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. 2023 Jan 6;51(D1):D690-D699.
doi: 10.1093/nar/gkac920.

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

Brian P Alcock  1   2   3 , William Huynh  1   2   3 , Romeo Chalil  1   2   3 , Keaton W Smith  1   2   3 , Amogelang R Raphenya  1   2   3 , Mateusz A Wlodarski  1   2   3 , Arman Edalatmand  1   2   3 , Aaron Petkau  4   5 , Sohaib A Syed  1   2   3 , Kara K Tsang  1   2   3 , Sheridan J C Baker  1   2   3 , Mugdha Dave  1   2   3 , Madeline C McCarthy  1   2   3 , Karyn M Mukiri  1   2   3 , Jalees A Nasir  1   2   3 , Bahar Golbon  1   2   3 , Hamna Imtiaz  1   2   3 , Xingjian Jiang  1   2   3 , Komal Kaur  1   2   3 , Megan Kwong  1   2   3 , Zi Cheng Liang  1   2   3 , Keyu C Niu  1   2   3 , Prabakar Shan  1   2   3 , Jasmine Y J Yang  1   2   3 , Kristen L Gray  6 , Gemma R Hoad  7 , Baofeng Jia  6 , Timsy Bhando  1   2   3 , Lindsey A Carfrae  1   2   3 , Maya A Farha  1   2   3 , Shawn French  1   2   3 , Rodion Gordzevich  1   2   3 , Kenneth Rachwalski  1   2   3 , Megan M Tu  1   2   3 , Emily Bordeleau  1   2   3 , Damion Dooley  8 , Emma Griffiths  8 , Haley L Zubyk  1   2   3 , Eric D Brown  1   2   3 , Finlay Maguire  9   10   11 , Robert G Beiko  9   10 , William W L Hsiao  6   8 , Fiona S L Brinkman  6 , Gary Van Domselaar  5   12 , Andrew G McArthur  1   2   3
Affiliations

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

Brian P Alcock et al. Nucleic Acids Res. .

Abstract

The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.

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Figures

Figure 1.
Figure 1.
Prevalence of individual AMR Gene Families in data collected by CARD:Live, broken down by predicted pathogen of the submitted genome sequences. Approximately 60% of submitted genome sequences have an ARG from the major facilitator superfamily (MFS) antibiotic efflux pumps.
Figure 2.
Figure 2.
Schematic workflow for CARD Resistomes and Variants. (A) Data is retrieved by downloading available genome assemblies for a list of pathogens from NCBI’s RefSeq database. Retrieved genome assemblies are subsequently parsed to identify plasmid- and chromosome-originating sequences, while genomic islands are identified separately through IslandViewer 4. (B) Each pathogen is specified using the NCBI Taxonomy Database ID and the genome data integrity is verified with an MD5 checksum. (C) Each genome is analyzed with RGI to generate a predicted resistome, which is then filtered to remove divergent or otherwise dissimilar homologs below the respective CARD model threshold for RGI (‘Loose’). (D) The remaining high-fidelity predictions (RGI ‘Perfect’ and ‘Strict’ categories) are parsed to integrate predicted resistome information and genomic sequences into the Broad Street PostgreSQL schema underlying CARD, where the data is contextualized through CARD and the ARO. These data are then uploaded to the CARD website where they are available publicly for viewing, download, or use by RGI’s metagenomic read mapping algorithms.
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References

    1. McArthur A.G., Waglechner N., Nizam F., Yan A., Azad M.A., Baylay A.J., Bhullar K., Canova M.J., De Pascale G., Ejim L.et al.. The Comprehensive Antibiotic Resistance Database. Antimicrob. Agents Chemother. 2013; 57:3348–3357. - PMC - PubMed
    1. Tacconelli E., Carrara E., Savoldi A., Harbarth S., Mendelson M., Monnet D.L., Pulcini C., Kahlmeter G., Kluytmans J., Carmeli Y.et al.. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect. Dis. 2018; 18:318–327. - PubMed
    1. CDC Antibiotic Resistance Threats in the United States, 2019. 2019; Atlanta, GA: U.S. Department of Health and Human Services, CDC.
    1. The Expert Panel on the Potential Socio-Economic Impacts of Antimicrobial Resistance in Canada When Antibiotics Fail. 2019; Ottawa, ON: Council of Canadian Academies.
    1. O’Neill J. Tackling drug-resistant infections globally: final report and recommendations. The Review on Antimicrobial Resistance. 2016; London.

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