ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes
Sushim K. Gupta,Babu Roshan Padmanabhan,Seydina M. Diene,Rafael López-Rojas,Marie Kempf,Luce Landraud,Jean-Marc Rolain +6 more
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.read more
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Dissertation
Investigation into compound(s) exhibiting Streptococcus mutans anti-biofilm activity
TL;DR: The S. mutans biofilm inhibitory activity in this study may have potential to be applied as an anti-dental caries agent and should be investigated further in the future.
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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
Ricky Indra Alfaray,B. Saruuljavkhlan,Kartika Afrida Fauzia,Roberto C. Torres,Kaisa Thorell,Selva Rosyta Dewi,Kirill A. Kryukov,Takashi Matsumoto,Junko Akada,Ratha-Korn Vilaichone,Muhammad Miftahussurur,Yoshio Yamaoka +11 more
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
Emily F. Wissel,B. M. Talbot,Noriko A. B. Toyosato,Robert A. Petit,Vicki S. Hertzberg,Anne L Dunlop,Timothy D. Read +6 more
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.
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Molecular characterisation of, and antimicrobial resistance in, Clostridioides difficile from Thailand, 2017-2018
Korakrit Imwattana,Korakrit Imwattana,Papanin Putsathit,Daniel R. Knight,Daniel R. Knight,Pattarachai Kiratisin,Thomas V. Riley +6 more
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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