Phenotypic and genotypic relationships between Shigella species and Escherichia coli O37:H10 isolates in Addis Ababa, Ethiopia.

Objective: This study aimed to investigate the genotypic and phenotypic differences between Shigella species and E. coli O37:H10, as well as their antimicrobial resistance (AMR) and virulence factors, in children aged under five with diarrhea in Addis Ababa, Ethiopia.

Results: Using whole genome sequencing (WGS), all 28 S. sonnei identified with antisera were also verified as S. sonnei, while all nine isolates of S. flexneri were found to be E. coli O37:H10. One S. flexneri sample, identified serologically, was excluded from WGS analysis because of low genome coverage. Most resistant genes were associated with beta-lactam and trimethoprim drugs. All S. sonnei isolates had genes that encoded blaEC-8 and blaZEG-1. The E. coli O37:H10 had the Extended-spectrum beta-lactamase (ESBL) blaEC-15 for cephalosporins, blaMIX-2, and blaMIX-6 for penicillin. In contrast to S. sonnei, the most prevalent plasmid type in E. coli O37:H10 isolates was IncFII, while virulence genes like gad were frequently detected. Composite transposons, such as cn_43599_IS621 and cn_3785_IS3, were detected in all S. sonnei and E. coli O37:H10. Generally, the study highlighted a significant discrepancy between phenotypic and genotypic AMR, as well as variations in serotypes and phylogenetic relationships with global isolates.