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
The challenges of defining the human nasopharyngeal resistome.
L. O'Connor,Robert S. Heyderman +1 more
TL;DR: In this article , the authors explore the current understanding of the nasopharyngeal resistome, particularly the role of MGEs in propagating antimicrobial resistance (AMR), explore the advantages and limitations of metagenomic sequencing technologies and bioinformatic pipelines for the NGS analysis, and highlight the key outstanding questions for future research.
Posted ContentDOI
Comparative genomic analysis of skin and soft tissue Streptococcus pyogenes isolates from low- and high-income settings
Saikou Y. Bah,Saikou Y. Bah,Alexander J Keeley,Edwin P. Armitage,Henna Khalid,Roy R. Chaudhuri,Elina Senghore,Jarra Manneh,Lisa Tilley,Michael Marks,Saffiatou Darboe,Abdul Karim Sesay,Thushan I de Silva,Thushan I de Silva,Claire E. Turner +14 more
TL;DR: In this article, a comparative whole genome analyses of S. pyogenes isolates from skin and soft tissue infections in The Gambia, West Africa, where there is a high burden of such infections is performed.
Journal ArticleDOI
Outbreak report of polymyxin-carbapenem-resistant Klebsiella pneumoniae causing untreatable infections evidenced by synergy tests and bacterial genomes.
Marisa Zenaide Ribeiro Gomes,Elisangela Martins de Lima,Caio Augusto Martins Aires,Polyana Silva Pereira,Ju Bin Yim,Caio Augusto Santos Rodrigues,T. R. T. E. Oliveira,Priscila Pinho da Silva,Cristiane Eller,Claudio Rocha de Souza,Michael J. Rybak,Rodolpho Mattos Albano,Antonio Miranda,Edson Machado,Marcos Catanho +14 more
TL;DR: In this paper , the authors reported a PCR-Kp outbreak causing untreatable infections descriptively correlated with bacterial genomes, which was reported from a time when there were no licensed drugs in the world to treat some of these infections.
Journal ArticleDOI
Genomic Profiling of Non-O157 Shiga Toxigenic Escherichia coli-Infecting Bacteriophages from South Africa.
Emmanuel W. Bumunang,Tim A. McAllister,Rodrigo Ortega Polo,Collins Njie Ateba,Kim Stanford,J. Schlechte,Matthew G. Walker,Kellie MacLean,Yan D. Niu +8 more
TL;DR: In this article , 10 non-O157-infecting phages previously isolated from feedlot cattle and dairy farms in the North-West province of South Africa were sequenced, and their genomes were analyzed.
Posted ContentDOI
Genomic investigation reveals contaminated detergent as the source of an ESBL-producing Klebsiella michiganensis outbreak in a neonatal unit
Paul Chapman,Brian M. Forde,Leah W. Roberts,Haakon Bergh,Debra Vasey,Amy V. Jennison,S. M. Moss,David L. Paterson,Scott A. Beatson,Patrick N A Harris +9 more
TL;DR: Environmental reservoirs may be an important source in outbreaks of multi-drug resistant organisms during an outbreak of extended-spectrum-β-lactamase-producing Klebsiella michiganensis colonizing neonates and can be instrumental in revealing routes of transmission and guiding infection control responses.
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.