Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases

Background Next-generation sequencing has considerably increased the number of genomes available in the public domain. However, efforts to use these genomes for surveillance of antimicrobial resistance have thus far been limited and geographically heterogeneous. We inferred global resistance trends in Escherichia coli in food animals using genomes from public databases. Methods We retrieved 7632 E. coli genomes from public databases (NCBI, PATRIC and EnteroBase) and screened for antimicrobial resistance genes (ARGs) using ResFinder. Selection bias towards resistance, virulence or specific strains was accounted for by screening BioProject descriptions. Temporal trends for MDR, resistance to antimicrobial classes and ARG prevalence were inferred using generalized linear models for all genomes, including those not subjected to selection bias. Results MDR increased by 1.6 times between 1980 and 2018, as genomes carried, on average, ARGs conferring resistance to 2.65 antimicrobials in swine, 2.22 in poultry and 1.58 in bovines. Highest resistance levels were observed for tetracyclines (42.2%-69.1%), penicillins (19.4%-47.5%) and streptomycin (28.6%-56.6%). Resistance trends were consistent after accounting for selection bias, although lower mean absolute resistance estimates were associated with genomes not subjected to selection bias (difference of 3.16%+/- 3.58% across years, hosts and antimicrobial classes). We observed an increase in extended-spectrum cephalosporin ARG bla(CMY-2) and a progressive substitution of tetB by tetA. Estimates of resistance prevalence inferred from genomes in the public domain were in good agreement with reports from systematic phenotypic surveillance. Conclusions Our analysis illustrates the potential of using the growing volume of genomes in public databases to track AMR trends globally.

Automated summary

This study inferred the global resistance trends in Escherichia coli in food animals using genomes from public databases. The results showed that multidrug resistance increased by 1.6 times between 1980 and 2018, with the highest resistance levels observed for tetracyclines, penicillins, and streptomycin. The resistance trends remained consistent after accounting for selection bias. Additionally, the estimated resistance prevalence inferred from genomes in the public domain was in good agreement with reports from systematic phenotypic surveillance.