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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CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database
Brian Alcock,William Huynh,Romeo Chalil,Keaton W Smith,Amogelang R. Raphenya,Mateusz A Wlodarski,Arman Edalatmand,Aaron Petkau,Sohaib A Syed,Kara K. Tsang,Sheridan J C Baker,Mugdha Dave,Madeline C. McCarthy,Karyn M Mukiri,Jalees A. Nasir,Bahar Golbon,Hamna Imtiaz,Xingjian Jiang,Komal Kaur,Megan Kwong,Zi Cheng Liang,Keyu C Niu,Prabakar Shan,Jasmine Y J Yang,Kristen L Gray,Gemma Hoad,Baoguo Jia,Timsy Bhando,Lindsey A. Carfrae,Maya A. Farha,Shawn French,Rodion Gordzevich,Kenneth Rachwalski,Megan M Tu,Emily Bordeleau,Damion M. Dooley,Emma Griffiths,Haley L. Zubyk,Eric D. Brown,Finlay Maguire,Robert G. Beiko,William C. Hsiao,Fiona S. L. Brinkman,Gary Van Domselaar,Andrew G. McArthur +44 more
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Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle.
Aleksandra Miłobędzka,Catarina Ferreira,Ivone Vaz-Moreira,David Calderón-Franco,Adrian Gorecki,Sabina Purkrtova,Jan Bartacek,Lukasz Dziewit,Caitlin M. Singleton,Per Halkjær Nielsen,David G. Weissbrodt,Célia M. Manaia +11 more
TL;DR: A review of the state of the art of antibiotic resistance (AR) monitoring methods, considering distinct needs, objectives and available resources, is presented in this paper, where the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts is discussed.
Journal ArticleDOI
TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis.
Karen E. Ross,Alessandro M. Varani,Erik Snesrud,Hongzhan Huang,Danillo Oliveira Alvarenga,Jian Zhang,Cathy H. Wu,Patrick McGann,Mick Chandler +8 more
TL;DR: TnCentral as mentioned in this paper is a web resource for prokaryotic transposable elements (TE) which contains ∼400 carefully annotated TE, including transposons from the Tn3, Tn7 and Tn402 families; compound transposions; integrons; and associated insertion sequences.
Journal ArticleDOI
Next generation sequencing approaches to evaluate water and wastewater quality.
Emily Garner,Benjamin C. Davis,Erin Milligan,Matthew Forrest Blair,Ishi Keenum,Ayella Maile-Moskowitz,Jin Pan,Mariah Gnegy,Krista Liguori,Suraj Gupta,Aaron J. Prussin,Linsey C. Marr,Lenwood S. Heath,Peter J. Vikesland,Liqing Zhang,Amy Pruden +15 more
TL;DR: The emergence of Next Generation Sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry as discussed by the authors, which can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop new assay for each target organism or gene.
Journal ArticleDOI
Reservoirs of antimicrobial resistance genes in retail raw milk.
Jinxin Liu,Yuanting Zhu,Michele T. Jay-Russell,Danielle G. Lemay,Danielle G. Lemay,Danielle G. Lemay,David A. Mills +6 more
TL;DR: Despite advertised “probiotic” effects, the results indicate that raw milk microbiota has minimal lactic acid bacteria.
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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