Investigation on the evolution of Shiga Toxin (Stx)-converting phages carrying different stx2 gene subtypes based on whole genome sequencing. Shiga Toxin (Stx)-converting phages

Bacteriophages are pivotal elements in the dissemination of virulence genes. The main virulence de-terminants of Shiga Toxin producing E. coli, Shiga Toxins (Stx), are encoded by genes localized in the genome of lambdoid bacteriophages. Stx comprise two antigenically different types, Stx1 and Stx2, further divided into subtypes. Among these, certain Stx2 subtypes appear to be more com-monly occurring in the most severe forms of the STEC disease, haemorrhagic colitis and haemolytic uremic syndrome.This study aimed at obtaining insights on the evolution of Stx2 bacteriophages, due to their rele-vance in public health, and we report here on the analysis of the genomic structure of Stx2 convert-ing phages in relation with the known reservoir of the E. coli strains harbouring them.Stx2 converting phages conveying the genes encoding different stx2 subtypes have been isolated from STEC strains and their whole genomes have been sequenced, analysed and compared to those of other Stx2 phages available in the public domain. The phages’ regions containing the stx2 genes has been analysed in depth allowing to make inference on the possible mechanisms of selection and maintenance of certain Stx2 phages in the reservoir.The “stx regions” of different stx2 gene subtypes grouped into three different evolutionary lines in the comparative analysis, reflecting the frequency with which these subtypes are found in different animal niches, suggesting that the colonization of specific reservoir by STEC strains could be influ-enced by the Stx phage that they carry.Noteworthy, we could identify the presence of nanS-p gene exclusively in the “stx regions” of the phages identified in STEC strains commonly found in cattle. As a matter of fact, this gene encodes for an esterase capable of metabolizing sialic acids produced by submaxillary glands of bovines and present in great quantities in their gastrointestinal tract.

噬菌体（bacteriophages）是毒力基因传播的核心要素。产志贺毒素大肠杆菌（Shiga Toxin producing E. coli, STEC）的主要毒力决定因子——志贺毒素（Shiga Toxins, Stx），由定位于λ样噬菌体（lambdoid bacteriophages）基因组中的基因编码。志贺毒素包含两种抗原性迥异的类型：Stx1与Stx2，二者尚可进一步划分为多个亚型。其中，部分Stx2亚型更常出现于STEC疾病的最严重表型：出血性结肠炎（haemorrhagic colitis）与溶血性尿毒症综合征（haemolytic uremic syndrome）。
本研究鉴于Stx2噬菌体在公共卫生（public health）领域的重要价值，旨在深入解析其演化机制，并在此报告针对携带stx2基因的转化噬菌体的基因组结构分析，以及其与携带该类噬菌体的大肠杆菌菌株已知宿主库的关联。
研究人员从STEC菌株中分离出携带不同stx2亚型编码基因的Stx2转化噬菌体，对其全基因组进行了测序、分析，并与公共数据库（public domain）中已公开的其他Stx2噬菌体基因组展开比对。团队对噬菌体中包含stx2基因的stx区域（stx regions）进行了深度剖析，由此可推断宿主库中特定Stx2噬菌体的选择与维持机制。
通过比较分析，不同stx2基因亚型的stx区域（stx regions）可划分为三种不同的演化谱系，这一结果反映出这些亚型在不同动物生态位中的检出频率，提示STEC菌株对特定宿主库的定殖能力可能受其所携带的Stx噬菌体影响。
值得注意的是，研究团队发现nanS-p基因（nanS-p gene）仅存在于牛源常见STEC菌株所分离噬菌体的stx区域（stx regions）中。事实上，该基因编码的酯酶（esterase）可代谢牛下颌下腺（submaxillary glands）产生、且在牛胃肠道（gastrointestinal tract）中大量存在的唾液酸（sialic acids）。