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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Journal ArticleDOI
Exploring Antibiotic Resistance Diversity in Leuconostoc spp. by a Genome-Based Approach: Focus on the lsa A Gene.
TL;DR: In this article, a total of 131 putative antibiotic resistance (AR) traits associated with the main clinically relevant antibiotics were detected, including clindamycin (CLI) and quinupristin-dalfopristin (QUD) resistance.
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Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes
TL;DR: In this paper , the authors used metagenome-assembled genomes (MAGs) extracted from pigs at multiple time points to identify the most commonly distributed metagenomic species, such as Collinsella, Sodaliphilus, and Prevotella.
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Extended-Spectrum β-Lactamases in Human Isolates of Multidrug-Resistant Non-typhoidal Salmonella enterica.
Anahit M. Sedrakyan,Zhanna A. Ktsoyan,Karine A. Arakelova,Magdalina K. Zakharyan,Alvard I. Hovhannisyan,Zaruhi Gevorgyan,Armine A. Mnatsakanyan,Elene Kakabadze,Khatuna Makalatia,Nina Chanishvili,Jean-Paul Pirnay,Arsen Arakelyan,Rustam Aminov +12 more
TL;DR: A total of 291 non-duplicate isolates of non-typhoidal Salmonella (NTS) were collected from the fecal samples of patients with salmonellosis in Armenia and Georgia during 1996-2016 as discussed by the authors.
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Carbendazim shapes microbiome and enhances resistome in the earthworm gut
Jiajin Song,Tongxin Li,Zhiruo Zheng,Wenjie Fu,Zhengnan Long,Nan Shi,Yuling Han,Luqing Zhang,Yunlong Yu,Hua Fang +9 more
TL;DR: In this paper , Eisenia fetida was selected to investigate the effects of CBD in the soil-earthworm systems using shotgun metagenomics and qPCR methods, which may provide a novel insight into the neglected ecotoxicological risk of the widely used agrochemicals on the gut resistome of earthworm dwelling in soil.
Journal ArticleDOI
Genome-Resolved Metagenomics and Antibiotic Resistance Genes Analysis in Reclaimed Water Distribution Systems
Changzhi Wang,Pei-Ying Hong +1 more
TL;DR: The metagenomic data suggest that low DOC is needed to maintain the biological stability of reclaimed water along the distribution network.
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