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通过哈夫尼亚属(Hafnia)的比较基因组分析揭示了阿尔维(alvei)和帕拉维(paralvei)之间的明确进化关系,并提供了致病性的见解-2019.10-3.501

DNA专题微生态专题案例分享研究前沿

关键词bacteria,Draft Genome,virulence

中文题目:通过哈夫尼亚属Hafnia的比较基因组分析揭示了阿尔维alvei和帕拉维paralvei之间的明确进化关系,并提供了致病性的见解

英文题目:Comparative genomic analysis of the Hafnia genus reveals an explicit

evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

名:BMC Genomics 发表时间:2019.10 IF3.501

作者单位南开大学

测序产品:细菌基因组

样品来源:Hafinia病原体

文章类型:报告类

DOL10.1186/s12864-019-6123-1

英文摘要

Background: The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis.

Results: One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei.

Conclusions: Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

中文摘要

背景:Hafnia属是一种条件致病菌,与医院感染和社区获得性感染有关。尽管Hafnia通常是从临床资料中分离出来的,但其分类仍然是一个未解之谜,Hafnia在人类疾病中的作用和重要性也不确定。在这里,我们使用比较基因组分析来定义Hafnia的分类学,识别可能是生态和致病专门化结果的物种特异基因,并揭示可能有助于致病的毒力相关基因图谱。

结果:获得了1个完整的Hafnia菌株基因组序列和19个基因组草图,并与27个公开获得的基因组组合通过构建基于单拷贝核心基因的系统发育和种群结构,结合全基因组平均核苷酸同源性,我们提供了高分辨率的分型方法,以鉴定两个远的哈夫尼亚种(alveiparalvei)和一个错误标记的菌株。开放的泛基因组和大量可移动的基因元素的存在表明,哈夫尼亚(Hafnia)已经经历了大规模的基因重排。与代谢和运输相关的物种特异性核心基因组的存在表明阿尔维(alvei)和帕拉维(paralvei)之间可能存在生态位分化。我们还鉴定了两种哈夫尼亚菌(Hafnia)的毒力相关谱,包括大分子分泌系统、毒力和抗药性。在大分子系统中,T1SS、鞭毛1Tad-pilusT6SS-1Hafnia中是保守的,而T4SST5SS和其它T6SS则表现出多样性的进化。Hafnia的毒力因子与粘附、毒素、铁吸收、应激适应和外排泵有关。已鉴定的耐药基因与氨基糖苷、β-内酰胺、杆菌肽、阳离子抗菌肽、氟喹诺酮和利福平有关。在基因组水平上鉴定出的这些毒力相关的图谱提供了对Hafnia发病机制和alveiparalvei之间的区别的见解。

结论:本研究利用核心基因组系统发育学和比较基因组学方法,对Hafnia种间的分类学和种特异性进行了综合分析。破译具有大分子分泌系统、毒力因子和与致病性相关的抗性基因库的Hafnia菌株的基因组,可以为解决其众多感染和制定对抗病原体的策略提供见解。

阿布魏 2019-11-14 09:04:34

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