Epidemiological typing of ST80 vancomycin-resistant Enterococcus faecium: core-genome multi-locus sequence typing versus single nucleotide polymorphism-based typing.

Abstract

OBJECTIVES\nVancomycin-resistant Enterococcus faecium (VRE) belonging to sequence type 80 (ST80) has been successfully disseminating in hospital settings. The present study aimed to explore whole-genome sequencing (WGS)-based approaches in epidemiological typing of VRE, by investigating a collection of ST80 strains.\n\n\nMETHODS\nIn total, 41 VRE isolates of ST80 in three suspected transmission chains were subjected to WGS. The genetic relationship of the isolates was analysed by core-genome multi-locus sequence typing (cgMLST) and single nucleotide polymorphisms (SNPs). The published genome sequence of a predominant ST80 clone in Copenhagen was also included in analyses.\n\n\nRESULTS\nIsolates in group 1 (n=10) were recovered in the same geographic area, in which two isolates were from an outbreak of vanA genotype. Isolates of group 2 (n=4) were detected from another outbreak. Group 3 consisted of three non-outbreak isolates and 24 representative isolates from an outbreak of vanB genotype. Our findings indicated ≥24 allelic difference and >16 SNPs as the cut-off for excluding VRE strains from an outbreak. cgMLST identified >200 differing alleles between genomes of the Copenhagen clone and outbreak strains in this study. Our findings also demonstrated that SNP analysis was not suitable in typing samples from different groups, even with the same ST, due to the lack of optimal reference genome.\n\n\nCONCLUSIONS\ncgMLST and SNPs provided comparable epidemiologic discrimination for isolates with suspected transmission chain. For diverse isolates, SNP analysis could be suboptimal. An approach by applying cgMLST as the first line typing method and SNPs as a complementary tool was suggested.