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
Antimicrobial resistance in enteric bacteria: current state and next-generation solutions
TL;DR: This review presents a comprehensive discussion on circulating resistance profiles and gene mobilization strategies of the most problematic species of enteric bacterial pathogens and emerging approaches toward surveillance of pathogens and their resistance elements as well as promising treatment strategies that can circumvent common resistance mechanisms.
Journal ArticleDOI
Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women
Colin J. Worby,Henry L. Schreiber,Timothy J. Straub,Lucas R. van Dijk,Ryan A. Bronson,Benjamin S Olson,Jerome S. Pinkner,C. Obernuefemann,Vanessa L. Muñoz,Alexandra E. Paharik,Philippe Azimzadeh,Bruce J. Walker,Christopher A. Desjardins,Wen-Chi Chou,Karla Bergeron,Sinéad B. Chapman,Aleksandra Klim,Abigail L. Manson,Thomas J. Hannan,Thomas M. Hooton,Andrew L. Kau,H. Henry Lai,Karen W. Dodson,Scott J. Hultgren,Ashlee M. Earl +24 more
TL;DR: In this paper , the role of the microbiota in recurrent urinary tract infections (rUTIs) remains unclear, and the authors conducted a year-long study of women with and without a history of rUTI, from whom they collected urine, blood and monthly faecal samples for metagenomic and transcriptomic interrogation.
Journal ArticleDOI
Antibiotic resistance: bioinformatics-based understanding as a functional strategy for drug design
TL;DR: Understanding the evolution of antibiotic resistance at the molecular level as a functional tool for bioinformatic-based drug design is an important step in the fight against antibiotic resistance.
Journal ArticleDOI
Impact of oxytetracycline on anaerobic wastewater treatment and mitigation using enhanced hydrolysis pretreatment.
TL;DR: It is demonstrated that the control of conventional pollutants and ARGs could be achieved simultaneously in the UASB reactor by employing enhanced hydrolysis pretreatment and chemical oxygen demand removal rate and antibiotic resistance genes level were found to be similar to those achieved with zero oxytetracycline treatment.
Journal ArticleDOI
Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen
Claire L. Gorrie,Mirjana Mirceta,Ryan R. Wick,Louise M. Judd,Margaret M. C. Lam,Ryota Gomi,Iain J. Abbott,Nicholas R. Thomson,Richard A. Strugnell,Nigel F. Pratt,Jill S. Garlick,Kerrie Watson,Peter Hunter,David Pilcher,Steven McGloughlin,Denis Spelman,Kelly L. Wyres,Adam Jenney,Kathryn E. Holt +18 more
TL;DR: In this paper , the authors conducted a year-long prospective surveillance study of K. pneumoniae clinical isolates in hospital patients and revealed a diverse pathogen population, including other species within the K pneumoniae species complex.
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