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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Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms.
Nicole Pearcy,Yue Hu,Michelle Baker,Alexandre Maciel-Guerra,Ning Xue,Wei Wang,Jasmeet Kaler,Zixin Peng,Fengqin Li,Tania Dottorini +9 more
TL;DR: In this article, the authors developed a computational pipeline that combines machine learning with genome-scale metabolic models (GSMs) to elucidate the systemic relationships between genetic determinants of resistance and metabolism beyond annotated drug resistance genes.
Journal ArticleDOI
Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections.
TL;DR: In this paper, the authors describe the whole-genome sequences of trimethoprim-resistant ExPEC from recurrent UTIs (67 in total) from patients attending a regional Australian hospital from 2006 to 2008.
Journal ArticleDOI
Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients With Cirrhosis.
Amirhossein Shamsaddini,Patrick M. Gillevet,Chathur Acharya,Andrew Fagan,Edith Gavis,Masoumeh Sikaroodi,Sara McGeorge,Alexander Khoruts,Somaya Albhaisi,Michael Fuchs,Richard K. Sterling,Jasmohan S. Bajaj +11 more
TL;DR: In this paper, the impact of ARGs in cirrhosis-related gut metagenome on outcomes and disease progression, study the effect of rifaximin on ARG burden, and compare ARG abundance patterns with chronic kidney disease (CKD) and diabetes.
Journal ArticleDOI
Metagenomics revealed the mobility and hosts of antibiotic resistance genes in typical pesticide wastewater treatment plants
TL;DR: In this article , the authors tried to clarify the mobile antibiotic resistome and ARG hosts in three typical pesticide wastewater treatment plants (PWWTPs) through metagenomics, and they found that ARGs associated with antibiotic efflux and multi-drug resistance generally dominated in the PWWTP, and the relative abundance of ARGs was generally higher in the water phase than that in sludge phase.
Journal ArticleDOI
Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers
Alaric W. D’Souza,Manish Boolchandani,Sanket Patel,Gianluca Galazzo,Jarne M van Hattem,Maris S. Arcilla,Damian C. Melles,Menno D. de Jong,Constance Schultsz,Gautam Dantas,John Penders,John Penders +11 more
TL;DR: In this paper, the authors investigated the effect of international travel on the Gut Resistome and found that travel significantly increased the abundance and diversity of AMR genes in the travelers' gut resistome.
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