Emergence and genetic characterization of KLUC-3 extended-spectrum β-lactamase-producing Escherichia coli ST95 High-Risk clone causing nosocomial infection in Japan

Abstract

Objectives

KLUC β-lactamase is a minor extended-spectrum β-lactamase (ESBL) derived from chromosome-encoded cefotaximase in Kluyvera cryocrescens. This study aimed to characterize the genetic context of KLUC-3-producing Escherichia coli and bla_KLUC-3-harboring plasmids and assess nosocomial transmission.

Methods

In a national genomic surveillance conducted in 2019 and 2020, KLUC-3-producing E. coli strains (JBEAACH-19-0093 and JBEAACH-19-0210) were recovered from two pediatric inpatients in a Japanese hospital. Short- and long-read sequencing analyses using the HiSeq X Five and GridION were performed to determine the complete genome sequences.

Results

JBEAACH-19-0093 and JBEAACH-19-0210 belong to the B2-O1:K1:H7-ST95-fimH41 global high-risk clones and carry virulence genes related to extraintestinal pathogenic and uropathogenic E. coli. Single nucleotide polymorphism analysis showed high homology (13 SNPs) between the strains, suggesting nosocomial transmission. The bla_KLUC-3 gene was flanked by ISEcp1 and Δorf477 on 100-kb IncB/O/K/Z plasmids with a complete sequence identity. Comparative analysis revealed ISEcp1-mediated transposition of bla_KLUC-3 into the IncB/O/K/Z plasmid; the complete plasmid sequence was highly similar to bla_CTX-M- and bla_CMY-2-harboring plasmids from E. coli ST131 isolates. In GenBank database, 26 Enterobacterales harbored bla_KLUC-1 to bla_KLUC-7, particularly in Asia. Among them, the genomic structure of bla_KLUC-orf477/Δorf477 is conserved in 23 strains. In 13 Enterobacterales, except K. cryocrescens, ISEcp1 was inserted upstream of bla_KLUC and 10 strains carried bla_KLUC on the plasmids.

Conclusion

This is the first case of nosocomial transmission of KLUC-3 producers outside China. The bla_KLUC-3 emergence in the virulent pandemic lineage ST95 is a public health problem highlighting the need for further investigations to prevent its potential dissemination.