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
A Quantitative Metagenomic Sequencing Approach for High Throughput Gene Quantification and Demonstration with Environmental Antibiotic Resistance Genes
TL;DR: In this article, a quantitative metagenomic next-generation sequencing (qmNGS) approach was developed and tested to determine the sequencing yield (Yseq), which can then be used to calculate absolute concentration of target genes in environmental samples.
Journal ArticleDOI
Colistin and Carbapenem-Resistant Acinetobacter baumannii Aci46 in Thailand: Genome Analysis and Antibiotic Resistance Profiling.
TL;DR: In this paper, the genotypic characteristics of Acinetobacter baumannii Aci46 were investigated using Next Generation Sequencing (NGS) to obtain whole genome data.
Posted ContentDOI
Genomic diversity and molecular epidemiology of a multidrug resistant Pseudomonas aeruginosa DMC30b isolated from hospitalized burn patient in Bangladesh
TL;DR: The complete genome sequence of a multidrug resistant P. aeruginosa DMC30b will aid in understanding the evolution and phylogeny of such high-risk clones and provide a solid basis for further research on MDR or extensively drug resistant strains.
Journal ArticleDOI
Mining therapeutic targets from the antibiotic-resistant Campylobacter coli and virtual screening of natural product inhibitors against its riboflavin synthase
Khurshid Jalal,Kanwal Waseem Khan,Ajmal Hayat,Diyar Ahmad,Ghallab Alotaibi,Reaz Uddin,Mutaib M Mashraqi,Ahmad A. Alzamami,M. Aurongzeb,Zarrin Basharat +9 more
TL;DR: G genomes of 89 antibiotic-resistant strains of C. coli were downloaded from the PATRIC database and compounds identified appear safe for targeting this pathogen and can be further validated by experimental analysis before clinical trials.
Journal ArticleDOI
Characterization of a Conjugative Multidrug Resistance IncP-2 Megaplasmid, pPAG5, from a Clinical Pseudomonas aeruginosa Isolate
TL;DR: Plasmid pPAG5 is the largest multidrug resistance plasmid ever sequenced in the Pseudomonas genus and is capable of transferring resistance genes to transconjugants and producing aMultidrug-resistant phenotype.
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