Aquatic Disease Control Division, National Fishery Products Quality Management Service, Busan, Republic of Korea.
Department of Aquatic Life Medicine, College of Fisheries Sciences, Pukyong National University, 45, Yongso-ro, Nam-Gu, Busan, Republic of Korea.
Curr Microbiol. 2021 Jun;78(6):2391-2399. doi: 10.1007/s00284-021-02490-0. Epub 2021 Apr 27.
Nocardiosis is a major problem affecting fish that are farmed in seacages as well as freshwater fish; therefore, deciphering the bacteriological features of Nocardia seriolae is crucial. In particular, a number of studies over the past two years have reported the genome sequence of N. seriolae, and a comparative genomics approach is expected to yield valuable information on its epidemiological characteristics. The purpose of this study was to perform whole-genome sequence analysis of N. seriolae MH196537 from the Japanese eel and to investigate the significant differences noted between strains isolated from freshwater fish and marine fish by using Random Forest, a reliable machine learning algorithm. The Pacbio platform was employed to sequence the MH196537 strain, and genomic information from the other 16 strains was used for comparative analyses. All coding sequences of the 17 strains were categorized in RASTtk Sub-systems. The MH196537 strain had one contig, and it shared a high average nucleotide identity (ANI) with the freshwater strains (0.9994 - 0.9999) rather than the seawater strains (0.9985 - 0.9994). Moreover, 22 RASTtk subsystems carried a different number of genes from each N. seriolae. The fatty acids, lipids, and isoprenoids subsystem showed the highest mean decrease in the Gini index of over 1.5. Interestingly, freshwater strains were found to harbor all of the genes for both the mevalonate (MVA) and non-mevalonate pathways (MEP), whereas only the MEP existed in strains from diseased marine fish. Considering the differences in the byproducts of isoprenoids from the different pathways, it is likely that this will affect host-pathogen interactions; therefore, harboring the different pathways for the synthesis of isoprenoids could be an important pathogenic factor of N. seriolae.
诺卡氏菌病是影响笼养海水鱼和淡水鱼的主要问题，因此解析诺卡氏菌的细菌学特征至关重要。特别是，过去两年的多项研究报告了诺卡氏菌的基因组序列，预计比较基因组学方法将为其流行病学特征提供有价值的信息。本研究的目的是对来自日本鳗鲡的诺卡氏菌 MH196537 进行全基因组序列分析，并利用可靠的机器学习算法随机森林（Random Forest）来研究从淡水鱼和海水鱼分离的菌株之间的显著差异。我们使用 Pacbio 平台对 MH196537 菌株进行测序，并将来自其他 16 株的基因组信息用于比较分析。17 株的所有编码序列均在 RASTtk Sub-systems 中进行分类。MH196537 菌株有一个连续体，与淡水菌株（0.9994-0.9999）的平均核苷酸同一性（ANI）较高，而与海水菌株（0.9985-0.9994）的 ANI 较低。此外，22 个 RASTtk 亚系统的基因数量与每株诺卡氏菌都不同。脂肪酸、脂类和异戊二烯亚系统的基尼指数平均降低超过 1.5。有趣的是，淡水菌株均含有甲羟戊酸（MVA）和非甲羟戊酸途径（MEP）的所有基因，而患病海水鱼的菌株中仅存在 MEP。考虑到不同途径产生的异戊二烯的副产物不同，这可能会影响宿主-病原体的相互作用；因此，异戊二烯合成的不同途径可能是诺卡氏菌的一个重要致病因素。
