Molecular Epidemiology and Virulence Profiling of Escherichia Coli from Cattle Carcasses and Slaughterhouse Environments in Abuja, Nigeria

Abstract

This study investigated the molecular characteristics, virulence gene profiles, phylogroup distribution, and genetic relatedness of Escherichia coli isolated from cattle carcasses and slaughterhouse environments in Abuja, Nigeria. A total of 540 swab samples were collected from processed carcasses and meat-contact surfaces, including butchers’ hands, knives, wheelbarrows, kill floors, washing water, and effluent, at a government-owned Gwagwalada slaughterhouse (n = 340) and a privately owned Dei-Dei slaughterhouse (n = 200). Standard microbiological methods were used for isolation and identification. Overall, 105 confirmed E. coli isolates were recovered, yielding a prevalence of 19.4% (18.5% in Gwagwalada and 21.0% in Dei-Dei). All isolates were screened by polymerase chain reaction (PCR) for eight virulence-associated genes (eaeA, EAST, traT, hly, omp, bfp, stx, and cnf) and classified into phylogroups using the Clermont quadruplex PCR method. The most prevalent virulence genes were omp (96.4%), cnf (74.5%), and stx (72.7%). Phylogroup analysis revealed predominance of B1 (38.1%) and A (28.6%), while virulence-associated phylogroups B2 and D accounted for 21.9% of isolates. No statistically significant association was observed between virulence gene carriage and sample source (p > 0.05). Genetic relatedness assessed using the unweighted pair group method with arithmetic mean (UPGMA) clustering demonstrated five major clusters and one singleton at an 80% similarity threshold. Clusters comprised isolation from carcasses, knives, effluent, and washing water, indicating potential intra-facility cross-contamination and shared contamination routes. The coexistence of diverse phylogroups and high prevalence of Shiga toxin and necro toxigenic determinants underscores significant food safety and occupational health risks. These findings highlight slaughterhouses as critical convergence points for pathogen amplification within animal–human–environment interfaces. Strengthening hygiene enforcement, wastewater treatment, and routine molecular surveillance under a One Health framework is essential to mitigate zoonotic and foodborne transmission in Nigeria and similar settings.