A core genome MLST scheme for high-resolution typing of Enterococcus faecium

Enterococcus faecium, a common inhabitant of the human gut, has emerged as an important multidrug-resistant nosocomial pathogen in the last two decades. Since the start of the 21(st) century, multi-locus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium. However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for inter-laboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium. cgMLST transfers genome-wide single nucleotide polymorphism (SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme contained 1,423 cgMLST target genes. To test the scheme's performance, we performed WGS analysis of 103 outbreak isolates from five different hospitals in The Netherlands, Denmark and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same ST, which denotes the higher discriminatory power of this cgMLST scheme over conventional MLST. We also show that, in terms of resolution, the E. faecium cgMLST scheme's performance is equivalent to that of a SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, high-resolution tracing of E. faecium outbreaks.