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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mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements
TL;DR: The analysis of bacterial mobile genetic elements (MGEs) in genomic data is a critical step toward profiling the root causes of antibiotic resistance, phenotypic or metabolic diversity, and the evolution of bacterial genera as discussed by the authors .
Journal ArticleDOI
A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome
Shuqin Zeng,Dhrati V. Patangia,Alexandre Almeida,Zhemin Zhou,Dezhi Mu,R. Paul Ross,Catherine Stanton,Shaopu Wang +7 more
TL;DR: The Early-Life Gut Genomes (ELGG) catalog as mentioned in this paper contains 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3 years old spanning delivery mode, gestational age, feeding pattern, and geography.
Journal ArticleDOI
Genomic Characterization of Extensively Drug-Resistant NDM-Producing Acinetobacter baumannii Clinical Isolates With the Emergence of Novel blaADC-257
Mai M. Zafer,Amira F. A. Hussein,Mohamed H. Al-Agamy,Mohamed H. Al-Agamy,Hesham H. Radwan,Samira M. Hamed +5 more
TL;DR: In this article, the authors investigated antimicrobial resistance determinants and their context in four extensively drug resistant NDM-producing Acinetobacter baumannii clinical isolates collected between July and October 2020 from Kasr Al-Ainy Hospital, Cairo, Egypt.
Journal ArticleDOI
Genomic Analysis of Aeromonas veronii C198, a Novel Mcr-3.41-Harboring Isolate from a Patient with Septicemia in Thailand.
Rujirat Hatrongjit,Anusak Kerdsin,Dan Takeuchi,Thidathip Wongsurawat,Thidathip Wongsurawat,Piroon Jenjaroenpun,Piroon Jenjaroenpun,Peechanika Chopjitt,Parichart Boueroy,Yukihiro Akeda,Shigeyuki Hamada +10 more
TL;DR: In insights into the genomic characteristics of human A. veronii isolates, the complete genome sequence of a clinical isolate obtained from a patient with septicemia was determined and found to harbor a novel mcr-3 gene, designated mCr-3.41.
Journal ArticleDOI
Complete genome sequence of a novel lytic phage infecting Aeromonas hydrophila, an infectious agent in striped catfish (Pangasianodon hypophthalmus).
Vinh Q Tu,Vinh Q Tu,Tan-Trung Nguyen,Tan-Trung Nguyen,Tan-Trung Nguyen,Xuan T.T. Tran,Xuan T.T. Tran,Andrew D. Millard,Huyen T Phan,Huyen T Phan,Nga P Le,Nga P Le,Oanh T H Dang,Hoang A. Hoang,Hoang A. Hoang +14 more
TL;DR: It is confirmed that PVN02 is a novel lytic phage that could potentially be used as an agent to control Aeromonas hydrophila in striped catfish in the Mekong Delta, Vietnam.
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