Salad Vegetables as a Reservoir of Antimicrobial-Resistant Enterococcus: Exploring Diversity, Resistome, Virulence, and Plasmid Dynamics

This study investigates the occurrence, antimicrobial resistance (AMR) profiles, virulence factors, and plasmid composition of <i>Enterococcus</i> species isolated from salad ingredients in the United Arab Emirates (UAE). Four hundred salad vegetable items collected from local markets, over ten months through 2023, were screened, yielding an <i>Enterococcus</i> detection rate of 85.5% (342/400). <i>E. casseliflavus</i> was the most commonly identified species (50%), followed by <i>E. faecium</i> (20%) and <i>E. faecalis</i> (16%). Among 85 <i>Enterococcus</i> isolates tested for antimicrobial susceptibility, 55.3% displayed resistance to at least one agent, with 18.8% classified as multidrug-resistant (MDR). All isolates were not resistant to ampicillin, linezolid, teicoplanin, tigecycline, and high-level gentamicin. Intrinsic phenotypic resistance to vancomycin was found in <i>E. gallinarum</i> and <i>E. casseliflavus</i>, while low-level (<5%) ciprofloxacin and erythromycin resistance was sporadically detected in <i>E. faecium</i> and <i>E. faecalis</i>. Whole-genome sequencing (WGS) of 14 isolates (nine <i>E. faecium</i>, four <i>E. faecalis</i>, and one <i>E. casseliflavus</i>) unveiled a complex resistome. We report the first detection in salad vegetables of vancomycin resistance genes (<i>vanC</i>, <i>vanXY-C2</i>) in a vancomycin-susceptible <i>E. faecalis</i> isolate. Identifying <i>tetM</i>, <i>ermB</i>, and <i>optrA</i> genes in the studied isolates further underscored emerging resistance to tetracyclines, macrolides, and oxazolidinones. Concurrently, virulence gene analysis revealed 74 putative virulence factors, with <i>E. faecalis</i> harboring a higher diversity of biofilm-related and exoenzyme-encoding genes. One <i>E. faecalis</i> strain carried the cytolysin cluster (<i>cylI</i>, <i>cylS</i>, <i>cylM</i>), highlighting its pathogenic potential. Plasmid profiling identified 19 distinct plasmids, ranging from 3845 bp to 133,159 bp. Among the genome-sequenced isolates, mobilizable plasmids (47.3%) commonly carried AMR genes, especially <i>tet</i>(<i>L</i>) and <i>tet</i>(<i>M</i>), whereas conjugative plasmids (10.5%) did not harbor resistance determinants. These findings highlight that salad vegetables can still harbor and potentially transmit <i>Enterococcus</i> strains with clinically relevant resistance determinants and virulence traits. Enhancing foodborne AMR surveillance with WGS and targeted interventions is key to controlling its spread in the food.