of these MDR organisms which may have life-threatening clinical significance. Nowadays, the prevalence of food-producing animals carrying ESC-R E. coli and ESC-R Salmonella (especially those producing CTX-M-type ESBLs and the CMY-2 pAmpC) has reached worryingly high values. More recently, the appearance of carbapenem-resistant isolates (i.e., VIM-1-producing Enterobacteriaceae and NDM-1 or OXA-23-producing Acinetobacter spp.) in livestock has even drawn greater concerns. In this review, we describe the aspects related to the spread of the above MDR organisms among pigs, cattle, and poultry, focusing on epidemiology, molecular mechanisms of resistance, impact of antibiotic use, and strategies to contain the overall problem. The link and the impact of ESC-R organisms of livestock origin for the human scenario are also discussed.
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Fecal carriage of ESBL-producing E. coli and K. pneumoniae in children in Guinea-Bissau: a hospital-based cross-sectional study. PLoS One 2012; 7:e51981. [PMID: 23284838 PMCID: PMC3527401 DOI: 10.1371/journal.pone.0051981] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/07/2012] [Indexed: 11/19/2022] Open
Abstract
Background In recent years, the world has seen a surge in extended-spectrum β-lactamase (ESBL)-producing bacteria. However, data on the dissemination of ESBL-producing Enterobacteriaceae in the community from systematically enrolled study subjects in Africa remains limited. To determine the prevalence, phenotypic resistance patterns and genetic characteristics of ESBL-producing E. coli and K. pneumoniae in fecal carriage and to analyze associated risk factors in children attending a pediatric emergency department in Guinea-Bissau. Methodology/Principal Findings From June to September 2010, children <5 years of age with fever or tachycardia attending a pediatric emergency ward during the day was screened for ESBL carriage in feces. Socio-demographic and health seeking behavior data was collected. Antibiotic susceptibility was tested with VITEK2 and EUCAST disk diffusion method, molecular characterization of ESBL-encoding genes was performed with multiplex PCR and clonal relatedness was established by automated rep-PCR. Of 408 enrolled children 133 (32.6%) were ESBL carriers. In total, 83 E. coli and 91 K. pneumoniae ESBL-producing isolates were obtained. Nearly all isolates were multidrug-resistant. Co-resistance to ciprofloxacin, trimethoprim-sulfamethoxazole and aminoglycosides was common. Of the isolates, 38.5% were co-resistant to these classes plus extended-spectrum cephalosporins, which infers resistance to all easily available antibiotic agents for treatment of gram-negative sepsis in Guinea-Bissau. The predominant resistance-encoding gene subgroup was blaCTX-M-1 and epidemiologic typing showed that the bacterial ESBL population was highly diverse both for E. coli and K. pneumoniae. Bed sharing with another child <5 years of age was a risk factor for ESBL carriage, indicating crowding as a potential risk factor for transmission of ESBL-producing bacteria. Conclusions/Significance Prevalence of ESBL-producing bacteria in this population was high and clonally diverse. This is alarming considering the limited diagnostic and treatment possibilities in Guinea-Bissau and other resource-poor countries.
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Birgand G, Radu C, Alkhoder S, Al Attar N, Raffoul R, Dilly MP, Nataf P, Lucet JC. Does a gentamicin-impregnated collagen sponge reduce sternal wound infections in high-risk cardiac surgery patients? Interact Cardiovasc Thorac Surg 2012; 16:134-41. [PMID: 23115102 DOI: 10.1093/icvts/ivs449] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Sternal wound infections occurring after cardiac surgery have a critical impact on morbidity, mortality and hospital costs. This study evaluated the efficacy of a gentamicin-collagen sponge in decreasing deep sternal-wound infections in high-risk cardiac surgery patients. METHODS We conducted a quasi-experimental single-centre prospective cohort study in diabetic and/or overweight patients undergoing coronary-artery bypass surgery with bilateral internal mammary artery grafts. The end-point was the rate of reoperation for deep sternal wound infection. The period from January 2006 to October 2008, before the introduction of the gentamicin sponge, was compared with the period from November 2008 to December 2010. RESULTS Of 552 patients (median body mass index, 31.5; 37.7% with diabetes requiring insulin), 68 (12.3%) had deep sternal wound infections. Reoperation for deep sternal wound infections occurred in 40/289 (13.8%) preintervention patients and 22/175 (12.6%) patients managed with the sponge. Independent risk factors were female sex and longer time on mechanical ventilation, but not use of the sponge (adjusted odds ratio, 0.95; 95% confidence interval, 0.52-1.73; P = 0.88). The group managed with the sponge had a higher proportion of gentamicin-resistant micro-organisms (21/27, 77.8%) compared with the other patients (23/56, 41.1%; P < 0.01). The median time to reoperation for wound infection was higher with the sponge (21 vs 17 days, P < 0.01). CONCLUSIONS A gentamicin-collagen sponge was not effective in preventing deep sternal wound infections in high-risk patients. Our results suggest that a substantial proportion of wound contaminations occur after bypass surgery with bilateral internal mammary artery grafts.
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Affiliation(s)
- Gabriel Birgand
- Infection Control Unit, Bichat-Claude Bernard Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.
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Extended-spectrum β-lactamase-producing Enterobacteriaceae in Cameroonian hospitals. Eur J Clin Microbiol Infect Dis 2012; 32:79-87. [PMID: 22886058 DOI: 10.1007/s10096-012-1717-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/25/2012] [Indexed: 10/28/2022]
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae have been described worldwide, but there are few reports on the carriage of these bacteria in Cameroon. In order to investigate the types of ESBLs and to analyse some risk factors associated with ESBL carriage, faecal samples were collected between 3 January and 3 April 2009 from hospitalised patients at Yaounde Central Hospital and at two hospitals in Ngaoundere, Cameroon. Enterobacterial isolates resistant to third-generation cephalosporins were screened for ESBL production using the double-disk synergy test. Polymerase chain reaction (PCR) and DNA sequencing were performed in order to find out the different types of ESBL genes in presumptive ESBL-positive isolates. During the study period, a total of 121 different patients were screened for ESBL carriage. The prevalence among these patients whose faecal samples were found to contain ESBL-producers was 55.3 % (67/121). According to a univariate analysis, hospitalisation during the previous year was found to be associated with ESBL carriage. Of the 71 bacteria isolated, Escherichia coli was predominant and represented 48 % of all isolates. ESBL characterisation revealed two types of ESBLs, CTX-M-15 (96 %) and SHV-12 (4 %). The present study emphasises the importance of screening for ESBLs in laboratories in African countries. The monitoring and detection of ESBL-producing bacteria are important in the setting up of appropriate treatment of patients and to ensure effective infection control efforts.
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Lonchel CM, Meex C, Gangoué-Piéboji J, Boreux R, Assoumou MCO, Melin P, De Mol P. Proportion of extended-spectrum ß-lactamase-producing Enterobacteriaceae in community setting in Ngaoundere, Cameroon. BMC Infect Dis 2012; 12:53. [PMID: 22405322 PMCID: PMC3329637 DOI: 10.1186/1471-2334-12-53] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 03/09/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is no information regarding the resistance mechanisms of extended-spectrum ß-lactamase (ESBL)-producing Enterobacteriaceae in community setting in Cameroon. The current study aimed to determine the proportion of ESBLs in Enterobacteriaceae isolated in the community and to analyse some risk factors associated with ESBL carriage. METHODS Faecal samples were collected from 208 different outpatients and 150 healthy student volunteers between 3 January and 3 April 2009. Enterobacterial isolates resistant to third-generation cephalosporins were screened for ESBL production by the double-disk synergy test. Presumptive ESBL-producing isolates with positive synergy test were identified by Mass Spectrometry using the BioTyper MALDI-TOF. For such ESBL positive isolates, antibiotic susceptibility was determined by the Vitek 2 system. PCR and sequencing were performed for the detection of different types of ESBL genes in presumptive ESBL-producing isolates. Statistical methods were used for the univariate calculation of risk factors. RESULTS During the study period, a total of 358 faecal samples were analysed; 58 of such samples (16%) showed an ESBL phenotype and were confirmed by PCR. The proportion of ESBL producers in faecal carriage was statistically different between outpatients and student volunteers (23.1% vs. 6.7%: p < 0.000). According to a univariate analysis, previous use of antibiotics (ciprofloxacin) appeared to be a risk factor for ESBL carriage (p < 0.05).Escherichia coli was the species most frequently isolated among the ESBL producers in outpatients (66.7%) and student volunteers (90%). Isolates showed additional resistance to gentamicin, ciprofloxacin and trimethoprim/sulfamethoxazole but none of them was resistant to temocillin, amikacin or meropenem. Most of the strains (97%) produced a CTX-M group 1 enzymes [CTX-M-15 (98%) or CTX-M-1 (2%)] and the remaining strains produced SHV-12 enzyme (3%). CONCLUSIONS The use of drugs such as amoxicillin, ciprofloxacin and trimethoprim/sulfamethoxazole does not seem appropriate for empirical treatment because of emerging resistance. The implementation in Cameroon or in other African countries of methods of screening ESBL-producing organisms in routine laboratories is of great importance in order for us to offer patients appropriate treatment and for infection control efforts to succeed.
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Affiliation(s)
- Carine Magoué Lonchel
- Laboratory of Medical Microbiology, University of Liège, CHU Sart-Tilman (B23), B-4000 Liege, Belgium.
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Aibinu I, Odugbemi T, Koenig W, Ghebremedhin B. Sequence Type ST131 and ST10 Complex (ST617) predominant among CTX-M-15-producing Escherichia coli isolates from Nigeria* *This study has been partially presented during the 51st Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC) in Chicago, IL, September 2011. Clin Microbiol Infect 2012; 18:E49-51. [DOI: 10.1111/j.1469-0691.2011.03730.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Markovska R, Schneider I, Ivanova D, Keuleyan E, Stoeva T, Sredkova M, Markova B, Bojkova K, Gergova R, Bauernfeind A, Mitov I. High prevalence of CTX-M-15-producing O25b-ST131 Escherichia coli clone in Bulgarian hospitals. Microb Drug Resist 2012; 18:390-5. [PMID: 22352448 DOI: 10.1089/mdr.2011.0186] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
According to the European Antimicrobial Resistance Surveillance System project results, Bulgaria has become one of the European countries with dramatically increasing rates of extended-spectrum beta-lactamase (ESBL) producers. The aim of this work was to investigate the epidemiology of ESBL-producing Escherichia coli clinical isolates in Bulgaria, collected from seven clinical centers in three towns, during two study periods: 2002-2003 and 2006-2009. For 193 ESBL-producing E. coli isolates random amplified polymorphic DNA (RAPD) analyses, phylogenetic typing, and screening for O25b-ST131 isolates were carried out. Antimicrobial susceptibility, ESBL-type and transferability of resistance determinants were analyzed. Four different ESBL-types, namely TEM-139, SHV-12, CTX-M-3, and CTX-M-15 were found. CTX-M-15 dominated, being found in 88% of the isolates. RAPD-typing revealed 35 types, among which type A dominated, comprising 65% of the isolates. Sixty-eight percent of the 193 isolates belonged to the O25b-ST131 clone, to the phylogenetic group B2, mostly showed RAPD-type A (92%) and were found in all participating hospitals. O25b-ST131 isolates predominantly produced CTX-M-15 (96%), and less SHV-12 (n=3) or TEM-139 (n=2). In conclusion, this study demonstrated for the first time the country-wide dissemination of a highly resistant B2 O25b-ST131 CTX-M-15 producing E. coli clone in Bulgaria.
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Sekizuka T, Matsui M, Yamane K, Takeuchi F, Ohnishi M, Hishinuma A, Arakawa Y, Kuroda M. Complete sequencing of the bla(NDM-1)-positive IncA/C plasmid from Escherichia coli ST38 isolate suggests a possible origin from plant pathogens. PLoS One 2011; 6:e25334. [PMID: 21966500 PMCID: PMC3179503 DOI: 10.1371/journal.pone.0025334] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 09/01/2011] [Indexed: 11/18/2022] Open
Abstract
The complete sequence of the plasmid pNDM-1_Dok01 carrying New Delhi metallo-β-lactamase (NDM-1) was determined by whole genome shotgun sequencing using Escherichia coli strain NDM-1_Dok01 (multilocus sequence typing type: ST38) and the transconjugant E. coli DH10B. The plasmid is an IncA/C incompatibility type composed of 225 predicted coding sequences in 195.5 kb and partially shares a sequence with bla(CMY-2)-positive IncA/C plasmids such as E. coli AR060302 pAR060302 (166.5 kb) and Salmonella enterica serovar Newport pSN254 (176.4 kb). The bla(NDM-1) gene in pNDM-1_Dok01 is terminally flanked by two IS903 elements that are distinct from those of the other characterized NDM-1 plasmids, suggesting that the bla(NDM-1) gene has been broadly transposed, together with various mobile elements, as a cassette gene. The chaperonin groES and groEL genes were identified in the bla(NDM-1)-related composite transposon, and phylogenetic analysis and guanine-cytosine content (GC) percentage showed similarities to the homologs of plant pathogens such as Pseudoxanthomonas and Xanthomonas spp., implying that plant pathogens are the potential source of the bla(NDM-1) gene. The complete sequence of pNDM-1_Dok01 suggests that the bla(NDM-1) gene was acquired by a novel composite transposon on an extensively disseminated IncA/C plasmid and transferred to the E. coli ST38 isolate.
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Affiliation(s)
- Tsuyoshi Sekizuka
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mari Matsui
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kunikazu Yamane
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Fumihiko Takeuchi
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Hishinuma
- Deparment of Infection Control and Clinical Laboratory Medicine, Dokkyo Medical University, Mibu, Tochigi, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Makoto Kuroda
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail:
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