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Open AccessArticle

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

1
Department of Veterinary Science, University for Development Studies, P. O. Box TL 1882, Tamale 00233, Ghana
2
Antimicrobial Research Unit, Infection Genomics and Applied Bioinformatics Division, University of KwaZulu-Natal, Durban 4000, South Africa
3
School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
*
Authors to whom correspondence should be addressed.
Genes 2020, 11(12), 1504; https://doi.org/10.3390/genes11121504
Received: 5 November 2020 / Revised: 29 November 2020 / Accepted: 3 December 2020 / Published: 14 December 2020
(This article belongs to the Special Issue Genetics and Genomics of Zoonotic Foodborne Pathogens)
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. View Full-Text
Keywords: genomics; virulome; stress response; clonality; phylogenetic analysis; E. coli; meat genomics; virulome; stress response; clonality; phylogenetic analysis; E. coli; meat
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MDPI and ACS Style

Adzitey, F.; Asante, J.; Kumalo, H.M.; Khan, R.B.; Somboro, A.M.; Amoako, D.G. Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana. Genes 2020, 11, 1504. https://doi.org/10.3390/genes11121504

AMA Style

Adzitey F, Asante J, Kumalo HM, Khan RB, Somboro AM, Amoako DG. Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana. Genes. 2020; 11(12):1504. https://doi.org/10.3390/genes11121504

Chicago/Turabian Style

Adzitey, Frederick; Asante, Jonathan; Kumalo, Hezekiel M.; Khan, Rene B.; Somboro, Anou M.; Amoako, Daniel G. 2020. "Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana" Genes 11, no. 12: 1504. https://doi.org/10.3390/genes11121504

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