Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan, ROC.
Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC.
Microb Genom. 2022 Apr;8(4). doi: 10.1099/mgen.0.000780.
is a causative agent of pleuropneumonia in pigs of all ages. . is divided into 19 serovars based on capsular polysaccharides (CPSs) and lipopolysaccharides. The serovars of isolates are commonly determined by serological tests and multiplex PCR. This study aimed to develop a genomic approach for typing by screening for the presence of the species-specific gene in whole-genome sequencing (WGS) reads and identifying capsule locus (KL) types in genome assemblies. A database of the . KL, including CPS synthesis and CPS export genes, was established and optimized for Kaptive. To test the developed genomic approach, WGS reads of 189 . isolates and those of 66 samples from 14 other bacterial species were analysed. ariba analysis showed that was detected in all 189 . samples. These -positive WGS reads were assembled into genome assemblies and assessed. A total of 105 . genome assemblies that passed the quality assessment were analysed by Kaptive analysis against the . KL database. The results showed that 97 assemblies were classified and predicted as 13 serovars, which matched the serovar information obtained from the literature. The six genome assemblies from previously nontypable isolates were typed and predicted as serovars 17 and 18. Notably, one of the two “” samples was positive, and its genome assembly was typed as KL03 with high identity and predicted as . serovar 3. Collectively, a genomic approach was established and could accurately determine the KL type of . isolates using WGS reads. This approach can be used with high-quality genome assemblies for predicting . serovars and for retrospective analysis.
是一种引起各年龄段猪传染性胸膜肺炎的病原体。 根据荚膜多糖（CPSs）和脂多糖，可将 分为 19 个血清型。通常通过血清学试验和多重 PCR 来确定分离株的血清型。本研究旨在通过筛选全基因组测序（WGS）读段中物种特异性 基因并在基因组组装中鉴定荚膜基因座（KL）类型，开发一种基于基因组的 分型方法。建立了一个包含 、CPS 合成和 CPS 输出基因的 KL 数据库，并针对 Kaptive 进行了优化。为了测试所开发的基因组方法，分析了 189 株 分离株的 WGS 读段和来自 14 个其他细菌物种的 66 个样本的 WGS 读段。 ariba 分析显示，所有 189 株 分离株均检测到 。这些阳性的 WGS 读段被组装成基因组组装，并进行了评估。对 105 个通过质量评估的 基因组组装进行了 Kaptive 分析，以针对 KL 数据库进行分析。结果表明，97 个组装体被分类并预测为 13 个血清型，与文献中获得的血清型信息相匹配。6 个来自先前未定型分离株的基因组组装被分型并预测为血清型 17 和 18。值得注意的是，两个“”样本之一为阳性，其基因组组装被分型为 KL03，同源性高，预测为 血清型 3。总之，建立了一种基因组方法，可使用 WGS 读段准确确定 分离株的 KL 型。该方法可用于高质量的基因组组装，用于预测 血清型和回溯分析。
