title: Comparison of Whole-Genome Sequencing Methods for Analysis of Three Methicillin-Resistant Staphylococcus aureus Outbreaks.
abstract: Whole-genome sequencing (WGS) can provide excellent resolution in global and local epidemiological investigations ofStaphylococcus aureusoutbreaks. A variety of sequencing approaches and analytical tools have been used; it is not clear which is ideal. We compared two WGS strategies and two analytical approaches to the standard method of SmaI restriction digestion pulsed-field gel electrophoresis (PFGE) for typingS. aureusForty-twoS. aureusisolates from three outbreaks and 12 reference isolates were studied. Near-complete genomes, assembledde novowith paired-end and long-mate-pair (8 kb) libraries were first assembled and analyzed utilizing an in-house assembly and analytical informatics pipeline. In addition, paired-end data were assembled and analyzed using a commercial software package. Single nucleotide variant (SNP) analysis was performed using the in-house pipeline. Two assembly strategies were used to generate core genome multilocus sequence typing (cgMLST) data. First, the near-complete genome data generated with the in-house pipeline were imported into the commercial software and used to perform cgMLST analysis. Second, the commercial software was used to assemble paired-end data, and resolved assemblies were used to perform cgMLST. Similar isolate clustering was observed using SNP calling and cgMLST, regardless of data assembly strategy. All methods provided more discrimination between outbreaks than did PFGE. Overall, all of the evaluated WGS strategies yielded statistically similar results forS. aureustyping.
authors.affiliation: Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Cunningham
authors.affiliation: Department of Surgery, Mayo Clinic, Rochester, Minnesota, USA.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Chia
authors.affiliation: Department of Surgery, Mayo Clinic, Rochester, Minnesota, USA.
authors.forename: Patricio R
authors.identifier: 0000-0003-0282-4217
authors.initials: PR
authors.lastname: Jeraldo
authors.affiliation: Advanced Analytics and Information Support, Information Technology, Mayo Clinic, Rochester, Minnesota, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Quest
authors.affiliation: Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, Minnesota, USA.
authors.forename: Julie A
authors.initials: JA
authors.lastname: Johnson
authors.affiliation: Minnesota Department of Health, Saint Paul, Minnesota, USA.
authors.forename: Dave J
authors.initials: DJ
authors.lastname: Boxrud
authors.affiliation: Minnesota Department of Health, Saint Paul, Minnesota, USA.
authors.forename: Angela J
authors.initials: AJ
authors.lastname: Taylor
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA.
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Jenkins
authors.affiliation: Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, Minnesota, USA.
authors.forename: Travis M
authors.initials: TM
authors.lastname: Drucker
authors.affiliation: Department of Surgery, Mayo Clinic, Rochester, Minnesota, USA.
authors.forename: Heidi
authors.initials: H
authors.lastname: Nelson
authors.affiliation: Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA patel.robin@mayo.edu.|Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.
authors.forename: Robin
authors.initials: R
authors.lastname: Patel
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004196:Disease Outbreaks; D006801:Humans; D055624:Methicillin-Resistant Staphylococcus aureus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D017720:Molecular Epidemiology / Q000379:methods*; D058889:Molecular Typing / Q000379:methods*; D013203:Staphylococcal Infections / Q000453:epidemiology* / Q000382:microbiology; D000073336:Whole Genome Sequencing / Q000379:methods*
keywords: MRSA; PFGE; Staphylococcus aureus; molecular typing; whole-genome sequencing