Chromosomal integration of bla_CTX-M genes in diverse Escherichia coli isolates recovered from river water in Japan

Abstract

Occurrence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBLEC) in environmental waters is of great concern. However, unlike clinical ESBLEC, their genetic characteristics, in particular the genetic contexts of ESBL genes, are not well understood. In this study, we sequenced and analyzed the genomes of CTX-M-producing E. coli isolates recovered from river water to fully characterize the genetic contexts of blaCTX-M genes. Among the 14 isolates with completed genomes, blaCTX-M genes were detected on the chromosome in nine isolates. All but one chromosomal blaCTX-M genes were associated with ISEcp1 and were carried on different transposition units (TPU) ranging in size from 2,855 bp to 11,093 bp; the exception, blaCTX-M-2, was associated with ISCR1. In many cases, the TPU were directly inserted into chromosomes. However, in one case, the TPU was part of a 36-kbp multiresistance region bracketed by IS26, and the whole multiresistance region was inserted into the chromosome. We also found a case where a chromosomally-located TPU and an adjacent region had transposed into another chromosomal location, leading to duplication of blaCTX-M. The remaining five isolates carried blaCTX-M genes on epidemic IncI1 plasmids of different STs (ST3, ST16, ST113, and ST167) (n = 4) or on an IncB/O/K/Z plasmid (n = 1). This study revealed that environmental E. coli carry blaCTX-M genes in diverse genetic contexts. Apparent high prevalence of chromosomal blaCTX-M potentially indicates that some environmental E. coli can stably maintain blaCTX-M genes in the absence of antibiotic selection pressure, though further studies are needed to confirm this.