CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
Brian 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 R Tran,Rafik El Werfalli,Jalees A. Nasir,Martins Oloni,David Speicher,Alexandra Florescu,Bhavya Singh,Mateusz Faltyn,Anastasia Hernández-Koutoucheva,Arjun N. Sharma,Emily Bordeleau,Andrew C. Pawlowski,Haley L. Zubyk,Damion M. Dooley,Emma Griffiths,Finlay Maguire,Geoffrey L. Winsor,Robert G. Beiko,Fiona S. L. Brinkman,William W. L. Hsiao,William W. L. Hsiao,Gary Van Domselaar,Gary Van Domselaar,Andrew G. McArthur +35 more
TLDR
A new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes, able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants.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.read more
Citations
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Molecular epidemiology of Clostridioides difficile in companion animals: Genetic overlap with human strains and public health concerns
Frederico Ramos Alves,Rita Castro,Miguel Pinto,Alexandra Nunes,Constança Pomba,Manuela Oliveira,Leonor de Sousa Dâmaso da Silveira,João Paulo Gomes,Mónica Oleastro +8 more
TL;DR: In this article , the authors describe the C. difficile strains circulating in canine and feline populations, and evaluate their genetic overlap with human strains to assess the possibility of interspecies transmission.
Journal ArticleDOI
Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis
TL;DR: In this article , a multidrug-resistant Vibrio alfacsensis strain was matched with an Escherichia coli strain, and then determined the complete genome sequences of the donor and the transconjugant strains.
Posted ContentDOI
Metrics for Public Health Perspective Surveillance of Bacterial Antibiotic Resistance in Low- and Middle-Income Countries
Olga Tosas Auguet,Rene Niehus,Hyun S. Gweon,James A. Berkley,Joseph Waichungo,Tsi Njim,Jonathan D. Edgeworth,Rahul Batra,Kevin K Chau,Jeremy Swann,Sarah Walker,Tim E. A. Peto,Derrick W. Crook,Sarah Lamble,Paul Turner,Ben S. Cooper,Nicole Stoesser +16 more
TL;DR: Intermittent metagenomics of pooled human samples could represent a powerful pragmatic and economical approach for determining and monitoring AMR in clinical infections, especially in resource-limited settings.
Journal ArticleDOI
Antimicrobial Susceptibility Testing Performed in RPMI 1640 Reveals Azithromycin Efficacy against Carbapenem-Resistant Acinetobacter baumannii and Predicts In Vivo Outcomes in Galleria mellonella
TL;DR: In this paper , the authors performed an AST in RPMI 1640, a more physiologically relevant culture medium, revealed that a substantial proportion of carbapenem-resistant Acinetobacter baumannii isolates were susceptible to azithromycin, a macrolide antibiotic not currently considered effective against A. baum annii.
Journal ArticleDOI
Phages from Genus Bruynoghevirus and Phage Therapy: Pseudomonas Phage Delta Case
Petar Knezevic,Aleksandra Petrovic Fabijan,Damir Gavric,Jovana Pejic,Zsolt Doffkay,Gábor Rákhely +5 more
TL;DR: The applicability and safety of bacteriophage Delta as a potential anti-Pseudomonas aeruginosa agent belonging to genus Bruynoghevirus (family Podoviridae) was characterised in this article.
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