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Published, Version of Record (VoR)CC BY V4.0, Open
Journal article
Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe
mBio, v 7(3), e00444-16
05 May 2016
PMID: 27150362
Featured in Collection : UN Sustainable Development Goals @ Drexel
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.
The spread of antibiotic-resistant bacteria is a public health emergency of global concern, threatening medical intervention at every level of health care delivery. Several recent studies have demonstrated the promise of routine whole-genome sequencing (WGS) of bacterial pathogens for epidemiological surveillance, outbreak detection, and infection control. However, as this technology becomes more widely adopted, the key challenges of generating representative national and international data sets and the development of bioinformatic tools to manage and interpret the data become increasingly pertinent. This study provides a road map for the integration of WGS data into routine pathogen surveillance. We emphasize the importance of large-scale routine surveys to provide the population context for more targeted or localized investigation and the development of open-access bioinformatic tools to provide the means to combine and compare independently generated data with publicly available data sets.
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Details
- Title
- Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe
- Creators
- David M Aanensen - Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United KingdomEdward J Feil - University of BathMatthew T G Holden - Wellcome Sanger InstituteJanina Dordel - Drexel UniversityCorin A Yeats - Imperial College LondonArtemij Fedosejev - Imperial College LondonRichard Goater - GenomicSantiago Castillo-Ramírez - Universidad Nacional Autónoma de MéxicoJukka Corander - Helsinki Institute for Information TechnologyCaroline Colijn - Imperial College LondonMonika A Chlebowicz - University Medical Center GroningenLeo Schouls - National Institute for Public Health and the EnvironmentMax Heck - National Institute for Public Health and the EnvironmentGerlinde Pluister - National Institute for Public Health and the EnvironmentRaymond Ruimy - Centre Hospitalier Universitaire de NiceGunnar Kahlmeter - Växjö KommunJenny Åhman - Växjö KommunErika Matuschek - Växjö KommunAlexander W Friedrich - University Medical Center GroningenJulian Parkhill - Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United KingdomStephen D Bentley - Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United KingdomBrian G Spratt - Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United KingdomHajo Grundmann - University of FreiburgEuropean SRL Working Group
- Publication Details
- mBio, v 7(3), e00444-16
- Publisher
- American Society for Microbiology (ASM)
- Grant note
- 089472 / Wellcome Trust 099202 / Wellcome Trust 098051 / Wellcome Trust Wellcome Trust G1000803 / Medical Research Council
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Biology
- Web of Science ID
- WOS:000383440300020
- Scopus ID
- 2-s2.0-84978959412
- Other Identifier
- 991021867508404721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Microbiology