Potential diarrheagenic Escherichia coli in stool specimens collected from patients attending primary healthcare facilities in Ethiopia: prevalence and whole-genome sequencing based molecular characterization

The diarrheagenic Escherichia coli (DEC) is the major cause of diarrheal diseases, which are a heavy burden in Africa, including Ethiopia. However, genetic diversity and phylogenetic characteristics of E. coli pathotypes found in Ethiopia have not been studied well. This study aimed to investigate the prevalence of potential diarrheagenic E. coli in stool specimens of patients attending primary healthcare units (n=260) in Addis Ababa and Hossana by PCR and to characterize PCR identified DEC (n = 32) based on whole-genome sequencing. Virulence-associated genes, phylogenetic groups, serogroups, and multi-locus sequence types (MLST) were analyzed from obtained whole-genome sequence data using web-based tools. Diarrheagenic E. coli specific genes were detected in 12.3% of the E. coli isolates tested. We identified four common pathotypes, with enteropathogenic E. coli (EPEC) being the predominant pathotype. Two different hybrid pathotypes were identified. The majority (59.3%) of DEC pathotypes belonged to the phylogenetic group B1, followed by group A (28.1%). The identified pathotypes belonged to 24 different serogroups, 4 of them were 'rough' and all 'rough' serotypes belonged to the phylogroup A. Further, 20 different MLSTs were detected, with ST10 being the most abundant. All tested DEC pathotypes were found to carry 10 to 37 virulence-associated genes. The result of this study showed high diversity in the population structure of DEC pathotypes in terms of phylogroup, serotypes, sequence types, and virulence-associated genes. The findings of this study are crucial for designing targeted interventions helping to reduce the diarrheal burden in Ethiopia.