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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Mechanisms of antibiotic resistance of Clostridioides difficile.
TL;DR: In this paper, the authors summarized the most recent advancements in the understanding of antibiotic resistance in CD and analyzed the antibiotic resistance factors present in genomes of a few representative well known, epidemic and MDR CD strains found predominantly in different regions of the world.
Journal ArticleDOI
Whole-genome sequence analysis of high-level penicillin-resistant strains and antimicrobial susceptibility of Neisseria gonorrhoeae clinical isolates from Thailand
Natakorn Nokchan,Thidathip Wongsurawat,Piroon Jenjaroenpun,Perapon Nitayanon,Chanwit Tribuddharat +4 more
TL;DR: The gonococcal population in Thailand showed high susceptibility to ceftriaxone and azithromycin, current dual therapy recommended for gonorrhea treatment, and the AMR determinants and genetic compositions of plasmids in 3 Gonococcal strains with high-level penicillin resistance were examined.
Journal ArticleDOI
Metagenomics as a Tool To Monitor Reclaimed-Water Quality.
TL;DR: Here, metagenomic approaches and studies that demonstrated their use for reclaimed-water quality monitoring are reviewed and recommendations on areas of improvement are provided that will allow metagenomics to significantly impact how the water industry performs reclaimed- water quality monitoring in the future.
Journal ArticleDOI
Effect of black pepper essential oil on quorum sensing and efflux pump systems in the fish-borne spoiler Pseudomonas psychrophila KM02 identified by RNA-seq, RT-qPCR and molecular docking analyses
Natalia Tomaś,Kamila Myszka,Łukasz Wolko,Katarzyna Nuc,Artur Szwengiel,Anna Grygier,Małgorzata Majcher +6 more
TL;DR: It was showed that BPEO major compounds affected the functioning of the QS and EP system in KM02 and consequently reduced the spoilage potential.
Journal ArticleDOI
Comparative genomics in infectious disease
TL;DR: Recent approaches that leverage large numbers of whole genome sequences to decipher the spread and pathogenesis of bacterial infectious diseases are reviewed.
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