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. Author manuscript; available in PMC: 2023 Dec 1.
Published in final edited form as: Regul Toxicol Pharmacol. 2022 Oct 4;136:105266. doi: 10.1016/j.yrtph.2022.105266

Table 2.

Summary of phylogenomic resources for virulence and antibiotic resistance factor identification.a.

Name Link Profiling Category Key Description and References
Virulence
Virulence Factors Database (VFDB) with VFanalyzer http://www.mgc.ac.cn/VFs/ Global virulence

  • Comprehensive collection of bacterial virulence factors with linkage to published studies (Liu et al., 2019a)

  • VFanalyzer web-based automatic analysis pipeline screening tool for complete/draft genomes

  • 1112 virulence factors for 74 pathogens; 3663 curated VF-related genes
Pathogen-host Interactions (PHI- base) with PHIB-BLAST http://www.phi-base.org/ Global virulence interactions

  • Curated broad gene functions by high-level phenotypic outcome terms affecting virulence in plant, human, animal, and insect hosts (Urban et al., 2020)

  • Covers Fungal, protist, bacterial pathogens

  • 6780 genes, 13801 interactions, 268 pathogens, 210 hosts
Pathosystems Resource Integration Center (PATRIC) VF module https://www.patricbrc.org/ Curated priority pathogens

  • Highly curated library from priority pathogens with linkage and support from published evidence

  • Includes global VFDB and Victor datasets for virulence and ARDB and CARD for resistance

  • Leverages robust integration with PATRIC analytical infrastructure for comparative -omics, pathways, host/disease repertoire (Mao et al.., 2015; Wattam et al., 2014)
Mobilization Targets
VRprofile https://bioinfo-mml.sjtu.edu.cn/VRprofile/ Contextual virulence

  • Virulence and antibiotic resistance in contextual relationship with transfer-related gene clusters, mobilome (Li et al., 2018)

  • Virulence pipeline powered by VFDB and Victor and with backend broad mobilome database sourcing
Pathogenicity Island Database (PAIDB) version 2.0 http://www.paidb.re.kr Horizontal gene transfer regions

  • Comprehensive database on all reported pathogenicity islands (PAIs) and candidate PAIs in prokaryotic genomes (Yoon et al., 2015)

  • Functionality extended to include resistance islands (REIs)

  • 223 PAIs, 88 REIs from 2673 prokaryotic genomes
ICEberg 2.0 https://db-mml.sjtu.edu.cn/ICEberg2/ Integrative and conjugative elements

  • Updated database of bacterial integrative and conjugative elements (Liu et al., 2019b)
PHAge Search Tool Enhanced Release (PHASTER) https://phaster.ca/ Prophages

  • Identification and annotation of prophage sequences within bacterial genomes and plasmids (Arndt et al., 2019)
INTEGRALL http://integrall.bio.ua.pt/ Integrons

  • Public genetic repository for interactive access to integration DNA sequences, molecular arrangements, and genetic contexts (Moura et al., 2009)
IS finder https://isfinder.biotoul.fr/ Insertion sequences

  • Database of insertion sequences and some transposons (Tn3) from bacteria and archae (Siguier et al., 2014)
Antibiotic Resistance
Antibiotic Resistance Genes Database (ARDB) http://ardb.cbcb.umd.edu/ b Global resistance

  • Manually curated AR gene subtype and ontologies (Liu and Pop, 2009)

  • Tool for common mutations conferring resistance

  • Last update in 2009 and does not contain recently discovered genes (i. e. blaNDM-1, mcr-1; Arango-Argoty et al., 2018)
Comprehensive Antibiotic Resistance Database (CARD) https://card.mcmaster.ca/ Global resistance

  • High quality, curated reference database and molecular resource, detection models, and bioinformatics tools (Alcock et al., 2020)

  • Updated monthly and considered to be comprehensive resource

  • Organized by gene ontology, homology and variant detection, and genome analysis with Resistance Gene Identifier (RGI) tool for genomic and metagenomic data
ResFinder and Pointfinder https://cge.food.dtu.dk/services/ResFinder/ Resistance genotype-to-phenotype

  • Identification of resistance genes acquired horizontally through Center for Genomic Epidemiology database

  • Flexible thresholds for raw sequencing read analysis

  • Detection of chromosomal mutations mediating resistance through Pointfinder

  • Combined tools intended to facilitate genome sequencing-based anti-biograms prediction (Bortolaia et al., 2020)
Antibiotic Resistance Gene Annotation (ARG-ANNOT) https://www.mediterranee-infection.com/acces-ressources/base-de-donnees/arg-annot-2/ Global resistance bioinformatic tool

  • Recursive database for download and simple/rapid local use (Gupta et al., 2014)

  • Detection of resistance genes with relaxed search criteria detection of putative new resistance genes

  • Some level of point mutation-based resistance detection possible although not automatic
Resfams http://www.dantaslab.org/resfams Resistance prediction and annotation

  • Curated database of protein families and associated profile hidden Markov models (HMMs)

  • Confirmed for antibiotic resistance function and organized by ontology (Gibson et al., 2015)

  • Powered by CARD and specialty β-lactamase databases
a

Current publicly available resources reflect rapidly changing landscape for genome annotation and hypothetical gene identification; list should not be considered exhaustive, but representative of categorical, commonly used platforms.

b

Last website of record.