Microbial cell-free DNA sequencing for diagnosing lung infections in immunocompromised patients.
6 affiliations
- 1Karius Inc., 975 Island Drive, Redwood City, CA, 94065, USA.
- 2Karius Inc., 975 Island Drive, Redwood City, CA, 94065, USA. [email protected].
- 3Providence Swedish Medical Center, 1124 Columbia St. #600, Seattle, WA, 98144, USA.
- 4Division of Allergy and Infectious Diseases, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.
- 5Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., Mail Stop E4-100, Seattle, WA, 98109, USA.
- 6Duke Clinical Research Institute, Duke University School of Medicine, DUMC 2629, 203 Research Dr MSRB1 Ste. 201B, Durham, NC, 27710, USA.
Abstract
Rationale
Rapid and comprehensive detection of respiratory pathogens is essential for immunocompromised patients with suspected pneumonia. Conventional diagnostic methods are limited in scope, often slow, and lack sensitivity, leading to reduced diagnostic yield.Objectives
To analytically and clinically validate a microbial cell-free DNA (mcfDNA) sequencing assay for bronchoalveolar lavage fluid (BALF) that enables broad and sensitive detection of pathogens causing pneumonia in immunocompromised patients.Methods
The BALF-mcfDNA assay detects more than 500 bacteria, DNA viruses, fungi, and parasites. Analytical validation used 324 contrived samples containing DNA from 11 representative organisms and 1,294 in-silico samples. Clinical validation compared BALF-mcfDNA sequencing with usual care (UC) testing in 118 immunocompromised adults with suspected pneumonia. An independent expert panel adjudicated the etiologic diagnoses.Measurements and main results
BALF-mcfDNA testing demonstrated high inclusivity (97%), exclusivity (96%), and precision (coefficient of variation < 15%), with linear quantification across four orders of magnitude. Limits of detection were consistent across taxa, GC content, and genome size. In clinical evaluation, BALF-mcfDNA sequencing identified probable pneumonia pathogens in 34% of participants versus 24% for UC testing, increasing diagnostic yield by 43% (57% when combined with UC). In 24% of concordant cases, mcfDNA sequencing provided additional clinically relevant information by identifying new or species-level pathogens.Conclusions
BALF-mcfDNA sequencing enables sensitive, comprehensive, and rapid pathogen detection from BALF specimens, outperforming conventional methods and improving etiologic diagnosis of pneumonia in immunocompromised hosts.
Related
- BALF-mNGS-Derived Microbial Detection Profiles and Their Associations with Clinical Severity in Immunocompromised Patients with Community-Acquired Pneumonia.
- Comparative evaluation of metagenomic and targeted next-generation sequencing for pathogen detection in bronchoalveolar lavage fluid from patients with lower respiratory tract infections: a retrospective cohort study.
- A nationwide study of pathogens in hospitalized patients with lower respiratory tract infections by metagenomic next-generation sequencing
- A 16-year retrospective investigation of granulomatous liver injury in immunocompetent and immunocompromised patients at a tertiary care center
- Outcomes of immunocompromised and non-immunocompromised patients in the ICU diverge late in the pandemic
BibTeX
@article{brick2026microbial,
title = {{Microbial cell-free DNA sequencing for diagnosing lung infections in immunocompromised patients.}},
author = {Kevin Brick and Kristin H Jarman and Frederick Nolte and Igor D Vilfan and Marla Lay Vaughn and Aga Zielinska and Victoria Portnoy and Bradley A Perkins and Sivan Bercovici and Timothy A Blauwkamp and Jason D Goldman and Joshua A Hill and Stephen P Bergin},
journal = {Respiratory research},
year = {2026},
month = aug,
doi = {10.1186/s12931-026-03832-x},
url = {https://europepmc.org/article/MED/42958246},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Microbial cell-free DNA sequencing for diagnosing lung infections in immunocompromised patients.
AU - Kevin Brick
AU - Kristin H Jarman
AU - Frederick Nolte
AU - Igor D Vilfan
AU - Marla Lay Vaughn
AU - Aga Zielinska
AU - Victoria Portnoy
AU - Bradley A Perkins
AU - Sivan Bercovici
AU - Timothy A Blauwkamp
AU - Jason D Goldman
AU - Joshua A Hill
AU - Stephen P Bergin
PY - 2026
DA - 2026/08/01
JO - Respiratory research
DO - 10.1186/s12931-026-03832-x
UR - https://europepmc.org/article/MED/42958246
AB - Rationale Rapid and comprehensive detection of respiratory pathogens is essential for immunocompromised patients with suspected pneumonia. Conventional diagnostic methods are limited in scope, often slow, and lack sensitivity, leading to reduced diagnostic yield.Objectives To analytically and clinically validate a microbial cell-free DNA (mcfDNA) sequencing assay for bronchoalveolar lavage fluid (BALF) that enables broad and sensitive detection of pathogens causing pneumonia in immunocompromised patients.Methods The BALF-mcfDNA assay detects more than 500 bacteria, DNA viruses, fungi, and parasites. Analytical validation used 324 contrived samples containing DNA from 11 representative organisms and 1,294 in-silico samples. Clinical validation compared BALF-mcfDNA sequencing with usual care (UC) testing in 118 immunocompromised adults with suspected pneumonia. An independent expert panel adjudicated the etiologic diagnoses.Measurements and main results BALF-mcfDNA testing demonstrated high inclusivity (97%), exclusivity (96%), and precision (coefficient of variation < 15%), with linear quantification across four orders of magnitude. Limits of detection were consistent across taxa, GC content, and genome size. In clinical evaluation, BALF-mcfDNA sequencing identified probable pneumonia pathogens in 34% of participants versus 24% for UC testing, increasing diagnostic yield by 43% (57% when combined with UC). In 24% of concordant cases, mcfDNA sequencing provided additional clinically relevant information by identifying new or species-level pathogens.Conclusions BALF-mcfDNA sequencing enables sensitive, comprehensive, and rapid pathogen detection from BALF specimens, outperforming conventional methods and improving etiologic diagnosis of pneumonia in immunocompromised hosts.
SN - 1465-9921
SN - 1465-993X
ER -