Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA.
J Clin Microbiol. 2012 Dec;50(12):3853-61. doi: 10.1128/JCM.01499-12. Epub 2012 Sep 19.
Mycobacterium bovis isolates carry restricted allelic variation yet exhibit a range of disease phenotypes and host preferences. Conventional genotyping methods target small hypervariable regions of the M. bovis genome and provide anonymous biallelic information that is insufficient to develop phylogeny. To resolve phylogeny and establish trait-allele associations, we interrogated 75 M. bovis and 61 M. tuberculosis genomes for single nucleotide polymorphisms (SNPs), using iPLEX MassArray (Sequenom Inc., CA) technology. We indexed nucleotide variations in 306 genic and 44 intergenic loci among isolates derived from outbreaks in the United States from 1991 to 2010 and isolated from a variety of mammalian hosts. Two hundred six variant SNPs classified the 136 isolates and 4 previously sequenced strains (AF2122/97, BCG Pasteur, H37Rv, and CDC1551) into 5 major "SNP cluster groups." M. bovis isolates clustered into three major lineages based on 118 variant SNPs, while 84 SNPs differentiated the M. bovis BCG lineage from the virulent isolates. Forty-nine of the 51 human M. tuberculosis isolates were identical at all 350 loci studied. Thus, SNP-based analyses resolved the genotypic differences within M. bovis strains and differentiated these strains from M. tuberculosis strains representing diversity in time and space, providing population genetic frameworks that may aid in identifying factors responsible for the wide host range and disease phenotypes of M. bovis.
牛分枝杆菌分离株携带有限的等位基因变异，但表现出多种疾病表型和宿主偏好。传统的基因分型方法针对牛分枝杆菌基因组的小高度可变区，提供的匿名双等位基因信息不足以构建系统发育。为了解决系统发育问题并建立与性状相关的等位基因关联，我们使用 iPLEX MassArray（Sequenom Inc.，CA）技术，对 75 株牛分枝杆菌和 61 株结核分枝杆菌基因组中的单核苷酸多态性（SNP）进行了检测。我们在 306 个基因和 44 个基因间位点索引了核苷酸变异，这些变异来自于 1991 年至 2010 年美国暴发的菌株和来自多种哺乳动物宿主的分离株。206 个变异 SNP 将 136 个分离株和 4 株已测序的菌株（AF2122/97、BCG Pasteur、H37Rv 和 CDC1551）分为 5 个主要的“SNP 聚类群”。基于 118 个变异 SNP，牛分枝杆菌分离株聚类为 3 个主要谱系，而 84 个 SNP 将牛分枝杆菌 BCG 谱系与毒力分离株区分开来。在研究的 350 个基因座中，51 株人结核分枝杆菌分离株的 49 株完全相同。因此，基于 SNP 的分析解决了牛分枝杆菌菌株内部的基因型差异，并将这些菌株与代表时间和空间多样性的结核分枝杆菌菌株区分开来，提供了种群遗传框架，可能有助于确定导致牛分枝杆菌广泛宿主范围和疾病表型的因素。
