title: Comparing whole-genome sequencing with Sanger sequencing for spa typing of methicillin-resistant Staphylococcus aureus.
abstract: spa typing of methicillin-resistant Staphylococcus aureus (MRSA) has traditionally been done by PCR amplification and Sanger sequencing of the spa repeat region. At Hvidovre Hospital, Denmark, whole-genome sequencing (WGS) of all MRSA isolates has been performed routinely since January 2013, and an in-house analysis pipeline determines the spa types. Due to national surveillance, all MRSA isolates are sent to Statens Serum Institut, where the spa type is determined by PCR and Sanger sequencing. The purpose of this study was to evaluate the reliability of the spa types obtained by 150-bp paired-end Illumina WGS. MRSA isolates from new MRSA patients in 2013 (n = 699) in the capital region of Denmark were included. We found a 97% agreement between spa types obtained by the two methods. All isolates achieved a spa type by both methods. Nineteen isolates differed in spa types by the two methods, in most cases due to the lack of 24-bp repeats in the whole-genome-sequenced isolates. These related but incorrect spa types should have no consequence in outbreak investigations, since all epidemiologically linked isolates, regardless of spa type, will be included in the single nucleotide polymorphism (SNP) analysis. This will reveal the close relatedness of the spa types. In conclusion, our data show that WGS is a reliable method to determine the spa type of MRSA.
authors.affiliation: Department of Clinical Microbiology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark MRSA Knowledge Center, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark mette.damkjaer@dadlnet.dk.
authors.forename: Mette Damkjær
authors.initials: MD
authors.lastname: Bartels
authors.affiliation: Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: Andreas
authors.initials: A
authors.lastname: Petersen
authors.affiliation: MRSA Knowledge Center, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark.
authors.forename: Peder
authors.initials: P
authors.lastname: Worning
authors.affiliation: Department of Clinical Microbiology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark MRSA Knowledge Center, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark.
authors.forename: Jesper Boye
authors.initials: JB
authors.lastname: Nielsen
authors.affiliation: MRSA Knowledge Center, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark.
authors.forename: Hanna
authors.initials: H
authors.lastname: Larner-Svensson
authors.affiliation: Department of Clinical Microbiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark Novo Nordisk Center for Biosustainability, The Technical University of Copenhagen, Hørsholm, Denmark.
authors.forename: Helle Krogh
authors.initials: HK
authors.lastname: Johansen
authors.affiliation: Department of Infection Control, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Leif Percival
authors.initials: LP
authors.lastname: Andersen
authors.affiliation: Department of Clinical Microbiology, Herlev Hospital, University of Copenhagen, Herlev, Denmark.
authors.forename: Jens Otto
authors.initials: JO
authors.lastname: Jarløv
authors.affiliation: Department of Clinical Microbiology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark.
authors.forename: Kit
authors.initials: K
authors.lastname: Boye
authors.affiliation: Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: Anders Rhod
authors.initials: AR
authors.lastname: Larsen
authors.affiliation: Department of Clinical Microbiology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark MRSA Knowledge Center, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Henrik
authors.initials: H
authors.lastname: Westh
mesh_terms: D003718:Denmark / Q000453:epidemiology; D006801:Humans; D055624:Methicillin-Resistant Staphylococcus aureus / Q000145:classification* / Q000235:genetics*; D017720:Molecular Epidemiology / Q000379:methods; D058889:Molecular Typing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013203:Staphylococcal Infections / Q000453:epidemiology / Q000382:microbiology; D013205:Staphylococcal Protein A / Q000235:genetics*
chemical_list: D013205:Staphylococcal Protein A