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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Will a Non-antibiotic Metalloid Enhance the Spread of Antibiotic Resistance Genes: The Selenate Story
TL;DR: The rapid emergence of antibiotic resistance genes (ARGs) has become an increasingly serious threat to public health as discussed by the authors, and previous studies illustrate the antibiotic-like effect of many substances.
Journal ArticleDOI
Identification of mobile colistin resistance genes (mcr-1.1, mcr-5 and mcr-8.1) in Enterobacteriaceae and Alcaligenes faecalis of human and animal origin, Nigeria.
Emmanuel O. Ngbede,Anil Poudel,Anwar Kalalah,Yi Yang,Folasade Adekanmbi,Alex A. Adikwu,A. M. Adamu,Levi M. Mamfe,Salem T. Daniel,Nicodemus M. Useh,Jacob K. P. Kwaga,Mohammed I. Adah,Patrick Kelly,Patrick Butaye,Patrick Butaye,Chengming Wang +15 more
TL;DR: This study is the first to report mCr-1 in Alcaligenes faecalis, and emergence of mcr-5 and mcr -8 in Nigeria, and highlight the global spread of colistin resistance, and emphasize the urgent need for coordinated global action to combat resistant bacteria.
Journal ArticleDOI
Selective concentrations for trimethoprim resistance in aquatic environments
Nadine Kraupner,Stefan Ebmeyer,Marion Hutinel,Jerker Fick,Carl-Fredrik Flach,D. G. Joakim Larsson +5 more
TL;DR: It is proposed that 1 µg/L would be a reasonably protective exposure limit for trimethoprim in aquatic environments, based on the present and other studies.
Journal ArticleDOI
Histamine production by the gut microbiota induces visceral hyperalgesia through histamine 4 receptor signaling in mice
Giada De Palma,Chiko Shimbori,David E. Reed,Yan Yu,Virginia Rabbia,Jun Luo,Nestor N. Jiménez-Vargas,J Sessenwein,Cintya Lopez-Lopez,Marc Pigrau,Josue Jaramillo-Polanco,Yong Zhang,Lauren Baerg,Ahmad Manzar,Julien Pujo,Xiao-Dong Bai,Maria Ines Pinto-Sanchez,Alberto Caminero,Karen Madsen,Michael G. Surette,Michael Beyak,Alan E. Lomax,Elena F. Verdu,Stephen M. Collins,Stephen J. Vanner,Premysl Bercik +25 more
TL;DR: Results suggest that therapeutic strategies directed against bacterial histamine could help treat visceral hyperalgesia in a subset of patients with IBS with chronic abdominal pain.
Journal ArticleDOI
Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion
TL;DR: This study shows that phage-plasmids carry a large diversity of clinically relevant antibiotic resistance genes that they can transfer across bacteria, and their integrons become genetic platforms for the acquisition of novel resistance genes.
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