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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Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation
Christopher J. Severyn,Benjamin A. Siranosian,S. Kong,Angel Antonio Moreno,Michelle Li,Nan Chen,Christine Duncan,Steven P. Margossian,Leslie Lehmann,Shan Sun,Tessa M. Andermann,O. Birbrayer,Sophie C. Silverstein,Soomin Kim,Niaz Banaei,Jerome Ritz,Anthony A. Fodor,Wendy B. London,Ami S. Bhatt,Jennifer Whangbo +19 more
TL;DR: In this paper , the impact of GD on gut microbiome composition and the incidence of acute graft-versus-host disease (aGVHD) in allogeneic hematopoietic cell transplantation (HCT) patients was examined.
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Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy.
Xiangning Bai,Aswathy Narayanan,Piotr Nowak,Piotr Nowak,Piotr Nowak,Shilpa Ray,Shilpa Ray,Ujjwal Neogi,Anders Sönnerborg,Anders Sönnerborg +9 more
TL;DR: In this paper, a deep shotgun metagenomics study with the aim to obtain a more precise landscape of gut microbiome dysbiosis in HIV-1 infection was performed, where a reduced tendency of alpha diversity and significantly higher beta diversity were found in HIV 1-infected individuals on antiretroviral therapy (ART) compared to HIV- 1-negative controls.
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Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese.
Werner Ruppitsch,Andjela Nisic,Patrick Hyden,Adriana Cabal,Jasmin Sucher,Anna Stöger,Franz Allerberger,Aleksandra Martinovic +7 more
TL;DR: In 2019, sixteen Leuconostoc spp. mesenteroides isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro as discussed by the authors.
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Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes.
Rachel E. Diner,Rachel E. Diner,Drishti Kaul,Ariel Rabines,Ariel Rabines,Hong Zheng,Joshua A. Steele,John F. Griffith,Andrew E. Allen,Andrew E. Allen +9 more
TL;DR: In this paper, a detailed profile of both prokaryotic and eukaryotic coastal microbial communities was established using metabarcoding, and pathogenic Vibrio spp. were frequently associated with distinct EKaryotic amplicon sequence variants (ASVs), including diatoms and copepods.
Posted ContentDOI
Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus
Henrique Machado,Yara Seif,George Sakoulas,Connor A. Olson,Richard Szubin,Bernhard O. Palsson,Victor Nizet,Adam M. Feist +7 more
TL;DR: This study bridges the gap of understanding between clinical and microbiological vancomycin resistance in S. aureus and expands the number of allelic variants that result in vancomytcin resistance phenotypes and confirms a bacteriological media-specific mechanism for vancomYcin resistance enabled by a mutated mprF.
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