Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease

TY - JOUR

T1 - Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease

AU - Joensen, K G

AU - Engsbro, A L Ø

AU - Lukjancenko, O

AU - Kaas, R S

AU - Lund, O

AU - Westh, H

AU - Aarestrup, F M

PY - 2017/7/1

Y1 - 2017/7/1

N2 - 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.

AB - 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.

KW - Adolescent

KW - Adult

KW - Aged

KW - Aged, 80 and over

KW - Child

KW - Child, Preschool

KW - Denmark

KW - Diarrhea/diagnosis

KW - Feces/microbiology

KW - Female

KW - High-Throughput Nucleotide Sequencing/methods

KW - Hospitals, University

KW - Humans

KW - Infant

KW - Infant, Newborn

KW - Male

KW - Middle Aged

KW - Molecular Diagnostic Techniques/methods

KW - Young Adult

U2 - 10.1007/s10096-017-2947-2

DO - 10.1007/s10096-017-2947-2

M3 - Journal article

C2 - 28285331

SN - 0934-9723

VL - 36

SP - 1325

EP - 1338

JO - European Journal of Clinical Microbiology & Infectious Diseases

JF - European Journal of Clinical Microbiology & Infectious Diseases

IS - 7

ER -