Institute of Hygiene, University Hospital Münster, Münster, Germany.
Institute of Hygiene, University Hospital Münster, Münster, Germany.
Clin Microbiol Infect. 2015 Apr;21(4):347.e1-4. doi: 10.1016/j.cmi.2014.11.005. Epub 2014 Nov 25.
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.
当使用下一代全基因组测序（WGS）时，从 WGS 数据中提取 spa 型对于与基于 Sanger 测序的耐甲氧西林金黄色葡萄球菌（MRSA）spa 分型的向后兼容性至关重要。我们使用两种在进行 spa 分型之前执行序列质量修剪和从头组装的管道，在一个多样化的 423 株 MRSA 分离株的集合中评估了基于 WGS 的 spa 分型，该协议使用 2×250 bp 方案。SeqSphere(+) 管道正确分型了 419 株分离株（99.1%），而 CLCbio 管道成功分型了 249 株分离株（58.9%）。总之，WGS 与优化的从头组装相结合，可以几乎完全与基于 Sanger 测序的 spa 分型数据兼容。
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