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Background  The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types.  bla  CTX-M  genes, encoding CTX-M-type ESBLs, are usually found on plasmids, but chromosomal location is becoming common. Given that  bla  CTX-M -harboring strains often exhibit multidrug resistance (MDR), it is important to investigate the association between chromosomally integrated  bla  CTX-M  and the presence of additional antimicrobial resistance (AMR) genes, and to identify other relevant genetic elements.    Methods  A 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,  bla  CTX-M  genes were categorized as either chromosomal or plasmid-borne.    Results  WGS-based genotyping identified 58 AMR genes, including four  bla  CTX-M  alleles (i.e.,  bla  CTX-M-14 ,  bla  CTX-M-15 ,  bla  CTX-M-27 , and  bla  CTX-M-55 ). Hierarchical clustering using selected phenotypic and genotypic characteristics suggested clonal dissemination of  bla  CTX-M  genes. Out of 45  bla  CTX-M  gene-carrying strains, 7 harbored the gene in their chromosome. In one  E. cloacae  and three  E. coli  strains, chromosomal  bla  CTX-M-15  was located on insertions longer than 10 kb. These insertions were bounded by IS Ecp1  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.    Conclusion  Our study revealed the co-occurrence of IS Ecp1 - bla  CTX-M-15  and multiple AMR genes on chromosomal insertions in  E. cloacae  and  E. coli , suggesting that ISE cp1  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.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13756-021-00941-8.

antimicrobial resistance and infection control

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