ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Martin Hunt,Alison E. Mather,Alison E. Mather,Leonor Sánchez-Busó,Andrew J. Page,Julian Parkhill,Jacqueline A. Keane,Simon R. Harris +7 more
- Vol. 3, Iss: 10
Reads0
Chats0
TLDR
A new tool is presented, ARIBA, that identifies AMR-associated genes and single nucleotide polymorphisms directly from short reads, and generates detailed and customizable output.Abstract:
Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the resistance of a bacterial isolate from sequencing data. Here we present a new tool, ARIBA, that identifies AMR-associated genes and single nucleotide polymorphisms directly from short reads, and generates detailed and customizable output. The accuracy and advantages of ARIBA over other tools are demonstrated on three datasets from Gram-positive and Gram-negative bacteria, with ARIBA outperforming existing methods.read more
Citations
More filters
Journal ArticleDOI
Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread
Sophia David,Sandra Reuter,Simon R. Harris,Corinna Glasner,Theresa Feltwell,Silvia Argimón,Khalil Abudahab,Richard Goater,Tommaso Giani,Giulia Errico,Marianne Aspbury,Sara Sjunnebo,Edward J. Feil,Gian Maria Rossolini,David M. Aanensen,Hajo Grundmann,Hajo Grundmann +16 more
TL;DR: Combined analysis of the genetic and geographic distances between isolates with different β-lactam resistance determinants suggests that the propensity of K. pneumoniae to spread in hospital environments correlates with the degree of resistance and that carbapenemase-positive isolates have the highest transmissibility.
Journal ArticleDOI
Sequencing-based methods and resources to study antimicrobial resistance.
TL;DR: Focusing on sequence-based discovery of antibiotic resistance genes, this Review discusses computational strategies and resources for resistance gene identification in genomic and metagenomic samples, including recent deep-learning approaches.
Journal ArticleDOI
Using Genomics to Track Global Antimicrobial Resistance.
Rene S. Hendriksen,Valeria Bortolaia,Heather Tate,Gregory H. Tyson,Frank Møller Aarestrup,Patrick F. McDermott +5 more
TL;DR: A scientific literature review is conducted and a description of examples of available tools and databases for antimicrobial resistance (AMR) detection and future perspectives and recommendations are presented.
Journal ArticleDOI
Genome-Based Prediction of Bacterial Antibiotic Resistance.
TL;DR: It is argued that standardization of WGS-AST by challenge with consistently phenotyped strain sets of defined genetic diversity is necessary to compare the efficacy of methods of prediction of antibiotic resistance based on genome sequences.
Journal ArticleDOI
Using machine learning to predict antimicrobial MICs and associated genomic features for nontyphoidal Salmonella
Marcus Nguyen,Marcus Nguyen,S. Wesley Long,S. Wesley Long,Patrick F. McDermott,Randall J. Olsen,Randall J. Olsen,Robert Olson,Robert Olson,Rick Stevens,Rick Stevens,Gregory H. Tyson,Shaohua Zhao,James J. Davis,James J. Davis +14 more
TL;DR: A collection of 5,278 nontyphoidal Salmonella genomes was used to generate extreme gradient boosting (XGBoost)-based machine learning models for predicting MICs for 15 antibiotics, showing that highly accurate MIC prediction models can be generated with less than 500 genomes.
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 Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Journal ArticleDOI
Clustal W and Clustal X version 2.0
Mark A. Larkin,Gordon Blackshields,Nigel P. Brown,R. Chenna,Paul A. McGettigan,Hamish McWilliam,Franck Valentin,Iain M. Wallace,Andreas Wilm,Rodrigo Lopez,J.D. Thompson,Toby J. Gibson,Desmond G. Higgins +12 more
TL;DR: The Clustal W and ClUSTal X multiple sequence alignment programs have been completely rewritten in C++ to facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Journal ArticleDOI
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna,Matthew Hanna,Eric Banks,Andrey Sivachenko,Kristian Cibulskis,Andrew Kernytsky,Kiran V. Garimella,David Altshuler,Stacey Gabriel,Mark J. Daly,Mark A. DePristo +10 more
TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.