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
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Investigation of a night soil compost psychrotrophic bacterium Glutamicibacter arilaitensis LJH19 for its safety, efficient hydrolytic and plant growth-promoting potential
Shruti Sinai Borker,Shruti Sinai Borker,Aman Thakur,Aman Thakur,Sanjeet Kumar,Sareeka Kumari,Rakshak Kumar,Sanjay Kumar +7 more
TL;DR: The strain LJH19, a psychrotrophic bacteria was proposed to be a potentially safe bioinoculant candidate for efficient degradation of night soil owing to its survivability in cold and its efficient hydrolytic and PGP potential.
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Natural selenium stress influences the changes of antibiotic resistome in seleniferous forest soils
Fangfang Wang,Guoping Liu,Fan Zhang,Zong-Ming Li,Xiao-Lin Yang,Chaoguang Yang,Jian-Lin Shen,Ji-Zheng He,B. L. Li,Jian-Guo Zeng +9 more
TL;DR: In this article , the authors show that exposure of microorganisms to varying concentrations of selenium (Se), an essential but potentially deleterious metal(loid) to living organisms, can influence the migration and distribution of ARGs in forest soils.
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The fate of sulfonamide resistance genes and anthropogenic pollution marker intI1 after discharge of wastewater into a pristine river stream
Sarah Haenelt,Gangan Wang,Jonas Coelho Kasmanas,Florin Musat,Hans H. Richnow,Ulisses Nunes da Rocha,Jochen F. Müller,Niculina Musat +7 more
TL;DR: In this paper , the authors used quantitative PCR and long-read nanopore sequencing to monitor the abundance of these indicator genes and ARGs present as class 1 integron gene cassettes in a river system from pristine source to WWTP-impacted water.
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Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids
TL;DR: In this article, a comparative genomics approach based on genes conserved among members of the SGI1 group was used to identify diverse genomic islands (GIs) distantly related to SGI 1 in several species of Vibrio, Aeromonas, Salmonella, Pokkaliibacter, and Escherichia.
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Genome characteristics of clinical Salmonella enterica population from a state public health laboratory, New Hampshire, USA, 2017–2020
Madison R. Turcotte,Joshua T. Smith,Jinfeng Li,Xinglu Zhang,Kristin L. Wolfe,Fengxiang Gao,Christopher Benton,Cheryl P. Andam +7 more
TL;DR: In this article , the authors present some of the initial results of New Hampshire's initiative to transition to whole genome sequencing (WGS) in tracking Salmonella enterica , a bacterial pathogen that is responsible for non-typhoidal foodborne infections and enteric fever.
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