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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Novel Approach for Microbiome Analysis Using Bacterial Replication Rates and Causal Inference with Applications
TL;DR: A novel approach for metagenomic analysis is introduced that integrates microbial community profiling, replication rate calculation, and causal structural learning to analyze the antibiotic response and applies it to the data from an infant gut microbiome study.
Journal ArticleDOI
Methicillin Resistant Staphylococci Isolated from Goats and Their Farm Environments in Saudi Arabia Genotypically Linked to Known Human Clinical Isolates: a Pilot Study
Wael M. El-Deeb,Rory Cave,Mahmoud Fayez,Naser A. Al-Humam,Sayed A Quadri,Hermine V. Mkrtchyan +5 more
TL;DR: It is highlighted that implementing a holistic approach to whole genome sequencing surveillance in livestock and farm environments would aid the understanding of the transmission of methicillin resistant staphylococci and, most importantly, allow us to implement appropriate infection control and hygiene practices.
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Antibiotic resistance genes in the aquaculture sector: global reports and research gaps
Justin O.G. Kemp,Jessica J. Taylor,Lisa A. Kelly,Renée Larocque,Armando Heriazon,Kevin H. D. Tiessen,Steven J. Cooke +6 more
TL;DR: Aquaculture has been one of the fastest-growing food production systems over the last decade and increased intensification of production has created conditions that favour disease outbreaks.
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Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil
Danitza Romero-Calle,Francisnei Pedrosa-Silva,Luiz Marcelo Ribeiro Tomé,Thiago de Jesus Sousa,Leila Thaise Santana de Oliveira Santos,V. A. de Carvalho Azevedo,Bertram Brenig,Raquel G. Benevides,Thiago M. Venancio,Craig Billington,Aristóteles Góes-Neto +10 more
TL;DR: In this paper , a hybrid sequence assembly approach was used for environmental Salmonella genome analysis using HiSeq and MinION data, which yielded 10 contigs with 99.98% identity with S. enterica serovar Enteritidis OLF-SE2-98984-6.
Journal ArticleDOI
Draft Genome Sequence of Bifidobacterium pseudocatenulatum Bif4, Isolated from Healthy Infant Feces.
Atul Munish Chander,Shashank K. Singh,Shikha Sharma,Vasvi Chaudhry,Sivasubramanian Rajarammohan,Shrikant Mantri,Mahendra Bishnoi,Sanjay Kumar Bhadada,Kanthi Kiran Kondepudi +8 more
TL;DR: The 2.24-Mb draft genome sequence of Bifidobacterium pseudocatenulatum Bif4, isolated from a fecal sample from a healthy infant revealed genes predictive of its probiotic attributes.
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