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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Phenotypic and Genetic Characterization of Klebsiella pneumoniae Isolates from Wild Animals in Central Italy
Alexandra Chiaverini,Alessandra Cornacchia,Gabriella Centorotola,Elga Ersilia Tieri,Nadia Sulli,Ilaria Del Matto,Giorgio Iannitto,Domenico Petrone,Antonio Petrini,Francesco Pomilio +9 more
TL;DR: This study highlights the link between humans, domestic animals, and wildlife, showing that the current knowledge on this ecological context is lacking and that the potential health risks are underestimated.
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Description of Chryseobacterium timonianum sp. nov., isolated from a patient with pneumonia
Rita Abou Abdallah,T. Cimmino,Sophie Alexandra Baron,Frédéric Cadoret,Caroline Michelle,Didier Raoult,Didier Raoult,Pierre-Edouard Fournier,Fadi Bittar +8 more
TL;DR: It is concluded that strain strain G972T represents a novel species for which the name Chryseobacterium timonianum is proposed, which is likely to be a new species with standing in nomenclature.
Journal ArticleDOI
Three challenging cases of infections by multidrug-resistant Serratia marcescens in patients admitted to intensive care units.
Kesia Esther da Silva,Luana Rossato,Sérgio Jorge,Natasha Rodrigues de Oliveira,Frederico Schmitt Kremer,Vinicius Farias Campos,Luciano da Silva Pinto,Odir Antônio Dellagostin,Simone Simionatto +8 more
TL;DR: In this paper, the authors report three cases of carbapenem-resistant S. marcescens infections with unfavorable clinical outcomes and provide a molecular description of the antibiotic resistance determinants at a genomic level.
Dissertation
Analysis of Genomic Islands and Other Features in Draft Versus Complete Bacterial Genomes
Journal ArticleDOI
Characterization of OXA-48-producing Klebsiella oxytoca isolates from a hospital outbreak in Tunisia.
Julia Guzmán-Puche,Rim Jenayeh,María Pérez-Vázquez,Manuel-Causse,Ferjani Asma,Boukadida Jalel,Jesús Oteo-Iglesias,Luis Martínez-Martínez +7 more
TL;DR: In this article, the authors describe the phenotypic and molecular characterization of OXA-48-producing Klebsiella oxytoca isolates that caused an outbreak in a hospital in Tunisia.
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