CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

TLDR

CARD is a curated resource that provides reference DNA and protein sequences, detection models, and bioinformatics tools for bacterial antimicrobial resistance, built on a controlled vocabulary (ARO) to support resistome analysis and prediction. This study describes recent updates and expansions to CARD and its biocuration process, including new resources that enable community biocuration of AMR molecular reference data. By incorporating resistance variants into CARD, the authors can summarize predicted resistance, identify trends in AMR mobility, and uncover previously undescribed and novel variants. Since 2017, CARD has added over 500 new AMR detection models, revised its ontological structure, introduced a new classification paradigm, expanded analytical tools, and launched a Resistomes & Variants module that analyzes predicted resistance variants from 82 pathogens and more than 100,000 genomes.

Abstract

The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD's Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.