Genetic diversity, biocide susceptibility and biofilm forming ability of Escherichia coli isolates from slaughterhouse environments in Nigeria

The transmission of foodborne pathogens via contact with contaminated surfaces in meat processing is a significant public health concern. This study characterizes Escherichia coli (n = 50) obtained before and after disinfection in slaughterhouses in Edo State, Nigeria, focusing on biocide and antimicrobial susceptibility, biofilm formation, and curli fimbriae and cellulose production. Whole genome sequencing (WGS) was employed to assess the genetic diversity, resistome, and virulome of the isolates. Biocide susceptibility testing did not suggest resistance, with minimum inhibitory and minimum bactericidal concentrations significantly lower than in-use concentrations. Isolates obtained after disinfection of slaughterhouse surfaces formed stronger biofilms on average, independent of curli fimbriae and cellulose production. Phylogenetic analysis revealed a broad variety of genotypes, including atypical enteropathogenic E. coli and extraintestinal pathogenic lineages such as the global lineage ST10. Notably, two E. coli harbouring bla CTX-M-15 were identified. Core genome MLST verified clonal spread within slaughterhouses as well as recurring isolation of clones over time. Venn analysis indicated that carrying virulence genes encoding effector delivery systems favoured strong biofilm formation. Our findings suggest that meat-processing environments can serve as reservoirs for E. coli carrying bla CTX-M-15 E. coli , contributing to the dissemination of pathogenic strains that pose significant environmental and public health risks. • E. coli from slaughterhouses belonged to 36 distinct core genome (cg)MLST profiles. • Atypical enteropathogenic and global extraintestinal pathogenic E. coli were detected. • E. coli carrying bla CTX-M-15 were found in meat-processing environments. • E. coli obtained after cleaning and disinfection showed enhanced biofilm formation. • Slaughterhouses are reservoirs for pathogenic E. coli , threatening public health.