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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Antibiotic resistance in the environment.
TL;DR: In this article, the authors present the current understanding of the roles of the environment, including antibiotic pollution, in resistance evolution, in transmission and as a mere reflection of the regional antibiotic resistance situation in the clinic.
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Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome.
Stephen Nayfach,David Paez-Espino,David Paez-Espino,Lee Call,Lee Call,Soo Jen Low,Hila Sberro,Natalia Ivanova,Natalia Ivanova,Amy D Proal,Michael A. Fischbach,Ami S. Bhatt,Philip Hugenholtz,Nikos C. Kyrpides,Nikos C. Kyrpides +14 more
TL;DR: The Metagenomic Gut Virus catalogue as discussed by the authors contains 189,680 genomes from 11,810 publicly available human stool metagenomes and identified 54,118 candidate viral species, 92% of which were not found in existing databases.
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Raw Cow Milk Bacterial Consortium as Bioindicator of Circulating Anti-Microbial Resistance (AMR).
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TL;DR: In this paper , the authors present a platform consisting of three modules, which are preconfigured bioinformatic pipelines, cloud toolsets, and online omics' courses, which combine analytic tools for metagenomics, genomes, transcriptome, proteomics and metabolomics.
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TL;DR: Antibiotics have been used to cure bacterial infections for more than 70 years, and these low-molecular-weight bioactive agents have also been used for a variety of other medicinal applications.
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