Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France.
Université de Lyon, ANSES, VetAgro Sup, UMR Mycoplasmoses animales, Lyon, France.
Microb Genom. 2023 Jul;9(7). doi: 10.1099/mgen.0.001067.
is a major aetiological agent of bovine respiratory disease worldwide. Genome-based analyses are increasingly being used to monitor the genetic diversity and global distribution of , complementing existing subtyping schemes based on locus sequencing. However, these analyses have so far provided limited information on the spatiotemporal and population dynamics of circulating subtypes. Here we applied a genome-wide phylodynamic approach to explore the epidemic dynamics of 88 French strains collected between 2000 and 2019 in France and belonging to the currently dominant subtype 2 (st2). A strong molecular clock signal detected in the genomic data enabled robust phylodynamic inferences, which estimated that the st2 population in France is composed of two lineages that successively emerged from independent introductions of international strains. The first lineage appeared around 2000 and supplanted the previously established antimicrobial-susceptible subtype 1. The second lineage, which is likely more transmissible, progressively replaced the first st2 lineage population from 2005 onward and became predominant after 2010. Analyses also showed a brief decline in this second st2 lineage population in around 2011, possibly due to the challenge from the concurrent emergence of subtype 3 in France. Finally, we identified non-synonymous mutations in genes associated with lineages, which raises prospects for identifying new surveillance molecular markers. A genome-wide phylodynamic approach provides valuable resources for monitoring the evolution and epidemic dynamics of circulating subtypes, and may prove critical for developing more effective surveillance systems and disease control strategies.
是一种主要的牛呼吸道疾病病原体，在全球范围内都是如此。基于基因组的分析越来越多地被用于监测 的遗传多样性和全球分布，补充了基于基因座测序的现有亚型划分方案。然而，这些分析迄今为止提供的关于循环亚型的时空和种群动态的信息有限。在这里，我们应用了一种全基因组系统发育动力学方法来探索 88 株法国 菌株的流行动态，这些菌株于 2000 年至 2019 年在法国采集，属于目前占主导地位的 2 型（st2）亚型。在基因组数据中检测到的强烈分子钟信号使稳健的系统发育推断成为可能，该推断估计法国的 st2 群体由两个谱系组成，它们分别由国际菌株的独立引入而出现。第一个谱系出现在 2000 年左右，取代了先前建立的抗微生物药物敏感的 1 型。第二个谱系可能更具传染性，从 2005 年开始逐渐取代第一个 st2 谱系群体，并在 2010 年后成为主要群体。分析还表明，第二个 st2 谱系群体在 2011 年左右短暂下降，可能是由于法国同时出现 3 型的挑战。最后，我们在与谱系相关的基因中鉴定了非同义突变，这为识别新的监测分子标记提供了前景。全基因组系统发育动力学方法为监测循环 亚型的进化和流行动态提供了有价值的资源，这对于开发更有效的监测系统和疾病控制策略可能至关重要。
