ArticleEuropean journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology2021
Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms.
Article in European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 29 citations in OpenAlex.
- Application of Metagenomic Next-Generation Sequencing inFrontiers in medicine · 2022Pooled it
- Microbiome and resistome characterization of patients colonized with carbapenem-resistant Enterobacterales by long-read metagenomic next-generation sequencing of rectal swabs.JAC-antimicrobial resistance · 2025Article
- Towards unraveling antimicrobial resistance dynamics: a longitudinal exploration of rectal swab metagenomes.BMC microbiology · 2025Article
- Application of MinION Long-Read Sequencer for Semi-targeted Detection of Foodborne Pathogens.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Gut microbiome features and resistome elements associated with colonization and infection with antibiotic-resistance threats.Gut microbes reports · 2025Article
- Benchmarking 16S rRNA Gene-Based Approaches to Bacterial Taxonomy Assignment Based on Amplicon Sequencing With Illumina and Oxford Nanopore.International journal of microbiology · 2025Article
- Considerations for Severe Acute Respiratory Syndrome Coronavirus 2 Genomic Surveillance: A Joint Consensus Recommendation of the Association for Molecular Pathology and Association of Public Health Laboratories.The Journal of molecular diagnostics : JMD · 2025Review
- Neural network-based predictions of antimicrobial resistance phenotypes in multidrug-resistantAntimicrobial agents and chemotherapy · 2024Article
- Nanopore R10.4 metagenomic detection of blaNature communications · 2024Article
- Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2024Article
- Applicability of Bronchoalveolar Lavage Fluid and Plasma Metagenomic Next-Generation Sequencing Assays in the Diagnosis of Pneumonia.Open forum infectious diseases · 2024Article
- Clinical Application of Metagenomic Next-Generation Sequencing (mNGS) in Patients with Early Pulmonary Infection After Liver Transplantation.Infection and drug resistance · 2024Article
- The Clinical Impact of Metagenomic Next-Generation Sequencing (mNGS) Test in Hospitalized Patients with Suspected Sepsis: A Multicenter Prospective Study.Diagnostics (Basel, Switzerland) · 2023Article
- Detection ofFrontiers in microbiology · 2023Article
- Exploring the Bacteriome and Resistome of Humans and Food-Producing Animals in Brazil.Microbiology spectrum · 2022Article
- Evaluation of Metagenomic and Targeted Next-Generation Sequencing Workflows for Detection of Respiratory Pathogens from Bronchoalveolar Lavage Fluid Specimens.Journal of clinical microbiology · 2022Article
- Article
- Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections.Journal of advanced research · 2022Review
- Long-read sequencing-based in silico phage typing of vancomycin-resistant Enterococcus faecium.BMC genomics · 2021Article
- High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings.Small methods · 2021Review
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Antimicrobial resistance (AMR) is a public health threat where efficient surveillance is needed to prevent outbreaks. Existing methods for detection of gastrointestinal colonization of multidrug-resistant organisms (MDRO) are limited to specific organisms or resistance mechanisms. Metagenomic next-generation sequencing (mNGS) is a more rapid and agnostic diagnostic approach for microbiome and resistome investigations. We determined if mNGS can detect MDRO from rectal swabs in concordance with standard microbiology results. We performed and compared mNGS performance on short-read Illumina MiSeq (N = 10) and long-read Nanopore MinION (N = 5) platforms directly from rectal swabs to detect vancomycin-resistant enterococci (VRE) and carbapenem-resistant Gram-negative organisms (CRO). We detected Enterococcus faecium (N = 8) and Enterococcus faecalis (N = 2) with associated van genes (9/10) in concordance with VRE culture-based results. We studied the microbiome and identified CRO, Pseudomonas aeruginosa (N = 1), Enterobacter cloacae (N = 1), and KPC-producing Klebsiella pneumoniae (N = 1). Nanopore real-time analysis detected the bla
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