Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark.
Department of Bacteria, Parasites & Fungi, Statens Serum Institutgrid.6203.7, Copenhagen, Denmark.
Microbiol Spectr. 2022 Dec 21;10(6):e0218922. doi: 10.1128/spectrum.02189-22. Epub 2022 Nov 9.
Sequencing of the gene of methicillin-resistant Staphylococcus aureus (MRSA) is used for assigning types to e.g., detect transmission and control outbreaks. Traditionally, typing is performed by Sanger sequencing but has in recent years been replaced by whole-genome sequencing (WGS) in some laboratories. typing by WGS involves assembly of millions of short sequencing reads into larger contiguous sequences, from which the type is then determined. The choice of assembly program therefore potentially impacts the typing result. In this study, WGS of 1,754 MRSA isolates was followed by assembly using the assembly programs SPAdes (with two different sets of parameters) and SKESA. The types were assigned and compared to the types obtained by Sanger sequencing, regarding the latter as the correct types. SPAdes with the two different settings resulted in assembly of the correct type for 84.8% and 97.6% of the isolates, respectively, while SKESA assembled the correct type in 98.6% of cases. The misassembled types were generally two repeats shorter than the correct type and mainly included types with repetition of the same repeats. WGS-based typing is thus very accurate compared to Sanger sequencing, when the best assembly program for this purpose is used. typing of methicillin-resistant Staphylococcus aureus (MRSA) is widely used by clinicians, infection control workers, and researchers both in local outbreak investigations and as an easy way to communicate and compare MRSA types between laboratories and countries. Traditionally, types are determined by Sanger sequencing, but in recent years a whole-genome sequencing (WGS)-based approach has become increasingly used. In this study, we compared typing by WGS using different methods for assembling the genome from short sequencing reads and compared to Sanger sequencing as the gold standard. We find substantial differences in correct assembly of types between the assembly methods. Our findings are therefore important for the quality of WGS based typing data being exchanged by clinical microbiology laboratories.
对耐甲氧西林金黄色葡萄球菌 (MRSA) 基因进行测序，用于对其进行分型，例如，检测传播并控制暴发。传统上，通过 Sanger 测序进行分型，但近年来，一些实验室已将其替换为全基因组测序 (WGS)。通过 WGS 进行分型涉及将数百万个短测序reads 组装成更大的连续序列，然后从中确定 类型。因此，组装程序的选择可能会影响 分型结果。在这项研究中，对 1754 株 MRSA 分离株进行 WGS 测序，然后使用 SPAdes（两种不同的参数集）和 SKESA 程序进行组装。将 类型分配并与通过 Sanger 测序获得的 类型进行比较，后者被认为是正确的 类型。使用两种不同设置的 SPAdes 分别对 84.8%和 97.6%的分离株进行了正确 类型的组装，而 SKESA 在 98.6%的情况下组装了正确的 类型。错误组装的 类型通常比正确 类型短两个重复，并且主要包括重复相同重复的 类型。与 Sanger 测序相比，使用最佳组装程序进行 WGS 分型非常准确。
耐甲氧西林金黄色葡萄球菌 (MRSA) 的 分型在临床医生、感染控制工作者和研究人员中广泛使用，无论是在本地暴发调查中，还是作为在实验室和国家之间交流和比较 MRSA 类型的简便方法。传统上，通过 Sanger 测序确定 类型，但近年来，全基因组测序 (WGS) 方法的应用越来越广泛。在这项研究中，我们比较了使用不同方法从短测序reads 组装基因组的 WGS 分型，并将其与作为金标准的 Sanger 测序进行比较。我们发现不同组装方法在正确组装 类型方面存在显著差异。因此，我们的研究结果对于临床微生物学实验室之间交换的基于 WGS 的 分型数据的质量非常重要。
