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
Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways
Kasey A Webb,Olusola Olagoke,Timothy Baird,Jane Neill,Amy Quynh Trang Pham,Timothy J. Wells,Kay A. Ramsay,Scott C. Bell,Derek S. Sarovich,Erin P. Price +9 more
TL;DR: Comparison genomics was used to develop a real-time PCR assay to permit rapid Prevotella species identification and quantification from cultures and clinical specimens, and the addition of 35 airway-derived Prevotlla genomes to public databases will enhance ongoing efforts to unravel the role of this diverse and enigmatic genus.
Journal ArticleDOI
Whole-Genome Sequencing of a Colistin-Resistant Acinetobacter baumannii Strain Isolated at a Tertiary Health Facility in Pretoria, South Africa
TL;DR: The mosaic of the virulence factors coupled with the resistance-associated genes and the phenotypic resistance profile highlights the risk that this strain is at this South African tertiary health facility.
Journal ArticleDOI
Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary
TL;DR: In this paper, the authors performed a comparative genome analysis of four methicillin-resistant S. aureus clinical isolates from Germany and Hungary based on their previous polyphasic characterization finding.
Posted ContentDOI
ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data
TL;DR: This work introduces ResistoXplorer, a user-friendly tool that integrates recent advancements in statistics and visualization, coupled with extensive functional annotations and phenotype collection, to enable high-throughput analysis of common outputs generated from metagenomic resistome studies.
Journal ArticleDOI
Phenotypic and Genotypic Analysis of Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Beef Cattle in Australia
Yohannes Equar Messele,M. Alkhallawi,Tania Veltman,Darren J. Trott,J. P. McMeniman,Stephen P. Kidd,Wai Yee Low,Kiro R. Petrovski +7 more
TL;DR: It is demonstrated that E. coli isolated from feedlot beef cattle can harbour AMR genes, but the low incidence of medically important resistance reflected the prudent antimicrobial use in the Australian industry.
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