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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Identification of antibiotic resistance proteins via MiCId's augmented workflow. A mass spectrometry-based proteomics approach
Gelio Alves,Aleksey Y. Ogurtsov,Roger Karlsson,Daniel Jaén-Luchoro,Beatriz Piñeiro-Iglesias,Francisco Salvà-Serra,Björn Andersson,Edward R. B. Moore,Yi-Kuo Yu +8 more
TL;DR: Yu et al. as discussed by the authors proposed a new version of the Microorganism Classification and Identification (MiCId) workflow, which has a sensitivity value around 85% with a lower bound at about 72% and a precision greater than 95% in the identification of antibiotic resistance proteins.
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Coastal water bacteriophages infect various sets of Vibrio parahaemolyticus sequence types
Kari A. Brossard Stoos,Jennifer Ren,Robin R. Shields-Cutler,Kelly L. Sams,Shannon Caldwell,Marvin B. Ho,Gregg Rivara,Cheryl A. Whistler,Stephen H. Jones,Martin Wiedmann,Jamie DeMent,Rodman G. Getchell,Hélène Marquis +12 more
TL;DR: In this article , bacteriophages were used as a proxy to monitor the presence of Vibrio parahaemolyticus in coastal waters, and four distinct phages were identified based on their ability to infect different sets of isolates.
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Phage controlling method against novel freshwater-derived Vibrio parahaemolyticus in ready-to-eat crayfish (Procambarus clarkii).
Lin Teng,Geng Zou,Yang Zhou,Jie Li,Zhiyong Song,Xing Xing Dong,Zhengxin Ma,Zhijie Zheng,Huanchun Chen,Jinquan Li +9 more
TL;DR: In this paper , the authors reported the presence of Vibrio parahaemolyticus in ready-to-eat (RTE) crayfish, which were rarely identified and investigated.
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Region-specific Genomic Signatures of Multidrug-Resistant Helicobacter pylori Isolated from East and South India.
Shakti Kumar,Tanshi Mehrotra,Daizee Talukdar,Jyoti Verma,Bipul Chandra Karmakar,Sangita Paul,Sujit Chaudhuri,Agila Kumari Pragasam,Susmita Bakshi,Shashi Kumari,Meenal Chawla,Ayushi Purohit,Sonali Porey Karmakar,Ankur Mutreja,Sayantan Banerjee,Animesh Ray,Thandavarayan Ramamurthy,Asish Mukhopadyay,Bhabatosh Das +18 more
TL;DR: In this paper , the authors analyzed the whole genome sequences of 143 H. pylori strains, of which 32 were isolated from two different regions (eastern and southern) of India.
Journal ArticleDOI
Emergence and Molecular Epidemiology of Campylobacter jejuni ST-2993 Associated with a Large Outbreak of Guillain-Barré Syndrome in Peru
Willi Quino,Junior Caro-Castro,Orson Mestanza,Verónica Hurtado,María Luz Zamudio,G. Cruz-Gonzales,Ronnie G. Gavilan +6 more
TL;DR: C. jejuni ST-2993 strains recovered from the GBS outbreak are closely related to Peruvian Amazon strains, showing the necessity to increase epidemiological tracking of these kinds of pathogens to detect them and avoid GBS outbreaks in the future.
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