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

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 FaltynAnastasia 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

Research output: Contribution to journal › Article › peer-review

2403 Citations (Scopus)

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.

Original language	English
Pages (from-to)	D517-D525
Journal	Nucleic Acids Research
Volume	48
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkz935
Publication status	Published - Jan 1 2020

Bibliographical note

Funding Information:
Canadian Institutes of Health Research [PJT-156214 to A.G.M.]; Genome Canada (to R.G.B., F.S.L.B, W.W.L.H.); Cisco Systems Canada, Inc., Cisco Research Chair in Bioinformatics (to A.G.M.); Ontario Graduate Scholarship (to K.K.T.); McMaster University’s MacDATA Institute Graduate Fellowship (to K.K.T.); Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Michael Kamin Hart Memorial Scholarship (to K.K.T.); Ontario Graduate Scholarship (to H.L.Z.); Frederick Banting and Charles Best Canada Graduate Scholarship (CGS-D) (to E.B.); Donald Hill Family Fellowship in Computer Science (to F.M.); Natural Sciences and Engineering Research Council Banting Postdoctoral Fellowship (to A.C.P.); Mi-tacs Globalink Research Internship (to A.H-K.); IIDR Summer Student Fellowship (to H-K.T., T.T.Y.L., A.N.S.); McMaster Service Lab; Canada Foundation for Innovation [34531 to A.G.M., in part]. Conflict of interest statement. None declared.

Publisher Copyright:
© 2019 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

ASJC Scopus Subject Areas

Genetics

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10.1093/nar/gkz935

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Alcock, B. P., Raphenya, A. R., Lau, T. T. Y., Tsang, K. K., Bouchard, M., Edalatmand, A., Huynh, W., Nguyen, A. L. V., Cheng, A. A., Liu, S., Min, S. Y., Miroshnichenko, A., Tran, H. K., Werfalli, R. E., Nasir, J. A., Oloni, M., Speicher, D. J., Florescu, A., Singh, B., ... McArthur, A. G. (2020). CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Research, 48(D1), D517-D525. https://doi.org/10.1093/nar/gkz935

Alcock, BP, Raphenya, AR, Lau, TTY, Tsang, KK, Bouchard, M, Edalatmand, A, Huynh, W, Nguyen, ALV, Cheng, AA, Liu, S, Min, SY, Miroshnichenko, A, Tran, HK, 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, GV & McArthur, AG 2020, 'CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database', Nucleic Acids Research, vol. 48, no. D1, pp. D517-D525. https://doi.org/10.1093/nar/gkz935

@article{d4c6337178524024920fd64c30816b5a,

title = "CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database",

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.",

author = "Alcock, {Brian P.} and Raphenya, {Amogelang R.} and Lau, {Tammy T.Y.} and Tsang, {Kara K.} and M{\'e}gane Bouchard and Arman Edalatmand and William Huynh and Nguyen, {Anna Lisa V.} and Cheng, {Annie A.} and Sihan Liu and Min, {Sally Y.} and Anatoly Miroshnichenko and Tran, {Hiu Ki} and Werfalli, {Rafik E.} and Nasir, {Jalees A.} and Martins Oloni and Speicher, {David J.} and Alexandra Florescu and Bhavya Singh and Mateusz Faltyn and Anastasia Hernandez-Koutoucheva and Sharma, {Arjun N.} and Emily Bordeleau and Pawlowski, {Andrew C.} and Zubyk, {Haley L.} and Damion Dooley and Emma Griffiths and Finlay Maguire and Winsor, {Geoff L.} and Beiko, {Robert G.} and Brinkman, {Fiona S.L.} and Hsiao, {William W.L.} and Domselaar, {Gary V.} and McArthur, {Andrew G.}",

note = "Funding Information: Canadian Institutes of Health Research [PJT-156214 to A.G.M.]; Genome Canada (to R.G.B., F.S.L.B, W.W.L.H.); Cisco Systems Canada, Inc., Cisco Research Chair in Bioinformatics (to A.G.M.); Ontario Graduate Scholarship (to K.K.T.); McMaster University{\textquoteright}s MacDATA Institute Graduate Fellowship (to K.K.T.); Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Michael Kamin Hart Memorial Scholarship (to K.K.T.); Ontario Graduate Scholarship (to H.L.Z.); Frederick Banting and Charles Best Canada Graduate Scholarship (CGS-D) (to E.B.); Donald Hill Family Fellowship in Computer Science (to F.M.); Natural Sciences and Engineering Research Council Banting Postdoctoral Fellowship (to A.C.P.); Mi-tacs Globalink Research Internship (to A.H-K.); IIDR Summer Student Fellowship (to H-K.T., T.T.Y.L., A.N.S.); McMaster Service Lab; Canada Foundation for Innovation [34531 to A.G.M., in part]. Conflict of interest statement. None declared. Publisher Copyright: {\textcopyright} 2019 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2020",

month = jan,

day = "1",

doi = "10.1093/nar/gkz935",

language = "English",

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T1 - CARD 2020

T2 - 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.

N1 - Funding Information: Canadian Institutes of Health Research [PJT-156214 to A.G.M.]; Genome Canada (to R.G.B., F.S.L.B, W.W.L.H.); Cisco Systems Canada, Inc., Cisco Research Chair in Bioinformatics (to A.G.M.); Ontario Graduate Scholarship (to K.K.T.); McMaster University’s MacDATA Institute Graduate Fellowship (to K.K.T.); Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Michael Kamin Hart Memorial Scholarship (to K.K.T.); Ontario Graduate Scholarship (to H.L.Z.); Frederick Banting and Charles Best Canada Graduate Scholarship (CGS-D) (to E.B.); Donald Hill Family Fellowship in Computer Science (to F.M.); Natural Sciences and Engineering Research Council Banting Postdoctoral Fellowship (to A.C.P.); Mi-tacs Globalink Research Internship (to A.H-K.); IIDR Summer Student Fellowship (to H-K.T., T.T.Y.L., A.N.S.); McMaster Service Lab; Canada Foundation for Innovation [34531 to A.G.M., in part]. Conflict of interest statement. None declared. Publisher Copyright: © 2019 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2020/1/1

Y1 - 2020/1/1

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.

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

Abstract

Bibliographical note

ASJC Scopus Subject Areas

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