The Comprehensive Antibiotic Resistance Database

By A. McArthur, Nicholas Waglechner, Fazmin Nizam, Austin Yan, M. A. Azad, A. Baylay, Kirandeep Bhullar, Marc J. Canova, Gianfranco De Pascale, L. Ejim and 17 more. Antimicrobial Agents and Chemotherapy, 2013

1,981 citations recorded by the source corpus.

Subfields: Molecular Biology, Molecular Medicine, Pollution

View Paper: https://www.semanticscholar.org/paper/3bbc9400429ad3d6bda6d12e4449053afa1114a2

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Molecular Medicine

In Pollution

Citations in the corpus

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology (2014, methodology): “The Antibiotic Resistance Database (ARDB; Liu and Pop, 2009) and CARD (McArthur et al., 2013) were used for comparison of Resfams profile HMMs to pairwise sequence alignment against known AR proteins.”
Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates (2019, methodology): “Others consist of collections of nucleotide or protein sequences of either individual resistance genes or resistance-related mobile elements (23, 24).”
ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes (2013, methodology): “Moreover, the Resﬁnder and CARD tools are unable to detect point mutations in target genes that are known to be associated with AR.”
MEGARes: an antimicrobial resistance database for high throughput sequencing (2016, methodology): “While the contribution of the Antibiotic Resistance Ontology (ARO) developed by the Comprehensive Antibiotic Resistance Database (CARD) (28) is a notable improvement in AMR biocuration, and such a classification scheme is very useful for functional annotation, the ARO’s highly descriptive and large ”
Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens (2018, background): “Indeed two databases, 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 an”
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities (2019, methodology): “Users can currently align against the reference gene sets from the Comprehensive Antibiotic Resistance Database (CARD) (50) and the Virulence Factor Database (VFDB) (51).”
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center (2016, methodology): “For instance, a BLASTbased comparison (22) is performed with several externally curated ‘Specialty Gene’ databases, including the Antibiotic Resistance Database (ARDB) (23) and the Comprehensive Antibiotic Resistance Database (CARD) (24) for antibiotic resistance proteins.”
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.”
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes (2016, methodology): “For proteins with no CARD resistance gene annotation, the best ResFams HMM hit above threshold was retained.”
PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens (2017, background): “CARD’sresistancegeneidentiﬁer(RGI)proteinvariant modelsusecuratedSNPmatricestodetectandreportmutations associatedwithresistance.”
Bacterial phylogeny structures soil resistomes across habitats (2014, background): “To generate more encompassing counts of general resistance functions (for example, b -lactamases),genecountsweresummedacrossallannotationsthatclearlybelonged totheparentfunction(forexample,classA b -lactamases,metallo b -lactamases,TEM b -lactamases),informedbyestablishedARGontology 37 .”
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”
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes (2015, methodology): “It searches against custom BLAST databases that have been built from ARDB 34 and CARD 35 for finding potential antibiotic resistance genes; DrugBank 36 and TTD 37 for finding potential drug targets; VFDB 38 ,Victors 39 and the PATRIC virulence factors 10,33 for finding potential virulence factors;…”