Genomic analysis of multidrug-resistant clinical Enterococcus faecalis isolates for antimicrobial resistance genes and virulence factors from the western region of Saudi Arabia

Abstract

Background: Enterococcus faecalis is a ubiquitous member of the gut microbiota and has emerged as a lifethreatening multidrug-resistant (MDR) nosocomial pathogen. The aim of this study was to survey the prevalence of multidrug-resistant and epidemiologically important strains of E. faecalis in the western region of Saudi Arabia using phenotypic and whole genome sequencing approaches. Methods: In total, 155 patients positive for E. faecalis infection were included in this study. The isolates were identified by MALDI-TOF, and screen for antimicrobial resistance using VITEK-2 system. Genome sequencing was performed with paired-end strategy using MiSeq platform. Results: Seventeen sequence types (STs) were identified through multilocus sequence typing (MLST) analysis of the E. faecalis genomes, including two novels STs (ST862 and ST863). The most common STs in the Saudi patients were ST179 and ST16 from clonal complex 16 (CC16). Around 96% (n = 149) isolates were MDR. The antibiotics quinupristin/dalfopristin, clindamycin, and erythromycin demonstrated almost no coverage, and high-level streptomycin, gentamycin, and ciprofloxacin demonstrated suboptimal coverage. Low resistance was observed against vancomycin, linezolid, and ampicillin. Moreover, 34 antimicrobial resistance genes and variants, and three families of insertion sequences were found in the E. faecalis genomes, which likely contributed to the observed antimicrobial resistance. Twenty-two virulence factors, which were mainly associated with biofilm formation, endocarditis, cell adherence, and colonization, were detected in the isolates. Conclusions: Diverse STs of E. faecalis, including strains associated with common nosocomial infections are circulating in the healthcare facility of Saudi Arabia and carried multi-drug resistance, which has important implications for infection control.

Drug Resistance Determinants in Clinical Isolates of Enterococcus faecalis in Bangladesh: Identification of Oxazolidinone Resistance Gene optrA in ST59 and ST902 Lineages

“…While resistance to penicillins and glycopeptides was absent, higher resistance rates were noted for ERY, TET, and LVX. The prevalence of ERY resistance (85.2%) was higher than in our previous study of puerperal infections in Bangladesh [11], and comparable to that reported for blood isolates in the US and Europe [31], and hospital isolates in the middle East [32]. The resistance rate to LVX (45.7%) was similar to that in our previous studies in Bangladesh [11] and the Middle East [32], but appears to be Figure 2.…”

“…The prevalence of ERY resistance (85.2%) was higher than in our previous study of puerperal infections in Bangladesh [11], and comparable to that reported for blood isolates in the US and Europe [31], and hospital isolates in the middle East [32]. The resistance rate to LVX (45.7%) was similar to that in our previous studies in Bangladesh [11] and the Middle East [32], but appears to be Figure 2. Schematic representation of the genetic background of optrA in the E. faecalis strain SJ82 (uppermost) and the genetic organization or components similar to that of SJ82 in other strains reported previously [30] or available in GenBank database.…”

Insights into the Microbiological Safety of Wooden Cutting Boards Used for Meat Processing in Hong Kong’s Wet Markets: A Focus on Food-Contact Surfaces, Cross-Contamination and the Efficacy of Traditional Hygiene Practices

“…Similarly, the prevalence of Enterococcus faecalis in the unprocessed imported meat also highlights the complex pathogenic profile of the species inhabiting these meat products. E. faecalis is usually associated with nosocomial infections and has been reported as being one of the most challenging pathogens to treat due to its drug resistance [48,49].…”

Vancomycin-Resistant Enterococcus: Issues in Human Health, Animal Health, Resistant Mechanisms and the Malaysian Paradox

“…It not only links epithelial cells to virulent characteristics and resistant determinants via plasmid exchange and colonization but also attaches to the network of extracellular proteins (Wagner et al, 2018). Different studies have provided evidence that E. faecalis harbors the agg gene most (Guzman Prieto et al, 2016;Lins et al, 2019;Farman et al, 2019).…”

“…Gelatinase hydrolyses collagen, bioactive peptides and gelatin. It as an extracellular Zn-metallo-endopeptidase which causes substantial damage to host tissue by splitting fibrin resulting in the dissemination of Enterococcus specifically E. faecalis (Farman et al, 2019) and involved in biofilm formation (Aladarose et al, 2019).…”