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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CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
Baofeng Jia,Amogelang R. Raphenya,Brian Alcock,Nicholas Waglechner,Peiyao Guo,Kara K. Tsang,Briony A. Lago,Biren M. Dave,Sheldon K. Pereira,Arjun N. Sharma,Sachin Doshi,Mélanie Courtot,Raymond Lo,Laura E. Williams,Jonathan G. Frye,Tariq Elsayegh,Daim Sardar,Erin L. Westman,Andrew C. Pawlowski,Timothy A. Johnson,Fiona S. L. Brinkman,Gerard D. Wright,Andrew G. McArthur +22 more
TL;DR: The Comprehensive Antibiotic Resistance Database (CARD) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR.
Journal ArticleDOI
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
Brian Alcock,Amogelang R. Raphenya,Tammy T. Y. Lau,Kara K. Tsang,Mégane Bouchard,Arman Edalatmand,William Huynh,Anna-Lisa V. Nguyen,Annie A. Cheng,Sihan Liu,Sally Y. Min,Anatoly Miroshnichenko,Hiu-Ki R Tran,Rafik El Werfalli,Jalees A. Nasir,Martins Oloni,David Speicher,Alexandra Florescu,Bhavya Singh,Mateusz Faltyn,Anastasia Hernández-Koutoucheva,Arjun N. Sharma,Emily Bordeleau,Andrew C. Pawlowski,Haley L. Zubyk,Damion M. Dooley,Emma Griffiths,Finlay Maguire,Geoffrey L. Winsor,Robert G. Beiko,Fiona S. L. Brinkman,William W. L. Hsiao,William W. L. Hsiao,Gary Van Domselaar,Gary Van Domselaar,Andrew G. McArthur +35 more
TL;DR: A new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes, able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants.
Journal ArticleDOI
Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health
Kathryn E. Holt,Heiman F. L. Wertheim,Ruth N. Zadoks,Stephen Baker,Chris A. Whitehouse,David A. B. Dance,Adam Jenney,Thomas R. Connor,Li Yang Hsu,Juliëtte A. Severin,Sylvain Brisse,Hanwei Cao,Jonathan J. Wilksch,Claire L. Gorrie,Mark B. Schultz,David J. Edwards,Kinh Van Nguyen,Trung Vu Nguyen,Trinh Tuyet Dao,Martijn Mensink,Vien Le Minh,Nguyen Thi Khanh Nhu,Constance Schultsz,Kuntaman Kuntaman,Paul N. Newton,Paul N. Newton,Catrin E. Moore,Catrin E. Moore,Richard A. Strugnell,Nicholas R. Thomson,Nicholas R. Thomson +30 more
TL;DR: The DNA sequence of K. pneumoniae isolates from around the world is determined and it is shown that there is a wide spectrum of diversity, including variation within shared sequences and gain and loss of whole genes, and there is an unrecognized association between the possession of specific gene profiles associated with virulence and antibiotic resistance.
Journal ArticleDOI
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Michael Inouye,Harriet Dashnow,Harriet Dashnow,Lesley Raven,Mark B. Schultz,Bernard J. Pope,Bernard J. Pope,Takehiro Tomita,Justin Zobel,Kathryn E. Holt +9 more
TL;DR: This work presents SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data, which is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment.
Journal ArticleDOI
Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates.
Michael Feldgarden,Vyacheslav Brover,Daniel H. Haft,Arjun B. Prasad,Douglas J. Slotta,Igor Tolstoy,Gregory H. Tyson,Shaohua Zhao,Chih-Hao Hsu,Patrick F. McDermott,Daniel A. Tadesse,Cesar A. Morales,Mustafa Simmons,Glenn E. Tillman,Jamie L. Wasilenko,Jason P. Folster,William Klimke +16 more
TL;DR: AMRFinder appears to be a highly accurate AMR gene detection system based on the consistency between predicted AMR genotypes from AMRFinder and resistance phenotypes from the National Antimicrobial Resistance Monitoring System.
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