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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Evaluation of an immunological assay for the identification of multiple carbapenemase-producing Gram-negative bacteria.
TL;DR: In this paper , the authors evaluated a rapid lateral flow immunoassay (LFIA) for detecting carbapenemase production in Gram-negative bacteria in hospital settings, particularly in intensive care units.
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A Strategy for the Rapid Development of a Safe Vibrio cholerae Candidate Vaccine Strain
Dmitry S. Karpov,A. V. Goncharenko,Evgenii V Usachev,Daria V. Vasina,Elizaveta V. Divisenko,Yaroslava Chalenko,Andrei A. Pochtovyi,Roman S Ovchinnikov,Valentin V. Makarov,Sergei M Yudin,Artem P. Tkachuk,Vladimir A. Gushchin,Vladimir A. Gushchin +12 more
TL;DR: In this paper, the authors comprehensively characterized two Vibrio cholerae isolates using genome sequencing, bioinformatic analysis, and microscopic, physiological, and biochemical tests.
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Draft Genome Sequence of Pandrug-Resistant Pseudomonas aeruginosa SPA03, Isolated from a Patient with Benign Prostatic Hyperplasia.
Chanakya Pachi Pulusu,Balaram Khamari,Manmath Lama,Arun Sai Kumar Peketi,Prakash Kumar,Valakunja Nagaraja,Valakunja Nagaraja,Eswarappa Pradeep Bulagonda +7 more
TL;DR: The draft genome of pandrug-resistant Pseudomonas aeruginosa strain SPA03, which belongs to global high-risk sequence type 357 (ST357) and was isolated from a patient with benign prostatic hyperplasia, is presented in this paper.
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C. Castaneda-Alvarez,Ricardo A. R. Machado,Patricia Morales-Montero,Anja Boss,Arthur Muller,S. Prodan,Alan Zamorano,Ernesto San-Blas,Vladimír Půža,Erwin Aballay +9 more
TL;DR: Results of biochemical, physiological, molecular and genomic analyses suggest that strain UCH-936T represents a new species, which is proposed to name Photorhabdus antumapuensis sp.
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Multi-omics analysis reveals the host–microbe interactions in aged rhesus macaques
Jue Xu,Yue Xuen. Lan,Xinqi Wang,Ke Shang,Xu Liu,Jiao Wang,Jing Li,Bisong Yue,Meiying Shao,Zhenxin Fan +9 more
TL;DR: It is determined that tryptophan metabolism is critical for the physiological health of agedCRs, suggesting that aged CRs face multiple metabolic problems, immunological disorders, and oral and gut diseases.
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