Unravelling Shiga toxin-producing and enteropathogenic serotypes of Escherichia coli in dried fish sold in markets in Bobo-Dioulasso, Burkina Faso

Dried fish is widely consumed in Burkina Faso, yet its microbial safety remains insufficiently documented. Escherichia coli, including Shiga toxin–producing strains (STEC) and enteropathogenic strains (EPEC), represents a major public health concern. This a prospective descriptive study. A prospective descriptive study was performed from July 2024 to September 2025 across ten markets in Bobo-Dioulasso. The Methodology applied is based on the collection of thirty dried-fish samples and the application of standard microbiological methods for the isolation and biochemical identification of E. coli. Antibiotic susceptibility testing was performed according to EUCAST/CA-SFM (2024) guidelines. Molecular screening for virulence genes (stx1, stx2, eaeA) was performed using PCR. The results show that contamination was highest in the Colma, Belle-Ville, and Koko markets (100%). All isolates were resistant to amoxicillin and fosfomycin, while sensitivity remained high for meropenem (95%) and amikacin (75%). Three isolates carried virulence genes: stx1 (11.1%), stx2 (5.6%). No strain was positive for eaeA. Molecular clustering revealed distinct clusters, with STEC strains forming a separate group. The genetic distance shows the degree of similarity between strains. Three main clusters are clearly distinguishable. The first one comprising isolates that lack virulence genes or 16S RNA and have been excluded from further analysis. The second cluster represent shigatoxigenic strains. All these strains carry the stx1 gene. The third cluster isolates represent strains that possessed 16S rRNA gene only. This study highlighted a high prevalence of E. coli contamination in dried fish in Bobo-Dioulasso, including STEC strains carrying stx1 and stx2. The presence of multidrug-resistant isolates highlights the need for improved hygiene practices, routine surveillance, and reinforced regulatory measures to minimize foodborne risks.