Global distribution of antimicrobial resistance genes in Escherichia coli isolated from wild animals using genomes available in public databases

Abstract

Antimicrobial resistance (AMR) is a pressing worldwide health challenge fueled by the improper and/or excessive use of antimicrobials in humans and animals. Wild animals can acquire AMR from waste released into the environment, being a good bioindicator of AMR pollution in that compartment. This study aimed to estimate the global distribution of antimicrobial-resistant genes (ARGs) in Escherichia coli (E. coli) isolated from wild animals (birds and mammals) and to assess their role as sentinels for the study of AMR in the environment. A total of 4436 E. coli genomes were retrieved from three public databases and screened for ARGs using ResFinder, revealing 159 unique ARGs. The tetracycline-resistant gene tet(A) was the most frequently detected (22.1 %). The highest burden of ARGs per genome was identified in Asia (5.9), followed by Africa (5.2) and South and Central America (5). Wild birds and carnivores harbored more ARGs per isolate than wild ungulates, bats and other mammals. Additionally, wild animals inhabiting aquatic environment carried a higher number ARGs per genome compared to terrestrial species. Furthermore, genomes from those groups of animals showed a higher level of predicted resistance to classes of antibiotics widely used in humans and animals, including beta-lactams, aminoglycosides, tetracyclines, sulfonamides, trimethoprim, and last-resort antibiotics like colistin and carbapenems. Given the higher burden and their presence in different ecosystems, wild animals, especially birds, carnivores, and those living in the aquatic environment, could be good sentinels for the study of AMR pollution in the environment.