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
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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
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Journal ArticleDOI
Market Chickens as a Source of Antibiotic-Resistant Escherichia coli in a Peri-Urban Community in Lima, Peru.
Matthew Murray,Guillermo Salvatierra,Alejandra Dávila-Barclay,Brenda Ayzanoa,Camila Castillo-Vilcahuaman,Michelle Huang,Monica J. Pajuelo,Monica J. Pajuelo,Andres G. Lescano,Lilia Cabrera,Maritza Calderon,Douglas E. Berg,Robert H. Gilman,Pablo Tsukayama +13 more
TL;DR: In this paper, the authors compared Escherichia coli from chickens and humans with varying levels of exposure to chicken meat in a low-income community in the southern outskirts of Lima, Peru and found that E. coli strains from market chickens are a potential source of ARGs that can be transmitted to human commensals.
Journal ArticleDOI
Machine Learning for Antimicrobial Resistance Prediction: Current Practice, Limitations, and Clinical Perspective
Jee-In Kim,Finlay Maguire,Kara K. Tsang,Theodore Gouliouris,Sharon J. Peacock,Tim A. McAllister,Andrew G. McArthur,Robert G. Beiko +7 more
TL;DR: In this paper , the authors advocate for the incorporation of ML into front-line settings but also highlight the further refinements that are necessary to safely and confidently incorporate these methods, and strongly advocate that the next set of AMR-ML studies should focus on the refinement of these limitations to be able to bridge the gap to diagnostic implementation.
Journal ArticleDOI
Isolation and characterization of a lytic bacteriophage against Pseudomonas aeruginosa.
Sonika Sharma,Sibnarayan Datta,Soumya Chatterjee,Moumita Dutta,Jhuma Samanta,Mohan G. Vairale,Rajeev Gupta,Vijay Veer,Sanjai K. Dwivedi +8 more
TL;DR: In this paper, the authors reported the isolation and detailed characterization of a highly lytic Pseudomonasphage DRL-P1 isolated from wastewater, which appeared as a member of the phage family Myoviridae.
Journal ArticleDOI
Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water.
Meghan Maguire,Julie A. Kase,Dwayne Roberson,Tim Muruvanda,Eric W. Brown,Marc W. Allard,Steven M. Musser,Narjol Gonzalez-Escalona +7 more
TL;DR: In this paper, the limits of detection and classification of Shiga toxin-producing Escherichia coli (STEC) by qPCR and nanopore sequencing using 24 hour enriched irrigation water artificially contaminated with E. coli O157:H7 (EDL 933) were determined.
Journal ArticleDOI
Genetic Plurality of OXA/NDM-Encoding Features Characterized From Enterobacterales Recovered From Czech Hospitals.
Katerina Chudejova,Lucie Kraftova,Vittoria Mattioni Marchetti,Jaroslav Hrabak,Costas C. Papagiannitsis,Ibrahim Bitar +5 more
TL;DR: In all four carbapenemase-producing isolates, a diverse number of additional replicons, some of these associated with important resistance determinants, like blaCTX–M–15, arr-2 and ermB, were identified and indicated the genetic plurality involved in the acquisition and dissemination of determinants encoding OXA/NDM carbapemases.
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