Multilocus Sequence Typing Scheme for Enterococcus faecium

Abstract

A multilocus sequence typing (MLST) scheme has been developed for Enterococcus faecium. Internal fragments from seven housekeeping genes of 123 epidemiologically unlinked isolates from humans and livestock and 16 human-derived isolates from several outbreaks in the United States, the United Kingdom, Australia, and The Netherlands were analyzed. A total of 62 sequence types were detected in vancomycin-sensitive E. faecium (VSEF) and vancomycin-resistant E. faecium (VREF) isolates. VSEF isolates were genetically more diverse than VREF isolates. Both VSEF and VREF isolates clustered in host-specific lineages that were similar to the host-specific clustering obtained by amplified fragment length polymorphism analysis. Outbreak isolates from hospitalized humans clustered in a subgroup that was defined by the presence of a unique allele from the housekeeping gene purK and the surface protein gene esp. The MLST results suggest that epidemic lineages of E. faecium emerged recently worldwide, while genetic variation in both VREF and VSEF was created by longer-term recombination. The results show that MLST of E. faecium provides an excellent tool for isolate characterization and long-term epidemiologic analysis.Vancomycin-resistant Enterococcus faecium (VREF) has recently emerged as an important threat in U.S. hospitals (5, 24). In Europe, VREF isolates are found relatively frequently in the community and farm animals, while prevalence in hospitals is generally low (14). The latter observation was explained by the use of the glycopeptide avoparcin as an antimicrobial growth promoter in animal feeding operations.Several molecular typing schemes have been developed to study the epidemiology of VREF. Of these, pulsed-field gel electrophoresis analysis of genomic restriction fragments has been considered the "gold standard" for the study of hospital outbreaks because of its high degree of isolate differentiation (15,17,20,23). However, due to this high degree of isolate differentiation, pulsed-field gel electrophoresis typing is less suitable for determining the degree of relatedness among epidemiologically unrelated isolates. Recently, amplified fragment length polymorphism (AFLP) analysis was applied as a new method for the typing of VREF (1, 33). AFLP analysis is a robust and fast typing technique with high intra-and interexperimental reproducibilities and appears to be discriminatory enough for the recognition of hospital outbreaks (1, 32, 33). In addition, AFLP analysis has allowed the detection of associations among different E. faecium genetic lineages and different human and animal hosts (33), suggesting the existence of host-specific VREF lineages. Whether this is also true for vancomycin-sensitive E. faecium (VSEF) is not known, since VSEF isolates were not included in that study. AFLP typing also disclosed two different human-associated lineages. One lineage comprised epidemic-related isolates recovered from hospitalized patients, while isolates of the other lineage were mainly from nonhospitalized persons. Interes...

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

“…GMD assembly sizes were unchanged using this approach. As another measure of completeness, we looked for and found all multiple locus sequence typing (MLST) loci of S. oralis and E. faecium (Homan et al 2002;Do et al 2009). …”

“…Based on our mapping data, assembly sizes, and recovery of all MLST loci, however, we believe we came very close to completion of all genomes derived from GMDs (Homan et al 2002;Do et al 2009). To demonstrate that the contigs removed via BLAST were correctly identified as contamination, we compared tetranucleotide frequencies of cleaned and uncleaned contigs.…”

Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data

“…Finally, B. pseudomallei (and closely related species), M. catarrhalis, Staphylococcus epidermidis, Vibrio vulnificus, Campylobacter jejuni, Enterococcus faecium, E. coli, and S. aureus showed consistently low mean levels of ρ( ≤15). Little information has been published on the first four of these species, but clonal (low recombination) and epidemic (sexual but superficially clonal) population structures have been proposed for C. jejuni (Suerbaum et al, 2001) and E. faecium (Homan et al, 2002). The frequency of recombination in E. coli, S. aureus, and H. influenzae is still debated: some studies suggest low rates or clonal structures (Whittam, 1995;Feil et al, 2001Feil et al, ,2003, while others indicate the opposite (Feil et al, 1999(Feil et al, ,2001Meats et al, 2003).…”

Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases

“…Therefore, MLST databases for a number of different species were searched for high-D SNP sets. Species subject to this analysis were Burkholderia pseudomallei/ Burkholderia mallei, Helicobacter pylori, Campylobacter jejuni, Streptococcus pneumoniae, Streptococcus pyogenes and Enterococcus faecium (Feil et al, 2000;Enright et al, 2001;Sa-Leao et al, 2001;Dingle et al, 2002;Homan et al, 2002;Godoy et al, 2003;Meats et al, 2003). Ten different sets of SNPs were identified for each species.…”