Pfeiffer Wayne, Braun Josephine, Burchell Jennifer, Witte Carmel L, Rideout Bruce A
San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America.
Wildlife Disease Laboratories, San Diego Zoo Global, San Diego, California, United States of America.
PLoS One. 2017 Mar 7;12(3):e0173464. doi: 10.1371/journal.pone.0173464. eCollection 2017.
Mycobacteria isolated from more than 100 birds diagnosed with avian mycobacteriosis at the San Diego Zoo and its Safari Park were cultured postmortem and had their whole genomes sequenced. Computational workflows were developed and applied to identify the mycobacterial species in each DNA sample, to find single-nucleotide polymorphisms (SNPs) between samples of the same species, to further differentiate SNPs between as many as three different genotypes within a single sample, and to identify which samples are closely clustered genomically.
Nine species of mycobacteria were found in 123 samples from 105 birds. The most common species were Mycobacterium avium and Mycobacterium genavense, which were in 49 and 48 birds, respectively. Most birds contained only a single mycobacterial species, but two birds contained a mixture of two species. The M. avium samples represent diverse strains of M. avium avium and M. avium hominissuis, with many pairs of samples differing by hundreds or thousands of SNPs across their common genome. By contrast, the M. genavense samples are much closer genomically; samples from 46 of 48 birds differ from each other by less than 110 SNPs. Some birds contained two, three, or even four genotypes of the same bacterial species. Such infections were found in 4 of 49 birds (8%) with M. avium and in 11 of 48 birds (23%) with M. genavense. Most were mixed infections, in which the bird was infected by multiple mycobacterial strains, but three infections with two genotypes differing by ≤ 10 SNPs were likely the result of within-host evolution. The samples from 31 birds with M. avium can be grouped into nine clusters within which any sample is ≤ 12 SNPs from at least one other sample in the cluster. Similarly, the samples from 40 birds with M. genavense can be grouped into ten such clusters. Information about these genomic clusters is being used in an ongoing, companion study of mycobacterial transmission to help inform management of bird collections.
从圣地亚哥动物园及其野生动物园100多只被诊断患有禽分枝杆菌病的鸟类中分离出分枝杆菌，在其死后进行培养，并对其全基因组进行测序。开发并应用了计算工作流程，以识别每个DNA样本中的分枝杆菌种类，找到同一物种样本之间的单核苷酸多态性（SNP），进一步区分单个样本中多达三种不同基因型之间的SNP，并确定哪些样本在基因组上紧密聚类。
在来自105只鸟类的123个样本中发现了9种分枝杆菌。最常见的物种是鸟分枝杆菌和日内瓦分枝杆菌，分别存在于49只和48只鸟中。大多数鸟类仅含有单一的分枝杆菌物种，但有两只鸟含有两种物种的混合物。鸟分枝杆菌样本代表了鸟分枝杆菌鸟型和鸟分枝杆菌人型的不同菌株，许多样本对在其共同基因组上相差数百或数千个SNP。相比之下，日内瓦分枝杆菌样本在基因组上更为接近；48只鸟中的46只的样本彼此之间的差异小于110个SNP。一些鸟类含有同一细菌物种的两种、三种甚至四种基因型。在49只感染鸟分枝杆菌的鸟中有4只（8%）以及在48只感染日内瓦分枝杆菌的鸟中有11只（23%）发现了这种感染。大多数是混合感染，即鸟类被多种分枝杆菌菌株感染，但三种差异≤10个SNP的两种基因型感染可能是宿主内进化的结果。来自31只感染鸟分枝杆菌鸟类的样本可分为九个聚类，其中任何一个样本与聚类中的至少一个其他样本的差异≤12个SNP。同样，来自40只感染日内瓦分枝杆菌鸟类的样本可分为十个这样的聚类。有关这些基因组聚类的信息正在一项正在进行的分枝杆菌传播配套研究中使用，以帮助为鸟类种群管理提供信息。
