Antimicrobial resistance and genomic characterization of Escherichia coli from pigs and chickens in Zhejiang, China

Abstract

<i>Escherichia coli</i> is considered an opportunistic pathogen and an indicator for antimicrobial resistance (AMR) monitoring. Despite many reports on its AMR monitoring, studies based on genome-based analysis of AMR genes are still insufficient. Here, 181 <i>E. coli</i> strains were isolated from anal swab samples collected from pigs and chickens of animal farms located in Eastern China and sequenced through the Illumina platform. The results showed that 87.85% (159/181) of the <i>E. coli</i> isolates were multidrug-resistant (MDR). Ampicillin (AMP)- spectinomycin (SPT)- tetracycline (TET)- florfenicol (FFC)- sulfisoxazole (SF)- trimethoprim/sulfamethoxazole (SXT) was the predominant AMR pattern. By whole-genome sequencing, we found that ST10 (10.49%, 19/181) and ST48 (7.18%, 13/181) were major sequence types. IncFIB and IncX1 were the most prevalent plasmid replicons. The AMR genes <i>bla</i> _NDM-5 (1.10%, 2/181), <i>mcr</i>-1 (1.10%, 2/181), <i>tet</i>(X4) (1.10%, 2/181), and <i>cfr</i> (6.08%, 2/181) were also found in these isolates. In addition, among the 169 virulence genes detected, we identified <i>ast</i>A (37.02%, 67/181), <i>hly</i>A (1.66%, 3/181), <i>hly</i>B (1.66%, 3/181) and <i>hly</i>D (1.66%, 3/181), which were closely related to heat-stable enterotoxin 1 and α-hemolysin. In addition, there were 33 virulence genes associated with the iron uptake system, and 46 were adhesion-related genes. Our study highlighted the need for routine surveillance of AMR with advanced genomic approaches, providing up-to-date data on the prevalence of AMR for the development and execution of antimicrobial stewardship policy.