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.
Highlights
Whole genome sequencing (WGS) is expected to transform the practice of clinical microbiology and infection control [1,2]
WGS is only performed at Hvidovre Hospital and all meticillin-resistant Staphylococcus aureus (MRSA) isolates from the two other Departments of Clinical Microbiology are sent to Hvidovre Hospital for WGS
A lacking sequence type (ST) (7 isolates) was caused by a gene being in two contigs, the identification of a new allele, or a new combination of alleles leading to a novel ST not listed in the multilocus sequence types (MLST) database
Summary
Whole genome sequencing (WGS) is expected to transform the practice of clinical microbiology and infection control [1,2]. While detailed bioinformatics analysis remains a challenge, commercial software and webbased solutions are available for performing multilocus sequence typing and screening for gene-based antibiotic resistance on the WGS data [3]. The sequence-based typing method staphylococcal protein A (spa)-typing of meticillin-resistant Staphylococcus aureus (MRSA) has been performed since 2003 at the MRSA Knowledge Center, Department of Clinical Microbiology, at Hvidovre Hospital [4]. In January 2013, this Sanger sequencing method was replaced by WGS of all MRSA isolates and we routinely produce 24 full genomes twice a week. Bioinformatics is used to determine direct repeat units (dru) types and multilocus sequence types (MLST). Single nucleotide polymorphism (SNP) analysis is used routinely to compare relatedness of MRSA isolates
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