Vibriosis, a hemorrhagic septicemic disease caused by the bacterium Vibrio anguillarum, is an important bacterial infection in Danish sea-reared rainbow trout. Despite of vaccination, outbreaks still occur, likely because the vaccine is based on V. anguillarum strains from abroad/other hosts than rainbow trout. Information about the genetic diversity of V. anguillarum specifically in Danish rainbow trout, is required to investigate this claim. Consequently, the aim of the present investigation was to sequence and to characterize a collection of 44 V. anguillarum strains obtained primarily from vibriosis outbreaks in Danish rainbow trout. The strains were sequenced, de novo assembled, and the genomes examined for the presence of plasmids, virulence, and acquired antibiotic resistance genes. To investigate the phylogeny, single nucleotide polymorphisms were identified, and the pan-genome was calculated. All strains carried tet(34) encoding tetracycline resistance, and 36 strains also contained qnrVC6 for increased fluoroquinolone/quinolone resistance. But interestingly, all strains were phenotypic sensitive to both oxytetracycline and oxolinic acid. Almost all serotype O1 strains contained a pJM1-like plasmid and nine serotype O2A strains carried the plasmid p15. The distribution of virulence genes was rather similar across the strains, although evident variance among serotypes was observed. Most significant, almost all serotype O2 and O3 strains, as well as the serotype O1 strain without a pJM1-like plasmid, carried genes encoding piscibactin biosynthesis. Hence supporting the hypothesis, that piscibactin plays a crucial role in virulence for pathogenic strains lacking the anguibactin system. The phylogenetic analysis and pan-genome calculations revealed great diversity within V. anguillarum. Serotype O1 strains were in general very similar, whereas considerable variation was found among serotype O2A strains. The great diversity within the V. anguillarum serotype O2A genomes is most likely the reason why vaccines provide good protection from some strains, but not from others. Hopefully, the new genomic data and knowledge provided in this study might help develop an optimized vaccine against V. anguillarum in the future to reduce the use of antibiotics, minimize economic losses and improve the welfare of the fish.

中文翻译：

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44 个鳗鲡基因组分析揭示高遗传多样性

弧菌病是一种由鳗弧菌引起的出血性败血症，是丹麦海养虹鳟鱼的一种重要细菌感染。尽管接种了疫苗，但仍会发生暴发，这可能是因为疫苗是基于来自国外/其他宿主而不是虹鳟鱼的鳗鲡菌株。需要有关 V. anguillarum 遗传多样性的信息，特别是在丹麦虹鳟鱼中的遗传多样性，以调查此声明。因此，本研究的目的是对主要从丹麦虹鳟鱼弧菌病爆发中获得的 44 V. anguillarum 菌株进行排序和表征。对菌株进行测序、从头组装，并检查基因组中是否存在质粒、毒力和获得的抗生素抗性基因。为了研究系统发育，鉴定了单核苷酸多态性，并计算了泛基因组。所有菌株都携带 tet(34) 编码四环素抗性，36 株还含有 qnrVC6 以增加氟喹诺酮/喹诺酮抗性。但有趣的是，所有菌株对土霉素和恶唑酸都具有表型敏感性。几乎所有血清型 O1 菌株都含有 pJM1 样质粒，9 种血清型 O2A 菌株携带质粒 p15。尽管观察到血清型之间的明显差异，但毒力基因的分布在菌株之间相当相似。最重要的是，几乎所有血清型 O2 和 O3 菌株，以及没有 pJM1 样质粒的血清型 O1 菌株，都携带编码 piscibactin 生物合成的基因。因此支持假设，piscibactin 在缺乏 anguibactin 系统的致病菌株的毒力中起着至关重要的作用。系统发育分析和泛基因组计算揭示了鳗鲡内的巨大多样性。血清型 O1 菌株通常非常相似，而在血清型 O2A 菌株之间发现相当大的差异。V. anguillarum 血清型 O2A 基因组内的巨大多样性很可能是疫苗对某些菌株提供良好保护但对其他菌株无效的原因。希望本研究中提供的新基因组数据和知识可能有助于未来开发针对鳗鲡的优化疫苗，以减少抗生素的使用，最大限度地减少经济损失并改善鱼类的福利。鳗鲡。血清型 O1 菌株通常非常相似，而在血清型 O2A 菌株之间发现相当大的差异。V. anguillarum 血清型 O2A 基因组内的巨大多样性很可能是疫苗对某些菌株提供良好保护但对其他菌株没有保护作用的原因。希望本研究中提供的新基因组数据和知识可能有助于未来开发针对鳗鲡的优化疫苗，以减少抗生素的使用，最大限度地减少经济损失并改善鱼类的福利。鳗鲡。血清型 O1 菌株通常非常相似，而在血清型 O2A 菌株之间发现相当大的差异。V. anguillarum 血清型 O2A 基因组内的巨大多样性很可能是疫苗对某些菌株提供良好保护但对其他菌株无效的原因。希望本研究中提供的新基因组数据和知识可能有助于未来开发针对鳗鲡的优化疫苗，以减少抗生素的使用，最大限度地减少经济损失并改善鱼类的福利。