Genomic Analysis of Carbapenemase-Producing Escherichia coli Isolates Analyzed by Whole Genome Sequencing

The increasing trend of Escherichia coli that produce extended-spectrum beta-lactamases and carbapenemases is a global public health concern. Sequence type (ST)131, a high-risk clone, is most likely responsible for the global distribution of E. coli that carry the carbapenemase gene such as bla _KPC. In this study, carbapenemase-producing E. coli (CPEC) isolates were recovered from the stool of patients in a tertiary care hospital in 2019 and 2020.

We randomly selected nine isolates among CPEC isolates carrying KPC, NDM and OXA-type carbapenemase genes for whole genome sequencing (WGS). WGS was performed using the Illumina system (Illumina, Inc., San Diego, CA, USA) at Macrogen (Seoul, Korea). De novo assembly and assembly validation were performed at Macrogen. The whole genome of isolates was analyzed using the Center for Genomic Epidemiology website (http://www.genomicepidemiology.org/).

Seven sequence types were detected: ST131, ST410, ST68, ST216, ST405, ST224 and ST409 variant. Six isolates harbored CTX-M-type genes such as bla _CTX-M-15, bla _CTX-M-14 and bla _CTX-M-27. Plasmid replicons such as IncFIA, IncFIB, IncFII and IncX3 types were detected.

The present study showed the diversity of the molecular characteristics of CPEC by analysis of the whole genome of bacteria. WGS is a useful tool that provides much information in the clinical microbiology.