ArticlePloS one2015
Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Computational paradigms for antimicrobial resistance prediction: integrating multi-omics, structural modeling, and foundation artificial intelligence systems.Briefings in bioinformatics · 2026Pooled it
- Interpreting antimicrobial resistance from bacterial whole-genome sequencing: prediction tools, database fragmentation, analytical trade-offs, and harmonized reporting.Frontiers in microbiology · 2026Review
- Microbial Dark Matter: from Discovery to Applications.Genomics, proteomics & bioinformatics · 2022Review
- A review: antimicrobial resistance data mining models and prediction methods study for pathogenic bacteria.The Journal of antibiotics · 2021Review
- Genetic variation and function: revealing potential factors associated with microbial phenotypes.Biophysics reports · 2021Article
- Facile accelerated specific therapeutic (FAST) platform develops antisense therapies to counter multidrug-resistant bacteria.Communications biology · 2021Article
- Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producingMicrobial genomics · 2021Article
- Antibiotic resistance: Global health crisis and metagenomics.Biotechnology reports (Amsterdam, Netherlands) · 2021Article
- Antibiotic resistance: Time of synthesis in a post-genomic age.Computational and structural biotechnology journal · 2021Review
- Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing.Nature microbiology · 2020Article
- CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.Nucleic acids research · 2020Article
- Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance.Frontiers in genetics · 2020Review
- sraX: A Novel Comprehensive Resistome Analysis Tool.Frontiers in microbiology · 2020Article
- MALDI-TOF Mass Spectrometry and Specific Biomarkers: Potential New Key for Swift Identification of Antimicrobial Resistance in Foodborne Pathogens.Microorganisms · 2019Review
- Sequencing-based methods and resources to study antimicrobial resistance.Nature reviews. Genetics · 2019Review
- Using Genomics to Track Global Antimicrobial Resistance.Frontiers in public health · 2019Review
- Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges.Frontiers in microbiology · 2019Review
- Indexed variation graphs for efficient and accurate resistome profiling.Bioinformatics (Oxford, England) · 2018Article
- Metagenome Analysis as a Tool to Study Bacterial Infection Associated with Acute Surgical Abdomen.Journal of clinical medicine · 2018Article
- DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data.Microbiome · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAntimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring.
resultsHere we present the Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR's application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei.
conclusionsWe have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we show that SEAR is effective in detecting antimicrobial resistance genes in metagenomic and isolate sequencing data from both environmental metagenomes and sequencing data from clinical isolates.
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