Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland
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The correct interpretation of microbial sequencing data applied to surveillance and outbreak investigation depends on accessible genomic databases to provide vital genetic context. Our aim was to construct and describe a UK MRSA database containing over 1,000 methicillin-resistant Staphylococcus aureus (MRSA) genomes drawn from England, Northern Ireland, Wales, Scotland and the Republic of Ireland over a decade. We sequenced 1,013 MRSA submitted to the British Society for Antimicrobial Chemotherapy by 46 laboratories between 2001 and 2010. Each isolate was assigned to a regional healthcare referral network in England, and otherwise grouped based on country of origin. Phylogenetic reconstructions were used to contextualise MRSA outbreak investigations, and to detect the spread of resistance. The majority of isolates (n=783, 77%) belonged to CC22, which contains the dominant UK epidemic clone (EMRSA-15). There was marked geographic structuring of EMRSA-15, consistent with widespread dissemination prior to the sampling decade followed by local diversification. The addition of MRSA genomes from two outbreaks and one pseudo-outbreak demonstrated the certainty with which outbreaks could be confirmed or refuted. We identified local and regional differences in antibiotic resistance profiles, with examples of local expansion, as well as widespread circulation of mobile genetic elements across the bacterial population. We have generated a resource for the future surveillance and outbreak investigation of MRSA in the UK and Ireland, and have shown the value of this during outbreak investigation and tracking of antimicrobial resistance.
Reuter , S , Török , E M , Holden , M T , Reynolds , R , Raven , K E , Blane , B , Donker , T , Bentley , S D , Aanensen , D M , Grundmann , H , Feil , E J , Spratt , B G , Parkhill , J & Peacock , S J 2016 , ' Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland ' Genome Research , vol 26 , no. 2 , pp. 263-270 . DOI: 10.1101/gr.196709.115
© 2016 Reuter et al.; Published by Cold Spring Harbor Laboratory Press This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
The study was supported by grants from the UKCRC Translational Infection Research Initiative, and the Medical Research Council Grant Number G1000803) with contributions to the Grant from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research on behalf of the Department of Health, and the Chief Scientist Office of the Scottish Government Health Directorate (to Prof. Peacock); and by Wellcome Trust grant number 098051 awarded to the Wellcome Trust Sanger Institute. MET is Clinician Scientist Fellow supported by the Academy of Medical Sciences and the Health Foundation.
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