Journal article
Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease
National Food Institute, Technical University of Denmark1
Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark2
Hvidovre Hospital3
Department of Bio and Health Informatics, Technical University of Denmark4
Genomic Epidemiology, Department of Bio and Health Informatics, Technical University of Denmark5
University of Copenhagen6
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.
Language: | English |
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Publisher: | Springer Berlin Heidelberg |
Year: | 2017 |
Pages: | 1325-1338 |
ISSN: | 14354373 and 09349723 |
Types: | Journal article |
DOI: | 10.1007/s10096-017-2947-2 |
ORCIDs: | Lukjancenko, Oksana , Kaas, Rolf Sommer , Lund, Ole and Aarestrup, Frank Møller |
Adolescent Adult Aged Aged, 80 and over Biomedicine Child Child, Preschool Denmark Diarrhea Diarrhea/diagnosis Faecal Sample Feces Feces/microbiology Female Healthy Control Sample High-Throughput Nucleotide Sequencing High-Throughput Nucleotide Sequencing/methods Hospitals, University Humans Infant Infant, Newborn Internal Medicine Male Medical Microbiology Metagenomic Sample Middle Aged Molecular Diagnostic Techniques Molecular Diagnostic Techniques/methods Routine Diagnostics SC3 Virulence Gene Young Adult