Mottawea Walid, Duceppe Marc-Olivier, Dupras Andrée A, Usongo Valentine, Jeukens Julie, Freschi Luca, Emond-Rheault Jean-Guillaume, Hamel Jeremie, Kukavica-Ibrulj Irena, Boyle Brian, Gill Alexander, Burnett Elton, Franz Eelco, Arya Gitanjali, Weadge Joel T, Gruenheid Samantha, Wiedmann Martin, Huang Hongsheng, Daigle France, Moineau Sylvain, Bekal Sadjia, Levesque Roger C, Goodridge Lawrence D, Ogunremi Dele
Department of Food Science and Agricultural Chemistry, McGill University, Ste Anne de Bellevue, QC, Canada.
Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.
Front Microbiol. 2018 May 4;9:836. doi: 10.3389/fmicb.2018.00836. eCollection 2018.
Non-typhoidal is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of 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 strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in . In this study, the prophage sequence diversity in different serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of representing 151 serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in genomes. Prophage sequences were highly variable among 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 . 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 subtypes during foodborne outbreaks.
非伤寒型[病原体名称]是全球食源性疾病的主要病因。迅速准确地识别导致疾病暴发的[病原体名称]来源对于减少感染和消除持续的污染源至关重要。当前的分型工具，包括单核苷酸多态性（SNP）分型，在某些情况下可能不足以在流行病学上不相关的[病原体名称]菌株之间提供所需的区分度。前噬菌体基因占细菌基因组中辅助基因的大部分，有潜力用作[病原体名称]的高区分度标记。在本研究中，调查了不同[病原体名称]血清型和遗传相关菌株中的前噬菌体序列多样性。利用代表151种[病原体名称]血清型和66种密切相关细菌的1760株分离株的全基因组序列，使用PHASTER从组装的重叠群中识别前噬菌体序列。我们在[病原体名称]基因组中检测到154种不同的前噬菌体。前噬菌体序列在[病原体名称]血清型之间高度可变，每个基因组的前噬菌体区域中位数±四分位间距（IQR）为5±3。虽然一些前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前噬菌体含量分别聚类。对来自七次暴发的肠炎沙门氏菌分离株的分析为每次暴发产生了不同的前噬菌体图谱。总体而言，前噬菌体序列的多样性与基因组多样性相关。前噬菌体库为食源性暴发期间区分[病原体名称]亚型提供了一个额外的标记。
