TY - JOUR
T1 - CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database
AU - Alcock, Brian P.
AU - Raphenya, Amogelang R.
AU - Lau, Tammy T.Y.
AU - Tsang, Kara K.
AU - Bouchard, Mégane
AU - Edalatmand, Arman
AU - Huynh, William
AU - Nguyen, Anna Lisa V.
AU - Cheng, Annie A.
AU - Liu, Sihan
AU - Min, Sally Y.
AU - Miroshnichenko, Anatoly
AU - Tran, Hiu Ki
AU - Werfalli, Rafik E.
AU - Nasir, Jalees A.
AU - Oloni, Martins
AU - Speicher, David J.
AU - Florescu, Alexandra
AU - Singh, Bhavya
AU - Faltyn, Mateusz
AU - Hernandez-Koutoucheva, Anastasia
AU - Sharma, Arjun N.
AU - Bordeleau, Emily
AU - Pawlowski, Andrew C.
AU - Zubyk, Haley L.
AU - Dooley, Damion
AU - Griffiths, Emma
AU - Maguire, Finlay
AU - Winsor, Geoff L.
AU - Beiko, Robert G.
AU - Brinkman, Fiona S.L.
AU - Hsiao, William W.L.
AU - Domselaar, Gary V.
AU - McArthur, Andrew G.
PY - 2019/10/29
Y1 - 2019/10/29
N2 - 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.
AB - 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.
U2 - 10.1093/nar/gkz935
DO - 10.1093/nar/gkz935
M3 - Article
C2 - 31665441
AN - SCOPUS:85077666133
SN - 0305-1048
VL - 48
SP - D517-D525
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -