title: Ensuring backwards compatibility: traditional genotyping efforts in the era of whole genome sequencing.
abstract: When using next-generation whole genome sequencing (WGS), extraction of spa types from WGS data is essential for backwards compatibility with Sanger sequencing-based spa typing of methicillin-resistant Staphylococcus aureus (MRSA). We evaluated WGS-based spa typing with a 2×250 bp protocol in a diverse collection of 423 MRSA isolates using two pipelines that executed sequence quality-trimming and de novo assembly before spa typing. The SeqSphere(+) pipeline correctly typed 419 isolates (99.1%) whereas the CLCbio pipeline succeeded in 249 isolates (58.9%). In summary, WGS combined with an optimized de novo assembly enables nearly full compatibility with Sanger sequencing-based spa typing data.
authors: Institute of Hygiene, University Hospital Münster, Münster, Germany.
authors: S
authors: S
authors: Bletz
authors: Institute of Hygiene, University Hospital Münster, Münster, Germany. Electronic address: mellmann@uni-muenster.de.
authors: A
authors: A
authors: Mellmann
authors: Ridom GmbH, Münster, Germany.
authors: J
authors: J
authors: Rothgänger
authors: Department of Periodontology, University Hospital Münster, Münster, Germany.
authors: D
authors: D
authors: Harmsen
mesh_terms: D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D055624:Methicillin-Resistant Staphylococcus aureus / Q000145:classification* / Q000235:genetics*; D017720:Molecular Epidemiology / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: Backwards compatibility; Staphylococcus aureus; methicillin-resistant Staphylococcus aureus; spa typing; whole genome sequencing