ArticleBioinformatics (Oxford, England)2018
Indexed variation graphs for efficient and accurate resistome profiling.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 2 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
35 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Computational paradigms for antimicrobial resistance prediction: integrating multi-omics, structural modeling, and foundation artificial intelligence systems.Briefings in bioinformatics · 2026Pooled it
- Systematic review of human gut resistome studies revealed variable definitions and approaches.Gut microbes · 2020Pooled it
- Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.NAR genomics and bioinformatics · 2026Article
- The Wastewater Resistome: A Shotgun Metagenomics Analysis of Urban Treatment Plants in Sicily.Antibiotics (Basel, Switzerland) · 2026Article
- StaLAENet: A stacked LSTM-nested deep-autoencoder network for identification of antimicrobial resistance of nosocomial pathogens.Journal of biosciences · 2026Article
- Comparative assessment of annotation tools reveals critical antimicrobial resistance knowledge gaps in Klebsiella pneumoniae.Scientific reports · 2025Article
- Deeper Exploration of Gut Microbiome: Profile of Resistome, Virome and Viral Auxiliary Metabolic Genes of Three Ethnic Indian Groups.Molecular biotechnology · 2025Article
- argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO).Bioinformatics (Oxford, England) · 2025Article
- ARGContextProfiler: extracting and scoring the genomic contexts of antibiotic resistance genes using assembly graphs.Frontiers in microbiology · 2025Article
- The gut microbiome, resistome, and mycobiome in preterm newborn infants and mouse pups: lack of lasting effects by antimicrobial therapy or probiotic prophylaxis.Gut pathogens · 2024Article
- Characteristics of the Fecal Microbiome of Piglets with Diarrhea Identified Using Shotgun Metagenomics Sequencing.Animals : an open access journal from MDPI · 2023Article
- Staphylococcal diversity in atopic dermatitis from an individual to a global scale.Cell host & microbe · 2023Article
- Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome.Cell reports. Medicine · 2022Article
- The Bacterial Urban Resistome: Recent Advances.Antibiotics (Basel, Switzerland) · 2022Review
- Effects of Dietary Antimicrobial Growth Promoters on Performance Parameters and Abundance and Diversity of Broiler Chicken Gut Microbiome and Selection of Antibiotic Resistance Genes.Frontiers in microbiology · 2022Article
- Metagenomic analysis of MWWTP effluent treated via solar photo-Fenton at neutral pH: Effects upon microbial community, priority pathogens, and antibiotic resistance genes.The Science of the total environment · 2021Article
- A review of the resistome within the digestive tract of livestock.Journal of animal science and biotechnology · 2021Review
- Shotgun-metagenomics based prediction of antibiotic resistance and virulence determinants in Staphylococcus aureus from periprosthetic tissue on blood culture bottles.Scientific reports · 2021Article
- Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner.Nature microbiology · 2021Article
- PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data.Microbiome · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Antimicrobial resistance (AMR) remains a major threat to global health. Profiling the collective AMR genes within a metagenome (the 'resistome') facilitates greater understanding of AMR gene diversity and dynamics. In turn, this can allow for gene surveillance, individualized treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools. Results: Our method combines a variation graph representation of gene sets with a locality-sensitive hashing Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, graphing Resistance Out Of meTagenomes (GROOT), and show it to be both faster and more accurate than a current reference-dependent tool for resistome profiling. GROOT runs on a laptop and can process a typical 2 gigabyte metagenome in 2 min using a single CPU. Our method is not restricted to resistome profiling and has the potential to improve current metagenomic workflows. Availability and implementation: GROOT is written in Go and is available at https://github.com/will-rowe/groot (MIT license). Supplementary information: Supplementary data are available at Bioinformatics online.
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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.