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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Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents
Haley Sanderson,Kristen L Gray,Alexander Manuele,Finlay Maguire,Amjad Khan,Chaoyue Liu,Chandana N. Rudrappa,John H. E. Nash,James D. Robertson,Kyrylo Bessonov,Martins Oloni,Brian Alcock,Amogelang R. Raphenya,Tim A. McAllister,Sharon J. Peacock,Kathy E. Raven,Theodore Gouliouris,Andrew G. McArthur,Fiona S. L. Brinkman,Ryan C. Fink,Rahat Zaheer,Robert G. Beiko +21 more
TL;DR: In this paper , features including resistance determinants, virulence factors, and mobile genetic elements (MGEs) were profiled in a set of 1273 E. faecium genomes from two disparate geographic locations (in the UK and Canada) from a range of agricultural, clinical, and associated habitats.
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Agronomic efficiency and genome mining analysis of the wheat-biostimulant rhizospheric bacterium Pseudomonas pergaminensis sp. nov. strain 1008T
Marisa Díaz,Teresa Bach,Gustavo Gonzalez Anta,Betina Cecilia Agaras,Daniel Wibberg,Fabián Noguera,Wilter Canciani,Claudio Valverde +7 more
TL;DR: Pseudomonas sp.
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ApmA Is a Unique Aminoglycoside Antibiotic Acetyltransferase That Inactivates Apramycin.
Emily Bordeleau,Peter J. Stogios,Peter J. Stogios,Elena Evdokimova,Elena Evdokimova,Kalinka Koteva,Alexei Savchenko,Alexei Savchenko,Gerard D. Wright +8 more
TL;DR: In this article, the authors show that apramycin is structurally unique among the previously described aminoglycoside-modifying enzymes and capable of conferring a high level of resistance to aparamycin.
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β-Lactamase–Producing, Ciprofloxacin-Resistant Neisseria meningitidis Isolated From a 5-Month-Old Boy in the United States
Gillian Taormina,Joseph M. Campos,John Sweitzer,Adam C. Retchless,Kristy Lunquest,Lucy A McNamara,Natashia Reese,Maria Karlsson,Benjamin Hanisch +8 more
TL;DR: The first known case of disease in the United States due to a β-lactamase-producing, ciprofloxacin-resistant N. meningitidis was recently identified, which has potential implications on standard laboratory testing and empiric management of meningococcal disease.
Journal ArticleDOI
Machine Learning Prediction of Resistance to Subinhibitory Antimicrobial Concentrations from Escherichia coli Genomes.
Sam Benkwitz-Bedford,Martin Palm,Talip Yasir Demirtas,Ville Mustonen,Ville Mustonen,Anne Farewell,Jonas Warringer,Leopold Parts,Danesh Moradigaravand +8 more
TL;DR: In this paper, the authors used machine learning to predict the population doubling time and cell growth yield of 1,407 genetically diverse E. coli strains under exposure to three subinhibitory concentrations of six classes of antimicrobials from single-nucleotide genetic variants, accessory gene variation, and the presence of known AMR genes.
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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