Monitoring meticillin resistant Staphylococcus aureus and its spread in Copenhagen, Denmark, 2013, through routine whole genome sequencing

M D Bartels; H Larner-Svensson; H Meiniche; K Kristoffersen; K Schønning; J B Nielsen; S M Rohde; L B Christensen; A W Skibsted; J O Jarløv; H K Johansen; L P Andersen; I S Petersen; D W Crook; R Bowden; K Boye; P Worning; H Westh

doi:10.2807/1560-7917.ES2015.20.17.21112

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Monitoring meticillin resistant Staphylococcus aureus and its spread in Copenhagen, Denmark, 2013, through routine whole genome sequencing
M D Bartels^1,2 , H Larner-Svensson^2,3 , H Meiniche³ , K Kristoffersen³ , K Schønning^1,4 , J B Nielsen^1,3 , S M Rohde³ , L B Christensen³ , A W Skibsted³ , J O Jarløv⁵ , H K Johansen⁶ , L P Andersen⁷ , I S Petersen⁵ , D W Crook⁸ , R Bowden⁹ , K Boye¹ , P Worning³ , H Westh^1,3,4
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Affiliations: ¹ Department of Clinical Microbiology, Hvidovre University Hospital, Denmark ² These authors contributed equally to this work ³ MRSA Knowledge Center, Hvidovre University Hospital, Denmark ⁴ Institute of Clinical Medicine, University of Copenhagen, Denmark ⁵ Department of Clinical Microbiology, Herlev University Hospital, Denmark ⁶ Department of Clinical Microbiology, Rigshospitalet, Denmark ⁷ Department of Infection control, Rigshospitalet, Denmark ⁸ Infectious Diseases and Microbiology Unit John Radcliffe Hospital, Oxford, United Kingdom ⁹ Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom

Correspondence:
M Bartels
mette.damkjaer dadlnet.dk
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Citation style for this article: Bartels M D, Larner-Svensson H, Meiniche H, Kristoffersen K, Schønning K, Nielsen J B, Rohde S M, Christensen L B, Skibsted A W, Jarløv J O, Johansen H K, Andersen L P, Petersen I S, Crook D W, Bowden R, Boye K, Worning P, Westh H. Monitoring meticillin resistant Staphylococcus aureus and its spread in Copenhagen, Denmark, 2013, through routine whole genome sequencing. Euro Surveill. 2015;20(17):pii=21112. https://doi.org/10.2807/1560-7917.ES2015.20.17.21112 Received: 12 Mar 2014

Abstract

Typing of meticillin resistant Staphylococcus aureus (MRSA) by whole genome sequencing (WGS) is performed routinely in Copenhagen since January 2013. We describe the relatedness, based on WGS data and epidemiological data, of 341 MRSA isolates. These comprised all MRSA (n?=?300) identified in Copenhagen in the first five months of 2013. Moreover, because MRSA of staphylococcal protein A (spa)-type 304 (t304), sequence type (ST) 6 had been associated with a continuous neonatal ward outbreak in Copenhagen starting in 2011, 41 t304 isolates collected in the city between 2010 and 2012 were also included. Isolates from 2013 found to be of t304, ST6 (n=14) were compared to the 41 earlier isolates. In the study, isolates of clonal complex (CC) 22 were examined in detail, as this CC has been shown to include the hospital-acquired epidemic MRSA (EMRSA-15) clone. Finally, all MRSA ST80 were also further analysed, as representatives of an important community-acquired MRSA in Europe. Overall the analysis identified 85 spa-types and 35 STs from 17 CCs. WGS confirmed the relatedness of epidemiologically linked t304 neonatal outbreak isolates. Several non-outbreak related patients had isolates closely related to the neonatal isolates suggesting unrecognised community chains of transmission and insufficient epidemiological data. Only four CC22 isolates were related to EMRSA-15. No community spread was observed among the 13 ST80 isolates. WGS successfully replaced conventional typing and added information to epidemiological surveillance. Creation of a MRSA database allows clustering of isolates based on single nucleotide polymorphism (SNP) calling and has improved our understanding of MRSA transmission.