ARDB—Antibiotic Resistance Genes Database

By Bo Liu, Mihai Pop. Nucleic Acids Res., 2008

1,195 citations recorded by the source corpus.

The treatment of infections is increasingly compromised by the ability of bacteria to develop resistance to antibiotics through mutations or through the acquisition of resistance genes. Antibiotic resistance genes also have the potential to be used for bio-terror purposes through genetically modified organisms. In order to facilitate the identification and characterization of these genes, we have created a manually curated database—the Antibiotic Resistance Genes Database (ARDB)—unifying most of the publicly available information on antibiotic resistance. Each gene and resistance type is annotated with rich information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. Our database also supports sequence similarity searches and implements an initial version of a tool for characterizing common mutations that confer antibiotic resistance. The information we provide can be used as compendium of antibiotic resistance factors as well as to identify the resistance genes of newly sequenced genes, genomes, or metagenomes. Currently, ARDB contains resistance information for 13 293 genes, 377 types, 257 antibiotics, 632 genomes, 933 species and 124 genera. ARDB is available at http://ardb.cbcb.umd.edu/.

Subfields: Molecular Biology, Molecular Medicine, Pharmacology

View Paper: https://www.semanticscholar.org/paper/d769ca2ac7b7057df74fdf9d4d0de91f1b07917d

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Citations in the corpus

Bacteria Antibiotic Resistance: New Challenges and Opportunities for Implant-Associated Orthopaedic Infections (2017, background): “The Antibiotic Resistance Genes Database currently lists the existence of more than 23,000 potential resistance genes of about 380 different types from available bacterial genome sequences.(21) Fortunately, the number of functional resistance genes is much smaller.”
In-feed antibiotic effects on the swine intestinal microbiome (2012, methodology): “Three COGs (0477, permeases of the major facilitator superfamily; 1289, predicted membrane protein; 3570, streptomycin 6-kinase) contain swine metagenomic genes that are annotated as resistance genes in the antibiotic resistance gene database (ARDB).”
Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology (2014, methodology): “We compared Resfams HMMs with pairwise sequence alignment (BLAST) against the ARDB (Liu and Pop, 2009) and CARD (McArthur et al.”
Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens (2018, background): “…the Antibiotic Resistance Database (ARDB) and the Comprehensive Antibiotic Resistance Database (CARD), assembled in the last decade (Liu and Pop, 2009; McArthur et al., 2013), are expected to provide computational tools for the rapid prediction of antibiotic resistance genes and their…”
SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways (2020, background): “Third, several databases for profiling specific gene families, such as ARDB (for antibiotic resistance genes) and NCycDB (for N cycling genes) were recently developed (Liu & Pop, 2009; Tu et al., 2019).”
ARGs‐OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes (2018, methodology): “One published database, Structured Antibiotic Resistance Genes (SARG) (Yang et al., 2016), was mainly derived from a combination of ARDB (Liu and Pop, 2009) and CARD databases (McArthur et al., 2013).”
ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes (2013, methodology): “However, this database has not been upgraded since 2009 and has a restricted sequence entry ( 5 kb) for BLAST that is not compatible with whole-genome sequence analysis (9).”
BacMet: antibacterial biocide and metal resistance genes database (2013, background): “Classical antibiotic compounds were excluded, as resistance genes to antibiotics are covered in other databases such as the Antibiotic Resistance Genes Database and the Comprehensive Antibiotic Resistance Database; however, genes providing resistance to both biocides and antibiotics were included.”
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome (2012, methodology): “In other analyses by the HMP, additional protein databases including MetaCyc [28], CAZy [21], virulence related proteins [69], and antibiotic resistance genes [70] were all processed using HUMAnN.”
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database (2016, background): “ARDB focussed on all antibiotic resistance genes but has not been updated since 2009, ARGO is concerned with resistance to two classes of antibiotics, BacMet specifically collects data on biocide and metal resistance genes, and APD3 concentrates on antimicrobial peptides.”
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database (2015, background): “Note that pathogen-associated genes can also be viewed in JBrowse alongside the predicted GIs and the link from JBrowse to the IslandViewer website shows these genes in the context of genomic islands, curated virulence factors and antimicrobial resistance genes identified from the Antibiotic Resista”
Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review. (2013, background): “a DM, drug modification; DE, drug efflux; TM, target modification; TP, target protection (Liu and Pop, 2009).”
Antibiotic resistance plasmids in wastewater treatment plants and their possible dissemination into the environment (2010, background): “edu/) estimates there are over 13000 antibiotic resistance genes (ARGs) identified in greater than 600 genomes of antibiotic resistance bacteria (ARB) (Liu and Pop, 2009).”