Pan-genome Analyses of the Species Salmonella enterica, and Identification of Genomic Markers Predictive for Species, Subspecies, and Serovar.
Pan-genome Analyses of the Species Salmonella enterica, and Identification of Genomic Markers Predictive for Species, Subspecies, and Serovar.
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肠炎沙门氏菌的全基因组分析，以及预测种、亚种和血清型的基因组标记鉴定。
DOI：
10.3389/fmicb.2017.01345
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发表时间：
2017
影响因子：
5.2
通讯作者：
Gannon VPJ
中科院分区：
文献类型：
--
作者：
Laing CR;Whiteside MD;Gannon VPJ
食品安全是一个全球关注的问题，每年有超过220万人死于肠道疾病。目前的全基因组测序平台允许对肠道病原体进行常规测序，用于监测和疫情期间；然而，仍然存在的挑战是确定能够预测对人类健康构成最重大威胁的菌株群或能够在特定环境中持续存在的菌株群的基因组标记。我们之前开发了软件程序Panseq，它可以识别一组序列中的泛基因组，以及SuperPhy平台，它利用这些泛基因组信息来识别预测细菌菌株组的生物标志物。在这项研究中，我们检测了4893个肠沙门氏菌基因组的泛基因组，这是一种肠道病原体，比任何其他肠道病原体造成的残疾调整生命年损失都要多。我们发现了一个25.3 Mbp的泛基因组，在所有基因组中都存在一个1.5 Mbp的严格核心，在至少96%的基因组中发现了一个3.2 Mbp的保守核心。我们还鉴定出404个1000 bp的基因组区域是肠球菌特有的。这些物种特异性区域被发现主要编码假设的蛋白质、效应物和其他与毒力相关的蛋白质。对于六个肠链球菌亚种中的每一个，都鉴定出了每个亚种特有的标记。没有一个血清型具有在其所有基因组中存在而在所有其他血清型中不存在的泛基因组区域；然而，每个血清型确实有基因组区域普遍存在于所有组成成员中，并在统计上预测该血清型。发现基于保守核心基因组内snp的系统发育与利用整个泛基因组的1000 bp区域的存在/缺失产生的系统发育高度一致。未来的研究可以使用这些预测区域作为预防沙门氏菌病的疫苗的组成部分，以及用于计算机和湿实验室应用的简单和快速诊断测试，其用途从食品安全到公共卫生。最后，本研究中描述的工具和方法可以作为泛基因组学框架应用于其他群体基因组研究，以寻找其他细菌物种及其亚群的标记。
Food safety is a global concern, with upward of 2.2 million deaths due to enteric disease every year. Current whole-genome sequencing platforms allow routine sequencing of enteric pathogens for surveillance, and during outbreaks; however, a remaining challenge is the identification of genomic markers that are predictive of strain groups that pose the most significant health threats to humans, or that can persist in specific environments. We have previously developed the software program Panseq, which identifies the pan-genome among a group of sequences, and the SuperPhy platform, which utilizes this pan-genome information to identify biomarkers that are predictive of groups of bacterial strains. In this study, we examined the pan-genome of 4893 genomes of Salmonella enterica, an enteric pathogen responsible for the loss of more disability adjusted life years than any other enteric pathogen. We identified a pan-genome of 25.3 Mbp, a strict core of 1.5 Mbp present in all genomes, and a conserved core of 3.2 Mbp found in at least 96% of these genomes. We also identified 404 genomic regions of 1000 bp that were specific to the species S. enterica. These species-specific regions were found to encode mostly hypothetical proteins, effectors, and other proteins related to virulence. For each of the six S. enterica subspecies, markers unique to each were identified. No serovar had pan-genome regions that were present in all of its genomes and absent in all other serovars; however, each serovar did have genomic regions that were universally present among all constituent members, and statistically predictive of the serovar. The phylogeny based on SNPs within the conserved core genome was found to be highly concordant to that produced by a phylogeny using the presence/absence of 1000 bp regions of the entire pan-genome. Future studies could use these predictive regions as components of a vaccine to prevent salmonellosis, as well as in simple and rapid diagnostic tests for both in silico and wet-lab applications, with uses ranging from food safety to public health. Lastly, the tools and methods described in this study could be applied as a pan-genomics framework to other population genomic studies seeking to identify markers for other bacterial species and their sub-groups.
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影响因子：
6.4
作者：
Golubeva YA;Ellermeier JR;Cott Chubiz JE;Slauch JM
通讯作者：
Slauch JM
影响因子：
6.4
作者：
Desai PT;Porwollik S;Long F;Cheng P;Wollam A;Bhonagiri-Palsikar V;Hallsworth-Pepin K;Clifton SW;Weinstock GM;McClelland M
通讯作者：
McClelland M
影响因子：
3
作者：
Laing C;Buchanan C;Taboada EN;Zhang Y;Kropinski A;Villegas A;Thomas JE;Gannon VP
通讯作者：
Gannon VP
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
9.9
作者：
Franz, Eelco;Gras, Lapo Mughini;Dallman, Tim
通讯作者：
Dallman, Tim