CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
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Raphenya, Amogelang R
Lau, Tammy TY
Tsang, Kara K
Bouchard, Megane
Edalatmand, Arman
Huynh, William
Nguyen, Anna-Lisa
Cheng, Annie A
Liu, Sihan
Min, Sally Y
Miroshnichenko, Anatoly
Tran, Hiu-Ki
Werfalli, Rafik E
Nasir, Jalees A
Oloni, Martins
Speicher, David J
Florescu, Alexandra
Singh, Bhavya
Faltyn, Mateusz
Hernandez-Koutoucheva, Anastasia
Sharma, Arjun N
Bordeleau, Emily
Pawlowski, Andrew C
Zubyk, Haley L
Dooley, Damion
Griffiths, Emma
Maguire, Finlay
Winsor, Geoff L
Beiko, Robert G
Brinkman, Fiona SL
Hsiao, William WL
Domselaar, Gary
McArthur, Andrew G
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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.
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Nucleic Acids Research
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48
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D1
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© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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Environmental sciences
Biological sciences
Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
ANTIMICROBIAL RESISTANCE
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Alcock, BP; Raphenya, AR; Lau, TTY; Tsang, KK; Bouchard, M; Edalatmand, A; Huynh, W; Nguyen, A-L; Cheng, AA; Liu, S; Min, SY; Miroshnichenko, A; Tran, H-K; Werfalli, RE; Nasir, JA; Oloni, M; Speicher, DJ; Florescu, A; Singh, B; Faltyn, M; Hernandez-Koutoucheva, A; Sharma, AN; Bordeleau, E; Pawlowski, AC; Zubyk, HL; Dooley, D; Griffiths, E; Maguire, F; Winsor, GL; Beiko, RG; Brinkman, FSL; Hsiao, WWL; Domselaar, G; McArthur, AG, CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database, Nucleic Acids Research, 2020, 48 (D1), pp. D517-D525