Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
6129472 | Clinical Microbiology and Infection | 2015 | 4 Pages |
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 2Ã250 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.
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Authors
S. Bletz, A. Mellmann, J. Rothgänger, D. Harmsen,