Whole genome sequencing-based characterization of Escherichia coli isolated from raw beef in selected butcher shops in Addis Ababa and Burayu, Ethiopia

Escherichia coli ( E. coli ) is a commensal bacterium commonly found in the intestines of humans and animals. Certain pathogenic E. coli strains can lead to severe food poisoning. While different studies have been conducted in Ethiopia with regard to the contamination of food of animal origin with E. coil , there are limited studies that tend to characterize E. coli at a genomic level. The objective of this study was to assess the diversity, virulence profile, pathotypes and antimicrobial resistance markers of E. coli isolated from raw beef samples. A total of 16 E. coli isolates were subject to whole genome sequence analysis. The genomes were analyzed using different bioinformatics tools including AMRFinderPlus, and PlasmidFinder that were used to identify Antimicrobial resistance (AMR) genes and plasmids, respectively. The two major serotypes identified were O157:H7 (25%) and O82:H8 (12.5%) accounting for 37.5% of all the isolates sequenced. The sequenced E. coli isolates were classified into 13 sequence types (ST) of which ST11 was the predominant one and it was exclusively isolated from the beef samples from Burayu butcher shop. Seven (43.8%) of the E. coli were diarrheagenic E. coli pathotypes (Enteropathogenic E. coli (EPEC), n = 4, and Shiga toxin-producing E. coli (STEC), n = 3). Two STEC isolates were assigned to ST101. Two major virulence genes were detected in both pathotypes- eae (4/16) and stx1 (3/16). Antimicrobial resistance genetic markers carried on mobile genetic elements such as aph (3’’)-Ib ( n = 3), aph(6)-Id ( n = 2), sul 2 ( n = 2), tet(B) ( n = 3), and blaTEM- 1 ( n = 3) were frequently detected in the study isolates. In conclusion , this study revealed that E. coli isolates obtained from meat samples were clonally related within the specified geographic location and certain sequence types appear to be found in different location indicating potential cross contamination.