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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Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost
Tian-Lei Qiu,Linhe Huo,Yajie Guo,Min Gao,Guoliang Wang,Dong Hu,Cheng Li,Zhan-he Wang,Guiming Liu,Xuming Wang +9 more
TL;DR: In this paper , metagenomic assembly and cross-sample mapping were used to comprehensively decipher the common resistome and its potential mobility and hosts in animal manure and composts.
Journal ArticleDOI
Biological Mitigation of Antibiotic Resistance Gene Dissemination by Antioxidant-Producing Microorganisms in Activated Sludge Systems.
TL;DR: In this article, the authors examined how antioxidant-producing microorganisms inoculated in replicate activated sludge systems can biologically mitigate the dissemination of ARGs through removing reactive oxygen species (ROS) through quantitative polymerase chain reaction (qPCR).
Journal ArticleDOI
Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain From Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain
Mireya Viviana Belloso Daza,Giovanni Milani,C. Cortimiglia,Ester Pietta,Daniele Bassi,Pier Sandro Cocconcelli +5 more
TL;DR: This work highlights the significance of constant monitoring of products of animal origin, especially RTE foodstuffs, to stimulate the development of novel strategies in the race for constraining the spread of antibiotic resistance.
Journal ArticleDOI
Isolation, characterization, molecular analysis and application of bacteriophage DW-EC to control Enterotoxigenic Escherichia coli on various foods
Marta Nisita Dewanggana,C. Evangeline,Maurita Delia Ketty,Diana Elizabeth Waturangi,Yogiara,Stella Magdalena +5 more
TL;DR: In this article , the application of bacteriophage isolated from Indonesian traditional Ready-to-Eat (RTE) food to control ETEC population in various foods was investigated.
Journal ArticleDOI
Safety Evaluation of Lactobacillus delbrueckii subsp. lactis CIDCA 133: a Health-Promoting Bacteria
Luís Cláudio Lima de Jesus,Thiago de Jesus Sousa,Nina Dias Coelho-Rocha,Rodrigo Profeta,Fernanda Alvarenga Lima Barroso,Mariana Martins Drumond,Pamela Mancha-Agresti,Enio Ferreira,Bertram Brenig,Flávia Figueira Aburjaile,Vasco Azevedo +10 more
TL;DR: In this article, the safety aspects of Lactobacillus delbrueckii subsp. lactis CIDCA 133 based on whole-genome sequence and phenotypic analysis was investigated to avoid future questions about the harmful effects of this strain consumption.
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