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Metagenomic next-generation sequencing as a diagnostic tool in the clinical routine of an infectious diseases department: a retrospective cohort study

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Title: Metagenomic next-generation sequencing as a diagnostic tool in the clinical routine of an infectious diseases department: a retrospective cohort study
Authors: Kalbitz, Sven, Ermisch, Jörg, Kellner, Nils, Nickel, Olaf, Borte, Stephan, Marx, Kathrin, Lübbert, Christoph
Source: Infection
Publisher Information: Springer Science and Business Media LLC, 2024.
Publication Year: 2024
Subject Terms: Male, Adult, Aged, 80 and over, 0301 basic medicine, Adolescent [MeSH], Female [MeSH], High-Throughput Nucleotide Sequencing/methods [MeSH], mNGS, HIV infection, Aged, 80 and over [MeSH], Immunodeficiency, Aged [MeSH], Adult [MeSH], Humans [MeSH], Infectious diseases, Retrospective Studies [MeSH], Middle Aged [MeSH], Bacteria/genetics [MeSH], Diagnostics, Communicable Diseases/virology [MeSH], Cohort Studies [MeSH], Brief Report, Male [MeSH], Bacteria/classification [MeSH], Young Adult [MeSH], Metagenomics/methods [MeSH], Bacteria/isolation, Communicable Diseases/diagnosis [MeSH], 0303 health sciences, Bacteria, Adolescent, High-Throughput Nucleotide Sequencing, Middle Aged, Communicable Diseases, Cohort Studies, Young Adult, 03 medical and health sciences, Humans, Female, Metagenomics, Retrospective Studies, Aged
Description: Background Metagenomic next-generation sequencing (mNGS) of circulating cell-free DNA from plasma is a hypothesis-independent broadband diagnostic method for identification of potential pathogens. So far, it has only been investigated in special risk populations (e.g. patients with neutropenic fever). Purpose To investigate the extent to which mNGS (DISQVER® platform) can be used in routine clinical practice. Methods We collected whole blood specimens for mNGS testing, blood cultures (BC), and pathogen-specific PCR diagnostics. Clinical data and pathogen diagnostics were retrospectively reviewed by an infectious disease expert panel regarding the adjustment of anti-infective therapy. Results In 55 selected patients (median age 53 years, 67% male) with heterogeneous diagnoses, a total of 66 different microorganisms and viruses were detected using mNGS (51% viruses, 38% bacteria, 8% fungi, 3% parasites). The overall positivity rate of mNGS was 53% (29/55). Fifty-two out of 66 (79%) potential pathogens detected by mNGS were found in patients with primary or secondary immunodeficiency. The concordance rates of BC and pathogen-specific PCR diagnostics with mNGS testing were 14% (4/28) and 36% (10/28), respectively (p Streptococcus agalactiae) could only be detected by BC. Therapeutic consequences regarding anti-infective therapy were drawn from 23 pathogens (35% of detections), with 18 of these detections occurring in patients with immunodeficiency. Conclusions We conclude that mNGS is a useful diagnostic tool, but should only be performed selectively in addition to routine diagnostics of infectious diseases. The limited number of patients and the retrospective study design do not allow any further conclusions.
Document Type: Article
Other literature type
Language: English
ISSN: 1439-0973
0300-8126
DOI: 10.1007/s15010-024-02300-2
Access URL: https://pubmed.ncbi.nlm.nih.gov/38777941
https://repository.publisso.de/resource/frl:6520359
Rights: CC BY
Accession Number: edsair.doi.dedup.....337c6da5b86429c383fce8f0b7d6a646
Database: OpenAIRE
Description
Abstract:Background Metagenomic next-generation sequencing (mNGS) of circulating cell-free DNA from plasma is a hypothesis-independent broadband diagnostic method for identification of potential pathogens. So far, it has only been investigated in special risk populations (e.g. patients with neutropenic fever). Purpose To investigate the extent to which mNGS (DISQVER® platform) can be used in routine clinical practice. Methods We collected whole blood specimens for mNGS testing, blood cultures (BC), and pathogen-specific PCR diagnostics. Clinical data and pathogen diagnostics were retrospectively reviewed by an infectious disease expert panel regarding the adjustment of anti-infective therapy. Results In 55 selected patients (median age 53 years, 67% male) with heterogeneous diagnoses, a total of 66 different microorganisms and viruses were detected using mNGS (51% viruses, 38% bacteria, 8% fungi, 3% parasites). The overall positivity rate of mNGS was 53% (29/55). Fifty-two out of 66 (79%) potential pathogens detected by mNGS were found in patients with primary or secondary immunodeficiency. The concordance rates of BC and pathogen-specific PCR diagnostics with mNGS testing were 14% (4/28) and 36% (10/28), respectively (p Streptococcus agalactiae) could only be detected by BC. Therapeutic consequences regarding anti-infective therapy were drawn from 23 pathogens (35% of detections), with 18 of these detections occurring in patients with immunodeficiency. Conclusions We conclude that mNGS is a useful diagnostic tool, but should only be performed selectively in addition to routine diagnostics of infectious diseases. The limited number of patients and the retrospective study design do not allow any further conclusions.
ISSN:14390973
03008126
DOI:10.1007/s15010-024-02300-2