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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Complete Genome Sequence of Weissella confusa LM1 and Comparative Genomic Analysis.
TL;DR: In this article, the authors identified W. confusa as the dominant lactic acid bacteria in the gut of the migratory locust and named this strain W confusa LM1, which is the first genome of an insect-derived W.confusa strain with one complete chromosome and one complete plasmid.
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Transcriptomics and metagenomics of common cutworm (Spodoptera litura) and fall armyworm (Spodoptera frugiperda) demonstrate differences in detoxification and development
Ruikang Tang,Fangyuan Liu,Yue Xuen. Lan,Jiao Wang,Lei Wang,Jing Li,Xu Liu,Zhenxin Fan,Tao Guo,Bisong Yue +9 more
TL;DR: In this paper , the authors performed RNA-seq of 15 S. litura individuals from larval (fifth and sixth instar larvae), chrysalis, and adult developmental stages.
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Dogs as carriers of virulent and resistant genotypes of Clostridioides difficile
S. Finsterwalder,Igor Loncaric,Adriana Cabal,Michael P. Szostak,Lisa-Marie Barf,Manuela Marz,Franz Allerberger,Iwan Burgener,Alexander Tichy,Andrea T. Feßler,Stefan Schwarz,Stefan Monecke,R. Ehrlich,Werner Ruppitsch,Joachim Spergser,Frank Künzel +15 more
TL;DR: The results indicate that dogs may carry virulent and antimicrobial‐resistant C. difficile strains isolated from humans in Austria.
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MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing
N. Bonin,Enrique Doster,Hannah Worley,Lee J. Pinnell,Jonathan E Bravo,Peter Ferm,Simone Marini,Mattia Prosperi,Noelle R. Noyes,Paul S. Morley,Christina Boucher +10 more
TL;DR: In this article , the authors present MEGARes v3.0, an update to their customized bioinformatic pipeline for high-throughput analysis of metagenomic data.
Posted ContentDOI
Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda
Gavin Ackers-Johnson,Daniel Kibombo,Brenda Kusiima,Moses L Nsubuga,Edgar Kigozi,Henry Kajumbula,David P. Kateete,Richard Walwema,Helen Louise Ackers,Ian Goodhead,Richard J. Birtles,Chloe E. James +11 more
TL;DR: By generating detailed information about the epidemiology of circulating S. aureus and their antibiotic susceptibility, this study has provided, for the first time, data on which evidence-based infection and AMR interventions at FPRRH can be based.
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