TY - JOUR
T1 - Comparing whole-genome sequencing with sanger sequencing for spa typing of methicillin-resistant staphylococcus aureus
AU - Bartels, Mette Damkjær
AU - Petersen, Andreas
AU - Worning, Peder
AU - Nielsen, Jesper Boye
AU - Larner-Svensson, Hanna
AU - Johansen, Helle Krogh
AU - Andersen, Leif Percival
AU - Jarløv, Jens Otto
AU - Boye, Kit
AU - Larsen, Anders Rhod
AU - Westh, Henrik
N1 - Publisher Copyright:
Copyright © 2014, American Society for Microbiology. All Rights Reserved.
PY - 2014/12/1
Y1 - 2014/12/1
N2 - 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.
AB - 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.
U2 - 10.1128/JCM.01979-14
DO - 10.1128/JCM.01979-14
M3 - Journal article
C2 - 25297335
AN - SCOPUS:84910145816
VL - 52
SP - 4305
EP - 4308
JO - Journal of clinical microbiology
JF - Journal of clinical microbiology
SN - 0095-1137
IS - 12
ER -