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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Molecular Detection of Metronidazole and Tetracycline Resistance Genes in Helicobacter pylori-Like Positive Gastric Samples from Pigs
Francisco Cortez Nunes,Emily Taillieu,Teresa Letra Mateus,Sílvia Teixeira,Freddy Haesebrouck,Irina Amorim +5 more
TL;DR: In this paper , the presence of antibiotic resistance genes, previously reported in Helicobacter pylori, in gastric samples of 36 pigs, in which DNA of H.pylori-like organisms had been detected.
Journal ArticleDOI
Isolation and Characterization of Lytic Bacteriophages Targeting Diverse Enterobacter spp. Clinical Isolates
Amanda G. Finney,Jalyne M. Perry,Daniel R. Evans,Kevin J. Westbrook,Christi L. McElheny,Alina Iovleva,Yohei Doi,Ryan K. Shields,Daria Van Tyne +8 more
TL;DR: The phages isolated expand the diversity of Enterobacter-targeting phages, and could be useful for treating antibiotic-resistant Enterobacteria infections.
Journal ArticleDOI
Data on the genome of Bacillus subtilis A1- Midalam from beach soil.
Sneha Pramod,Rhea Thomas Thommana,Harini Kulanthaivelu Kanagam,Ashmitha Suresh Kumar,Santha Kalaikumari S,Elavarashi Elangovan,Kumar Perumal +6 more
TL;DR: The draft genome sequence of Bacillus subtilis A1, isolated from beach soil, has been shown to produce biofilm as discussed by the authors, and the genome size is 4,215,114 bp with an average G+C content of 43.5%.
Journal ArticleDOI
Can beta-lactamase resistance genes in anaerobic Gram-negative gut bacteria transfer to gut aerobes?
Journal ArticleDOI
Screening of colistin-resistant bacteria in livestock animals from France
Afaf Hamame,Bernard Davoust,Bouthaina Hasnaoui,David Lupande Mwenebitu,Jean-Marc Rolain,Seydina M. Diene +5 more
TL;DR: In this article , the emergence of colistin resistant (mcr)-1 and mcr-3 genes in pigs has been tracked using re-collected faecal samples from pigs in the south of France.
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