Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA.
Present address: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Microb Genom. 2024 Aug;10(8). doi: 10.1099/mgen.0.001279.
is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared genomes for 99 samples from 6 countries (Australia, Bosnia and Herzegovina, Brazil, China, France and USA) and 4 host species (domestic sheep, domestic goats, bighorn sheep and caribou). Core genome sequences of assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4 %) of accessory genes (i.e. genes found only in a subset of assemblies) compared to core genes (i.e. genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall, our results suggest that adaptation of has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species.
在全球范围内，与野生和家养的 Caprinae 动物的呼吸道疾病有关，在宿主物种内和物种之间疾病结果的差异很大。为了深入了解这种细菌的系统发育结构和致病性机制，我们比较了来自 6 个国家（澳大利亚、波斯尼亚和黑塞哥维那、巴西、中国、法国和美国）和 4 个宿主物种（家养绵羊、家养山羊、大角羊和北美驯鹿）的 99 个样本的基因组。来自家养绵羊和山羊的组装核心基因组序列分为两个得到很好支持的系统发育分支，它们之间的差异足以被认为是不同的细菌物种，这与这两个分支中的每一个都起源于不同的宿主物种相一致。大角羊和北美驯鹿的基因组组装也属于这两个分支，表明存在多次溢出事件，最常见的是从家养绵羊中溢出。泛基因组分析表明，与核心基因（即在所有组装中发现的基因）相比，辅助基因（即仅在一部分组装中发现的基因）的比例很高（91.4%），这可能表明该病原体有适应宿主内环境的倾向。此外，许多与碳代谢相关的基因，这是支原体的一个毒力因子，表现出同源重组的证据，这是适应的潜在特征。绵羊和山羊分支之间的注释基因的存在或缺失非常相似，只有两个注释基因与分支显著相关。然而，来自阿拉斯加无症状北美驯鹿的三个基因组组装在绵羊分支内形成了一个高度分化的亚分支，与其他组装相比，该亚分支缺少 23 个注释基因，其中许多基因具有与碳代谢相关的功能。总的来说，我们的研究结果表明，的适应涉及碳代谢途径的进化和与这些途径相关的毒力机制。参与这些途径的基因，以及本研究中确定的其他可能与毒力有关的基因，是未来研究宿主物种内和物种之间疾病结果高度变化的可能基因组基础的潜在目标。
