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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Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs
Nattinee Kittiwan,Jessica K. Calland,Evangelos Mourkas,Matthew D. Hitchings,Susan Murray,Pakpoom Tadee,Phacharaporn Tadee,Kwanjit Duangsonk,Guillaume Méric,Samuel K. Sheppard,Prapas Patchanee,Ben Pascoe +11 more
TL;DR: In this paper , a collection of pigs from Chiang Mai province, Northern Thailand were sampled and sequenced to identify growing antimicrobial resistance (AMR) among invasive S. suis.
Journal ArticleDOI
Genomics of Tenacibaculum Species in British Columbia, Canada
Joseph P. Nowlan,Ashton N. Sies,Scott R. Britney,Andrew D. S. Cameron,Ahmed Siah,John S. Lumsden,S. Russell +6 more
TL;DR: In this article , the authors used the MinION platform for whole-genome sequencing of 10 species of Tenacibaculum from Atlantic salmon with mouthrot in British Columbia, Canada.
Journal ArticleDOI
Quantification of antibiotic resistance genes (ARGs) in clouds at a mountain site (puy de Dôme, central France)
TL;DR: In this article , the presence of antibiotic resistant genes (ARGs) in clouds was assessed as an indicator of long-distance travel potential of antibiotic resistance in the atmosphere, and it was shown that a variety of ARGs can reach the altitude of clouds mainly located within the free troposphere.
Journal ArticleDOI
Predictive Power of Long-Read Whole-Genome Sequencing for Rapid Diagnostics of Multidrug-Resistant Brachyspira hyodysenteriae Strains
Nick Vereecke,Nadine Botteldoorn,Charlotte Brossé,Caroline Bonckaert,Hans Nauwynck,Freddy Haesebrouck,Filip Boyen,Dominiek Maes,Sebastiaan Theuns +8 more
TL;DR: In this paper , the authors used a Bonito base-calling model to identify Brachyspira hyodysenteriae (B. hydysentiae) field isolates.
Journal ArticleDOI
Molecular Characterization of Salmonella Detected along the Broiler Production Chain in Trinidad and Tobago
Anisa S. Khan,Rian Pierneef,Narjol Gonzalez-Escalona,Meghan Maguire,Cong Li,Gregory H. Tyson,Sherry Ayers,Karla Georges,Woubit Abebe,Abiodun A. Adesiyun +9 more
TL;DR: This cross-sectional study determined the serovars, antimicrobial resistance genes, and virulence factors of Salmonella isolated from hatcheries, broiler farms, processing plants, and retail outlets in Trinidad and Tobago to help future source tracking during epidemiological investigations associated withSalmonella foodborne outbreaks in the region and worldwide.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
BLAST+: architecture and applications.
Christiam Camacho,George Coulouris,Vahram Avagyan,Ning Ma,Jason S. Papadopoulos,Kevin Bealer,Thomas L. Madden +6 more
TL;DR: The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences.
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