Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain.
Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain.
Front Cell Infect Microbiol. 2021 Nov 18;11:775402. doi: 10.3389/fcimb.2021.775402. eCollection 2021.
Bacteriophages (phages) are viruses that infect bacteria. They are the most abundant biological entity on Earth (current estimates suggest there to be perhaps 10 particles) and are found nearly everywhere. Temperate phages can integrate into the chromosome of their host, and prophages have been found in abundance in sequenced bacterial genomes. Prophages may modulate the virulence of their host in different ways, e.g., by the secretion of phage-encoded toxins or by mediating bacterial infectivity. Some 70% of (the pneumococcus)-a frequent cause of otitis media, pneumonia, bacteremia and meningitis-isolates harbor one or more prophages. In the present study, over 4000 genomes were examined for the presence of prophages, and nearly 90% were found to contain at least one prophage, either defective (47%) or present in full (43%). More than 7000 complete putative integrases, either of the tyrosine (6243) or serine (957) families, and 1210 full-sized endolysins (among them 1180 enzymes corresponding to 318 amino acid-long -acetylmuramoyl-L-alanine amidases [LytA]) were found. Based on their integration site, 26 different pneumococcal prophage groups were documented. Prophages coding for tRNAs, putative virulence factors and different methyltransferases were also detected. The members of one group of diverse prophages (PPH090) were found to integrate into the 3' end of the host gene encoding the major autolysin without disrupting it. The great similarity of the and genes (85-92% identity) allowed them to recombine, an apparent integrase-independent mechanism, to produce different DNA rearrangements within the pneumococcal chromosome. This study provides a complete dataset that can be used to further analyze pneumococcal prophages, their evolutionary relationships, and their role in the pathogenesis of pneumococcal disease.
噬菌体（phages）是感染细菌的病毒。它们是地球上最丰富的生物实体（目前的估计表明，可能有 10 亿个粒子），几乎无处不在。温和噬菌体可以整合到宿主的染色体中，并且在测序的细菌基因组中发现了丰富的原噬菌体。原噬菌体可以通过分泌噬菌体编码的毒素或以介导细菌感染性的方式以不同的方式调节宿主的毒力。大约 70%的（肺炎球菌）-一种常见的中耳炎、肺炎、菌血症和脑膜炎的病原体-分离株携带一个或多个原噬菌体。在本研究中，检查了超过 4000 个基因组中是否存在原噬菌体，发现近 90%的基因组至少含有一个原噬菌体，要么是缺陷的（47%），要么是完整的（43%）。发现了超过 7000 个完整的推定整合酶，酪氨酸（6243）或丝氨酸（957）家族的，以及 1210 个全长内切酶（其中 1180 个酶对应于 318 个氨基酸长的乙酰氨酰基 muramoyl-L-丙氨酸酰胺酶 [LytA]）。根据它们的整合位点，记录了 26 个不同的肺炎球菌原噬菌体群。还检测到编码 tRNA、推定毒力因子和不同甲基转移酶的原噬菌体。一组多样化原噬菌体（PPH090）的成员被发现整合到宿主编码主要自溶素的基因 3'端而不破坏它。和 基因（85-92%的同一性）的高度相似性允许它们通过一种明显的整合酶独立机制重组，在肺炎球菌染色体内产生不同的 DNA 重排。本研究提供了一个完整的数据集，可以用于进一步分析肺炎球菌原噬菌体、它们的进化关系以及它们在肺炎球菌病发病机制中的作用。
