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Whole-genome sequencing revealed independent emergence of vancomycin-resistant Enterococcus faecium causing sequential outbreaks over 3 years in a tertiary care hospital

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Abstract

Vancomycin-resistant Enterococcus faecium (VREfm) emerged as an important cause of nosocomial infections worldwide. Previous studies based on molecular typing revealed that VREfm outbreaks are mainly associated with a particular genetic lineage, namely clonal complex 17 (CC17), which harbours either vanA or vanB gene cluster. The University Hospital of Lausanne faced several VREfm episodes of transmissions between 2014 and 2017. In this study, we used whole-genome sequencing (WGS) to investigate the relatedness of 183 VREfm isolates collected from 156 patients. Sequence types (ST) 17, ST80 and ST117 were the most predominant clones. Based on epidemiological data, 10 outbreaks were identified, which were caused by at least 13 distinct genotypes. The majority of isolates involved in outbreaks (91%) differed by only 0 to 3 SNPs. Four outbreaks involved more than one genotype and half of the cases considered as sporadic were possibly linked to an outbreak. By sequencing all isolates, we were able to better understand our local epidemiology of VREfm. The polyclonal structure observed between the different outbreaks strains, the high level of recombination detected in isolates, the time elapsed between admission and the first VREfm detection and the negative screening at admission support the hypothesis of the emergence of new VREfm clones within the hospitalised population.

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Funding

The Service of Hospital Preventive Medicine of the Lausanne University Hospital funded this project.

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Author notes

  1. Mohamed H. H. Abdelbary

    Present address: Division of Oral Microbiology and Immunology, Department of Operative and Preventive Dentistry and Periodontology, RWTH Aachen University Hospital, Aachen, Germany

Authors and Affiliations

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

    Mohamed H. H. Abdelbary, Laurence Senn, Gregory Chaillou, Estelle Moulin & Dominique S. Blanc

  2. Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland

    Gilbert Greub

Authors
  1. Mohamed H. H. Abdelbary
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  2. Laurence Senn
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  3. Gilbert Greub
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  4. Gregory Chaillou
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  5. Estelle Moulin
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  6. Dominique S. Blanc
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Corresponding author

Correspondence to Dominique S. Blanc.

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The authors declare that they have no conflict of interest.

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All procedures performed in this study involving human participants were in accordance with the ethical standards of the regional and national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

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ESM 1

(PDF 704 kb)

Table S1

Patient’s epidemiological data. (XLSX 20 kb)

Table S2

Entire resistance and virulence factors detected in the 183 VREfm isolates. (XLSX 90 kb)

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Abdelbary, M.H.H., Senn, L., Greub, G. et al. Whole-genome sequencing revealed independent emergence of vancomycin-resistant Enterococcus faecium causing sequential outbreaks over 3 years in a tertiary care hospital. Eur J Clin Microbiol Infect Dis 38, 1163–1170 (2019). https://doi.org/10.1007/s10096-019-03524-z

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  • DOI: https://doi.org/10.1007/s10096-019-03524-z

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