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
More filters
Journal ArticleDOI
ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics
TL;DR: This work presents ProPan, a public database covering 23 archaeal species and 1,481 bacterial species for comprehensively profiling prokaryotic pan-genome dynamics and develops a very user-friendly interface, flexible retrieval and multi-level real-time statistical visualization, which will serve as a weighty resource for the studies of proKaryoticPanGenome dynamics, taxonomy and identification as well as environmental adaptation.
Journal ArticleDOI
Soil Collected in the Great Smoky Mountains National Park Yielded a Novel Listeria sensu stricto Species, L. swaminathanii
Catharine R Carlin,Jingqiu Liao,Lauren K. Hudson,Tracey L. Peters,Thomas G. Denes,Renato H. Orsi,Xiao-chun Guo,Martin Wiedmann +7 more
TL;DR: Phenotypic and genotypic characterization results indicate that this species is nonpathogenic, and the novel Listeria species described here is phenotypically nonhemolytic and negative for phosphatidylinositol-specific phospholipase C activity.
Journal ArticleDOI
Genetic Diversity of Antimicrobial Resistance and Key Virulence Features in Two Extensively Drug-Resistant Acinetobacter baumannii Isolates
Massimiliano Marazzato,Daniela Scribano,Meysam Sarshar,Francesca Brunetti,Silvia Fillo,Antonella Fortunato,Florigio Lista,Anna Teresa Palamara,Carlo Zagaglia,Cecilia Ambrosi +9 more
TL;DR: Interestingly, the lack of some important virulence determinants did not abrogate their adhesive abilities to abiotic and biotic surfaces, as reported before; indeed, strains retained these capacities, although to a different extent, suggesting the presence of distinct vicarious genes.
Journal ArticleDOI
Performance Characteristics of Next-Generation Sequencing for the Detection of Antimicrobial Resistance Determinants in Escherichia coli Genomes and Metagenomes
Ashley Rooney,Amogelang R. Raphenya,Roberto G. Melano,Christine Seah,N. Yee,Derek R. MacFadden,Andrew G. McArthur,Pierre H. H. Schneeberger,Bryan Coburn +8 more
TL;DR: Analysis of sequencing depths from recent studies assessing ARG content in metagenomic samples demonstrated that sequencing depths had a median estimated detection frequency of 84% (interquartile range: 30%–92%) for a relative abundance of 1%.
Journal ArticleDOI
Natural selenium stress influences the changes of antibiotic resistome in seleniferous forest soils
Fang-Fang Wang,Guoming Liu,Fan Zhang,Zong-Ming Li,Xiaolin Yang,Chaoguang Yang,Jian-Lin Shen,Ji-Zheng He,B. Larry Li,Jian-Guo Zeng +9 more
TL;DR: In this paper , the authors show that exposure of microorganisms to varying concentrations of selenium (Se), an essential but potentially deleterious metal(loid) to living organisms, can influence the migration and distribution of ARGs in forest soils.
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.
Related Papers (5)
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Trimmomatic: a flexible trimmer for Illumina sequence data
The RAST Server: Rapid Annotations using Subsystems Technology
Ramy K. Aziz,Ramy K. Aziz,Daniela Bartels,Aaron A. Best,Matthew DeJongh,Terrence Disz,Terrence Disz,Robert Edwards,Kevin Formsma,Svetlana Gerdes,Elizabeth M. Glass,Michael Kubal,Folker Meyer,Folker Meyer,Gary J. Olsen,Gary J. Olsen,Robert Olson,Robert Olson,Andrei L. Osterman,Ross Overbeek,Leslie Klis McNeil,Daniel Paarmann,Tobias Paczian,Bruce Parrello,Gordon D. Pusch,Claudia I. Reich,Rick Stevens,Rick Stevens,Olga Vassieva,Veronika Vonstein,Andreas Wilke,Olga Zagnitko +31 more