Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland
- Sandra Reuter1,2,
- M. Estée Török1,3,4,
- Matthew T.G. Holden2,5,
- Rosy Reynolds6,7,
- Kathy E. Raven1,
- Beth Blane1,
- Tjibbe Donker8,
- Stephen D. Bentley2,
- David M. Aanensen9,
- Hajo Grundmann8,10,
- Edward J. Feil11,
- Brian G. Spratt9,
- Julian Parkhill2 and
- Sharon J. Peacock1,2,3,4,12
- 1Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom;
- 2Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom;
- 3Public Health England, Microbiology Services Division, Addenbrooke's Hospital, Cambridge CB2 0QW, United Kingdom;
- 4Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom;
- 5School of Medicine, University of St. Andrews, St. Andrews KY16 9TF, United Kingdom;
- 6British Society for Antimicrobial Chemotherapy, B1 3NJ, United Kingdom;
- 7North Bristol NHS Trust, Bristol BS10 5NB, United Kingdom;
- 8Department of Medical Microbiology, University Medical Centre Groningen, Rijksuniversiteit Groningen, 9713 GZ Groningen, The Netherlands;
- 9Faculty of Medicine, School of Public Health, Imperial College, London W2 1PG, United Kingdom;
- 10Department of Hospital Epidemiology, Institute for Environmental Medicine and Hospital Hygiene, University Hospital Freiburg, 79106 Freiburg, Germany;
- 11The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom;
- 12London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
- Corresponding authors: sr731{at}medschl.cam.ac.uk; sjp97{at}medschl.cam.ac.uk
Abstract
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 United Kingdom MRSA database containing over 1000 methicillin-resistant Staphylococcus aureus (MRSA) genomes drawn from England, Northern Ireland, Wales, Scotland, and the Republic of Ireland over a decade. We sequenced 1013 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 was otherwise grouped based on country of origin. Phylogenetic reconstructions were used to contextualize MRSA outbreak investigations and to detect the spread of resistance. The majority of isolates (n = 783, 77%) belonged to CC22, which contains the dominant United Kingdom 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 United Kingdom and Ireland and have shown the value of this during outbreak investigation and tracking of antimicrobial resistance.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.196709.115.
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Freely available online through the Genome Research Open Access option.
- Received July 8, 2015.
- Accepted December 14, 2015.
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/.
