Genome-Wide Diversity and Phylogeography of Mycobacterium avium subsp. paratuberculosis in Canadian Dairy Cattle.

Genome-Wide Diversity and Phylogeography of Mycobacterium avium subsp. paratuberculosis in Canadian Dairy Cattle.

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative bacterium of Johne’s disease (JD) in ruminants. The control of JD in the dairy industry is challenging, but can be improved with a better understanding of the diversity and distribution of MAP subtypes. Previously established molecular typing techniques used to differentiate MAP have not been sufficiently discriminatory and/or reliable to accurately assess the population structure. In this study, the genetic diversity of 182 MAP isolates representing all Canadian provinces was compared to the known global diversity, using single nucleotide polymorphisms identified through whole genome sequencing. MAP isolates from Canada represented a subset of the known global diversity, as there were global isolates intermingled with Canadian isolates, as well as multiple global subtypes that were not found in Canada. One Type III and six “Bison type” isolates were found in Canada as well as one Type II subtype that represented 86% of all Canadian isolates. Rarefaction estimated larger subtype richness in Québec than in other Canadian provinces using a strict definition of MAP subtypes and lower subtype richness in the Atlantic region using a relaxed definition. Significant phylogeographic clustering was observed at the inter-provincial but not at the intra-provincial level, although most major clades were found in all provinces. The large number of shared subtypes among provinces suggests that cattle movement is a major driver of MAP transmission at the herd level, which is further supported by the lack of spatial clustering on an intra-provincial scale.

鸟分枝杆菌副结核亚种（MAP）是反刍动物约翰氏病（JD）的病原菌。乳业中对约翰氏病的防控具有挑战性，但更好地了解MAP亚型的多样性和分布可改善防控效果。先前建立的用于区分MAP的分子分型技术在区分能力和/或可靠性方面不足，无法准确评估种群结构。在本研究中，利用全基因组测序确定的单核苷酸多态性，将代表加拿大所有省份的182株MAP分离株的遗传多样性与已知的全球多样性进行了比较。来自加拿大的MAP分离株是已知全球多样性的一个子集，因为有全球分离株与加拿大分离株混合在一起，并且有多种全球亚型在加拿大未被发现。在加拿大发现了1株III型和6株“野牛型”分离株，以及1株II型亚型，该亚型占加拿大所有分离株的86%。通过对MAP亚型的严格定义，稀释曲线估计魁北克的亚型丰富度高于加拿大其他省份；通过宽松定义，估计大西洋地区的亚型丰富度较低。在省际层面观察到显著的系统地理聚类，但在省内层面未观察到，尽管大多数主要分支在所有省份都有发现。各省之间大量共享的亚型表明，牛的流动是牛群层面MAP传播的主要驱动因素，省内规模上缺乏空间聚类进一步支持了这一点。