Antimicrobial resistance genes and associated mobile genetic elements in Escherichia coli from human, animal and environment

Abstract

The global rise of antimicrobial resistance (AMR) poses a significant threat to human health. The environment plays an essential role in transmission of antimicrobial resistance genes (ARGs) between human and animal. Bacterial communities harbour diverse ARGs, carried by mobile genetic elements (MGEs) like plasmids and insertion sequences (ISs). Here, a total of 2199 Escherichia coli (E. coli) whole genome sequences from human, animal, bird and environment were retrieved globally to investigate ARG prevalence and assess their genetic framework. The study highlights how the genetic background including plasmids, IS elements and transposons surrounding ARGs influences their transmission potential. The maximum number of ARGs was found in United Kingdom followed by USA, majorly in human hosts. However, IS-associated ARGs were most prevalent in bird hosts. ARGs like aph(6)-ld, aph(3″)-lb, bla_CTX-M, bla_NDM were widespread across all hosts. Tn2 was the most prevalent, majorly carried by IncFIB plasmids. The IS26 and ISVsa3 carried diverse ARGs, primarily linked to aminoglycoside and β-lactam resistance. The combinations like mph(A)_IS6100 and bla_NDM-5_IS5 showed fixed IS-ARG associations. ARGs like bla_NDM, bla_CTX-M variants displayed strong association with IS elements. The study highlights possible mechanism of transmission due to close proximity of AMR genes to MGEs, offering promising strategies to combat AMR by predicting and addressing future resistance determinants.