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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Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland.
TL;DR: It was revealed that strain B8 might survive atmospheric methane concentration and had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate synthesis, and heavy metal resistance, which might enable its survival in wetland environments.
Posted ContentDOI
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: The limits of detection and classification of STECs by qPCR and nanopore sequencing using enriched irrigation water artificially contaminated with E. coli O157:H7 were determined and the bacterial species in the un-spiked enrichment were identified, including antimicrobial resistance genes, which could have important implications to food safety.
Journal ArticleDOI
Isolation and characterization of bacteriophages from the human skin microbiome that infect Staphylococcus epidermidis
Luca G Valente,Melissa Pitton,Monika Fürholz,Simone Oberhaensli,Rémy Bruggmann,Stephen L. Leib,Stephan M. Jakob,Grégory Resch,Yok-Ai Que,David R. Cameron +9 more
TL;DR: An efficient method to isolate bacteriophages present within the human skin microbiome, by using niche-specific S. epidermidis as the host for phage propagation, and identified novel genes including a putative N-acetylmuramoyl-L-alanine amidase amidase gene.
Journal ArticleDOI
The Antimicrobial Susceptibility of Porphyromonas gingivalis: Genetic Repertoire, Global Phenotype, and Review of the Literature
Georg Conrads,Tim Klomp,Dongmei Deng,Johannes-Simon Wenzler,Andreas Braun,Mohamed M. H. Abdelbary +5 more
TL;DR: In this paper, the in vitro antimicrobial susceptibility of 29 strains of the major periodontal pathogen Porphyromonas gingivalis and three P. gulae (as an ancestor) to nine antibiotics (amoxicillin, amoxicillin/clavulanate, clindamycin, metronidazole, moxifloxacin, doxycycline, azithromycin, imipenem, and cefoxitin) was evaluated by e-testing of minimal inhibitory concentration according to international standards.
Journal ArticleDOI
Emerging Threat of Antimicrobial Resistance in β-Hemolytic Streptococci.
TL;DR: W Whole genome sequencing of the erythromycin and clindamycin resistant bacterial population revealed a substantial phylogenetic diversity in S. agalactiae and S. dysgalactiae, suggesting a dissemination of antimicrobial resistance predominantly through conjugative transfer rather than clonal expansion of resistant strains in these two species.
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