Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits
Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits
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DOI：
10.1038/ismej.2013.90
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发表时间：
2013-10-01
期刊：
影响因子：
11
通讯作者：
Le Roux, Frederique
中科院分区：
文献类型：
--
作者：
Goudenege, David;Labreuche, Yannick;Le Roux, Frederique
黑腹弧菌是新喀里多尼亚和印度-太平洋其他地区养殖对虾的新病原体。黑腹弧菌致病性的分子决定因素尚不清楚；然而，分子流行病学研究表明，致病性与特定的谱系有关。在这里，我们对16株黑色弧菌进行了基于高通量测序的比较基因组分析，以探索含有病原体的谱系的基因组多样性和进化历史，并确定病原体特异的遗传元件。我们的系统发育分析揭示了三个含有病原体的黑色弧菌分支，其中包括两个先前从新喀里多尼亚发现的分支和一个新的分支，其中包括来自马达加斯加败血症对虾的疑似致病分离物。这三个分支之间相似的遗传距离表明，它们大致同时从一个祖先群体中分化出来，重组分析表明，这些基因组过去曾共享一个共同的基因库，并交换了基因。由于每个同时代的谱系都由几乎相同的菌株组成，比较基因组学允许区分不同严重程度的对虾发病特有的遗传因素。值得注意的是，在所有高致病性(HP)菌株中只有一个大的质粒编码毒素。虽然较少的/非致病菌株含有相关的质粒，但它们是通过一个假定的毒素位点来区分的。非致病的黑色弧菌表达该基因会产生有毒的培养上清，这通常是幽门螺杆菌菌株的独有特征。因此，这种蛋白质，在这里被称为‘nigritoxin’，在一定程度上被牵连，但在黑腹弧菌的毒性中仍有待准确确定。
Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.