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

Brian P Alcock; Amogelang R Raphenya; Tammy T Y Lau; Kara K Tsang; Mégane Bouchard; Arman Edalatmand; William Huynh; Anna-Lisa V Nguyen; Annie A Cheng; Sihan Liu; Sally Y Min; Anatoly Miroshnichenko; Hiu-Ki Tran; Rafik E Werfalli; Jalees A Nasir; Martins Oloni; David J Speicher; Alexandra Florescu; Bhavya Singh; Mateusz Faltyn; Anastasia Hernandez-Koutoucheva; Arjun N Sharma; Emily Bordeleau; Andrew C Pawlowski; Haley L Zubyk; Damion Dooley; Emma Griffiths; Finlay Maguire; Geoff L Winsor; Robert G Beiko; Fiona S L Brinkman; William W L Hsiao; Gary V Domselaar; Andrew G McArthur

doi:10.1093/nar/gkz935

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

Nucleic Acids Res. 2020 Jan 8;48(D1):D517-D525. doi: 10.1093/nar/gkz935.

Authors

Brian P Alcock^{1

2

3}, Amogelang R Raphenya^{1

2

3}, Tammy T Y Lau^{2

3}, Kara K Tsang^{1

2

3}, Mégane Bouchard^{2

4}, Arman Edalatmand^{2

3}, William Huynh^{2

3}, Anna-Lisa V Nguyen^{2

4}, Annie A Cheng^{2

3}, Sihan Liu^{2

3}, Sally Y Min^{2

3}, Anatoly Miroshnichenko^{2

3}, Hiu-Ki Tran^{2

3}, Rafik E Werfalli^{2

3}, Jalees A Nasir^{2

3}, Martins Oloni^{2

3}, David J Speicher^{2

3}, Alexandra Florescu^{2

4}, Bhavya Singh⁵, Mateusz Faltyn^{2

6}, Anastasia Hernandez-Koutoucheva⁷, Arjun N Sharma^{2

3}, Emily Bordeleau^{1

2

3}, Andrew C Pawlowski⁸, Haley L Zubyk^{1

2

3}, Damion Dooley⁹, Emma Griffiths¹⁰, Finlay Maguire¹¹, Geoff L Winsor¹⁰, Robert G Beiko¹¹, Fiona S L Brinkman¹⁰, William W L Hsiao^{9

10

12}, Gary V Domselaar^{13

14}, Andrew G McArthur^{1

2

3}

Affiliations

¹ David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
² M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
³ Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
⁴ Bachelor of Health Sciences Program, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
⁵ Honours Biology Program, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
⁶ Bachelor of Arts & Science Program, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
⁷ Center for Genome Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos 62210, Mexico.
⁸ Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
⁹ Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, V6T 2B5, British Columbia, Canada.
¹⁰ Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.
¹¹ Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, B3H 1W5, Canada.
¹² British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, V5Z 4R4, Canada.
¹³ National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada.
¹⁴ Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacteria / drug effects
Bacteria / genetics
Bacterial Proteins / chemistry
Bacterial Proteins / genetics
Bacterial Proteins / metabolism
Databases, Genetic*
Drug Resistance, Bacterial*
Genes, Bacterial*
Software*

Substances

Bacterial Proteins