Genome-associations of extended-spectrum ß-lactamase producing (ESBL) or AmpC producing E. coli in small and medium pig farms from Khon Kaen province, Thailand
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Published:2022-10-20
Issue:1
Volume:22
Page:
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ISSN:1471-2180
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Container-title:BMC Microbiology
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language:en
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Short-container-title:BMC Microbiol
Author:
Pires João,Huber Laura,Hickman Rachel A.,Dellicour Simon,Lunha Kamonwan,Leangapichart Thongpan,Jiwakanon Jatesada,Magnusson Ulf,Sunde Marianne,Järhult Josef D.,Van Boeckel Thomas P.
Abstract
AbstractThailand is undergoing rapid intensification of livestock production where small subsistence farms and medium sized commercial farms coexist. In medium farms, antimicrobials are prescribed by a veterinarian, whereas in small farms antimicrobial use remains largely unsupervised. The impact of these differences as well as other farming practices on the emergence and composition of antimicrobial resistance genes (ARGs) remains largely unknown. We analyzed 363 genomes of extended-spectrum ß-lactamase producing (ESBL) and/or AmpC producing Escherichia coli recovered from humans and pigs at small and medium farms from the Khon Kaen province, Thailand. We tested for genome-wide associations to identify links between ARGs, host, and farm size. Pig isolates from small farms were associated with mcr and qnr genes conferring resistance to colistin and fluoroquinolones, respectively. In contrast, pig isolates from medium farms were associated with ARGs conferring resistance to drugs commonly used on medium farms (i.e., streptomycin). ESBL plasmids from small farms co-carried ARGs conferring resistance to critically important antimicrobials more frequently compared to plasmid from medium farms. Frequent ARG combinations included blaCTX-M-55 + qnrS1 (29.8% vs 17.5% in small and medium farms, respectively), blaCTX-M-55 + qnrS1 + mcr-3.19 (5% vs 0%), blaCTX-M-14 + qnrS1 (9.3% vs 6.2%), and blaCTX-M-14 + qnrS1 + mcr-1.1 (3.1% vs 0%). The co-location on plasmids of ARGs conferring resistance to critically important antimicrobials as defined by the World Health Organization is concerning, and actions to curb their spread are urgently needed. Legislation on limiting antimicrobial sales and initiatives to better inform farmers and veterinarians on appropriate antimicrobial usage and farm biosecurity could help reduce antimicrobial use on farms.
Funder
Fonds De La Recherche Scientifique - FNRS
Fonds voor Wetenschappelijk Onderzoek-Vlaanderen
European Union Horizon 2020
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
Branco Weiss Fellowship – Society in Science
Swiss Federal Institute of Technology Zurich
Publisher
Springer Science and Business Media LLC
Subject
Microbiology (medical),Microbiology
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