Phenotypic and genomic characterization of antimicrobial resistance in vancomycin-resistant Enterococcus faecalis

Enterococcus faecalis has emerged as a significant nosocomial pathogen with increasing relevance at the human-animal interface. This study investigated the antimicrobial resistance (AMR) profiles and genomic characteristics of E. faecalis isolated from cattle farms in Punjab, India.

A total of 288 samples, comprising cattle feces (239), cattle handler hand swabs (34), and handler stool samples (15), were processed using standard bacteriological protocols. Presumptive isolates were confirmed as E. faecalis by culture characteristics and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). Antimicrobial susceptibility testing (AST) was performed using the Kirby-Bauer disk diffusion method, and vancomycin resistance was confirmed by minimum inhibitory concentration (MIC) testing. Resistance genes were screened by polymerase chain reaction (PCR) and vancomycin-resistant isolates underwent whole-genome sequencing (WGS) for detailed genomic characterization. Overall, 51 E. faecalis isolates were recovered from 288 samples, yielding an overall prevalence of 17.70% (51/288). Sample-wise prevalence was 19.24% (46/239) in cattle feces, 8.82% (3/34) in hand swabs, and 13.33% (2/15) in stool samples. AST revealed high resistance rates to erythromycin (72.54%), linezolid (31.37%), ciprofloxacin and penicillin G (29.41% each), and tetracycline (27.45%). Phenotypic vancomycin resistance was identified in 5.88% (3/51) of isolates. PCR screening detected vanC1 in 31.37% and vanC2/C3 in 33.33% of isolates, although their presence was not uniformly associated with phenotypic resistance.WGS of three vancomycin-resistant E. faecalis isolates identified resistance genes, virulence determinants, and a shared multilocus sequence type (MLST), ST-387, among isolates from cattle and handlers.

These findings highlight cattle farms as reservoirs of multidrug resistant (MDR) and virulent E. faecalis strains, emphasizing the importance of genomic surveillance to prevent the dissemination of these strains into healthcare settings.