Comparing Whole-Genome Sequencing with Sanger Sequencing for spa Typing of Methicillin-Resistant Staphylococcus aureus
Comparing Whole-Genome Sequencing with Sanger Sequencing for spa Typing of Methicillin-Resistant Staphylococcus aureus
复制标题
DOI：
10.1128/jcm.01979-14
复制
发表时间：
2014-12-01
影响因子：
9.4
通讯作者：
Westh, Henrik
中科院分区：
文献类型：
--
作者：
Bartels, Mette Damkjaer;Petersen, Andreas;Westh, Henrik
耐甲氧西林金黄色葡萄球菌（MRSA）的spa分型传统上是通过PCR扩增和spa重复区域的Sanger测序来完成的。在丹麦Hvidovre医院，自2013年1月以来，对所有MRSA分离株进行了常规的全基因组测序（WGS），并通过内部分析管道确定spa类型。由于国家监测，所有MRSA分离株被送到Statens血清研究所，在那里通过PCR和Sanger测序确定spa类型。本研究的目的是评估150 bp对端Illumina WGS获得spa类型的可靠性。纳入2013年丹麦首都地区新发MRSA患者（n = 699）的MRSA分离株。我们发现两种方法获得的spa类型之间有97%的一致性。通过两种方法分离得到的菌株均为spa型。通过两种方法分离的19株菌株在spa类型上存在差异，这在大多数情况下是由于在全基因组测序的分离株中缺乏24bp重复序列。这些相关但不正确的温泉类型在疫情调查中应该没有影响，因为所有流行病学上相关的分离株，无论温泉类型如何，都将包括在单核苷酸多态性（SNP）分析中。这将揭示温泉类型的密切关系。总之，我们的数据表明WGS是一种可靠的方法来确定MRSA的spa类型。
spa typing of methicillin-resistant Staphylococcus aureus (MRSA) has traditionally been done by PCR amplification and Sanger sequencing of the spa repeat region. At Hvidovre Hospital, Denmark, whole-genome sequencing (WGS) of all MRSA isolates has been performed routinely since January 2013, and an in-house analysis pipeline determines the spa types. Due to national surveillance, all MRSA isolates are sent to Statens Serum Institut, where the spa type is determined by PCR and Sanger sequencing. The purpose of this study was to evaluate the reliability of the spa types obtained by 150-bp paired-end Illumina WGS. MRSA isolates from new MRSA patients in 2013 (n = 699) in the capital region of Denmark were included. We found a 97% agreement between spa types obtained by the two methods. All isolates achieved a spa type by both methods. Nineteen isolates differed in spa types by the two methods, in most cases due to the lack of 24-bp repeats in the whole-genome-sequenced isolates. These related but incorrect spa types should have no consequence in outbreak investigations, since all epidemiologically linked isolates, regardless of spa type, will be included in the single nucleotide polymorphism (SNP) analysis. This will reveal the close relatedness of the spa types. In conclusion, our data show that WGS is a reliable method to determine the spa type of MRSA.