PDF(Pubmed)
Abstract：
Mycobacterium avium subsp. paratuberculosis (MAP) is the pathogen responsible for paratuberculosis or Johne\'s Disease (JD) in ruminants, which is responsible for substantial economic losses worldwide. MAP transmission primarily occurs through the fecal-oral route, and the introduction of an MAP infected animal into a herd is an important transmission route. In the current study, we characterized MAP isolates from 67 cows identified in 20 herds from the provinces of Quebec and Ontario, Canada. Whole genome sequencing (WGS) was performed and an average genome coverage (relative to K-10) of ∼14.9 fold was achieved. The total number of SNPs present in each isolate varied from 51 to 132 and differed significantly between herds. Isolates with the highest genetic variability were generally present in herds from Quebec. The isolates were broadly separated into two main clades and this distinction was not influenced by the province from which they originated. Analysis of 8 MIRU-VNTR loci and 11 SSR loci was performed on the 67 isolates from the 20 dairy herds and publicly available references, notably major genetic lineages and six isolates from the province of Newfoundland and Labrador. All 67 field isolates were phylogenetically classified as Type II (C-type) and according to MIRU-VNTR, the predominant type was INMV 2 (76.1%) among four distinct patterns. Multilocus SSR typing identified 49 distinct INMV SSR patterns. The discriminatory index of the multilocus SSR typing was 0.9846, which was much higher than MIRU-VNTR typing (0.3740). Although multilocus SSR analysis provides good discriminatory power, the resolution was not informative enough to determine inter-herd transmission. In select cases, SNP-based analysis was the only approach able to document disease transmission between herds, further validated by animal movement data. The presence of SNPs in several virulence genes, notably for PE, PPE, mce and mmpL, is expected to explain differential antigenic or pathogenetic host responses. SNP-based studies will provide insight into how MAP genetic variation may impact host-pathogen interactions. Our study highlights the informative power of WGS which is now recommended for epidemiological studies and to document mixed genotypes infections.
摘要：
鸟分枝杆菌亚种。副结核病（MAP）是引起反刍动物副结核病或约翰病（JD）的病原体，这在全球范围内造成了巨大的经济损失。MAP传播主要通过粪便-口腔途径发生，将MAP感染的动物引入畜群是重要的传播途径。在目前的研究中,我们对来自魁北克和安大略省20个牧群的67头奶牛的MAP分离株进行了表征，加拿大。进行全基因组测序（WGS），平均基因组覆盖率（相对于K-10）达到约14.9倍。每个分离株中存在的SNP总数在51至132之间变化，并且在牧群之间显着不同。遗传变异性最高的分离株通常存在于魁北克的牧群中。分离株被广泛分为两个主要分支，这种区别不受它们起源的省的影响。对来自20个乳牛群的67个分离株和公开文献进行了8个MIRU-VNTR基因座和11个SSR基因座的分析，特别是主要的遗传谱系和来自纽芬兰和拉布拉多省的六个分离株。所有67个野外分离株都被系统发育分类为II型（C型），根据MIRU-VNTR，在四种不同的模式中，主要类型是INMV2(76.1%)。多位点SSR分型鉴定出49种不同的INMVSSR模式。多位点SSR分型的判别指数为0.9846，远高于MIRU-VNTR分型(0.3740)。尽管多位点SSR分析提供了良好的鉴别力，该决议的信息不足以确定牧间传播。在某些情况下，基于SNP的分析是唯一能够记录牛群之间疾病传播的方法，动物运动数据进一步验证。在几个毒力基因中存在SNP，特别是对于PE，PPE,MCE和MMPL,预计将解释不同的抗原或致病性宿主反应。基于SNP的研究将深入了解MAP遗传变异如何影响宿主-病原体相互作用。我们的研究强调了WGS的信息能力，现在推荐用于流行病学研究和记录混合基因型感染。
