Complete genome sequence of an emerging fish pathogen Acinetobacter pittii strain Ap-W20 and its virulence characteristics
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摘要: 皮特不动杆菌是一种新兴的鱼源致病菌，为了对该菌的致病机理进行研究并为该菌引起的鱼类疾病防治提供技术储备，实验选取皮特不动杆菌菌株Ap-W20进行了全基因组测序，并对其毒力特征进行了分析。结果发现，Ap-W20全基因组序列总长为4 399 705 bp，GC含量为38.78%，共预测到4 230个编码序列(CDS)，存在4个质粒，GenBank数据库登录号为CP027658~CP027662。ANI分析结果证实，Ap-W20属于皮特不动杆菌，且Ap-W20与已知人源皮特不动杆菌AP_882(96.69%)和环境源皮特不动杆菌PHEA-2(96.55%)相似度较高。Ap-W20与AP_882、PHEA-2的比较基因组学分析发现，Ap-W20中的基因岛、前噬菌体和质粒数量最多，这很可能与它们各自的分离环境和致病力有关。通过与毒力因子数据库(VFDB)比对，在Ap-W20全基因组中预测到286个毒力基因，主要与黏附和抗吞噬等有关。Ap-W20中还存在Ⅰ、Ⅱ和Ⅵ型分泌系统、多套双组分调控系统以及细菌素合成基因簇等，表明鱼源皮特不动杆菌可能存在复杂的致病机制。本研究对鱼源皮特不动杆菌全基因组进行了毒力特征分析，为该菌引起的鱼类疾病防治奠定了基础。Abstract: In order to make a further study of the pathogenic mechanism of Acinetobacter pittii an emerging fish pathogen and provide technical reserves for the prevention and control of fish diseases caused by A. pittii, we selected A. pittii strain Ap-W20 for the whole genome sequencing and analysis of its virulence characteristics. The results showed that strain Ap-W20 contained a chromosome of 4 399 705 bp with an average G+C content of 38.78% and 4 230 coding sequences (CDS). Particularly, Ap-W20 carries four previously unreported plasmids. The GenBank accession numbers of Ap-W20 are CP027658–CP027662. The ANI analysis result confirmed that Ap-W20 belonged to A. pittii, and Ap-W20 had close similarities with A. pittii AP_882 from human (96.69%) and A. pittii PHEA-2 (96.55%) from environment. Comparative genomic analysis of Ap-W20 with AP_882 and PHEA-2 found that the numbers of gene islands, prophages and plasmids in Ap-W20 were the largest, which is likely related to their respective isolation environments and specific pathogenicity. In comparison with the VFDB database, 286 virulence genes were predicted in the entire genome of Ap-W20, mainly related to adhesion and anti-phagocytosis. Ap-W20 also has Type I, II and VI secretion systems, multiple sets of two-component regulatory system, and bacteriocin synthesis gene cluster, etc., which suggests that there may be complex pathogenic mechanisms in A. pittii derived from fish. This study demonstrates the complete genome sequence and the virulence characteristics of A. pittii from fish, which may provide a basis for the disease control caused by A. pittii.
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图 2 28株不动杆菌的平均核苷酸分析
Figure 2. Average nucleotide identity of 28 strains of Acinetobacter
图 3 Ap-W20的COG功能分类
Figure 3. Gene distribution based on COG function classification of strain Ap-W20
图 4 Ap-W20的GO功能分类
Figure 4. Gene distribution based on GO function function classification of strain Ap-W20
图 5 Ap-W20的KEGG功能分类
Figure 5. Gene distribution based on KEGG function classification of strain Ap-W20
图 6 Ap-W20、AP_882和PHEA-2共线性分析
Figure 6. Collinear analysis result of strains Ap-W20, AP_882 and PHEA-2
表 1 Ap-W20基因组基本信息
Table 1. Genome features of A. pittii strain Ap-W20
特征
features染色体
chromosome质粒 plasmid pApW20-1 pApW20-2 pApW20-3 pApW20-4 长度/bp length 3 991 129 237 519 147 574 8 123 7 680 GC含量/% G+C content 38.80 37.92 40.33 36.26 33.11 CDS数量 no. of CDS 3 811 257 165 12 10 tRNA数量 no. of tRNAs 73 - - - - rRNA数量 no. of rRNAs 18 - - - - GenBank登录号 accession numbers CP027658 CP027659 CP027660 CP027661 CP027662 
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表 2 Ap-W20、AP_882和PHEA-2基因组中可移动元件的比较
Table 2. Comparison of the mobile elements in the genomes of strains Ap-W20, AP_882 and PHEA-2
菌株
strain质粒数/个
plasmid number基因岛数目/个 island number 完整的前噬菌体/个
intact prophage不完整的前噬菌体/个
incomplete prophage染色体
chromosome质粒
plasmidAp-W20 4 34 5 2 3 AP_882 2 12 3 0 1 PHEA-2 0 13 0 0 0
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表 3 Ap-W20的毒力基因预测分类统计表
Table 3. Virulence genes of A. pittii strain Ap-W20 predicted by VFDB
毒力因子一级分类
level 1毒力因子二级分类
level 2基因数量/个
gene no.防御性毒力因子 defensive virulence factors 抗吞噬 anti-phagocytosis 16 压力蛋白 stress protein 8 细胞代谢 cellular metabolism 1 进攻性毒力因子 offensive virulence factors 黏附 adherence 48 分泌系统 secretion system 17 毒素 toxin 3 入侵 invasion 3 非特异性毒力因子 nonspecific virulence factor 铁摄取系统 iron uptake system 39 毒力调节相关基因 regulation of virulence-associated genes 调节 regulation 7 其他 others 144
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