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Research article - Peer-reviewed, 2022

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

Pires, Joao; Huber, Laura; Hickman, Rachel A.; Dellicour, Simon; Lunha, Kamonwan; Leangapichart, Thongpan; Jiwakanon, Jatesada; Magnusson, Ulf; Sunde, Marianne; Jarhult, Josef D.; Van Boeckel, Thomas P.;


Thailand 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 bla(CTX-M-55) + qnrS1 (29.8% vs 17.5% in small and medium farms, respectively), bla(CTX-M-55) + qnrS1 + mcr-3.19 (5% vs 0%), bla(CTX-M-14) + qnrS1 (9.3% vs 6.2%), and bla(CTX-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.


Antimicrobial resistance; Pig; Farms; Antimicrobial use; Escherichia coli; ESBL

Published in

BMC Microbiology

2022, volume: 22, article number: 253
Publisher: BMC

Authors' information

Pires, Joao
Swiss Federal Institute of Technology (ETH Zürich)
Huber, Laura
Auburn University
Hickman, Rachel A.
Uppsala University
Dellicour, Simon
Universite Libre de Bruxelles
Dellicour, Simon
KU Leuven
Lunha, Kamonwan
Swedish University of Agricultural Sciences, Department of Clinical Sciences
Leangapichart, Thongpan
Norwegian Veterinary Institute
Jiwakanon, Jatesada
Khon Kaen University
Swedish University of Agricultural Sciences, Department of Clinical Sciences
Sunde, Marianne
Norwegian Veterinary Institute
Jarhult, Josef D.
Uppsala University
Van Boeckel, Thomas P.
ETH Zurich
Van Boeckel, Thomas P.
Ctr Dis Dynam Econ and Policy

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