Kayansamruaj Pattanapon, Dong Ha Thanh, Hirono Ikuo, Kondo Hidehiro, Senapin Saengchan, Rodkhum Channarong
Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand; Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand.
Department Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
Infect Genet Evol. 2017 Oct;54:7-17. doi: 10.1016/j.meegid.2017.06.012. Epub 2017 Jun 15.
Flavobacterium columnare is one of the deadliest fish pathogens causing devastating mortality in various freshwater fish species globally. To gain an insight into bacterial genomic contents and structures, comparative genome analyses were performed using the reference and newly sequenced genomes of F. columnare including genomovar I, II and I/II strains isolated from Thailand, Europe and the USA. Bacterial genomes varied in size from 3.09 to 3.39Mb (2714 to 3101 CDSs). The pan-genome analysis revealed open pan-genome nature of F. columnare strains, which possessed at least 4953 genes and tended to increase progressively with the addition of a new genome. Genomic islands (GIs) present in bacterial genomes were diverse, in which 65% (39 out of 60) of possible GIs were strain-specific. A CRISPR/cas investigation indicated at least two different CRISPR systems with varied spacer profiles. On the other hand, putative virulence genes, including those related to gliding motility, type IX secretion system (T9SS), outer membrane proteins (Omp), were equally distributed among F. columnare strains. The MLSA scheme categorized bacterial strains into nine different sequence types (ST 9-17). Phylogenetic analyses based on either 16S rRNA, MLSA and concatenated SNPs of core genome revealed the diversity of F. columnare strains. DNA homology analysis indicated that the estimated digital DNA-DNA hybridization (dDDH) between strains of genomovar I and II can be as low as 42.6%, while the three uniquely tilapia-originated strains from Thailand (1214, NK01 and 1215) were clearly dissimilar to other F. columnare strains as the dDDH values were only 27.7-30.4%. Collectively, this extensive diversity among bacterial strains suggested that species designation of F. columnare would potentially require re-emendation.
柱状黄杆菌是最致命的鱼类病原体之一，在全球各种淡水鱼物种中造成毁灭性的死亡。为了深入了解细菌的基因组内容和结构，我们使用柱状黄杆菌的参考基因组和新测序基因组进行了比较基因组分析，这些基因组包括从泰国、欧洲和美国分离的基因变种I、II和I/II菌株。细菌基因组大小在3.09至3.39Mb之间（2714至3101个编码序列）。泛基因组分析揭示了柱状黄杆菌菌株的开放泛基因组性质，其拥有至少4953个基因，并且随着新基因组的加入而逐渐增加。细菌基因组中存在的基因组岛（GIs）多种多样，其中65%（60个中的39个）可能的GIs是菌株特异性的。CRISPR/cas研究表明至少有两种不同的CRISPR系统，其间隔序列不同。另一方面，推定的毒力基因，包括那些与滑行运动、IX型分泌系统（T9SS）、外膜蛋白（Omp）相关的基因，在柱状黄杆菌菌株中分布均匀。多位点序列分型（MLSA）方案将细菌菌株分为九种不同的序列类型（ST 9 - 17）。基于16S rRNA、MLSA和核心基因组串联单核苷酸多态性的系统发育分析揭示了柱状黄杆菌菌株的多样性。DNA同源性分析表明，基因变种I和II菌株之间估计的数字DNA - DNA杂交（dDDH）可低至42.6%，而来自泰国的三个独特的罗非鱼源菌株（1214、NK01和1215）与其他柱状黄杆菌菌株明显不同，因为dDDH值仅为27.7 - 30.4%。总体而言，细菌菌株之间的这种广泛多样性表明，柱状黄杆菌的物种命名可能需要重新修订。
