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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WGS based analysis of acquired antimicrobial resistance in human and non-human Acinetobacter baumannii isolates from a German perspective
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Evaluating the emergence of nonsusceptibility among Pseudomonas aeruginosa respiratory isolates from a phase-3 clinical trial for treatment of nosocomial pneumonia (ASPECT-NP).
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TL;DR: In this paper, the emergence of nonsusceptibility to ceftolozane/tazobactam and meropenem was evaluated among Pseudomonas aeruginosa lower respiratory tract isolates obtained from participants in the ASPECT-NP clinical trial.
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An integrated in silico based subtractive genomics and reverse vaccinology approach for the identification of novel vaccine candidate and chimeric vaccine against XDR Salmonella typhi H58.
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A metallo-β-lactamase enzyme for internal detoxification of the antibiotic thienamycin.
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TL;DR: In this paper, the thnS gene was expressed and investigated its activities against various substrates, and it was shown that ThnS belongs to the superfamily of metallo-β-lactamase fold proteins, and exhibited lower affinity and less efficiency toward penicillin G and cefotaxime, while imipenem is more actively hydrolysed.
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fosM, a new family of fosfomycin resistance gene identified in bacterial species isolated from human microbiota
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TL;DR: A new family of potential chromosomal fosfomycin resistance genes is reported, named fosM, named after the drug itself, which was cloned into a susceptible Escherichia coli strain.
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