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Open AccessJournal ArticleDOI

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

TLDR
A concise database for BLAST using a Bio-Edit interface that can detect AR genetic determinants in bacterial genomes and can rapidly and easily discover putative new AR geneticeterminants is created.
Abstract
ARG-ANNOT (Antibiotic Resistance Gene-ANNOTation) is a new bioinformatic tool that was created to detect existing and putative new antibiotic resistance (AR) genes in bacterial genomes. ARG-ANNOT uses a local BLAST program in Bio-Edit software that allows the user to analyze sequences without a Web interface. All AR genetic determinants were collected from published works and online resources; nucleotide and protein sequences were retrieved from the NCBI GenBank database. After building a database that includes 1,689 antibiotic resistance genes, the software was tested in a blind manner using 100 random sequences selected from the database to verify that the sensitivity and specificity were at 100% even when partial sequences were queried. Notably, BLAST analysis results obtained using the rmtF gene sequence (a new aminoglycoside-modifying enzyme gene sequence that is not included in the database) as a query revealed that the tool was able to link this sequence to short sequences (17 to 40 bp) found in other genes of the rmt family with significant E values. Finally, the analysis of 178 Acinetobacter baumannii and 20 Staphylococcus aureus genomes allowed the detection of a significantly higher number of AR genes than the Resfinder gene analyzer and 11 point mutations in target genes known to be associated with AR. The average time for the analysis of a genome was 3.35 ± 0.13 min. We have created a concise database for BLAST using a Bio-Edit interface that can detect AR genetic determinants in bacterial genomes and can rapidly and easily discover putative new AR genetic determinants.

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Dissertation

Investigation into compound(s) exhibiting Streptococcus mutans anti-biofilm activity

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Posted ContentDOI

A resistome roadmap: from the human body to pristine environments

TL;DR: In this paper, the authors studied the resistome of 771 samples from five major body parts (skin, nares, vagina, gut and oral cavity) of healthy subjects from the Human Microbiome Project and addressed the potential dispersion of ARGs in pristine environments.
Journal ArticleDOI

Global Antimicrobial Resistance Gene Study of Helicobacter pylori: Comparison of Detection Tools, ARG and Efflux Pump Gene Analysis, Worldwide Epidemiological Distribution, and Information Related to the Antimicrobial-Resistant Phenotype

TL;DR: In this paper , a global-scale study was conducted to identify H. pylori antimicrobial-resistant genes (ARG), address their global distribution, and understand their effect on the antimicrobial resistance (AMR) phenotypes of the clinical isolates.

hAMRoaster: a tool for comparing performance of AMR gene detection software

TL;DR: Wissel et al. as mentioned in this paper developed a software pipeline, hAMRoaster (Harmonized AMR Output compAriSon Tool ER), for assessing accuracy of prediction of antibiotic resistance phenotypes.
Posted ContentDOI

Molecular characterisation of, and antimicrobial resistance in, Clostridioides difficile from Thailand, 2017-2018

TL;DR: There was a large proportion of C. difficile RT 017 in Thailand and significant AMR among these strains, and a significant correlation between resistance genotype and phenotype for moxifloxacin and rifampicin was revealed.
References
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Journal ArticleDOI

Basic Local Alignment Search Tool

TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI

Identification of acquired antimicrobial resistance genes

TL;DR: A web server providing a convenient way of identifying acquired antimicrobial resistance genes in completely sequenced isolates was created, and the method was evaluated on WGS chromosomes and plasmids of 30 isolates.
Journal ArticleDOI

Improved microbial gene identification with GLIMMER

TL;DR: Significant technical improvements to GLIMMER are reported that improve its accuracy still further, and a comprehensive evaluation demonstrates that the accuracy of the system is likely to be higher than previously recognized.
Journal ArticleDOI

Antibiotic resistance is ancient

TL;DR: Target metagenomic analyses of rigorously authenticated ancient DNA from 30,000-year-old Beringian permafrost sediments are reported and show conclusively that antibiotic resistance is a natural phenomenon that predates the modern selective pressure of clinical antibiotic use.
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