The Comprehensive Antibiotic Resistance Database has been updated, http://card.mcmaster.ca
CARD Curation: Addition of HERA, TRU, & ACI beta-lactamases, sul4, and new quinolone efflux pumps.
Antibiotic Resistance Ontology: Expanded to include an entirely new branch describing AMR phenotypic testing methods. ARO additionally now officially available at the OBO Foundry, allowing formal integration with other ontological resources, most notably the Genomic Epidemiology Application Ontology (GenEpiO), https://github.com/genepio/genepio.
Resistance Gene Identifier: Resistome prediction for low quality or low coverage assemblies, merged metagenomics reads, and small plasmids or assembly contigs. Includes prediction of partial AMR genes. Support added for Docker operating-system-level virtualization (i.e. containerization).
Prevalence, Resistomes, & Variants: Expanded to 67 important pathogens, with a focus on ESKAPEs, WHO Priority Pathogens, and agents of sepsis.
The Comprehensive Antibiotic Resistance Database has been updated, http://card.mcmaster.ca
This February 2018 release is our largest to date and includes new data types, a new classification system, an entirely new version of the Resistance Gene Identifier, and website improvements.
CARD Curation: 37 new ADC beta-lactamases, 21 PDC beta-lactamases, new MCR proteins, 23 rRNA mutations, resistant isoleucyl-tRNA synthetases, hundreds of new resistance mutations, and more. While in past releases all curated AMR mutations were those characterized from clinical isolates, CARD now additionally includes mutations discovered via in vitro selection experiments. Ontological improvements have been made to enable an entirely new classification system for CARD data and RGI results: resistance determinants are now systematically categorized by AMR Gene Family, Drug Class, and Resistance Mechanism. The Antibiotic Resistance Ontology is now additionally available via GitHub, https://github.com/arpcard.
Resistance Gene Identifier: Entirely new codebase, compatible with CARD data (card.json) version 2.0.0 and up (download separately). Open Reading Frame (ORF) prediction using Prodigal, homolog detection using BLAST (default) or DIAMOND, and Strict significance based on CARD curated bitscore cut-offs. Addition of rRNA mutation and efflux over-expression models. Hits of 95% identity or better are automatically listed as Strict. All results organized by revised ARO classification: AMR Gene Family, Drug Class, and Resistance Mechanism. Revised documentation, command line menu, and website graphical interface. The Resistance Gene Identifier is now additionally available via GitHub, https://github.com/arpcard.
Prevalence, Genomes, & Variants: Expansion of our computer-generated data set on the prevalence of AMR genes and variants among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI for clinically important pathogens. CARD Prevalence 2.0.0 is based on sequence data acquired from NCBI on August 28, 2017, analyzed using RGI 4.0.0 (DIAMOND homolog detection) and CARD 2.0.0. Now includes results for protein overexpression models and rRNA mutations. All results organized by the revised ARO classification: AMR Gene Family, Drug Class, and Resistance Mechanism. Download files now include 35000+ genome annotations and all predicted sequence variants.