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CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

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.

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Actively replicating gut bacteria identified by 5-ethynyl-2’-deoxyuridine (EdU) click chemistry and cell sorting

TL;DR: In this article , a combination of 5-ethynyl-2'-deoxyuridine (EdU) click chemistry and fluorescence-activated cell sorting and sequencing (FACS-Seq) was used to characterize replicating gut bacteria.
Journal ArticleDOI

Actively replicating gut bacteria identified by 5-ethynyl-2’-deoxyuridine (EdU) click chemistry and cell sorting

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Complete Genome Sequence of Morganella morganii CTX51T, Isolated from a Human Cecal Adenocarcinoma

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Top-Down Genomic Surveillance Approach to Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of<i>Enterococcus faecium</i>Detected in Cancer Patients in Arkansas

TL;DR: In this article , a comprehensive analysis of over one hundred E. faecium isolates collected from 66 cancer patients at the University of Arkansas for Medical Sciences (UAMS) between June, 2018 and May, 2019 is presented.
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