Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level.
Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level.
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通过分枝杆菌亚种的整个基因组测序鉴定的串联重复键入的局限性。国家和牛群的旁结核病。
DOI：
10.1186/s12864-015-1387-6
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发表时间：
2015-03-08
期刊：
影响因子：
4.4
通讯作者：
De Buck J
中科院分区：
文献类型：
--
作者：
Ahlstrom C;Barkema HW;Stevenson K;Zadoks RN;Biek R;Kao R;Trewby H;Haupstein D;Kelton DF;Fecteau G;Labrecque O;Keefe GP;McKenna SL;De Buck J
鸟分枝杆菌副结核病（MAP）是奶牛约翰氏病的病原菌，在加拿大乳制品行业中广泛存在，对经济和动物福利具有重大影响。了解MAP的种群动态可用于识别引入事件，改善控制工作和目标传播途径，尽管这需要充分了解MAP的多样性和畜群之间和全国范围内的分布。全基因组测序（WGS）提供了一个详细的评估SNP水平的多样性和分离株的遗传关系，而一些分子分型技术用于调查MAP的分子流行病学，如可变数目的串联重复序列（VNTR）分型，目标基因组中相对不稳定的重复元件，可能是太不可预测的，得出准确的结论。本研究的目的是评估的多样性牛MAP分离株在加拿大奶牛群使用WGS，然后确定VNTR分型是否可以区分真正相关和不相关的菌株。基于通过WGS对124个MAP分离株识别的3，039个SNP进行的系统发育分析，在来自加拿大7个省的奶牛群中识别出了8种遗传上不同的亚型，其中优势类型包括超过80%的MAP分离株。527个MAP分离株的VNTR分型鉴定出12个类型，包括来自7个不同畜群的“野牛型”分离株。在全国范围内，MAP分离株之间存在1-2至239-240个SNP，无论它们属于相同还是不同的VNTR类型。MAP分离株的一项单水平分析表明，VNTR分型可能高估和低估了在单个牛群中发现的MAP分离株的相关性。在加拿大存在多个MAP亚型表明多个引入该国，包括现在已成为一个主导类型，这是约翰氏病控制的重要发现。VNTR分型往往无法识别密切相关和远亲的分离株，限制了使用这种分型方案在国家和国家一级研究MAP的分子流行病学的适用性。
Mycobacterium avium subsp. paratuberculosis (MAP), the causative bacterium of Johne’s disease in dairy cattle, is widespread in the Canadian dairy industry and has significant economic and animal welfare implications. An understanding of the population dynamics of MAP can be used to identify introduction events, improve control efforts and target transmission pathways, although this requires an adequate understanding of MAP diversity and distribution between herds and across the country. Whole genome sequencing (WGS) offers a detailed assessment of the SNP-level diversity and genetic relationship of isolates, whereas several molecular typing techniques used to investigate the molecular epidemiology of MAP, such as variable number of tandem repeat (VNTR) typing, target relatively unstable repetitive elements in the genome that may be too unpredictable to draw accurate conclusions. The objective of this study was to evaluate the diversity of bovine MAP isolates in Canadian dairy herds using WGS and then determine if VNTR typing can distinguish truly related and unrelated isolates. Phylogenetic analysis based on 3,039 SNPs identified through WGS of 124 MAP isolates identified eight genetically distinct subtypes in dairy herds from seven Canadian provinces, with the dominant type including over 80% of MAP isolates. VNTR typing of 527 MAP isolates identified 12 types, including “bison type” isolates, from seven different herds. At a national level, MAP isolates differed from each other by 1–2 to 239–240 SNPs, regardless of whether they belonged to the same or different VNTR types. A herd-level analysis of MAP isolates demonstrated that VNTR typing may both over-estimate and under-estimate the relatedness of MAP isolates found within a single herd. The presence of multiple MAP subtypes in Canada suggests multiple introductions into the country including what has now become one dominant type, an important finding for Johne’s disease control. VNTR typing often failed to identify closely and distantly related isolates, limiting the applicability of using this typing scheme to study the molecular epidemiology of MAP at a national and herd-level.
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影响因子：
4.4
作者：
Ahlstrom, Christina;Barkema, Herman W.;De Buck, Jeroen
通讯作者：
De Buck, Jeroen
影响因子：
9.4
作者：
Amonsin, A;Li, LL;Kapur, V
通讯作者：
Kapur, V
影响因子：
2.1
作者：
Arnold, C;Thorne, N;Gharbia, S
通讯作者：
Gharbia, S
影响因子：
3.7
作者：
Bryant JM;Schürch AC;van Deutekom H;Harris SR;de Beer JL;de Jager V;Kremer K;van Hijum SA;Siezen RJ;Borgdorff M;Bentley SD;Parkhill J;van Soolingen D
通讯作者：
van Soolingen D
影响因子：
4.3
作者：
Aandahl RZ;Reyes JF;Sisson SA;Tanaka MM
通讯作者：
Tanaka MM