Fong Karen, Lu Yu Tong, Brenner Thomas, Falardeau Justin, Wang Siyun
Food, Nutrition and Health, The University of British Columbia, Vancouver, BC, Canada.
Front Microbiol. 2022 Jul 22;13:853703. doi: 10.3389/fmicb.2022.853703. eCollection 2022.
Prophages have long been regarded as an important contributor to the evolution of and Verotoxin-producing (VTEC), members of the that cause millions of cases of foodborne illness in North America. In . Typhimurium, prophages provide many of the genes required for invasion; similarly, in VTEC, the Verotoxin-encoding genes are located in cryptic prophages. The ability of prophages to quickly acquire and lose genes have driven their rapid evolution, leading to highly diversified populations of phages that can infect distantly-related bacterial hosts. To defend against foreign genetic materials (i.e., phages), bacteria have evolved Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immunity, consisting of variable spacer regions that match short nucleic acid sequences of invaders previously encountered. The number of spacer regions varies widely amongst , and there is currently no clear consensus if the accumulation of spacers is linked to genomic prophage abundance. Given the immense prophage diversity and contribution to bacterial host phenotypes, we analyzed the prophage sequences within 118 strains of and VTEC, 117 of which are of agricultural origin. Overall, 130 unique prophage sequences were identified and they were found to be remarkably diverse with <50% nucleotide similarity, particularly with the Gifsy-1 group which was identified in several serovars and interestingly, a strain of VTEC. Additionally, we identified a novel plasmid-like phage that carried antibiotic resistance and bacteriocin resistance genes. The strains analyzed carried at least six distinct spacers which did not possess homology to prophages identified in the same genome. In fact, only a fraction of all identified spacers (14%) possessed significant homology to known prophages. Regression models did not discern a correlation between spacer and prophage abundance in our strains, although the relatively high number of spacers in our strains (an average of 27 in and 19 in VTEC) suggest that high rates of infection may occur in agricultural niches and be a contributing driver in bacterial evolution. Cumulatively, these results shed insight into prophage diversity of and VTEC, which will have further implications when informing development of phage therapies against these foodborne pathogens.
原噬菌体长期以来一直被视为导致北美数百万例食源性疾病的肠出血性大肠杆菌（VTEC）进化的重要贡献者。在鼠伤寒沙门氏菌中，原噬菌体提供了许多入侵所需的基因；同样，在VTEC中，编码志贺毒素的基因位于隐秘原噬菌体中。原噬菌体快速获取和丢失基因的能力推动了它们的快速进化，导致了高度多样化的噬菌体群体，这些噬菌体可以感染远缘相关的细菌宿主。为了抵御外来遗传物质（即噬菌体），细菌进化出了成簇规律间隔短回文重复序列（CRISPR）免疫，它由可变间隔区组成，这些间隔区与先前遇到的入侵者的短核酸序列相匹配。不同细菌中间隔区的数量差异很大，目前对于间隔区的积累是否与基因组原噬菌体丰度相关尚无明确共识。鉴于原噬菌体的巨大多样性及其对细菌宿主表型的贡献，我们分析了118株肠出血性大肠杆菌和VTEC中的原噬菌体序列，其中117株来自农业来源。总体而言，共鉴定出130个独特的原噬菌体序列，发现它们差异显著，核苷酸相似度低于50%，特别是在几个血清型以及一株VTEC中鉴定出的Gifsy-1组。此外，我们鉴定出一种携带抗生素抗性和细菌素抗性基因的新型质粒样噬菌体。所分析的菌株携带至少六个不同的间隔区，这些间隔区与同一基因组中鉴定出的原噬菌体没有同源性。事实上，所有鉴定出的间隔区中只有一小部分（14%）与已知原噬菌体具有显著同源性。回归模型未发现我们所分析菌株中间隔区和原噬菌体丰度之间存在相关性，尽管我们菌株中间隔区数量相对较多（肠出血性大肠杆菌平均为27个，VTEC平均为19个），这表明在农业生态位中可能发生高感染率，并且是细菌进化的一个促成因素。总的来说，这些结果深入了解了肠出血性大肠杆菌和VTEC的原噬菌体多样性，这对于指导针对这些食源性病原体的噬菌体疗法的开发具有进一步的意义。
