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Whole-genome sequencing revealed independent emergence of vancomycin-resistant Enterococcus faecium causing

Mohamed H H Abdelbary1,2, Laurence Senn1, Gilbert Greub3

  • 1Service of hospital preventive medicine, Lausanne University Hospital, Rue du Bugnon 46, 1011, Lausanne, Switzerland.

European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology
|March 20, 2019
PubMed

Insights

Whole-genome sequencing revealed complex Vancomycin-resistant Enterococcus faecium (VREfm) epidemiology. Multiple genotypes caused outbreaks, suggesting new VREfm clones emerge within hospitals.

Area of Science:

  • Infectious Diseases
  • Microbiology
  • Genomics

Background:

  • Vancomycin-resistant Enterococcus faecium (VREfm) is a significant cause of hospital-acquired infections globally.
  • Previous studies linked VREfm outbreaks to the CC17 lineage carrying vanA or vanB genes.
  • The University Hospital of Lausanne experienced VREfm transmissions between 2014 and 2017.

Purpose of the Study:

  • To investigate the genetic relatedness and epidemiology of VREfm isolates at the University Hospital of Lausanne.
  • To utilize whole-genome sequencing (WGS) for detailed outbreak analysis.
  • To understand the local VREfm transmission dynamics and clonal structure.

Main Methods:

  • Whole-genome sequencing (WGS) was performed on 183 VREfm isolates from 156 patients.
  • Epidemiological data was analyzed in conjunction with WGS results.
  • Single Nucleotide Polymorphism (SNP) analysis was used to assess isolate relatedness.

Main Results:

  • ST 17, ST80, and ST117 were the predominant sequence types.
  • Ten outbreaks were identified, involving at least 13 distinct genotypes.
  • Most outbreak isolates (91%) differed by 0–3 SNPs, indicating close relatedness within outbreaks.
  • Four outbreaks included multiple genotypes, and sporadic cases were potentially linked to outbreaks.
  • High recombination levels and polyclonal structures were observed.

Conclusions:

  • WGS provided a comprehensive understanding of local VREfm epidemiology.
  • The polyclonal nature of outbreaks and high recombination suggest the emergence of new VREfm clones within the hospital population.
  • Findings support the hypothesis of de novo VREfm clone emergence in hospitalized patients, challenging solely clonal spread models.
Keywords:
Enterococcus faeciumGenome sequencingInfection controlOutbreakTransmissionVancomycin resistance

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