Data_Sheet_1_Characterization and Genomic Analysis of SFPH2, a Novel T7virus Infecting Shigella.pdf

Shigellosis, caused by Shigella, is a major global health concern, with nearly 164.7 million cases and over a million deaths occurring annually worldwide. Shigella flexneri is one of the most common subgroups of Shigella with a high incidence of multidrug-resistance. The phage therapy approach is an effective method for controlling multidrug-resistant bacteria. However, only a few Shigella phages have been described to date. In this study, a novel lytic bacteriophage SFPH2 was isolated from a sewage sample obtained from a hospital in Beijing, China, using a multidrug-resistant S. flexneri 2a strain (SF2) isolated from the fecal sample of a dysentery patient. SFPH2 is a member of the Podoviridae virus family with an icosahedral capsid and a short, non-contractile tail. It was found to be stable over a wide range of temperatures (4–50°C) and pH values (pH 3–11). Moreover, SFPH2 could infect two other S. flexneri serotypes (serotypes 2 variant and Y). High-throughput sequencing revealed that SFPH2 has a linear double-stranded DNA genome of 40,387 bp with 50 open reading frames. No tRNA genes were identified in the genome. Comparative analysis of the genome revealed that the SFPH2 belongs to the subfamily Autographivirinae and genus T7virus. The genome shows high similarity with other enterobacterial T7virus bacteriophages such as Citrobacter phage SH4 (95% identity and 89% coverage) and Cronobacter phage Dev2 (94% identity and 92% coverage). A comparison of the fiber proteins showed that minor differences in the amino acid residues might specify different protein binding regions and determine host species. In conclusion, this is the first report of a T7virus that can infect Shigella; SFPH2 has a functional stability under a wide range of temperatures and pH values, showing the potential to be widely applied to control Shigella–associated clinical infections and reduce the transmission rates of S. flexneri serotype 2a and its variants in the environment.

志贺菌感染，由志贺菌引起，是全球公共卫生领域的一大关注点，全球每年约有1.647亿病例，超过一百万死亡病例。志贺菌弗氏亚种是志贺菌中最常见的亚种之一，具有高比例的多药耐药性。噬菌体疗法是一种有效的控制多药耐药细菌的方法。然而，迄今为止，仅描述了少数志贺菌噬菌体。在本研究中，从中国北京一家医院的污水样本中分离出一种新型溶菌性噬菌体SFPH2，该噬菌体是从一名痢疾患者的粪便样本中分离出的多药耐药性弗氏亚种2a菌株（SF2）中获得的。SFPH2是二十面体衣壳和短的非收缩尾的Podoviridae病毒家族成员。研究发现，SFPH2在广泛的温度范围（4–50°C）和pH值（pH 3–11）下具有良好的稳定性。此外，SFPH2能够感染两种其他弗氏亚种血清型（2变异型和Y型）。高通量测序显示，SFPH2具有40,387碱基对的线性双链DNA基因组，含有50个开放阅读框。基因组中未检测到tRNA基因。基因组比较分析表明，SFPH2属于Autographivirinae亚科和T7virus属。其基因组与其它肠杆菌T7virus噬菌体，如柠檬酸杆菌噬菌体SH4（95%同源性和89%覆盖率）和克罗诺杆菌噬菌体Dev2（94%同源性和92%覆盖率）具有较高的相似性。纤维蛋白的比较表明，氨基酸残基的细微差异可能指定不同的蛋白结合区域并决定宿主物种。综上所述，这是首次报道能够感染志贺菌的T7virus；SFPH2在广泛的温度和pH值下具有功能稳定性，显示出广泛应用于控制与志贺菌相关的临床感染以及降低环境中介的弗氏亚种2a及其变异株传播率的潜力。