Chromosomal integration of bla(CTX-M) genes in diverse Escherichia coli isolates recovered from river water in Japan

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 bla(CTX-M) genes. Among the 14 isolates with completed genomes, bla(CTX-M) genes were detected on the chromosome in nine isolates. All but one chromosomal bla(CTX-M) genes were associated with ISEcp1 and were carried on different transposition units ranging in size from 2,855 bp to 11,093 bp; the exception, bla(CTX-M-2), was associated with ISCR1. The remaining five isolates carried bla(CTX-M) genes on epidemic IncI1 plasmids of different sequence types (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 bla(CTX-M) genes in diverse genetic contexts. Apparent high prevalence of chromosomal bla(CTX-M) potentially indicates that some E. coli can stably maintain bla(CTX-M) genes in environmental waters, though further studies are needed to confirm this.