Whole genome sequencing analysis of non-O157 Shiga toxin-producing Escherichia coli in milk in Kwara State, Nigeria

Background: Escherichia coli is a major cause of poor microbial quality of milk, often resulting from unhygienic milk handling. Milk contamination poses public health concerns. Shiga toxin-producing Escherichia coli (STEC) strains in food products, particularly milk, is a critical concern for public health. Limited information exists on the detection of non-O157 E. coli pathotypes in milk sold by local processors in Nigeria. Aims: This study aimed to explore the diversity of non-O157 STEC isolates found in commercially available milk in Kwara State, Nigeria, to find the genetic diversity and potential risks associated with these strains. Methods: A subgroup of 18 representative non-O157 STEC isolated from milk samples (n=1225) was selected for whole genome sequencing (WGS) analysis. Results: Four novel sequence types (ST): ST398, ST540, ST1727, and ST9891 of non-O157 E. coli involving five serotypes: O176:H30, O176:H20, O8:H20, O21:H45, and O22:H7, carrying variable proportions of virulence factors, antimicrobial resistance genes, and plasmids, were identified. Conclusion: This investigation contributes valuable data to the ongoing efforts to ensure food safety and prevent the transmission of E. coli strains through dairy products. The findings have implications for public health policies and food quality standards in Kwara State, Nigeria. Improved hygienic practices during milk handling are recommended.