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
Reads0
Chats0
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
Citations
More filters
Journal ArticleDOI
A fatal outbreak of neonatal sepsis caused by mcr-10 carrying Enterobacter kobei in a tertiary care hospital in Nepal.
Sulochana Manandhar,Q. Nguyen,Duy Thanh Pham,Puja Amatya,Maia A. Rabaa,Sabina Dongol,Buddha Basnyat,Sameer Dixit,Stephen Baker,Abhilasha Karkey +9 more
TL;DR: In this paper , the authors reported the emergence of carbapenem and colistin non-susceptible E. kobei carrying mcr-10 gene as a cause of nosocomial neonatal sepsis in a NICU.
The Human Gut Antibiotic Resistome in the Metagenomic Era: Progress and Perspectives
Yongfei Hu,Baoli Zhu +1 more
TL;DR: This review of the recent research findings on the human gut antibiotic resistome is summarized, with an emphasis on progress achieved using the culture-independent metagenomic strategy.
Journal ArticleDOI
Population structure of blaKPC-harbouring IncN plasmids at a New York City medical centre and evidence for multi-species horizontal transmission.
Angela Gomez-Simmonds,Medini K. Annavajhala,Nina Tang,Felix D. Rozenberg,Mehrose Ahmad,Heekuk Park,Allison J. Lopatkin,Anne-Catrin Uhlemann +7 more
TL;DR: Genomic analysis of blaKPC-harbouring IncN plasmids revealed the presence of several distinct sublineages as well as substantial host diversity within plasmid clusters suggestive of frequent mobilization.
Posted ContentDOI
Bactopia: a flexible pipeline for complete analysis of bacterial genomes
Robert A. Petit,Timothy D. Read +1 more
TL;DR: A new series of pipelines called Bactopia is built using Nextflow workflow software, to provide efficient comparative genomic analyses for bacterial species or genera, and is an open source system that can scale from projects as small as one bacterial genome to thousands.
Posted ContentDOI
Extended spectrum β-lactamase and carbapenemase genes are substantially and sequentially reduced during conveyance and treatment of urban sewage
Liguan Li,Joseph Nesme,Marcos Quintela-Baluja,Sabela Balboa,Syed A. Hashsham,Maggie R. Williams,Zhuofeng Yu,Søren J. Sørensen,David W. Graham,Jesús L. Romalde,Arnaud Dechesne,Barth F. Smets +11 more
TL;DR: This first documentation of a substantial ARG reduction during sewage conveyance provides opportunities for antibiotic resistance management and a caution for sewage-based ARG surveillance.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
The RAST Server: Rapid Annotations using Subsystems Technology
Ramy K. Aziz,Ramy K. Aziz,Daniela Bartels,Aaron A. Best,Matthew DeJongh,Terrence Disz,Terrence Disz,Robert Edwards,Kevin Formsma,Svetlana Gerdes,Elizabeth M. Glass,Michael Kubal,Folker Meyer,Folker Meyer,Gary J. Olsen,Gary J. Olsen,Robert Olson,Robert Olson,Andrei L. Osterman,Ross Overbeek,Leslie Klis McNeil,Daniel Paarmann,Tobias Paczian,Bruce Parrello,Gordon D. Pusch,Claudia I. Reich,Rick Stevens,Rick Stevens,Olga Vassieva,Veronika Vonstein,Andreas Wilke,Olga Zagnitko +31 more
TL;DR: A fully automated service for annotating bacterial and archaeal genomes that identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user.
Journal ArticleDOI
Identification of acquired antimicrobial resistance genes
Ea Zankari,Henrik Hasman,Salvatore Cosentino,Martin Vestergaard,Simon Rasmussen,Ole Lund,Frank Møller Aarestrup,Mette Voldby Larsen +7 more
TL;DR: A web server providing a convenient way of identifying acquired antimicrobial resistance genes in completely sequenced isolates was created, and the method was evaluated on WGS chromosomes and plasmids of 30 isolates.
Journal ArticleDOI
Improved microbial gene identification with GLIMMER
TL;DR: Significant technical improvements to GLIMMER are reported that improve its accuracy still further, and a comprehensive evaluation demonstrates that the accuracy of the system is likely to be higher than previously recognized.
Journal ArticleDOI
Antibiotic resistance is ancient
Vanessa M. D'Costa,Christine E. King,Lindsay Kalan,Mariya Morar,Wilson W L Sung,Carsten Schwarz,Duane G. Froese,Grant D. Zazula,Fabrice Calmels,Régis Debruyne,G. Brian Golding,Hendrik N. Poinar,Gerard D. Wright +12 more
TL;DR: Target metagenomic analyses of rigorously authenticated ancient DNA from 30,000-year-old Beringian permafrost sediments are reported and show conclusively that antibiotic resistance is a natural phenomenon that predates the modern selective pressure of clinical antibiotic use.