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

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.

Genomic Analysis of Antibiotic-Resistant Staphylococcus epidermidis Isolates From Clinical Sources in the Kwazulu-Natal Province, South Africa

“…Prediction of isolates’ pathogenicity toward human hosts yielded a high average probability score ( P score ≈ 0.937), close to 1.00. This pathogenicity score juxtaposed with the several virulence genes possessed by isolates, supporting their pathogenic potential to humans ( Adzitey et al, 2020 ).…”

Phenotypic Antimicrobial Susceptibility of Escherichia coli from Raw Meats, Ready-to-Eat Meats, and Their Related Samples in One Health Context

“…Resistance genes, such as bla CTX-M and bla TEM (beta-lactamase), tet (A) and tet (B) (tetracycline), aph (3")-Ib and apha (6) (aminoglycoside), dfrA17 and dfrA14 (trimethoprim) and mdf(A) macrolide, have been found in E. coli isolated from Ghana [23,24]. In addition, virulence factors, such as lpfA, gad, mchF, iha, mchB, mchC eilA, iss, cftB and mcmA, have been associated with E. coli isolates from various meat samples in Ghana [45], revealing the potential and possibility of E. coli isolates from this study to be pathogenic, although this study did not seek to establish that. The developments of resistances are elicited by factors including the inappropriate use of antimicrobials and poor hygiene practices in healthcare and food chain setups [19,20], facilitating the transfer of resistant E. coli.…”

Virulence Determinants and Plasmid-Mediated Colistin Resistance mcr Genes in Gram-Negative Bacteria Isolated From Bovine Milk

“…However, previous studies have indicated the occurrence of some virulence factors on plasmids of E. coli ( Rodriguez-Siek et al., 2005 ; Johnson et al., 2006 ; Mellata et al., 2010 ; Cyoia et al., 2015 ), K. pneumoniae ( Dolejska et al., 2013 ; Chen et al., 2020 ), Aeromonas species ( Brown et al., 1997 ), and P. aeruginosa ( Morales-Espinosa et al., 2012 ). E. coli strains possess virulence genes that play a significant role in the survival and pathogenesis of the strain in the host through bacterial adhesion ( ipfA ), hemolysis ( hlyF ), iron acquisition ( iroN and ireA ), and increased serum survival and resistance to phagocytosis ( iss and traT ) ( Sarowska et al., 2019 ; Adzitey et al., 2020 ). K. pneumoniae hypervirulent strains possess different genes that determine virulence and severity of infection in the host.…”