Comparing whole-genome sequencing to pulsed-field gel electrophoresis for vancomycin-resistant Enterococcus faecium hospital surveillance.

UNLABELLED: Vancomycin-resistant enterococci (VREs) have emerged as an important public health concern and a leading cause of healthcare-associated infections. Accurately distinguishing between closely related VRE strains is imperative for infection control measures in the setting of hospital outbreaks. Although pulsed-field gel electrophoresis (PFGE) is considered the gold standard for VRE strain typing, recent studies have identified whole-genome sequencing (WGS) as a promising alternative with greater resolution. In this study, we report on the validation and utility of a WGS and single-nucleotide polymorphism (SNP) analysis pipeline toward vancomycin-resistant Enterococcus faecium (VREfm) strain typing in a large academic medical center. Using PFGE as the reference method, we identified a conservative threshold of ≤10 SNPs as robustly identifying related VREfm isolates with 98.5% sensitivity and 93.1% specificity. Comparing VREfm infection control surveillance pre- and post-WGS SNP strain typing revealed a proportionally greater number of isolates with related strain types and epidemiological links in the post-WGS SNP group. These findings suggest that WGS SNP analysis can improve the resolution of emerging hospital outbreaks and infection control measures, as compared to PFGE.

IMPORTANCE: Distinguishing between closely related antibiotic-resistant bacteria is an important task toward infection control measures in a hospital environment. This study focused on strains of one particular antibiotic-resistant bacterium (vancomycin-resistant Enterococcus faecium) and assessed the utility of a whole-genome sequencing analysis pipeline toward distinguishing strain relatedness compared to the gold standard reference method. The results showed that strain typing with whole-genome sequencing identified a proportionally greater number of transmission/outbreak events compared to the reference method over a similar time period. The findings suggest that a whole-genome sequencing pipeline, when available, can improve hospital infection control measures.