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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Staphylococcus aureus lineages associated with a free-ranging population of the fruit bat Pteropus livingstonii retained over 25 years in captivity
Kay Fountain,Alberto Rodriguez Barbon,Marjorie J. Gibbon,David Lloyd,Anette Loeffler,Edward J. Feil +5 more
TL;DR: In this article , the genomes of Staphylococcus aureus colonising critically endangered Livingstone's fruit bats (Pteropus livingstonii) were compared with those from bats in the endemic founder population free ranging in the Comoros Republic.
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Role of Institut Hospitalo-Universitaire Méditerranée Infection in the surveillance of resistance to antibiotics and training of students in the Mediterranean basin and in African countries.
TL;DR: The role of the Institut Hospitalo-Universitaire Méditerranée Infection created in 2011 in the identification and description of multidrug-resistant bacteria thanks to collaborations and training of students from the Mediterranean basin and from African countries is reported.
Posted ContentDOI
The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi
Megan E Carey,To Nguyen Thi Nguyen,Tran Do Hoang Nhu,Zoe A. Dyson,Pham Thanh Duy,Elli Mylona,Satheesh Nair,Marie Anne Chattaway,Stephen Baker +8 more
TL;DR: Detailed phylogenetic and phylodynamic analyses on contemporary genome sequences from S. Typhi indicate that the prototype H58 organisms were multi-drug resistant (MDR), suggesting that the first H58 organism was generated during chronic carriage.
Dissertation
Computational Tools for Annotating Antibiotic Resistance in Metagenomic Data
Arango Argoty,Gustavo Alonso +1 more
TL;DR: NanoARG, an online computational resource that takes advantage of the long reads produced by nanopore sequencing technology to provide insights into mobility, co-selection, and pathogenicity, is introduced.
Journal ArticleDOI
The functional convergence of antibiotic resistance in β‐lactamases is not conferred by a simple convergent substitution of amino acid
Vivek Keshri,Kevin Arbuckle,Kevin Arbuckle,Olivier Chabrol,Jean-Marc Rolain,Didier Raoult,Pierre Pontarotti,Pierre Pontarotti +7 more
TL;DR: The functional activity of antibiotic resistance mediated by β‐lactamase has evolved in a convergent manner within molecular classes, but is not associated with any single amino acid substitution, which suggests that the dynamics of convergent evolution in this system can vary between the functional and molecular levels.
References
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