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

Abstract Background The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types.blaCTX-Mgenes, encoding CTX-M-type ESBLs, are usually found on plasmids, but chromosomal location is becoming common. Given thatblaCTX-M-harboring strains often exhibit multidrug resistance (MDR), it is important to investigate the association between chromosomally integratedblaCTX-Mand the presence of additional antimicrobial resistance (AMR) genes, and to identify other relevant genetic elements. Methods A total of 46 clinical isolates of cefotaxime-resistantEnterobacteriaceae(1Enterobacter cloacae, 9Klebsiella pneumoniae, and 36Escherichia coli) from Zambia were subjected to whole-genome sequencing (WGS) using MiSeq and MinION. By reconstructing nearly complete genomes,blaCTX-Mgenes were categorized as either chromosomal or plasmid-borne. Results WGS-based genotyping identified 58 AMR genes, including fourblaCTX-Malleles (i.e.,blaCTX-M-14,blaCTX-M-15,blaCTX-M-27, andblaCTX-M-55). Hierarchical clustering using selected phenotypic and genotypic characteristics suggested clonal dissemination ofblaCTX-Mgenes. Out of 45blaCTX-Mgene-carrying strains, 7 harbored the gene in their chromosome. In oneE. cloacaeand threeE. colistrains, chromosomalblaCTX-M-15was located on insertions longer than 10 kb. These insertions were bounded by ISEcp1at 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. Conclusion Our study revealed the co-occurrence of ISEcp1-blaCTX-M-15and multiple AMR genes on chromosomal insertions inE. cloacaeandE. coli, suggesting that ISEcp1may 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 theseEnterobacteriaceaespecies.