Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana.

Frederick Adzitey,Jonathan Asante,Anou M Somboro,Hezekiel M Kumalo,Rene B Khan,Daniel G Amoako

doi:10.3390/genes11121504

Frederick Adzitey, Jonathan Asante + Show 4 more

Open Access

https://doi.org/10.3390/genes11121504

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Abstract

Escherichia coli are among the most common foodborne pathogens associated with infections reported from meat sources. This study investigated the virulome, pathogenicity, stress response factors, clonal lineages, and the phylogenomic relationship of E. coli isolated from different meat sources in Ghana using whole-genome sequencing. Isolates were screened from five meat sources (beef, chevon, guinea fowl, local chicken, and mutton) and five areas (Aboabo, Central market, Nyorni, Victory cinema, and Tishegu) based in the Tamale Metropolis, Ghana. Following microbial identification, the E. coli strains were subjected to whole-genome sequencing. Comparative visualisation analyses showed different DNA synteny of the strains. The isolates consisted of diverse sequence types (STs) with the most common being ST155 (n = 3/14). Based Upon Related Sequence Types (eBURST) analyses of the study sequence types identified four similar clones, five single-locus variants, and two satellite clones (more distantly) with global curated E. coli STs. All the isolates possessed at least one restriction-modification (R-M) and CRISPR defence system. Further analysis revealed conserved stress response mechanisms (detoxification, osmotic, oxidative, and periplasmic stress) in the strains. Estimation of pathogenicity predicted a higher average probability score (Pscore ≈ 0.937), supporting their pathogenic potential to humans. Diverse virulence genes that were clonal-specific were identified. Phylogenomic tree analyses coupled with metadata insights depicted the high genetic diversity of the E. coli isolates with no correlation with their meat sources and areas. The findings of this bioinformatic analyses further our understanding of E. coli in meat sources and are broadly relevant to the design of contamination control strategies in meat retail settings in Ghana.

Highlights

Escherichia coli (E. coli) are Gram-negative, rod shape, facultative anaerobic bacteria of the Enterobacteriaceae family [1,2]
A total of 14 isolates obtained from five meat sources [beef (n = 3), chevon (n = 3), guinea fowl (n = 3), local chicken (n = 3), and mutton (n = 2)] and five areas [Aboabo (n = 2), Central market (n = 3), Nyorni (n = 3), Victory cinema (n = 2), and Tishegu (n = 4)] based in the Tamale Metropolis, Ghana (Table 1) were selected for further bioinformatic and comparative analyses
E. coli are among the most common foodborne pathogens associated with infections reported from meat sources

Summary

Introduction

Escherichia coli (E. coli) are Gram-negative, rod shape, facultative anaerobic bacteria of the Enterobacteriaceae family [1,2]. They are naturally found in the gastrointestinal tract of animals and their droppings [2,3], and can cross-contaminate meat, especially under faulty processing conditions [4]. E. coli group includes subtypes, such as neonatal meningitis associated E. coli, uropathogenic E. coli, and sepsis-associated E. coli [6,7]. Their various virulence genes differentiate these pathotypes

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