Resistome, mobilome, virulome analysis and phylogenomics of Enterococcus faecalis isolated from raw muscle foods of beef origin in Gauteng, South Africa

dc.contributor.authorMatle, Itumeleng
dc.contributor.authorAtanda, Abimbola Comfort
dc.contributor.authorPierneef, Rian Ewald
dc.contributor.authorMagwedere, Kudakwashe
dc.contributor.authorMafuna, Thendo
dc.date.accessioned2024-07-01T11:16:10Z
dc.date.available2024-07-01T11:16:10Z
dc.date.issued2023-11-13
dc.descriptionDATA AVAILABILITY : The whole Genome Shotgun project has been deposited at GenBank under the accession JARXOI000000000-JARXOP000000000 (Table S1) .en_US
dc.description.abstractEnterococcus faecalis is a ubiquitous bacterium found in various environments, including processed beef meat, and is known for its importance in both food safety and public health. This pivotal significance stems not solely from its virulence but also from its adeptness in eliciting multidrug-resistant infections in humans. The aim of this study was to investigate the population structure, resistome, mobilome, and virulome of E. faecalis obtained from processed beef meat sources in South Africa. A total of eight genomes sequenced in this study were examined, alongside 78 publicly available, high-quality genomes of E. faecalis, with a comprehensive analysis conducted to identify antimicrobial resistance (AMR) determinants, virulence factors, and mobile genetic elements (MGE). Six distinct sequence types (STs) (ST79, ST860, ST40, ST238, ST21, and ST700) and 41 core virulence factors were found across all the genomes. The virulence factors included genes encoding adherence (ace, asa1, Ef0485, ebpA, ebpB, ebpC, srtC); exoenzyme (Ef3023, Ef0818, gelE, sprE); immunomodulation (cpsA, cpsB, cpsC, cpsD, cpsE, cpsF, cpsG, cpsH, cpsI, cpsK), and biofilm formation (bopD, fsrA, fsrB, fsrC). In addition, AMR genes were identified across all genomes, which include aminoglycoside resistance (ant(6)-Ia), trimethoprim resistance (dfrA), drug and biocide resistance (efrA and efrB), multidrug efflux pump (emeA), clindamycin quinupristin-dalfopristin, dalfopristin resistance (lsaA), and tetracycline resistance (tetM). The genomes of E. faecalis sequenced here contained a variety of MGEs, including Insertion Sequences (ISs), transposons, prophages, and plasmids, which may have facilitated genetic exchange within and between these species. The results highlight that beef meat products act as a reservoir for virulent E. faecalis strains possessing antibiotic-resistance traits. This study provides insight into the genomic characteristics, antimicrobial resistance genes, virulence factors, and genetic mobile elements associated with eight E. faecalis isolates from processed beef meat in the Gauteng province of South Africa.en_US
dc.description.departmentBiochemistryen_US
dc.description.departmentGeneticsen_US
dc.description.departmentMicrobiology and Plant Pathologyen_US
dc.description.librarianam2024en_US
dc.description.sdgSDG-02:Zero Hungeren_US
dc.description.sdgSDG-03:Good heatlh and well-beingen_US
dc.description.sponsorshipThe Gauteng Department of Agriculture and Rural Development.en_US
dc.description.urihttp://www.elsevier.com/locate/ygenoen_US
dc.identifier.citationMatle, I., Atanda, A.C., Pierneef, R. et al. 2023, 'Resistome, mobilome, virulome analysis and phylogenomics of Enterococcus faecalis isolated from raw muscle foods of beef origin in Gauteng, South Africa', Genomics, vol. 115, art. 110742, pp. 1-9. https://DOI.org/10.1016/j.ygeno.2023.110742en_US
dc.identifier.issn0888-7543
dc.identifier.other10.1016/j.ygeno.2023.110742
dc.identifier.urihttp://hdl.handle.net/2263/96738
dc.language.isoenen_US
dc.publisherElsevieren_US
dc.rights© 2023 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license.en_US
dc.subjectEnterococcusen_US
dc.subjectAntimicrobial resistanceen_US
dc.subjectVirulence factorsen_US
dc.subjectMobile genetic elementsen_US
dc.subjectProcessed meaten_US
dc.subjectWhole genome sequencing (WGS)en_US
dc.subjectSDG-02: Zero hungeren_US
dc.subjectSDG-03: Good health and well-beingen_US
dc.titleResistome, mobilome, virulome analysis and phylogenomics of Enterococcus faecalis isolated from raw muscle foods of beef origin in Gauteng, South Africaen_US
dc.typeArticleen_US

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