Ensuring backwards compatibility: Traditional genotyping efforts in the era of whole genome sequencing
Bletz S., Mellmann A., Rothgänger J., Harmsen D.
Research article (journal) | Peer reviewedAbstract
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.
Details about the publication
Journal: Clinical microbiology and infection: the official publication of the European Society of Clinical Microbiology and Infectious Diseases (Clin Microbiol Infect)
Volume: 21
Issue: 4
Page range: 347.e1-347.e4
Status: Published
Release year: 2015
Language in which the publication is written: English
Link to the full text: http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=84928579555&origin=inward
Keywords: Backwards compatibility; Methicillin-resistant Staphylococcus aureus; Spa typing; Staphylococcus aureus; Whole genome sequencing
Authors from the University of Münster
| Bletz, Stefan | Institute of Hygiene |
| Harmsen, Dag | Department of Periodontology |
| Mellmann, Alexander | Institute of Hygiene |