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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A Glyphosate-Based Herbicide Cross-Selects for Antibiotic Resistance Genes in Bacterioplankton Communities
TL;DR: In this paper , the effects of glyphosate-based herbicides on ARGs were investigated in natural aquatic communities, which are often contaminated with pesticides from agricultural runoff, and the results showed that GBHs may have the unintended consequence of selecting for antibiotic resistance genes (ARGs).
Journal ArticleDOI
Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions.
Lucas Palma Perez Braga,Roberta Verciano Pereira,Layla Farage Martins,Livia Maria Silva Moura,Fabio Beltrame Sanchez,José S. L. Patané,Aline Maria Da Silva,João C. Setubal +7 more
TL;DR: In this article, 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level.
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A Peek into the Plasmidome of Global Sewage.
TL;DR: The plasmidome of 24 samples (22 countries, 5 continents) from the global sewage surveillance project was investigated in this article. But, the results showed that only about 90% of the circular DNA elements did not have any similarity to known plasmids.
Journal ArticleDOI
Genomics and pathotypes of the many faces of Escherichia coli
TL;DR: A birds-eye view of the E. coli species is taken, characterizing it from historical, clinical, and genetic perspectives, and advocating streamlining efforts for clinical reporting of ExPEC and emphasizing the pathogenic potential that exists throughout the entire species.
Journal ArticleDOI
Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema.
Zhaoyan Chen,Hang Cheng,Zhao Cai,Qingjun Wei,Jinlong Li,Jinhua Liang,Wenshu Zhang,Zhijian Yu,Dongjing Liu,Lei Liu,Zhenqiang Zhang,Ke Wang,Liang Yang +12 more
TL;DR: In this article, the authors carried out a metagenomic snapshot of the pleural effusion from 45 empyema patients by Illumina sequencing platform to assess its taxonomic, and antibiotic resistome structure.
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