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Updated: Apr 17, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Ensuring backwards compatibility: traditional genotyping efforts in the era of whole genome sequencing
S Bletz1, A Mellmann1, J Rothgänger2
1Institute of Hygiene, University Hospital Münster, Münster, Germany.
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.
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