Antimicrobial Resistance and Comparative Genome Analysis of High-Risk Escherichia coli Strains Isolated from Egyptian Children with Diarrhoea

TL;DR

This study analyzes the genomes of multidrug-resistant Escherichia coli strains from Egyptian children with diarrhea, revealing high-risk clones and resistance genes.

Contribution

The paper provides genome sequences and resistance profiles of ten high-risk MDR E. coli strains from Egyptian children, highlighting their pathogenic and resistance characteristics.

Findings

The E. coli strains carry resistance genes including blaNDM and blaOXA, likely on IncX3 and IncF plasmids.

Many strains belong to high-risk ExPEC clones ST167, ST410, and ST617.

The findings emphasize the need for increased surveillance of MDR pathogens in Egypt.

Abstract

Escherichia coli is an important human pathogen that is able to cause a variety of infections, which can result in diarrhoea, urinary tract infections, sepsis, and even meningitis, depending on the pathotype of the infecting strain. Like many Gram-negative bacteria, E. coli is becoming increasingly resistant to many frontline antibiotics, including third-generation cephalosporins and carbapenems, which are often considered the antibiotics of last resort for these infections. This is particularly the case in Egypt, where multidrug-resistant (MDR) E. coli is highly prevalent. However, in spite of this, few Egyptian MDR E. coli strains have been fully characterised by genome sequencing. Here, we present the genome sequences of ten highly MDR E. coli strains, which were isolated from children who presented with diarrhoea at the Outpatients Clinic of Assiut University Children’s Hospital in Assiut, Egypt. We report that they carry multiple antimicrobial resistance genes, which includes extended spectrum β-lactamase genes, as well as blaNDM and blaOXA carbapenemase genes, likely encoded on IncX3 and IncF plasmids. Many of these strains were also found to be high-risk extra-intestinal pathogenic E. coli (ExPEC) clones belonging to sequence types ST167, ST410, and ST617. Thus, their presence in the Egyptian paediatric population is particularly worrying, and this highlights the need for increased surveillance of high-priority pathogens in this part of the world.

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