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
Citations
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Comparing resistome profiles from anthropogenically impacted and non-impacted areas of two South Shetland Islands - Maritime Antarctica.
TL;DR: In this paper , the authors compared resistome profiles of impacted and non-impacted areas in Deception Island (Whalers Bay, Crater Lake, and Fumarole Bay) and Livingston Island (Hannah Point) in order to investigate the microbiome tolerance/resistance mechanisms selected as a function of environmental drivers.
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Tracking the Origin of Austrian Human Brucellosis Cases Using Whole Genome Sequencing.
Justine Schaeffer,Sandra Revilla-Fernández,Erwin Hofer,Romana Posch,Anna Stoeger,Christoph Leth,Friedrich Schmoll,Vesna Djordjevic,Brankica Lakicevic,Kazimir Matovic,Peter Hufnagl,Alexander Indra,Franz Allerberger,Werner Ruppitsch +13 more
TL;DR: In this paper, 21 B. melitensis strains isolated in Austria between 2005 and 2019 were collected, 17 strains from 15 different patients and four strains from cattle, combined with core-genome MLST analysis was used to characterize these strains.
Journal ArticleDOI
Non-Penicillin-Susceptible Streptococcus suis Isolated from Humans
Nichari Bamphensin,Peechanika Chopjitt,Rujirat Hatrongjit,Parichart Boueroy,Nahuel Fittipaldi,Marcelo Gottschalk,Anusak Kerdsin +6 more
TL;DR: In this article, S. suis isolates recovered from human infections in Thailand were characterized with regard to their antimicrobial susceptibility and antimicrobial resistance genes, including, for non-penicillin-susceptible isolates, sequence analyses of five genes encoding penicillinbinding proteins (pbp1a, pbp1b, pBP1b and pBP2a), and pbp2x).
Journal ArticleDOI
Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant
Paul Jankowski,Jaydon Gan,Tri Le,Michaela McKennitt,Audrey Garcia,Kadir Yanaç,Qiuyan Yuan,Miguel I. Uyaguari-Diaz +7 more
TL;DR: In this article , the authors characterized the resistome, the distribution of classes 1-3 integron-integrase genes (intI1, intI2, and intI3) as mobile genetic element biomarkers, and the bacterial and phage community compositions in the North End Sewage Treatment Plant in Winnipeg, Manitoba.
Journal ArticleDOI
Restoring carbapenem efficacy: a novel carbapenem companion targeting metallo-β-lactamases in carbapenem-resistant Enterobacterales
Nicola Ooi,Victoria E Lee,Nathan Chalam-Judge,Rebecca Newman,Andrew J Wilkinson,Ian R. Cooper,David Orr,Sally Lee,Victoria J. Savage +8 more
TL;DR: A series of rationally designed MBLIs that restore activity of carbapenems against NDM/IMP/VIM-producing Enterobacterales is developed, warranting further development towards a novel combination therapy that combats antibiotic-resistant organisms, which pose a critical threat to human health.
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