Whole-genome sequencing for routine pathogen surveillance in Public Health: a population snapshot of invasive staphylococcus aureus in Europe

ESCMID Study Group on Molecular Epidemiological Markers (ESGEM), European Staphylococcal Reference Laboratory Working Group

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Abstract

The implementation of routine whole-genome sequencing (WGS) promises to transform our ability to monitor the emergence and spread of bacterial pathogens. Here we combined WGS data from 308 invasive Staphylococcus aureus isolates corresponding to a pan-European population snapshot, with epidemiological and resistance data. Geospatial visualization of the data is made possible by a generic software tool designed for public health purposes that is available at the project URL (http://www.microreact.org/project/EkUvg9uY?tt=rc). Our analysis demonstrates that high-risk clones can be identified on the basis of population level properties such as clonal relatedness, abundance, and spatial structuring and by inferring virulence and resistance properties on the basis of gene content. We also show that in silico predictions of antibiotic resistance profiles are at least as reliable as phenotypic testing. We argue that this work provides a comprehensive road map illustrating the three vital components for future molecular epidemiological surveillance: (i) large-scale structured surveys, (ii) WGS, and (iii) community-oriented database infrastructure and analysis tools.
Original languageEnglish
Article numbere00444-16
Number of pages15
JournalmBio
Volume7
Issue number3
Early online date5 May 2016
DOIs
Publication statusPublished - 30 Jun 2016

Keywords

  • microbiology
  • epidemiology

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    ESCMID Study Group on Molecular Epidemiological Markers (ESGEM), & European Staphylococcal Reference Laboratory Working Group (2016). Whole-genome sequencing for routine pathogen surveillance in Public Health: a population snapshot of invasive staphylococcus aureus in Europe. mBio, 7(3), [e00444-16]. https://doi.org/10.1128/mBio.00444-16