ArticleEuropean journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology2017
Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease.
Article in European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Metagenomics enables parallel detection of 176 clinically relevant targets from faecal samples.Frontiers in cellular and infection microbiology · 2026Article
- Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC.Microbiology spectrum · 2025Article
- Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens.Gut pathogens · 2025Article
- Evaluation of shotgun metagenomics as a diagnostic tool for infectious gastroenteritis.PloS one · 2025Article
- Virulence genes and pulsed-field gel electrophoresis profiles of Shiga toxin-producingIranian journal of microbiology · 2024Article
- Metagenomic analysis of sewage for surveillance of bacterial pathogens: A release experiment to determine sensitivity.PloS one · 2024Article
- Application of metagenomic next-generation sequencing and targeted metagenomic next-generation sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients.Frontiers in cellular and infection microbiology · 2024Article
- Article
- Safety, efficacy, and impact on gut microbial ecology of aFrontiers in nutrition · 2023Article
- Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool.Microorganisms · 2022Article
- Culture-Free Detection of Antibiotic Resistance Markers from Native Patient Samples by Hybridization Capture Sequencing.Microorganisms · 2021Article
- Using next-generation sequencing to develop a Shigella species threshold and profile faecal samples from suspected diarrhoea cases.Folia microbiologica · 2021Article
- Temporal dynamics of the plasma microbiome in recipients at early post-liver transplantation: a retrospective study.BMC microbiology · 2021Article
- The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling.International journal of molecular sciences · 2021Review
- A Comparison of Blood Pathogen Detection Among Droplet Digital PCR, Metagenomic Next-Generation Sequencing, and Blood Culture in Critically Ill Patients With Suspected Bloodstream Infections.Frontiers in microbiology · 2021Article
- Childhood diarrhoeal diseases in developing countries.Heliyon · 2020Review
- Phenotypic and genotypic characterization of Salmonella Typhimurium isolates from humans and foods in Brazil.PloS one · 2020Article
- Metagenomic Next-Generation Sequencing versus Traditional Pathogen Detection in the Diagnosis of Peripheral Pulmonary Infectious Lesions.Infection and drug resistance · 2020Article
- Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms.EFSA journal. European Food Safety Authority · 2019Article
- Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study.Annals of clinical microbiology and antimicrobials · 2018Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The accurate microbiological diagnosis of diarrhoea involves numerous laboratory tests and, often, the pathogen is not identified in time to guide clinical management. With next-generation sequencing (NGS) becoming cheaper, it has huge potential in routine diagnostics. The aim of this study was to evaluate the potential of NGS-based diagnostics through direct sequencing of faecal samples. Fifty-eight clinical faecal samples were obtained from patients with diarrhoea as part of the routine diagnostics at Hvidovre University Hospital, Denmark. Ten samples from healthy individuals were also included. DNA was extracted from faecal samples and sequenced on the Illumina MiSeq system. Species distribution was determined with MGmapper and NGS-based diagnostic prediction was performed based on the relative abundance of pathogenic bacteria and Giardia and detection of pathogen-specific virulence genes. NGS-based diagnostic results were compared to conventional findings for 55 of the diarrhoeal samples; 38 conventionally positive for bacterial pathogens, two positive for Giardia, four positive for virus and 11 conventionally negative. The NGS-based approach enabled detection of the same bacterial pathogens as the classical approach in 34 of the 38 conventionally positive bacterial samples and predicted the responsible pathogens in five of the 11 conventionally negative samples. Overall, the NGS-based approach enabled pathogen detection comparable to conventional diagnostics and the approach has potential to be extended for the detection of all pathogens. At present, however, this approach is too expensive and time-consuming for routine diagnostics.
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