Reads-based Virulence Factors' Scanner

A web-based pipeline for identifying virulence factor genes from sequencing reads


24 Pathogens, 2456 VFGs, 439 VFs, 31670 Reference Genomes, 2847624 VFG Sequences

The effective identification of virulence factor genes (VFGs) of high frequency and important pathogenic bacteria in clinical samples helps to identify potential pathogenic bacteria, assess the virulence intensity of pathogenicity of clinical strains, diagnosis and implementation of accurate treatment and prognostic management of infectious diseases. Furthermore, in the field of public health, profiling bacterial virulence by VFGs detection provides useful information for the surveillance of bacteria infections, the judgment of outbreak probability and the assessment of epidemic severity, and facilitates the proposal and implementation of reasonable disease control and prevention.

In order to identify VFGs of 24 pathogenic bacteria in clinical samples, Reads-based Virulence Factors' Scanner (RVFscan) provides a multi-annotation system, including a curated VFGs database composed of 27470 representative VFG sequences, VF functional and clinical characteristics, and a pipeline for identifying the important VFGs based on clinical metagenomic next-generation sequencing (mNGS) short-reads data. This tool can be used to identify 2456 VFGs of 24 pathogenic bacteria at one time.
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Virulence Factor Result:
Virulence Factor CN Virulence Factor Category Species CN Species Gram 主要基因比对 Reads
产气菌素 Aerobactin 铁摄取 肺炎克雷伯菌 Klebsiella pneumoniae G- iucC,iucB,iucA 4
杀白细胞素 leukotoxin 外毒素 金黄色葡萄球菌 Staphylococcus aureus G+ lukD,lukS-PV,lukF-PV 3
黏液表型调节因子 regulator of mucoid phenotype 荚膜 肺炎克雷伯菌 Klebsiella pneumoniae G- rmpA2,rmpA 4
葡萄球菌肠毒素 staphylococcal enterotoxin 外毒素 金黄色葡萄球菌 Staphylococcus aureus G+ sell,selk,see 10
Virulence Factor Genus:
1、产气菌素: 产气菌素是肺炎克雷伯菌最强的铁摄取系统因子,是增强其毒力的主要物质,可使毒力增强100倍(小鼠体内),是增强其毒力的主要物质,产气菌素突变缺失菌株在体外培养(人腹水培养液、人血清、尿液)和体内培养(注射全身感染的小鼠)时,不能合成气杆菌素的毒力显著下降。产气菌素受体由基因簇iucABCD-iutA编码,常与rmpA共同位于毒力质粒pLVPK,其中iutA编码产气菌素特定的外膜蛋白受体。
2、杀白细胞素: 杀白细胞素(Panton-Valentine leukocidin,PVL)是金葡菌分泌产生的一种双组份外毒素,具有促进中性粒细胞溶解的作用,产PVL的金葡菌毒力非常强,容易导致皮肤、软组织化脓性感染,严重者可导致坏死性肺炎,致死率较高。pvl基因被认为是金葡菌的主要毒力基因,在金葡菌化脓性肌炎中的决定性作用,但也有研究说明pvl不能说明一定具有强致病力。PVL由两个基因编码(lukF-PV、lukS-PV)。
3、黏液表型调节因子: 肺炎克雷伯菌黏液性状以及与黏液性状相关的毒力基因rmpA的存在是致肝脓肿肺炎克雷伯菌的重要特征,是导致人类肝脓肿的主要原因,其编码的蛋白辅助荚膜合成,参与对黏液性状的调控。敲除该基因后荚膜合成能力降低甚至缺失,失去高黏液表型的特征,致病性降低。由于血液中肺炎克雷伯菌易随血流播散之其他部位形成感染,若为高黏液表型的菌株,毒力强,可导致严重的侵袭性感染,如眼内炎、脑膜炎等,高黏液表型的肺炎克雷菌被认为是高毒力菌株。位于毒力质粒pLVPK,并非单独发挥作用,而是与TerW、IutA、SilS等共同影响形成肝脓肿时的毒力作用。
4、葡萄球菌肠毒素: 肠毒素(enterotoxins,SEs)与金葡菌致病性密切相关,是一组毒力相似、结构相关,但抗原性不同的胞外蛋白质,SEs可与肠道神经细胞受体作用刺激呕吐中枢导致以呕吐为主要症状的急性肠胃炎,是引起人类细菌性食物中毒的主要原因。此外,非月经相关的中毒性休克综合征(TSS)病例大部分是由肠毒素引起的。属于超抗原毒素,超抗原毒素的基因位于可移动基因元件上,如致病岛、噬菌体和质粒上。
Reference:
[1]吴翰欣, 丁家伟, 高淩, 等. 高毒力肺炎克雷伯菌的毒力机制研究进展[J]. 生物技术通讯, 2018, 029(001):119-122.
[2]孙琛, 王亚娟, 杨鑫, 等. 新生儿金黄色葡萄球菌感染致病株分子特征研究[J]. 中国小儿急救医学, 2019, 26(11):813-819.
[3]沈定霞, 李东冬, 郭玲,等. 高黏液表型肺炎克雷伯菌的荚膜分型与毒力基因的检测[J]. 中华检验医学杂志, 2014(5):379-382.
[4]刘颖超, 杨鑫, 王丽娟, 等. 儿童金黄色葡萄球菌皮肤软组织感染临床分离株的分子及耐药特征研究[J]. 中华实用儿科临床杂志, 2018, 033(007):513-519.
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Department of Bioinformatics
Hugobiotech Co., Ltd.
Beijing,China
tel:010-87227805
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