一株鲫鱼源致病性希瓦氏菌(Shewanella sp.) XWfb1生长特性、全基因组测序及比较基因组分析

Whole genome sequencing, growth characterization, and comparative genomic analysis of pathogenic Shewanella sp. XWfb1 isolated from Crucian auratus

摘要:

背景 希瓦氏菌(Shewanella sp.)是广泛分布于水产环境中的革兰氏阴性条件致病菌，可感染鲫鱼(Carassius auratus)等经济鱼类，引发体表溃烂、败血症等疾病。目的 研究希瓦氏菌XWfb1的生长特性，解析菌株XWfb1的全基因组信息，基于基因组数据解析其进化地位，挖掘其毒力与耐药基因分布特征，为阐明致病机制及耐药风险防控提供理论依据。方法 观察对比希瓦氏菌XWfb1的生长曲线和环境胁迫下的生长特性。结合Illumina和PacBio平台对菌株XWfb1进行全基因组测序，利用混合组装策略完成基因组拼接，进行基因预测、功能注释并采用PCR验证关键基因表达；通过系统发育树和比较基因组学分析其进化关系。结果 希瓦氏菌XWfb1对短期热激耐受能力良好，可以适应中高盐度环境[3% NaCl]，基因组总长度为5 036 139 bp，G+C含量45.31%，包含4 282个编码基因和138个非编码基因。功能注释显示各数据库分别注释基因4 282 (NR)、1 476 (GO)、3 544 (COG)、2 508 (KEGG)和2 660个(SWISS)。系统发育分析表明，菌株XWfb1与虹鳟希瓦氏菌(Shewanella oncorhynchi) Z-P2亲缘关系最近[平均核苷酸一致性(average nucleotide identity, ANI)值97.39%，数字DNA-DNA杂交(digital DNA-DNA hybridization, dDDH)值87.50%]，基因组共线性分析显示其与近缘种存在局部重排现象。PCR验证确认关键毒力基因lon、luxS、dksA、hem和fur均呈现高表达特征，并检出耐药基因mcr-4和Sul1。结论 通过全基因组测序结果和比较基因组学分析，菌株XWfb1可能属于S. oncorhynchi，目前此菌种在GenBank仅有4株基因组数据，本研究丰富了水产微生物资源库，并揭示了其以运动性和免疫调控为主的毒力特征及多重耐药风险，为水产致病菌的分子机制研究及精准防控提供了重要遗传学基础。

Abstract:

Background Shewanella sp. is a Gram-negative conditional pathogen widely distributed in aquatic environments. It can infect economically important fish species such as crucian carp (Carassius auratus), causing diseases like ulcerative skin lesions and septicemia.Objective To investigate the growth characteristics, whole genome information, genome data-based evolutionary status, and distribution characteristics of virulence and antibiotic resistance genes of Shewanella sp. XWfb1, thereby providing a theoretical basis for elucidating its pathogenic mechanisms and guiding the prevention of antibiotic resistance risks.Methods We systematically evaluated the growth curve and environmental stress tolerance (including heat shock and salinity) of XWfb1. Illumina and PacBio platforms were used for the whole genome sequencing of XWfb1, followed by genome assembly via a hybrid strategy. Gene prediction, functional annotation, and PCR validation of key genes were then conducted. Phylogenetic and comparative genomic analyses were performed to clarify its evolutionary relationship.Results XWfb1 exhibited strong short-term heat shock tolerance and adaptability to moderate-high salinity environments (3% NaCl). The genome of this strain had a total length of 5 036 139 bp and the G+C content of 45.31%, containing 4 282 coding genes and 138 non-coding genes. Functional annotation against different databases identified 4 282 (NR), 1 476 (GO), 3 544 (COG), 2 508 (KEGG), and 2 660 (SWISS) genes. Phylogenetic analysis revealed that XWfb1 was most closely related to S. oncorhynchi Z-P2 [(average nucleotide identity (ANI, 97.39%), digital DNA-DNA hybridization (dDDH, 87.50%)]. Synteny analysis indicated local genomic rearrangements compared with closely related species. PCR validation confirmed high expression of key virulence genes (lon, luxS, dksA, hem, and fur) and detected antibiotic resistance genes (mcr-4 and Sul1).Conclusion Whole genome sequencing and comparative genomic analysis suggest that strain XWfb1 is a member of S. oncorhynchi. Only four genome sequences of S. oncorhynchi have been deposited in GenBank to date. This study enriches the aquatic microbial resource library, elucidates the virulence characteristics associated with motility and immune regulation, and predicts the potential risk of multidrug resistance of S. oncorhynchi. These findings provide a critical genetic foundation for advancing research on the molecular mechanisms of aquatic pathogens and developing precise prevention and control strategies.