Quinolone resistance genesqnr,aac(6′)-Ib-cr,oqxAB, andqepAin environmentalEscherichia coli: insights into their genetic contexts from comparative genomics

Abstract

ABSTRACTPrevious studies have reported the occurrence of transferable quinolone resistance determinants in environmentalEscherichia coli. However, little is known about their vectors and genetic contexts. To gain insights into these genetic characteristics, we analyzed the complete genomes of 53 environmentalE. coliisolates containing one or more transferable quinolone resistance determinants, including 20 sequenced in this study and 33 sourced from RefSeq. The studied genomes carried the following transferable quinolone resistance determinants alone or in combination:aac(6′)-Ib-cr,oqxAB,qepA1,qnrA1,qnrB4,qnrB7,qnrB19,qnrD1,qnrS1, andqnrS2, withqnrS1being predominant. These resistance genes were detected on plasmids of diverse replicon types; however,aac(6′)-Ib-cr,qnrS1, andqnrS2were also detected on the chromosome. The genetic contexts surrounding these genes included not only those found in clinical isolates but also novel contexts, such asqnrD1embedded within a composite transposon-like structure bounded by Tn3-derived inverted-repeat miniature elements (TIMEs). This study provides deep insights into mobile genetic elements associated with transferable quinolone resistance determinants, highlighting the importance of genomic surveillance of antimicrobial resistant bacteria in the environment.