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Mills RO, Dadzie I, Le-Viet T, Baker DJ, Addy HPK, Akwetey SA, Donkoh IE, Quansah E, Semanshia PS, Morgan J, Mensah A, Adade NE, Ampah EO, Owusu E, Mwintige P, Amoako EO, Spadar A, Holt KE, Foster-Nyarko E. Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana. J Antimicrob Chemother 2024; 79:1529-1539. [PMID: 38751093 PMCID: PMC11215549 DOI: 10.1093/jac/dkae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/09/2024] [Indexed: 07/02/2024] Open
Abstract
OBJECTIVES Comprehensive data on the genomic epidemiology of hospital-associated Klebsiella pneumoniae in Ghana are scarce. This study investigated the genomic diversity, antimicrobial resistance patterns, and clonal relationships of 103 clinical K. pneumoniae isolates from five tertiary hospitals in Southern Ghana-predominantly from paediatric patients aged under 5 years (67/103; 65%), with the majority collected from urine (32/103; 31%) and blood (25/103; 24%) cultures. METHODS We generated hybrid Nanopore-Illumina assemblies and employed Pathogenwatch for genotyping via Kaptive [capsular (K) locus and lipopolysaccharide (O) antigens] and Kleborate (antimicrobial resistance and hypervirulence) and determined clonal relationships using core-genome MLST (cgMLST). RESULTS Of 44 distinct STs detected, ST133 was the most common, comprising 23% of isolates (n = 23/103). KL116 (28/103; 27%) and O1 (66/103; 64%) were the most prevalent K-locus and O-antigen types. Single-linkage clustering highlighted the global spread of MDR clones such as ST15, ST307, ST17, ST11, ST101 and ST48, with minimal allele differences (1-5) from publicly available genomes worldwide. Conversely, 17 isolates constituted novel clonal groups and lacked close relatives among publicly available genomes, displaying unique genetic diversity within our study population. A significant proportion of isolates (88/103; 85%) carried resistance genes for ≥3 antibiotic classes, with the blaCTX-M-15 gene present in 78% (n = 80/103). Carbapenem resistance, predominantly due to blaOXA-181 and blaNDM-1 genes, was found in 10% (n = 10/103) of the isolates. CONCLUSIONS Our findings reveal a complex genomic landscape of K. pneumoniae in Southern Ghana, underscoring the critical need for ongoing genomic surveillance to manage the substantial burden of antimicrobial resistance.
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Affiliation(s)
- Richael O Mills
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Isaac Dadzie
- Department of Medical Laboratory Technology, University of Cape Coast, Cape Coast, Ghana
| | - Thanh Le-Viet
- Quadram Institute Biosciences, Norwich Research Park, Norwich NR4 7UQ, UK
| | - David J Baker
- Quadram Institute Biosciences, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Humphrey P K Addy
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Samuel A Akwetey
- Department of Clinical Microbiology, University of Development Studies, Tamale, Ghana
| | - Irene E Donkoh
- Department of Medical Laboratory Technology, University of Cape Coast, Cape Coast, Ghana
| | - Elvis Quansah
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
- Anhui Provincial Laboratory of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Prince S Semanshia
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Jennifer Morgan
- Department of Medical Laboratory Technology, University of Cape Coast, Cape Coast, Ghana
| | - Abraham Mensah
- Department of Microbiology and Immunology, University of Cape Coast, Cape Coast, Ghana
| | - Nana E Adade
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Microbiology, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Emmanuel O Ampah
- Microbiology Department, Greater Accra Regional Hospital, Ridge, Accra, Ghana
| | - Emmanuel Owusu
- Microbiology Department, Greater Accra Regional Hospital, Ridge, Accra, Ghana
| | - Philimon Mwintige
- Microbiology Laboratory, Cape Coast Teaching Hospital, Cape Coast, Ghana
| | - Eric O Amoako
- Public Health Laboratory, Effia Nkwanta Regional Hospital, Sekondi-Takoradi, Ghana
| | - Anton Spadar
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | - Kathryn E Holt
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | - Ebenezer Foster-Nyarko
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
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Uwanibe JN, Olawoye IB, Happi CT, Folarin OA. Genomic Characterization of Multidrug-Resistant Pathogenic Enteric Bacteria from Healthy Children in Osun State, Nigeria. Microorganisms 2024; 12:505. [PMID: 38543556 PMCID: PMC10974654 DOI: 10.3390/microorganisms12030505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 04/01/2024] Open
Abstract
Antimicrobial resistance (AMR) is responsible for the spread and persistence of bacterial infections. Surveillance of AMR in healthy individuals is usually not considered, though these individuals serve as reservoirs for continuous disease transmission. Therefore, it is essential to conduct epidemiological surveillance of AMR in healthy individuals to fully understand the dynamics of AMR transmission in Nigeria. Thirteen multidrug-resistant Citrobacter spp., Enterobacter spp., Klebsiella pneumoniae, and Escherichia coli isolated from stool samples of healthy children were subjected to whole genome sequencing (WGS) using Illumina and Oxford nanopore sequencing platforms. A bioinformatics analysis revealed antimicrobial resistance genes such as the pmrB_Y358N gene responsible for colistin resistance detected in E. coli ST219, virulence genes such as senB, and ybtP&Q, and plasmids in the isolates sequenced. All isolates harbored more than three plasmid replicons of either the Col and/or Inc type. Plasmid reconstruction revealed an integrated tetA gene, a toxin production caa gene in two E. coli isolates, and a cusC gene in K. quasivariicola ST3879, which induces neonatal meningitis. The global spread of AMR pathogenic enteric bacteria is of concern, and surveillance should be extended to healthy individuals, especially children. WGS for epidemiological surveillance will improve the detection of AMR pathogens for management and control.
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Affiliation(s)
- Jessica N. Uwanibe
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Oshogbo 232102, Osun State, Nigeria; (J.N.U.); (I.B.O.); (C.T.H.)
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Oshogbo 232102, Osun State, Nigeria
| | - Idowu B. Olawoye
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Oshogbo 232102, Osun State, Nigeria; (J.N.U.); (I.B.O.); (C.T.H.)
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Oshogbo 232102, Osun State, Nigeria
| | - Christian T. Happi
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Oshogbo 232102, Osun State, Nigeria; (J.N.U.); (I.B.O.); (C.T.H.)
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Oshogbo 232102, Osun State, Nigeria
| | - Onikepe A. Folarin
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Oshogbo 232102, Osun State, Nigeria; (J.N.U.); (I.B.O.); (C.T.H.)
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Oshogbo 232102, Osun State, Nigeria
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3
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Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli. Nat Commun 2023; 14:1400. [PMID: 36918537 PMCID: PMC10011798 DOI: 10.1038/s41467-023-36337-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/23/2023] [Indexed: 03/16/2023] Open
Abstract
Escherichia coli is a frequent member of the healthy human gastrointestinal microbiota, as well as an important human pathogen. Previous studies have focused on the genomic diversity of the pathogenic E. coli and much remains unknown about the non-diarrheagenic E. coli residing in the human gut, particularly among young children in low and middle income countries. Also, gaining additional insight into non-diarrheagenic E. coli is important for understanding gut health as non-diarrheagenic E. coli can prevent infection by diarrheagenic bacteria. In this study we examine the genomic diversity of non-diarrheagenic fecal E. coli from male and female children with or without diarrhea from countries in sub-Saharan Africa and south Asia as part of the Global Enteric Multicenter Study (GEMS). We find that these E. coli exhibit considerable genetic diversity as they were identified in all E. coli phylogroups and an Escherichia cryptic clade. Although these fecal E. coli lack the characteristic virulence factors of diarrheagenic E. coli pathotypes, many exhibit remarkable genomic similarity to previously described diarrheagenic isolates with differences attributed to mobile elements. This raises an important question of whether these non-diarrheagenic fecal E. coli may have at one time possessed the mobile element-encoded virulence factors of diarrheagenic pathotypes or may have the potential to acquire these virulence factors.
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Takawira FT, Pitout JDD, 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. Faecal carriage of ESBL producing and colistin resistant Escherichia coli in avian species over a 2-year period (2017-2019) in Zimbabwe. Front Cell Infect Microbiol 2022; 12:1035145. [PMID: 36619741 PMCID: PMC9816332 DOI: 10.3389/fcimb.2022.1035145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/31/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Extended spectrum beta-lactamase (ESBL) producing Escherichia coli have become widespread among food producing animals. These strains serve as a reservoir of antibiotic resistance genes (ARGs) and act as a possible source of infection to humans as transmission can occur by direct or indirect contact. Methods This study investigated the faecal carriage of ESBL producing and colistin resistant E. coli in poultry over a 2-year period (2017-2019) from Zimbabwe. A total of 21 ESBL positive isolates from poultry cloacal specimens were selected for whole genome sequencing from animal E. coli isolates bio-banked at the National Microbiology Reference laboratory using phenotypic susceptibility testing results from the National Escherichia coli Surveillance Program to provide representation of different geographical regions and year of isolation. Cloacal swabs were collected from 3000 broiler live birds from farm 1 and from farm 2, 40 backyard chickens and 10 ducks were sampled. Antimicrobial susceptibility and ESBL testing were performed as per Clinical Laboratory Standards Institute guidelines. Whole genome sequencing of ESBL producing isolates was used to determine sequence types (STs), ARGs, and phylogroups. Results Twenty-one of the included E. coli isolates were confirmed as ESBL producers. Three defined sequence type clonal complexes (CCs) were identified (ST10CC, ST155CC and ST23CC), with ST10CC associated with the most antibiotic resistant profile. The ESBL phenotype was linked to the presence of either cefotaximase-Munich-14 (CTX-M-14) or CTX-M-79. Plasmid mediated quinolone resistant determinants identified were qnrB19 and qnrS1 and one ST10CC isolate from farm 1 broiler chickens harbored a mobile colistin resistance gene (mcr-1). Phylogenetic groups most identified were B1, A and unknown. Discussions The avian ESBL producing E. coli belonged to a diverse group of strains. The detection of several ARGs highlights the importance of implementing enhanced control measures to limit the spread in animals, environment, and humans. This is the first report of mcr-1 in Zimbabwe, which further underscores the importance of the One Health approach to control the spread and development of AMR.
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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 D. D. 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, United Kingdom
| | - 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,Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa
| | | | - Marleen M. Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa,Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa,*Correspondence: Marleen M. Kock,
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5
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Foster-Nyarko E, Pallen MJ. The microbial ecology of Escherichia coli in the vertebrate gut. FEMS Microbiol Rev 2022; 46:fuac008. [PMID: 35134909 PMCID: PMC9075585 DOI: 10.1093/femsre/fuac008] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.
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Affiliation(s)
- Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, United Kingdom
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6
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Giannattasio-Ferraz S, Ene A, Gomes VJ, Queiroz CO, Maskeri L, Oliveira AP, Putonti C, Barbosa-Stancioli EF. Escherichia coli and Pseudomonas aeruginosa Isolated From Urine of Healthy Bovine Have Potential as Emerging Human and Bovine Pathogens. Front Microbiol 2022; 13:764760. [PMID: 35330764 PMCID: PMC8940275 DOI: 10.3389/fmicb.2022.764760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The study of livestock microbiota has immediate benefits for animal health as well as mitigating food contamination and emerging pathogens. While prior research has indicated the gastrointestinal tract of cattle as the source for many zoonoses, including Shiga-toxin producing Escherichia coli and antibiotic resistant bacteria, the bovine urinary tract microbiota has yet to be thoroughly investigated. Here, we describe 5 E. coli and 4 Pseudomonas aeruginosa strains isolated from urine of dairy Gyr cattle. While both species are typically associated with urinary tract infections and mastitis, all of the animals sampled were healthy. The bovine urinary strains were compared to E. coli and P. aeruginosa isolates from other bovine samples as well as human urinary samples. While the bovine urinary E. coli isolates had genomic similarity to isolates from the gastrointestinal tract of cattle and other agricultural animals, the bovine urinary P. aeruginosa strains were most similar to human isolates suggesting niche adaptation rather than host adaptation. Examination of prophages harbored by these bovine isolates revealed similarity with prophages within distantly related E. coli and P. aeruginosa isolates from the human urinary tract. This suggests that related urinary phages may persist and/or be shared between mammals. Future studies of the bovine urinary microbiota are needed to ascertain if E. coli and P. aeruginosa are resident members of this niche and/or possible sources for emerging pathogens in humans.
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Affiliation(s)
- Silvia Giannattasio-Ferraz
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Vitor Júnio Gomes
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Cid Oliveira Queiroz
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Laura Maskeri
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | | | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Edel F. Barbosa-Stancioli
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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7
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Thomson NM, Gilroy R, Getino M, Foster-Nyarko E, van Vliet AH, La Ragione RM, Pallen MJ. Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens. PeerJ 2022; 10:e12935. [PMID: 35251780 PMCID: PMC8896058 DOI: 10.7717/peerj.12935] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/23/2022] [Indexed: 01/11/2023] Open
Abstract
The genus Escherichia has been extensively studied and it is known to encompass a range of commensal and pathogenic bacteria that primarily inhabit the gastrointestinal tracts of warm-blooded vertebrates. However, the presence of E. coli as a model organism and potential pathogen has diverted attention away from commensal strains and other species in the genus. To investigate the diversity of Escherichia in healthy chickens, we collected fecal samples from antibiotic-free Lohmann Brown layer hens and determined the genome sequences of 100 isolates, 81 of which were indistinguishable at the HC0 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing scheme. Despite initial selection on CHROMagar Orientation medium, which is considered selective for E. coli, in silico phylotyping and core genome single nucleotide polymorphism analysis revealed the presence of at least one representative of all major clades of Escherichia, except for E. albertii, Shigella, and E. coli phylogroup B2 and cryptic clade I. The most frequent phylogenomic groups were E. coli phylogroups A and B1 and E. ruysiae (clades III and IV). We compiled a collection of reference strains isolated from avian sources (predominantly chicken), representing every Escherichia phylogroup and species, and used it to confirm the phylogeny and diversity of our isolates. Overall, the isolates carried low numbers of the virulence and antibiotic resistance genes typically seen in avian pathogenic E. coli. Notably, the clades not recovered are ones that have been most strongly associated with virulence by other studies.
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Affiliation(s)
| | - Rachel Gilroy
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom,Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom,Department of Infection Biology, London School of Hygiene & Tropical Medicine, University of London, London, United Kingdom
| | - Arnoud H.M. van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Roberto M. La Ragione
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom,Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom,Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
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8
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Milenkov M, Rasoanandrasana S, Rahajamanana LV, Rakotomalala RS, Razafindrakoto CA, Rafalimanana C, Ravelomandranto E, Ravaoarisaina Z, Westeel E, Petitjean M, Mullaert J, Clermont O, Raskine L, Samison LH, Endtz H, Andremont A, Denamur E, Komurian-Pradel F, Armand-Lefevre L. Prevalence, Risk Factors, and Genetic Characterization of Extended-Spectrum Beta-Lactamase Escherichia coli Isolated From Healthy Pregnant Women in Madagascar. Front Microbiol 2021; 12:786146. [PMID: 35003019 PMCID: PMC8740230 DOI: 10.3389/fmicb.2021.786146] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
Antimicrobial resistance is a major public health concern worldwide affecting humans, animals and the environment. However, data is lacking especially in developing countries. Thus, the World Health Organization developed a One-Health surveillance project called Tricycle focusing on the prevalence of ESBL-producing Escherichia coli in humans, animals, and the environment. Here we present the first results of the human community component of Tricycle in Madagascar. From July 2018 to April 2019, rectal swabs from 492 pregnant women from Antananarivo, Mahajanga, Ambatondrazaka, and Toamasina were tested for ESBL-E. coli carriage. Demographic, sociological and environmental risk factors were investigated, and E. coli isolates were characterized (antibiotic susceptibility, resistance and virulence genes, plasmids, and genomic diversity). ESBL-E. coli prevalence carriage in pregnant women was 34% varying from 12% (Toamasina) to 65% (Ambatondrazaka). The main risk factor associated with ESBL-E. coli carriage was the rainy season (OR = 2.9, 95% CI 1.3-5.6, p = 0.009). Whole genome sequencing was performed on 168 isolates from 144 participants. bla CTX-M-15 was the most frequent ESBL gene (86%). One isolate was resistant to carbapenems and carried the bla NDM-5 gene. Most isolates belonged to commensalism associated phylogenetic groups A, B1, and C (90%) and marginally to extra-intestinal virulence associated phylogenetic groups B2, D and F (10%). Multi locus sequence typing showed 67 different sequence types gathered in 17 clonal complexes (STc), the most frequent being STc10/phylogroup A (35%), followed distantly by the emerging STc155/phylogroup B1 (7%), STc38/phylogroup D (4%) and STc131/phylogroup B2 (3%). While a wide diversity of clones has been observed, SNP analysis revealed several genetically close isolates (n = 34/168) which suggests human-to-human transmissions. IncY plasmids were found with an unusual prevalence (23%), all carrying a bla CTX-M-15. Most of them (85%) showed substantial homology (≥85%) suggesting a dissemination of IncY ESBL plasmids in Madagascar. This large-scale study reveals a high prevalence of ESBL-E. coli among pregnant women in four cities in Madagascar associated with warmth and rainfall. It shows the great diversity of E. coli disseminating throughout the country but also transmission of specific clones and spread of plasmids. This highlights the urgent need of public-health interventions to control antibiotic resistance in the country.
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Affiliation(s)
- Milen Milenkov
- Fondation Mérieux, Lyon, France
- Université de Paris, IAME, INSERM UMR 1137, Paris, France
| | - Saida Rasoanandrasana
- Laboratoire de Bactériologie, CHU Joseph Raseta Befelatanana, RESAMAD Network, Antananarivo, Madagascar
| | | | | | | | - Christian Rafalimanana
- Laboratoire de Bactériologie, CHU Joseph Ravoahangy Andrianavalona, RESAMAD Network, Antananarivo, Madagascar
| | - Emile Ravelomandranto
- Laboratoire de Bactériologie, CHRR Alaotra Mangoro, RESAMAD Network, Ambatondrazaka, Madagascar
| | | | | | | | - Jimmy Mullaert
- Université de Paris, IAME, INSERM UMR 1137, Paris, France
| | | | | | - Luc Hervé Samison
- Centre d’Infectiologie Charles Mérieux, University of Antananarivo, Antananarivo, Madagascar
| | - Hubert Endtz
- Fondation Mérieux, Lyon, France
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, Netherlands
| | | | - Erick Denamur
- Université de Paris, IAME, INSERM UMR 1137, Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, Paris, France
| | | | - Laurence Armand-Lefevre
- Université de Paris, IAME, INSERM UMR 1137, Paris, France
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, Paris, France
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