title: Core Genome Multilocus Sequence Typing Scheme for High-  Resolution Typing of Enterococcus faecium.
abstract: Enterococcus faecium, a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus 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 interlaboratory 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 consists of 1,423 cgMLST target genes. To test the performance of the scheme, 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 sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks.
authors.forename: Mark
authors.initials: M
authors.lastname: de Been
authors.forename: Mette
authors.initials: M
authors.lastname: Pinholt
authors.forename: Janetta
authors.initials: J
authors.lastname: Top
authors.forename: Stefan
authors.initials: S
authors.lastname: Bletz
authors.forename: Alexander
authors.initials: A
authors.lastname: Mellmann
authors.forename: Willem
authors.initials: W
authors.lastname: van Schaik
authors.forename: Ellen
authors.initials: E
authors.lastname: Brouwer
authors.forename: Malbert
authors.initials: M
authors.lastname: Rogers
authors.forename: Yvette
authors.initials: Y
authors.lastname: Kraat
authors.forename: Marc
authors.initials: M
authors.lastname: Bonten
authors.forename: Jukka
authors.initials: J
authors.lastname: Corander
authors.forename: Henrik
authors.initials: H
authors.lastname: Westh
authors.forename: Dag
authors.initials: D
authors.lastname: Harmsen
authors.forename: Rob J L
authors.initials: RJ
authors.lastname: Willems
mesh_terms: D019295:Computational Biology / Q000379:methods; D003428:Cross Infection / Q000453:epidemiology / Q000382:microbiology; D003718:Denmark / Q000453:epidemiology; D004196:Disease Outbreaks; D016984:Enterococcus faecium / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D016680:Genome, Bacterial; D005858:Germany / Q000453:epidemiology; D016908:Gram-Positive Bacterial Infections / Q000453:epidemiology / Q000382:microbiology; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods; D058885:Multilocus Sequence Typing / Q000379:methods*; D009426:Netherlands / Q000453:epidemiology; D020641:Polymorphism, Single Nucleotide