Genomic characterization of fecal Escherichia coli isolates with reduced susceptibility to beta-lactam antimicrobials from wild hogs and Coyotes

This study was carried out to determine the antimicrobial resistance (AMR) genes and mobile genetic elements of 16 Escherichia coli isolates with reduced susceptibility to ceftazidime and imipenem that were recovered from the fecal samples of coyotes and wild hogs from West Texas. Using whole-genome sequencing, all the isolates were distinct isolates with unrelated sequence type and serotypes. All the isolates were carriers of the multi-drug resistant mdf(A) gene. Five isolates contained 3 beta-lactamase genes (2 bla_CMY-2, 2 bla_CTX-M-55, 1 bla_CTX-M-27) that confer resistance to beta-lactam antimicrobials. Some isolates were carriers of genes conferring resistance to tetracyclines (tetA, tetB, tetC), aminoglycosides (aac(3)-IId, aadA1, aadA5, aadA22, aph(3")-lb, aph(6)-ld), sulfonamides (sul2, sul3), amphenicol (floR), trimethoprim (dfrA1, dfrA17) and macrolide, lincosamide, streptogramin B (MLSB) agents (Inu(F), mph(A)). Nine isolates showed chromosomal mutations in the promoter region G of ampC beta-lactamase gene while 3 isolates showed mutations in gyrA, parC, and parE quinolone resistance-determining regions which confers resistance to quinolones. We also detected ten incompatibility plasmid groups with incF most common. Different types of virulence genes were detected including those that enhance bacterial fitness and pathogenicity. One bla_CMY-2 positive isolate from a wild hog was Shiga-toxin-producing E. coli and was a carrier of stx2A, stx2B, and stx2 virulence toxin subtypes. We report the detection of bla_CMY-2, bla_CTX-M-55, and bla_CTX-M-27 beta-lactamase genes in E. coli from coyotes for the first time. This study demonstrates the importance of wildlife as reservoirs of important multi-drug-resistant bacteria and provide information for future comparative genomic analysis with limited literature on antimicrobial resistance dynamics in wildlife such as coyotes.