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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Journal ArticleDOI
Genomic Characteristics of Stx2e-Producing Escherichia coli Strains Derived from Humans, Animals, and Meats
Xi Yang,Yannong Wu,Qian Liu,Hui Sun,Ming Luo,Yanwen Xiong,Andreas Matussek,Bin Hu,Xiangning Bai +8 more
TL;DR: Wang et al. as mentioned in this paper analyzed the prevalence and genetic characteristics of Stx2e-producing Escherichia coli (Stx 2e-STEC) strains from humans compared to strains from animals and meats in China.
Journal ArticleDOI
Metagenomics-Based Analysis of the Age-Related Cumulative Effect of Antibiotic Resistance Genes in Gut Microbiota.
Lei Wu,Lei Wu,Xinqiang Xie,Ying Li,Tingting Liang,Tingting Liang,Haojie Zhong,Jun Ma,Jun Ma,Lingshuang Yang,Juan Yang,Juan Yang,Longyan Li,Yu Xi,Haixin Li,Jumei Zhang,Xuefeng Chen,Yu Ding,Qingping Wu +18 more
TL;DR: In this article, a comprehensive antibiotic resistome catalog was established using fecal samples from 246 healthy individuals from world's longevity township in Jiaoling, China, in total, 606 antibiotic resistance genes were detected.
Journal ArticleDOI
Coexistence of two blaCTX-M-14 genes in a blaNDM-5-carrying multidrug-resistant Escherichia coli strain recovered from a bloodstream infection in China
TL;DR: In this article, the authors reported the first genome sequence of a multidrug-resistant E. coli carrying blaNDM-5 and two copies of blaCTX-M-14 gene recovered from a bloodstream infection in China.
Journal ArticleDOI
The First Report of mcr-1-Carrying Escherichia coli Originating from Animals in Serbia.
Dusan Misic,Ferenc Kiskaroly,Michael P. Szostak,Adriana Cabal,Werner Ruppitsch,Tanja Bernreiter-Hofer,Viktoria Milovanovic,Andrea T. Feßler,Franz Allerberger,Joachim Spergser,Elke Müller,Stefan Schwarz,Sascha D. Braun,Stefan Monecke,Ralf Ehricht,Maciej Korus,Damir Benković,Małgorzata Korzeniowska,Igor Loncaric +18 more
TL;DR: In this paper, the presence of mcr-1 in five E. coli isolates originating from healthy turkeys was observed in two farms in Northern Vojvodina, Serbia from 1 January 1 to 1 October 2020.
Posted ContentDOI
A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile
Korakrit Imwattana,Korakrit Imwattana,César Rodríguez,Thomas V. Riley,Daniel R. Knight,Daniel R. Knight +5 more
TL;DR: In this article, the authors provided the first species-wide snapshot of AMR genomic epidemiology in C. difficile using 10,330 publicly-available C.difficile genomes from strains isolated worldwide.
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