Determining Streptococcus suis serotype from short-read whole-genome sequencing data.
Determining Streptococcus suis serotype from short-read whole-genome sequencing data.
复制标题
从短读全基因组测序数据中确定SUIS血清型链球菌。
DOI：
10.1186/s12866-016-0782-8
复制
发表时间：
2016-07-22
期刊：
影响因子：
4.2
通讯作者：
Fittipaldi N
中科院分区：
文献类型：
--
作者：
Athey TB;Teatero S;Lacouture S;Takamatsu D;Gottschalk M;Fittipaldi N
根据对荚膜多糖（CPS）的血清学反应，猪链球菌分为29个血清型。针对cps基因座的多重PCR检测也用于确定S。但它们不能区分血清型1和14以及血清型2和1/2。在这里，我们开发了一个管道，允许从全基因组测序（WGS）短读段数据中进行计算机血清型测定，可以很容易地识别所有29个S。猪血清型。我们对代表所有29种已知沙门氏菌的121个菌株的基因组进行了测序。猪血清型。接下来，我们将可用的软件组合到自动化流水线中，允许通过短读段测序数据与定制的S. suis cps位点数据库。血清型对1和14，2和1/2的菌株可以通过cpsK基因中的错义突变来区分。我们报告在我们收集的菌株中，凝固酶和管道确定的血清型之间99%匹配。我们使用了375个额外的S。从NCBI的Sequence Read Archive（SRA）下载的猪基因组来验证管道。使用SRA WGS数据的验证结果为92%匹配。包括管道子程序，使我们能够评估菌株毒力标志物的内容，并获得多位点序列分型直接从WGS数据。我们的管道可以快速准确地测定S。suis血清型和其他谱系信息，直接来自WGS数据。通过区分血清型1和14，以及血清型2和1/2，我们的方法解决了三十年来长期存在的S。sui打字问题。本文的在线版本（doi：10.1186/s12866-016-0782-8）包含补充材料，可供授权用户使用。
Streptococcus suis is divided into 29 serotypes based on a serological reaction against the capsular polysaccharide (CPS). Multiplex PCR tests targeting the cps locus are also used to determine S. suis serotypes, but they cannot differentiate between serotypes 1 and 14, and between serotypes 2 and 1/2. Here, we developed a pipeline permitting in silico serotype determination from whole-genome sequencing (WGS) short-read data that can readily identify all 29 S. suis serotypes. We sequenced the genomes of 121 strains representing all 29 known S. suis serotypes. We next combined available software into an automated pipeline permitting in silico serotyping of strains by differential alignment of short-read sequencing data to a custom S. suis cps loci database. Strains of serotype pairs 1 and 14, and 2 and 1/2 could be differentiated by a missense mutation in the cpsK gene. We report a 99 % match between coagglutination- and pipeline-determined serotypes for strains in our collection. We used 375 additional S. suis genomes downloaded from the NCBI’s Sequence Read Archive (SRA) to validate the pipeline. Validation with SRA WGS data resulted in a 92 % match. Included pipeline subroutines permitted us to assess strain virulence marker content and obtain multilocus sequence typing directly from WGS data. Our pipeline permits rapid and accurate determination of S. suis serotype, and other lineage information, directly from WGS data. By discriminating between serotypes 1 and 14, and between serotypes 2 and 1/2, our approach solves a three-decade longstanding S. suis typing issue. The online version of this article (doi:10.1186/s12866-016-0782-8) contains supplementary material, which is available to authorized users.