Prophages distribution and genome evolution of Shigella flexneri in China
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摘要:
目的 前噬菌体是细菌基因组中重要可移动原件，在细菌毒力和宿主适应性方面发挥着重要作用。 由噬菌体介导的福氏志贺菌血清型转化频繁发生，给志贺菌的监测、诊断和预防工作带来不便。 为了探究我国福氏志贺菌基因组进化与其前噬菌体相关的血清型别转换之间的关系，利用生物信息学方法将前噬菌体在福氏志贺菌基因组中的分布与进化进行关联分析。 方法 在中国17省（市、自治区）选取的294株福氏志贺菌具有丰富的血清型多态性。 通过比较不同血清型福氏志贺菌基因组中原噬菌体及血清型转换噬菌体的覆盖度，统计分析其分布规律。 结果 部分菌株可携带多种前噬菌体，同一种前噬菌体也可分布在不同血清型菌株中；部分菌株虽携带血清型转换噬菌体却并未发生血清型转换事件。 不同血清型转换噬菌体在福氏志贺菌进化树中成簇出现，表明该部分菌株出现了血清型集中转换现象。 结论 本研究有助于揭示前噬菌体的遗传多样性及与福氏志贺菌进化和血清型变异之间的关系，对预防和控制志贺菌的感染具有重要意义。 Abstract: Prophage is an mobile genetic elements carried on bacterial genome, which plays an important role in bacterial virulence and host adaptability. Phage-mediated serotype conversion occurs frequently, which brings inconvenience to the surveillance, diagnosis and prevention of Shigella. In order to explore the relationship between the serotype-converting phages of Shigella flexneri and genome evolution, we analyzed correlation between the distribution of prophage and the phylogenetic tree of Shigella flexneri. In total of 294 Shigella flexneri with different serotypes from 17 provinces in China were selected. We compared the coverage of prophages and serotype-converting phages in the different genome of Shigella flexneri. Correlation analysis were did about the phage distribution in phylogenetic tree. The results showed that multiple kinds of prophages were carried by Shigella flexneri, and the same prophage may distributed in different serotype strains. Some strains carried bacteriophages without serotype-converting events. The bacteriophages appeared in clusters in the evolutionary tree, indicating a concentrated serotype-converting events. We indicated the close relationship between serotype-converting phages and the evolution of Shigella flexneri. Our research is of great significant to prevent and control Shigella infection.-
Key words:
- Shigella flexneri /
- Prophage /
- Serotype conversion /
- Bacterial genome /
- Evolution
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图 1 不同血清型福氏志贺菌前噬菌体分布
注：热图顶端颜色标签按照294株福氏志贺菌不同的血清型划分。热图内部颜色代表菌株中含有右侧噬菌体的个数，具体个数见左侧颜色标尺
Figure 1. Distribution of prophages among Shigella flexneri with different serotypes
图 2 不同血清型福氏志贺菌基因组中志贺菌相关前噬菌体分布
注：热图顶端颜色标签按照294株福氏志贺菌不同的血清型划分。热图内部颜色代表菌株中含有右侧噬菌体的个数，具体见左侧颜色标尺
Figure 2. Distribution of Shigella associated prophages among Shigella flexneri with different serotypes
图 3 福氏志贺菌进化树与前噬菌体分布情况
注：最内圈表述菌株宿主信息，第二圈表示菌株血清型分类。外圈热图由外向内分别表示噬菌体sfx、Stx2-converting_phage_86、Stx2-converting_phage_1717、Stx1_converting_phage_DNA、Shigella_phage_Ss-VASD、Shigella_phage_SfII，Shigella_phage_Sf6、Shigella_phage_SHSML-45、Shigella_phage_POCJ13、Shigella_phage_75_02_Stx、Enterobacteria_phage_SfV、Enterobacteria_phage_SfI、Enterobacteria_phage_Sf6及Enterobacteria_phage_Sf101在福氏志贺菌基因组的比对相似度
Figure 3. Maximum likelihood tree of the 294 isolates and distribution of prophages
表 1 不同省(市、自治区）挑选的福氏志贺菌血清型分布
Table 1. Serotypes distribution of Shigella flexneri from different provinces
血清型 省 份 总计 安徽 北京 福建 甘肃（动物菌株＋人菌株） 贵州 黑龙江 河南 湖北 江苏 辽宁 青海 陕西 上海 山西 四川 西藏 浙江 1a 2 1 1 4＋0 1 1 15 1 1 − 4 − − 7 − − − 38 1b − − − 2＋2 − − 3 − 1 − − − − − − − − 8 1d 1 − − − − − 2 − − − − − − − − − 1 4 2a 4 1 4 5＋4 4 4 17 1 3 − 1 − − 6 − 1 − 55 2b 2 2 2 15＋0 1 2 8 1 3 2 7 − − 3 1 1 − 49 3a − − − 0＋2 2 1 3 1 − − − − − − − − − 9 4a − − − − 1 − − − − − − − − − − − − 1 4av − − − − − − 1 − − − − − − − − − − 1 4b − − − − − − − − − − − − − − 1 − − 1 7b − − − − − − 1 − − − − − − − − − − 1 X 2 − − 0＋2 1 2 11 − − − − − − − − − − 18 Xv 12 3 5 8＋15 − 3 22 2 1 2 3 3 1 11 − 1 1 93 Y 1 − − 0＋1 − 1 4 − − − − − − − − − − 7 Y-gtrI − − − − − − 1 − − − − − − − − − − 1 Y-gtrII − 1 − − 1 − 1 − − − − − − − − − − 3 Yv − − 1 − − − − − − − − − − − − − − 1 Yv-gtrII 1 − − − − − 2 − − − − − − − − − − 3 合计 25 8 13 60（34＋26） 11 14 91 6 9 4 15 3 1 27 2 3 2 294 注：-. 表示该省（市、自治区）没有分离到该血清型菌株 
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