Novel chromosomal insertions of ISEcp1-blaCTX-M-15 and diverse antimicrobial resistance genes in Zambian clinical isolates of Enterobacter cloacae and Escherichia coli

Bernard Hang’ombe,Hideaki Higashi,Yoshikazu Furuta,Misheck Shawa,Evans Mulenga,Manyando Simbotwe,Christone Kaile,Atmika Paudel,Tuvshinzaya Zorigt,Maron Mubanga,Gillan Mulenga

doi:10.1186/s13756-021-00941-8

Abstract

BackgroundThe epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types. blaCTX-M genes, encoding CTX-M-type ESBLs, are usually found on plasmids, but chromosomal location is becoming common. Given that blaCTX-M-harboring strains often exhibit multidrug resistance (MDR), it is important to investigate the association between chromosomally integrated blaCTX-M and the presence of additional antimicrobial resistance (AMR) genes, and to identify other relevant genetic elements.MethodsA total of 46 clinical isolates of cefotaxime-resistant Enterobacteriaceae (1 Enterobacter cloacae, 9 Klebsiella pneumoniae, and 36 Escherichia coli) from Zambia were subjected to whole-genome sequencing (WGS) using MiSeq and MinION. By reconstructing nearly complete genomes, blaCTX-M genes were categorized as either chromosomal or plasmid-borne.ResultsWGS-based genotyping identified 58 AMR genes, including four blaCTX-M alleles (i.e., blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, and blaCTX-M-55). Hierarchical clustering using selected phenotypic and genotypic characteristics suggested clonal dissemination of blaCTX-M genes. Out of 45 blaCTX-M gene-carrying strains, 7 harbored the gene in their chromosome. In one E. cloacae and three E. coli strains, chromosomal blaCTX-M-15 was located on insertions longer than 10 kb. These insertions were bounded by ISEcp1 at one end, exhibited a high degree of nucleotide sequence homology with previously reported plasmids, and carried multiple AMR genes that corresponded with phenotypic AMR profiles.ConclusionOur study revealed the co-occurrence of ISEcp1-blaCTX-M-15 and multiple AMR genes on chromosomal insertions in E. cloacae and E. coli, suggesting that ISEcp1 may be responsible for the transposition of diverse AMR genes from plasmids to chromosomes. Stable retention of such insertions in chromosomes may facilitate the successful propagation of MDR clones among these Enterobacteriaceae species.

Highlights

The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types. blaCTX-M genes, encoding CTX-M-type ESBLs, are usually found on plasmids, but chromosomal location is becoming common
Multilocus sequence typing (MLST) revealed high genetic diversity among strains This study examined 46 cefotaxime-resistant Enterobacteriaceae strains isolated from various clinical samples among patients at the University Teaching Hospital (UTH), Zambia (Table 1)
Data obtained in previous studies indicate that the chromosomal incorporation of blaCTX-M is usually mediated by ISEcp1; the co-occurrence of ISEcp1-blaCTX-M and additional antimicrobial resistance (AMR) genes has never been reported in E. cloacae or E. coli

Summary

Introduction

The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types. blaCTX-M genes, encoding CTX-M-type ESBLs, are usually found on plasmids, but chromosomal location is becoming common. The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types. Given that blaCTX-M-harboring strains often exhibit multidrug resistance (MDR), it is important to investigate the association between chromosomally integrated blaCTX-M and the presence of additional antimicrobial resistance (AMR) genes, and to identify other relevant genetic elements. Extended-spectrum β-lactamases (ESBLs) are bacterial enzymes capable of degrading most β-lactam antibiotics, rendering them therapeutically useless. A high ESBL burden has been observed in France and China, where local hospitals reported prevalence figures of 17.7% [10] and 68.2% [11], respectively. In reports from Zambia, ESBL-associated multidrug resistance (MDR) was observed in all 45 Klebsiella pneumoniae isolates obtained from neonates [15] and in all 15 diarrhoeagenic Escherichia coli isolates from under-five children [16] at the University Teaching Hospital (UTH)

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Results

Discussion

Conclusion