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
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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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Journal ArticleDOI
Whole genome sequencing of coagulase positive staphylococci from a dog-and-owner screening survey.
Judit Sahin-Tóth,Eszter Kovács,Adrienn Tóthpál,János Juhász,János Juhász,Barbara Forró,Krisztián Bányai,Kata Havril,Andrea Horváth,Ágoston Ghidán,Orsolya Dobay +10 more
TL;DR: In this article, the authors used pulsed-field gel electrophoresis (PFGE) to identify co-carriage between S. aureus and S. pseudintermedius.
Journal ArticleDOI
Incubation trial indicated the earthworm intestinal bacteria as promising biodigestor for mitigating tetracycline resistance risk in anthropogenic disturbed forest soil.
TL;DR: Wang et al. as mentioned in this paper collected forest soil in the Yangtze River Delta, China, and its resident Metaphire guillelmi to investigate the interaction between tetracycline (50 μg kg-1) and the bacteria in worm gut and soil.
Journal ArticleDOI
Genome analysis and antimicrobial resistance characteristics of Chryseobacterium aquaticum isolated from farmed salmonids
TL;DR: It is concluded that antimicrobial resistance could be of intrinsic nature and demonstrated a strong correlation between these genes in the genome of C-174 and mortality in the rainbow trout.
Proceedings ArticleDOI
KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data
Mattia Prosperi,Simone Marini +1 more
TL;DR: KARGA as mentioned in this paper is a multi-platform Java toolkit for identifying ARGs from metagenomic short read data, which uses an efficient double-lookup strategy, statistical filtering on false positives, and provides individual read classification as well as covering the database resistome.
Journal ArticleDOI
Exploring antimicrobial resistance to beta-lactams, aminoglycosides and fluoroquinolones in E. coli and K. pneumoniae using proteogenomics
Dimard E. Foudraine,Nikolaos Strepis,Christoph Stingl,Marian T. ten Kate,Annelies Verbon,Corné H. W. Klaassen,Wil H. F. Goessens,Theo M. Luider,Lennard J. M. Dekker +8 more
TL;DR: In this paper, a multi-omics approach was proposed to analyze resistance against frequently used antibiotics within the beta-lactam, aminoglycoside and fluoroquinolone group in E. coli and K. pneumoniae isolates.
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