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
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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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Antibiotic Susceptibility Profiles of Pediococcus pentosaceus from Various Origins and Their Implications for the Safety Assessment of Strains with Food-Technology Applications.
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Investigation of next-generation sequencing data of Klebsiella pneumoniae using web-based tools.
Eva Brhelová,Mariya Antonova,Filip Pardy,Iva Kocmanová,Jiri Mayer,Jiri Mayer,Zdenek Racil,Zdenek Racil,Martina Lengerová,Martina Lengerová +9 more
TL;DR: Applying appropriate web‐based online tools to NGS data enables the rapid extraction of comprehensive information that can be used for more efficient diagnosis and treatment of patients, while data processing is free of charge, easy and time‐efficient.
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Vancomycin gene selection in the microbiome of urban Rattus norvegicus from hospital environment
Thomas Arn Hansen,Tejal Joshi,Anders Rhod Larsen,Paal Skytt Andersen,Klaus Harms,Sarah Mollerup,Eske Willerslev,Kurt Fuursted,Lars Peter Nielsen,Anders J. Hansen +9 more
TL;DR: In this paper, the authors investigated faecal samples of R. norvegicus from three major cities for the presence of antibiotic resistance genes and found that despite the shared resistome within samples from the same geographic locations, samples from hospital area carry significantly abundant vancomycin resistance genes.
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Molecular Characterization 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: In this article, the authors characterized AMR among clinical C. difficile strains in Thailand, where antimicrobial use remains inadequately regulated and the presence of erm-class genes was associated with high-level clindamycin and erythromycin resistance.
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