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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Molecular dissemination of emerging antibiotic, biocide, and metal co-resistomes in the Himalayan hot springs.
TL;DR: In this article , a metagenomic approach has been employed to understand the causes, dissemination, and effects of antibiotic, metal, and biocide resistomes on the microbial ecology of three hot springs, Borong, Lingdem, and Yumthang, located at different altitudes of the Sikkim Himalaya.
Journal ArticleDOI
Overcoming bacterial resistance to antibiotics: the urgent need - a review
Magdalena Stachelek,Magdalena Zalewska,Magdalena Zalewska,Ewelina Kawecka-Grochocka,Tomasz Sakowski,Emilia Bagnicka +5 more
TL;DR: This review begins with the discovery of antibiotics, covers the modes of action of select antimicrobials, and ends with a literature review of the newest potential alternative approaches to overcoming the drug resistance phenomenon.
Journal ArticleDOI
Genomic Characterization of Clinical Extensively Drug-Resistant Acinetobacter pittii Isolates.
Peechanika Chopjitt,Nuntiput Putthanachote,Ratchadaporn Ungcharoen,Rujirat Hatrongjit,Parichart Boueroy,Yukihiro Akeda,Kazunori Tomono,Shigeyuki Hamada,Anusak Kerdsin +8 more
TL;DR: In this article, the authors used multilocus sequence typing with the Pasteur scheme to characterize clinical isolates of Carbinem-resistant Acinetobacter pittii (CRAP) from a tertiary hospital in Northeast Thailand.
Journal ArticleDOI
Antibiotic Resistance Genes in River Biofilms: A Metagenomic Approach toward the Identification of Sources and Candidate Hosts
TL;DR: Shooter metagenomics is employed to track ARG and taxonomic markers in river biofilms along a gradient of fecal pollution depicted by crAssphage signatures and finds strong evidence for an impact of wastewater effluents on both community composition and resistomes.
Journal ArticleDOI
Insight Into Whole Genome of Aeromonas veronii Isolated From Freshwater Fish by Resistome Analysis Reveal Extensively Antibiotic Resistant Traits.
Rungnapa Sakulworakan,Putita Chokmangmeepisarn,Nguyen Dinh-Hung,Elayaraja Sivaramasamy,Ikuo Hirono,Rungthip Chuanchuen,Pattanapon Kayansamruaj,Channarong Rodkhum +7 more
TL;DR: Aeromonas veronii outbreaks in tilapia farming caused relatively high mortalities, and the bacteria was resistant to many kinds of antimicrobials used in Thailand aquaculture as mentioned in this paper.
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