VRprofile


35524563	VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens. [PMID: 35524563] Meng Wang, Ying-Xian Goh, Cui Tai, Hui Wang, Zixin Deng, Hong-Yu Ou Abstract VRprofile2 is an updated pipeline that rapidly identifies diverse mobile genetic elements in bacterial genome sequences. Compared with the previous version, three major improvements were made. First, the user-friendly visualization could aid users in investigating the antibiotic resistance gene cassettes in conjunction with various mobile elements in the multiple resistance region with mosaic structure. VRprofile2 could compare the predicted mobile elements to the collected known mobile elements with similar architecture. A new mobilome indicator was proposed to give an overall estimation of the mobilome size in individual bacterial genomes. Second, the relationship between antibiotic resistance genes, mobile elements, and host strains would be efficiently examined with the aid of predicted strain's sequence typing, the incompatibility group and the transferability of plasmids. Finally, the updated back-end database, MobilomeDB2, now collected nearly a thousand active mobile elements retrieved from literature or based on prediction. The pre-computed results of the antibiotic resistance gene-carrying mobile elements of >5500 ESKAPEE genomes were also provided. We expect that VRprofile2 will provide better support for researchers interested in bacterial mobile elements and the dissemination of antibiotic resistance. VRprofile2 is freely available to all users without any login requirement at https://tool2-mml.sjtu.edu.cn/VRprofile. Nucleic Acids Res. 2022:50(W1) \| 50 Citations (from Europe PMC, 2025-03-22)
28077405	VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria. [PMID: 28077405] Jun Li, Cui Tai, Zixin Deng, Weihong Zhong, Yongqun He, Hong-Yu Ou, Abstract VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes, as well as extends these trait transfer-related genetic contexts, in newly sequenced pathogenic bacterial genomes. The used backend database MobilomeDB was firstly built on sets of known gene cluster loci of bacterial type III/IV/VI/VII secretion systems and mobile genetic elements, including integrative and conjugative elements, prophages, class I integrons, IS elements and pathogenicity/antibiotic resistance islands. VRprofile is thus able to co-localize the homologs of these conserved gene clusters using HMMer or BLASTp searches. With the integration of the homologous gene cluster search module with a sequence composition module, VRprofile has exhibited better performance for island-like region predictions than the other widely used methods. In addition, VRprofile also provides an integrated Web interface for aligning and visualizing identified gene clusters with MobilomeDB-archived gene clusters, or a variety set of bacterial genomes. VRprofile might contribute to meet the increasing demands of re-annotations of bacterial variable regions, and aid in the real-time definitions of disease-relevant gene clusters in pathogenic bacteria of interest. VRprofile is freely available at http://bioinfo-mml.sjtu.edu.cn/VRprofile. Brief. Bioinformatics. 2017:() \| 68 Citations (from Europe PMC, 2025-03-22)

VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens. [PMID: 35524563]

Meng Wang, Ying-Xian Goh, Cui Tai, Hui Wang, Zixin Deng, Hong-Yu Ou

VRprofile2 is an updated pipeline that rapidly identifies diverse mobile genetic elements in bacterial genome sequences. Compared with the previous version, three major improvements were made. First, the user-friendly visualization could aid users in investigating the antibiotic resistance gene cassettes in conjunction with various mobile elements in the multiple resistance region with mosaic structure. VRprofile2 could compare the predicted mobile elements to the collected known mobile elements with similar architecture. A new mobilome indicator was proposed to give an overall estimation of the mobilome size in individual bacterial genomes. Second, the relationship between antibiotic resistance genes, mobile elements, and host strains would be efficiently examined with the aid of predicted strain's sequence typing, the incompatibility group and the transferability of plasmids. Finally, the updated back-end database, MobilomeDB2, now collected nearly a thousand active mobile elements retrieved from literature or based on prediction. The pre-computed results of the antibiotic resistance gene-carrying mobile elements of >5500 ESKAPEE genomes were also provided. We expect that VRprofile2 will provide better support for researchers interested in bacterial mobile elements and the dissemination of antibiotic resistance. VRprofile2 is freely available to all users without any login requirement at https://tool2-mml.sjtu.edu.cn/VRprofile.

Nucleic Acids Res. 2022:50(W1) | 50 Citations (from Europe PMC, 2025-03-22)

VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria. [PMID: 28077405]

Jun Li, Cui Tai, Zixin Deng, Weihong Zhong, Yongqun He, Hong-Yu Ou,

Abstract

VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes, as well as extends these trait transfer-related genetic contexts, in newly sequenced pathogenic bacterial genomes. The used backend database MobilomeDB was firstly built on sets of known gene cluster loci of bacterial type III/IV/VI/VII secretion systems and mobile genetic elements, including integrative and conjugative elements, prophages, class I integrons, IS elements and pathogenicity/antibiotic resistance islands. VRprofile is thus able to co-localize the homologs of these conserved gene clusters using HMMer or BLASTp searches. With the integration of the homologous gene cluster search module with a sequence composition module, VRprofile has exhibited better performance for island-like region predictions than the other widely used methods. In addition, VRprofile also provides an integrated Web interface for aligning and visualizing identified gene clusters with MobilomeDB-archived gene clusters, or a variety set of bacterial genomes. VRprofile might contribute to meet the increasing demands of re-annotations of bacterial variable regions, and aid in the real-time definitions of disease-relevant gene clusters in pathogenic bacteria of interest. VRprofile is freely available at http://bioinfo-mml.sjtu.edu.cn/VRprofile.

Brief. Bioinformatics. 2017:() | 68 Citations (from Europe PMC, 2025-03-22)

URL:	https://tool2-mml.sjtu.edu.cn/VRprofile
Full name:	profiling of virulence and antibiotic resistance traits
Description:	The antibiotic resistance genes (ARGs) often gain mobility through associating with a set of mobile genetic elements (mobilome). Their concerted activities significantly contribute to the promiscuous spread of ARGs throughout the microbial community. Here, we report the release of VRprofile version 2.0, which offers three major enhancements: (i) graphical representation of the multiple resistance regions with mosaic structures and comparison to the known MGEs with similar architecture; (ii) aid to explore the relationships of antibiotic resistance genes, mobile elements, and host strains; (iii) pre-computed mobilome of more than 5500 ESKAPEE bacterial genomes.
Year founded:	2018
Last update:	2022-05-07
Version:	v2.0
Accessibility:	Accessible
Country/Region:	China

Data type:	DNA
Data object:	Bacteria
Database category:	Gene genome and annotation Health and medicine Interaction
Major species:	Enterococcus faecium Staphylococcus aureus Klebsiella pneumoniae Acinetobacter baumannii Pseudomonas aeruginosa Enterobacter soli Escherichia coli
Keywords:	pathogenic bacteria virulence and antibiotic resistance

University/Institution:	Shanghai Jiao Tong University
Address:	State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China.
City:	Shanghai
Province/State:	Shanghai
Country/Region:	China
Contact name (PI/Team):	Hong-Yu Ou
Contact email (PI/Helpdesk):	hyou@sjtu.edu.cn

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