Multilocus short sequence repeat sequencing approach for differentiating among Mycobacterium avium subsp paratuberculosis strains
Multilocus short sequence repeat sequencing approach for differentiating among Mycobacterium avium subsp paratuberculosis strains
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DOI：
10.1128/jcm.42.4.1694-1702.2004
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发表时间：
2004-04-01
影响因子：
9.4
通讯作者：
Kapur, V
中科院分区：
文献类型：
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作者：
Amonsin, A;Li, LL;Kapur, V
我们描述了一种多位点短序列重复序列（MLSSR）测序方法的鸟分枝杆菌亚种的基因分型。副结核分枝杆菌（M.副结核杆菌）菌株。初步分析确定了分散在整个M.副结核杆菌基因组中有78个完全重复序列。对6株M.来自不同宿主物种和地理位置的副结核分离株鉴定出11个多态性短序列重复序列（SSR）的子集，每个位点平均3.2个等位基因。这11个基因座的比较测序被用来对33个M的集合进行基因分型。代表IS900基因座（MPIL）或扩增片段长度多态性（AFLP）类型的不同多重PCR的副结核病分离株。分析区分了33 M。副结核分离株分为20个不同的MLSSR类型，符合地理和流行病学的相关性和歧视指数为0.96。MLSSR分析也能清楚地区分绵羊和牛的M.结果表明，该菌株的MPIL基因型（A18）和AFLP基因型（Z1和Z2）分别占优势。如前所述的副结核。总而言之，我们的研究结果表明，MLSSR测序能够对M进行简单且可重复的高分辨率亚型分型。用于分子流行病学和群体遗传学分析的副结核病分离株。
We describe a multilocus short sequence repeat (MLSSR) sequencing approach for the genotyping of Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) strains. Preliminary analysis identified 185 mono-, di-, and trinucleotide repeat sequences dispersed throughout the M. paratuberculosis genome, of which 78 were perfect repeats. Comparative nucleotide sequencing of the 78 loci of six M. paratuberculosis isolates from different host species and geographic locations identified a subset of 11 polymorphic short sequence repeats (SSRs), with an average of 3.2 alleles per locus. Comparative sequencing of these 11 loci was used to genotype a collection of 33 M. paratuberculosis isolates representing different multiplex PCR for IS900 loci (MPIL) or amplified fragment length polymorphism (AFLP) types. The analysis differentiated the 33 M. paratuberculosis isolates into 20 distinct MLSSR types, consistent with geographic and epidemiologic correlates and with an index of discrimination of 0.96. MLSSR analysis was also clearly able to distinguish between sheep and cattle isolates of M. paratuberculosis and easily and reproducibly differentiated strains representing the predominant MPIL genotype (genotype A18) and AFLP genotypes (genotypes Z1 and Z2) of M. paratuberculosis described previously. Taken together, the results of our studies suggest that MLSSR sequencing enables facile and reproducible high-resolution subtyping of M. paratuberculosis isolates for molecular epidemiologic and population genetic analyses.