Ong Chian Teng, Blackall Patrick J, Boe-Hansen Gry B, deWet Sharon, Hayes Ben J, Indjein Lea, Korolik Victoria, Minchin Catherine, Nguyen Loan To, Nordin Yusralimuna, Siddle Hannah, Turni Conny, Venus Bronwyn, Westman Mark E, Zhang Zhetao, Tabor Ala E
Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia.
Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Dutton Park, QLD, Australia.
Front Microbiol. 2024 Sep 12;15:1452564. doi: 10.3389/fmicb.2024.1452564. eCollection 2024.
Bovine Genital Campylobacteriosis (BGC), caused by subsp. venerealis, is a sexually transmitted bacterium that significantly impacts cattle reproductive performance. However, current detection methods lack consistency and reliability due to the close genetic similarity between subsp. venerealis and subsp. fetus. Therefore, this study aimed to utilize complete genome analysis to distinguish genetic features between subsp. venerealis and other subspecies, thereby enhancing BGC detection for routine screening and epidemiological studies.
This study reported the complete genomes of four subsp. fetus and five subsp. venerealis, sequenced using long-read sequencing technologies. Comparative whole-genome analyses ( = 25) were conducted, incorporating an additional 16 complete genomes from the NCBI database, to investigate the genomic differences between these two closely related subspecies. Pan-genomic analyses revealed a core genome consisting of 1,561 genes and an accessory pangenome of 1,064 genes between the two subspecies. However, no unique predicted genes were identified in either subspecies. Nonetheless, whole-genome single nucleotide polymorphisms (SNPs) analysis identified 289 SNPs unique to one or the subspecies. After the removal of SNPs located on putative genomic islands, recombination sites, and those causing synonymous amino acid changes, the remaining 184 SNPs were functionally annotated. Candidate SNPs that were annotated with the KEGG "Peptidoglycan Biosynthesis" pathway were recruited for further analysis due to their potential association with the glycine intolerance characteristic of subsp. venerealis and its biovar variant. Verification with 58 annotated genomes, both complete and incomplete, from RefSeq, successfully classified these seven SNPs into two groups, aligning with their phenotypic identification as CFF ( subsp. fetus) or CFV/CFVi ( subsp. venerealis and its biovar variant). Furthermore, we demonstrated the application of mraY SNPs for detecting subspecies using a quantitative PCR assay.
Our results highlighted the high genetic stability of subspecies. Nevertheless, subsp. venerealis and its biovar variants encoded common SNPs in genes related to glycine intolerance, which differentiates them from subsp. fetus. This discovery highlights the potential of employing a multiple-SNP assay for the precise differentiation of subspecies.
由胎儿弯曲杆菌性病亚种引起的牛生殖道弯曲杆菌病（BGC）是一种性传播细菌，对牛的繁殖性能有重大影响。然而，由于胎儿弯曲杆菌性病亚种与胎儿弯曲杆菌胎儿亚种在基因上极为相似，当前的检测方法缺乏一致性和可靠性。因此，本研究旨在利用全基因组分析来区分胎儿弯曲杆菌性病亚种与其他亚种之间的基因特征，从而加强用于常规筛查和流行病学研究的BGC检测。
本研究报告了利用长读测序技术测序的4个胎儿弯曲杆菌胎儿亚种和5个胎儿弯曲杆菌性病亚种的全基因组。进行了比较全基因组分析（n = 25），纳入了来自NCBI数据库的另外16个完整基因组，以研究这两个密切相关的弯曲杆菌亚种之间的基因组差异。泛基因组分析显示，这两个弯曲杆菌亚种之间的核心基因组由1561个基因组成，附属泛基因组有1064个基因。然而，在任何一个亚种中都未发现独特的预测基因。尽管如此，全基因组单核苷酸多态性（SNP）分析确定了一个或另一个亚种特有的289个SNP。在去除位于假定基因组岛、重组位点以及导致同义氨基酸变化的SNP后，对其余184个SNP进行了功能注释。由于与胎儿弯曲杆菌性病亚种及其生物变种的甘氨酸不耐受特征潜在相关，对注释有KEGG“肽聚糖生物合成”途径的候选SNP进行了进一步分析。利用来自RefSeq的58个注释过的完整和不完整基因组进行验证，成功地将这7个SNP分为两组，与它们作为CFF（胎儿弯曲杆菌胎儿亚种）或CFV/CFVi（胎儿弯曲杆菌性病亚种及其生物变种）的表型鉴定一致。此外，我们展示了利用定量PCR检测法应用mraY SNP来检测弯曲杆菌亚种。
我们的结果突出了弯曲杆菌亚种的高遗传稳定性。然而，胎儿弯曲杆菌性病亚种及其生物变种在与甘氨酸不耐受相关的基因中编码了共同的SNP，这使它们与胎儿弯曲杆菌胎儿亚种区分开来。这一发现凸显了采用多SNP检测法精确区分弯曲杆菌亚种的潜力。
