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Study

Study Name: Human feces microbial communities from patient with diarrhoea and healthy adults in Hvidovre University Hospital, Denmark

Projects

Biosamples

Organisms

Biosamples: 65 Seq. Projects: 65
STUDY INFORMATION
GOLD Study ID Gs0141916
Study Name Human feces microbial communities from patient with diarrhoea and healthy adults in Hvidovre University Hospital, Denmark
Other Names
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
SRA Studies
SRA Study Id ERP015638
Study Title Evaluating the Potential of using Next-Generation Sequencing for Direct Clinical Diagnostics of Faecal Samples from Patients with Diarrhoea
Study Abstract Diarrhoea is a major global disease burden and rapid, precise identification of the causative pathogens is important to initiate patient treatment and to discover and handle potential outbreaks. The current diagnostics involve numerous procedures and often the pathogen is not identified in time to guide clinical management. Furthermore, in many clinical cases pathogens are never identified. 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. Species distribution was determined with MGmapper (http://cge.cbs.dtu.dk/services/MGmapper/) and NGS-based diagnostic prediction was performed based on 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 responsible pathogens in five of 11 conventionally negative samples. Overall, the NGS-based approach enabled pathogen detection comparable to the conventional diagnostics, and the approach has potential to be extended for detection of all pathogens. At present, however, this approach is too expensive and time-consuming for routine diagnostics.
  
Legacy ER Study ID
Legacy GOLD ID
Added By JGI automated process on 2019-02-28
Last Modified By
PI
Description The aim of this study is to evaluate the potential of NGS-based diagnostics through direct sequencing of faecal samples.
Relevance
Study Information Link
Study Information Visibility Public
Metagenomic Study Yes
Publication
Is GEBA
Is HMP
ECOSYSTEM CLASSIFICATION
Ecosystem Host-associated
Ecosystem Category Human
Ecosystem Type Digestive system
Ecosystem Subtype Large intestine
Specific Ecosystem Fecal
STUDY COMPOSITION
Number of Biosamples 65
Number of Organisms 0
Number of Seq Projects 65
Number of Analysis Projects 0
Number of Related Studies 0

 

 

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