Dataset Information

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.

SUBMITTER: Alcock BP

PROVIDER: S-EPMC7145624 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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

Alcock Brian P BP Raphenya Amogelang R AR Lau Tammy T Y TTY Tsang Kara K KK Bouchard Mégane M Edalatmand Arman A Huynh William W Nguyen Anna-Lisa V AV Cheng Annie A AA Liu Sihan S Min Sally Y SY Miroshnichenko Anatoly A Tran Hiu-Ki HK Werfalli Rafik E RE Nasir Jalees A JA Oloni Martins M Speicher David J DJ Florescu Alexandra A Singh Bhavya B Faltyn Mateusz M Hernandez-Koutoucheva Anastasia A Sharma Arjun N AN Bordeleau Emily E Pawlowski Andrew C AC Zubyk Haley L HL Dooley Damion D Griffiths Emma E Maguire Finlay F Winsor Geoff L GL Beiko Robert G RG Brinkman Fiona S L FSL Hsiao William W L WWL Domselaar Gary V GV McArthur Andrew G AG

Nucleic acids research 20200101 D1

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 fo ...[more]

PMID: 31665441

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Project description:PurposeThis study aimed to report on in vitro susceptibility patterns among corneal isolates collected in the Antibiotic Resistance Monitoring in Ocular micRoorganisms (ARMOR) study.MethodsEach year, from 2009 to 2019, Staphylococcus aureus, coagulase-negative staphylococci (CoNS), Streptococcus pneumoniae, Pseudomonas aeruginosa, and Haemophilus influenzae isolates cultured from patients with ocular infections at participating ARMOR sites were submitted to a central laboratory for species confirmation and antibiotic susceptibility testing. In this analysis of corneal isolates, odds ratios for concurrent resistance were based on sample proportions, one-way ANOVA was used to evaluate resistance by patient age, and Cochran-Armitage tests were used to examine changes in antibiotic resistance over time.ResultsA total of 1499 corneal isolates were collected from 61 sites over the 11-year period. Overall, 34.5% (148 of 429) of S. aureus and 41.9% (220 of 525) of CoNS isolates were methicillin resistant and had higher odds ratios for concurrent resistance to azithromycin (17.44 and 5.67), ciprofloxacin (39.63 and 12.81), and tobramycin (19.56 and 19.95), respectively, relative to methicillin-susceptible isolates (P < .001, all); also, a high proportion of methicillin-resistant S. aureus (85.1%) and methicillin-resistant CoNS (81.8%) were multidrug resistant (at least three classes of antibiotics). Resistance among S. pneumoniae isolates was highest for azithromycin (33.1%), whereas P. aeruginosa and H. influenzae isolates demonstrated low resistance overall. Among staphylococci, antibiotic resistance differed by patient age (S. aureus: F = 6.46, P < .001; CoNS: F = 4.82, P < .001), and few small changes in resistance (≤3.60% per year), mostly decreases, were observed over time.ConclusionsAlthough rates of in vitro antibiotic resistance among presumed keratitis isolates obtained in ARMOR seemed stable between 2009 and 2019, resistance among staphylococci and pneumococci remains high (and should be considered when treating keratitis).

Dataset Information

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

Publications

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

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