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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Susceptibility (re)-testing of a large collection of Listeria monocytogenes from foods in China from 2012 to 2015 and WGS characterization of resistant isolates
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TL;DR: Data showed that this bacterium can acquire resistance by horizontal gene transfer in and between species, and may necessitate a re-evaluation of risk to public health, associated with this bacterial species.
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Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods.
Bert Bogaerts,Stéphanie Nouws,Bavo Verhaegen,Sarah Denayer,Julien Van Braekel,Raf Winand,Qiang Fu,Florence Crombé,Denis Pierard,Kathleen Marchal,Kathleen Marchal,Nancy H. C. Roosens,Sigrid C. J. De Keersmaecker,Kevin Vanneste +13 more
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Identification of polysaccharide capsules among extensively drug-resistant genitourinary Haemophilus parainfluenzae isolates.
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TL;DR: This study describes for the first time a capsular operon in H. parainfluenzae, a major determinant of pathogenicity that may contribute to increased virulence in XDR clinical isolates and phylogenetic analysis suggests the possible spread of an XDR-encapsulated strain in Europe.
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Use of online tools for antimicrobial resistance prediction by whole-genome sequencing in methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE)
Ahmed Babiker,Mustapha M. Mustapha,Marissa P Pacey,Kathleen A. Shutt,Chinelo Ezeonwuka,Sara L. Ohm,Vaughn S. Cooper,Jane W. Marsh,Yohei Doi,Lee H. Harrison +9 more
TL;DR: WGS can be used as a reliable predicator of phenotypic resistance both for MRSA and VRE using readily available online tools.
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Draft genome and description of Merdibacter massiliensis gen.nov., sp. nov., a new bacterium genus isolated from the human ileum.
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