Genomic Characterization of International High-Risk Clone ST410 Escherichia coli Co-Harboring ESBL-Encoding Genes and blaNDM-5 on IncFIA/IncFIB/IncFII/IncQ1 Multireplicon Plasmid and Carrying a Chromosome-Borne blaCMY-2 from Egypt

The accelerated dispersion of multidrug-resistant (MDR) Escherichia coli due to the production of extended-spectrum beta-lactamases (ESBLs) or AmpC enzymes has been noted in Egypt, presenting a serious treatment challenge. In this study, we investigate the prevalence of ESBLs and AmpC enzymes among 48 E. coli isolates collected from patients with urinary tract infections admitted to a teaching hospital in Alexandria. Phenotypic and genotypic methods of detection are conducted. Isolates producing both enzymes are tested for the mobilization of their genes by a broth mating experiment. Whole genome sequencing (WGS) is performed for isolate EC13655. The results indicate that 80% of the isolates are MDR, among which 52% and 13% were ESBL and AmpC producers, respectively. Conjugation experiments fail to show the mobilization of bla(CMY-2) in EC13655, which was chosen for WGS. In silico analysis reveals that the isolate belongs to a ST410-H24Rx high-risk clone. It coharbors the ESBL-encoding genes bla(CTX-M-15), bla(TEM-1), bla(OXA-1) and bla(NDM-5) on an IncFIA/IncFIB/IncFII/IncQ1 multireplicon plasmid. The chromosomal location of bla(CMY-2) is detected with a flanking upstream copy of ISEcp1. This chromosomal integration of bla(CMY-2) establishes the stable maintenance of the gene and thus, necessitates an imperative local surveillance to reduce further spread of such strains in different clinical settings.

Automated summary

This study investigates the prevalence and genetic characteristics of ESBLs and AmpC enzymes in multidrug-resistant E. coli isolates from urinary tract infection patients in Egypt. The results show a high percentage of MDR isolates, with a significant proportion producing ESBLs and AmpC enzymes. Whole genome sequencing reveals the presence of high-risk clones carrying multiple resistance genes on both plasmids and chromosomes. These findings emphasize the importance of surveillance and control measures for multidrug-resistant strains in the region.