ArticleMicrobial genomics2017
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads.
Article in Microbial genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 448 papers.
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Who cites it
448 citing papers in PubMed.
- Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial.BMC biology · 2023Trial
- A Simplified Guide to Whole-Genome Sequence Analysis of Salmonella on the Command Line.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Pre-existing β-lactamase gene diversity is associated with lower risk of ESBL-producing Enterobacterales colonization in patients exposed to ceftriaxone.Gut microbes · 2026Article
- Genomic profile of extraintestinal pathogenicVirulence · 2026Article
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- Escherichia coli ST131 Drives Carbapenem Use for E. coli Bloodstream Infections.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
- Nationwide spread of multidrug resistant Klebsiella pneumoniae across US communities.Nature communications · 2026Article
- A more complete picture: capturing single nucleotide variant diversity in extended-spectrum beta-lactamase producingMicrobial genomics · 2026Article
- Phenotypic and genotypic characterization of antimicrobial resistance in coagulase-negative staphylococci from bone lesions in broiler chickens.BMC veterinary research · 2026Article
- Increased Diversity and Introduction of Multidrug-Resistant Strains of Neisseria gonorrhoeae Following Cessation of COVID-19 Pandemic-Related Travel Restrictions: An Observational Genomic Epidemiologic Study.The Journal of infectious diseases · 2026Observational
- Whole-genome sequencing to investigate the prevalence and transmission of multidrug-resistant Gram-negative pathogens in an adult intensive care unit in the UK.Microbial genomics · 2026Article
- Evolution of pandemic cholera at its global source.Nature · 2026Article
- Artificial intelligence based approaches for prediction of antimicrobial resistance in ruminant host pathogens.World journal of microbiology & biotechnology · 2026Article
- Laboratory evaluation of the Allplex NG & DR assay for detection ofSexually transmitted infections · 2026Article
- Genome-sequencing of ocular fluid in a patient with syphilitic uveitis: Strain identification and antimicrobial resistance detection.American journal of ophthalmology case reports · 2026Article
- Preferred evolutionary routes of convergence in Klebsiella pneumoniae favor siderophore acquisition over hypervirulence.Research square · 2026Article
- The emergence and spread of a novel sequence type of Corynebacterium diphtheriae in Vietnam.Scientific reports · 2026Article
388 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.