Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping.
Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping.
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DOI：
10.3389/fmicb.2018.00836
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发表时间：
2018
影响因子：
5.2
通讯作者：
Ogunremi D
中科院分区：
文献类型：
--
作者：
Mottawea W;Duceppe MO;Dupras AA;Usongo V;Jeukens J;Freschi L;Emond-Rheault JG;Hamel J;Kukavica-Ibrulj I;Boyle B;Gill A;Burnett E;Franz E;Arya G;Weadge JT;Gruenheid S;Wiedmann M;Huang H;Daigle F;Moineau S;Bekal S;Levesque RC;Goodridge LD;Ogunremi D
非伤寒沙门氏菌是全世界食源性疾病的主要原因。及时准确地识别导致疾病爆发的沙门氏菌来源对于最大限度地减少感染和消除持续的污染源至关重要。在某些情况下，当前的亚型分型工具（包括单核苷酸多态性 (SNP) 分型）可能不足以对流行病学上不相关的沙门氏菌菌株进行所需的区分。原噬菌体基因代表了细菌基因组中的大多数辅助基因，并且有潜力用作沙门氏菌的高辨别标记。在本研究中，研究了不同沙门氏菌血清型和遗传相关菌株的原噬菌体序列多样性。使用代表 151 种沙门氏菌血清型和 66 种密切相关细菌的 1,760 个肠沙门氏菌分离株的全基因组序列，使用 PHASTER 从组装的重叠群中鉴定出原噬菌体序列。我们在肠沙门氏菌基因组中检测到 154 种不同的前噬菌体。原噬菌体序列在肠沙门氏菌血清型中差异很大，每个基因组的中值±四分位距（IQR）为5±3个原噬菌体区域。虽然一些原噬菌体序列在特定血清型的菌株中高度保守，但很少有区域是谱系特异性的。因此，属于每个血清型的菌株可以根据其原噬菌体含量单独聚类。对七次爆发的肠炎沙门氏菌分离株的分析为每次爆发产生了不同的原噬菌体谱。总而言之，原噬菌体序列的多样性与基因组多样性相关。原噬菌体库为食源性暴发期间区分肠沙门氏菌亚型提供了额外的标记。
Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP) typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella. In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR) of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific serovars, few regions were lineage specific. Therefore, strains belonging to each serovar could be clustered separately based on their prophage content. Analysis of S. Enteritidis isolates from seven outbreaks generated distinct prophage profiles for each outbreak. Taken altogether, the diversity of the prophage sequences correlates with genome diversity. Prophage repertoires provide an additional marker for differentiating S. enterica subtypes during foodborne outbreaks.
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影响因子：
168.9
作者：
Feasey, Nicholas A.;Dougan, Gordon;Kingsley, Robert A.;Heyderman, Robert S.;Gordon, Melita A.
通讯作者：
Gordon, Melita A.
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：
56.9
作者：
Diard, Mederic;Bakkeren, Erik;Hardt, Wolf-Dietrich
通讯作者：
Hardt, Wolf-Dietrich
影响因子：
3.6
作者：
Figueroa-Bossi, N;Uzzau, S;Bossi, L
通讯作者：
Bossi, L
影响因子：
10.7
作者：
Bobay LM;Rocha EP;Touchon M
通讯作者：
Touchon M