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

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.

Automated summary

Thailand is experiencing differences in antimicrobial use and the composition of antimicrobial resistance genes (ARGs) between small and medium farms. Pig isolates from small farms are more associated with genes conferring resistance to colistin and fluoroquinolones, while pig isolates from medium farms are associated with genes conferring resistance to drugs commonly used on medium farms. ARGs conferring resistance to critically important antimicrobials are more frequently co-carried on plasmids from small farms compared to plasmids from medium farms. Actions to curb the spread of these ARGs are urgently needed.