Abstract:
Enterococcus 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.
