Serovar detector. Serotyping of Actinobacillus pleuropneumoniae based on whole genome sequencing – validation of a bioinformatic tool

Serovar detector is a new bioinformatic tool for determining the serovar of Actinobacillus pleuropneumoniae using whole genome sequencing. The cps operons of isolates are compared to the serovar reference strains and the outcome is determined both by the number of common genes as well as the similarities between the homologous genes. The validation of the bioinformatic tool utilizes a broad collection of 732 isolates including representatives from all described serovars. The isolates included have earlier been characterized by conventional serotyping, PCR tests or different bioinformatic tools. It also includes isolates that have been difficult to allocate to a serovar using serology in order to test the pipeline’s performance when potential new varieties or combinations of cps genes are present. Out of the 732 isolates included in the investigation, only 36 isolates (4.9%) could not be allocated to the 19 recognized serovars. The validation showed that Serovar detector represents a robust method for determining the serovar of an isolate and also a valuable tool for further characterization of the genetic heterogeneity both within the serovars as well as within the A. pleuropneumoniae species.

血清型检测工具（Serovar Detector）是一款基于全基因组测序技术，用于鉴定猪胸膜肺炎放线杆菌（Actinobacillus pleuropneumoniae）血清型的新型生物信息学工具。该工具通过将分离株的cps操纵子（cps operons）与血清型参考菌株进行比对，基于共同基因的数量以及同源基因间的序列相似性来判定最终结果。为验证该生物信息学工具的性能，研究团队收集了涵盖所有已报道血清型的732株分离株作为验证集。本次验证纳入的分离株，前期均已通过传统血清分型、PCR检测或其他生物信息学工具完成表型与基因型鉴定。此外，为测试该分析流程在潜在新型cps基因变异体或组合存在时的性能，验证集还纳入了部分难以通过血清学方法分配至已知血清型的分离株。在本次研究纳入的732株分离株中，仅36株（占比4.9%）无法归类至目前已确认的19种血清型。验证结果表明，血清型检测工具（Serovar Detector）不仅是一种可靠的分离株血清型鉴定方法，同时也是解析猪胸膜肺炎放线杆菌各血清型内乃至整个菌种内遗传异质性的实用工具。