Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements
Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements
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DOI：
10.1038/ismej.2013.186
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发表时间：
2014-04-01
期刊：
影响因子：
11
通讯作者：
Verner-Jeffreys, David W.
中科院分区：
文献类型：
--
作者：
Brynildsrud, Ola;Feil, Edward J.;Verner-Jeffreys, David W.
鲑鱼肾杆菌是细菌性肾病的病原体，是全世界鲑科鱼类的主要病原体。种内遗传多样性水平非常低，阻碍了了解这种革兰氏阳性细菌的传播动力学和近期进化史的努力。我们利用新一代测序技术的最新进展，从代表广泛地理和时间范围以及不同宿主物种的 68 个不同的鲑鱼红鲑分离株中生成全基因组单核苷酸多态性 (SNP) 数据。系统发育分析有力地描绘了两个谱系（谱系 1 和谱系 2）；此外，年代测定分析估计所有分离株的最近祖先的时间为1239年前（95%可信区间（CI）为444-2720年前）。我们的数据揭示了谱系1在上个世纪的洲际传播，同时伴随着用于水产养殖目的和休闲渔业放养的活鱼、饲料和卵子的人为移动，而谱系2似乎在商业活动之前在野生东大西洋鲑鱼种群中流行。基于 SNP 的高分辨率分析使我们能够分离出与邻近养鱼场密切相关的分离株，表明它们构成了单一暴发的一部分。我们能够证明，从挪威和英国分离出来的鲑鱼主要谱系 1 亚群可能代表了与 40 年前类似的对这些地区的引入。这项研究证明了该技术在分析兽医和环境微生物以及人类病原体的微观和中尺度进化关系方面的前景。
Renibacterium salmoninarum is the causative agent of bacterial kidney disease, a major pathogen of salmonid fish species worldwide. Very low levels of intra-species genetic diversity have hampered efforts to understand the transmission dynamics and recent evolutionary history of this Gram-positive bacterium. We exploited recent advances in the next-generation sequencing technology to generate genome-wide single-nucleotide polymorphism (SNP) data from 68 diverse R. salmoninarum isolates representing broad geographical and temporal ranges and different host species. Phylogenetic analysis robustly delineated two lineages (lineage 1 and lineage 2); futhermore, dating analysis estimated that the time to the most recent ancestor of all the isolates is 1239 years ago (95% credible interval (CI) 444-2720 years ago). Our data reveal the intercontinental spread of lineage 1 over the last century, concurrent with anthropogenic movement of live fish, feed and ova for aquaculture purposes and stocking of recreational fisheries, whilst lineage 2 appears to have been endemic in wild Eastern Atlantic salmonid stocks before commercial activity. The high resolution of the SNP-based analyses allowed us to separate closely related isolates linked to neighboring fish farms, indicating that they formed part of single outbreaks. We were able to demonstrate that the main lineage 1 subgroup of R. salmoninarum isolated from Norway and the UK likely represent an introduction to these areas similar to 40 years ago. This study demonstrates the promise of this technology for analysis of micro and medium scale evolutionary relationships in veterinary and environmental microorganisms, as well as human pathogens.