Plasma microbial cell-free DNA sequencing in immunocompromised patients with pneumonia: A prospective observational study Journal Article
| Authors: | Bergin, S. P.; Chemaly, R. F.; Dadwal, S. S.; Hill, J. A.; Lee, Y. J.; Haidar, G.; Luk, A.; Drelick, A.; Chin-Hong, P. V.; Benamu, E.; Khawaja, F.; Nanayakkara, D.; Papanicolaou, G. A.; Small, C. B.; Fung, M.; Barron, M. A.; Davis, T.; McClain, M. T.; Maziarz, E. K.; Madut, D. B.; Bedoya, A. D.; Gilstrap, D. L.; Todd, J. T.; Barkauskas, C. E.; Bigelow, R.; Leimberger, J. D.; Tsalik, E. L.; Wolf, O.; Mughar, M.; Hollemon, D.; Duttagupta, R.; Lupu, D. S.; Bercovici, S.; Perkins, B. A.; Blauwkamp, T. A.; Fowler, V. B. Jr; Holland, T. L. |
| Article Title: | Plasma microbial cell-free DNA sequencing in immunocompromised patients with pneumonia: A prospective observational study |
| Abstract: | Background Pneumonia is a common cause of morbidity and mortality, yet a causative pathogen is identified in a minority of cases. Plasma microbial cell-free DNA sequencing may improve diagnostic yield in immunocompromised patients with pneumonia. Methods In this prospective, multicenter, observational study of immunocompromised adults undergoing bronchoscopy to establish a pneumonia etiology, plasma microbial cell-free DNA sequencing was compared to standardized usual care testing. Pneumonia etiology was adjudicated by a blinded independent committee. The primary outcome, additive diagnostic value, was assessed in the Per Protocol population (patients with complete testing results and no major protocol deviations) and defined as the percent of patients with an etiology of pneumonia exclusively identified by plasma microbial cell-free DNA sequencing. Clinical additive diagnostic value was assessed in the Per Protocol subgroup with negative usual care testing. Results Of 257 patients, 173 met Per Protocol criteria. A pneumonia etiology was identified by usual care in 52/173 (30.1%), plasma microbial cell-free DNA sequencing in 49/173 (28.3%) and the combination of both in 73/173 (42.2%) patients. Plasma microbial cell-free DNA sequencing exclusively identified an etiology of pneumonia in 21/173 patients (additive diagnostic value 12.1%, 95% confidence interval [CI], 7.7% to 18.0%, P <.001). In the Per Protocol subgroup with negative usual care testing, plasma microbial cell-free DNA sequencing identified a pneumonia etiology in 21/121 patients (clinical additive diagnostic value 17.4%, 95% CI, 11.1% to 25.3%). Conclusions Non-invasive plasma microbial cell-free DNA sequencing significantly increased diagnostic yield in immunocompromised patients with pneumonia undergoing bronchoscopy and extensive microbiologic and molecular testing. Clinical Trials Registration NCT04047719. |
| Keywords: | prospective studies; hematopoietic stem cell transplantation; confidence intervals; hematologic neoplasms; bronchoscopy; descriptive statistics; funding source; communicable diseases; nonexperimental studies; microbiological techniques; dna -- analysis; human; bloodborne pathogens; sequence analysis -- methods; pneumonia -- etiology; immunocompromised host -- drug effects; cell-free nucleic acids -- blood; pneumonia -- therapy; microbial culture and sensitivity tests -- methods |
| Journal Title: | Clinical Infectious Diseases |
| Volume: | 78 |
| Issue: | 3 |
| ISSN: | 1058-4838 |
| Publisher: | Oxford University Press |
| Date Published: | 2024-03-15 |
| Start Page: | 775 |
| End Page: | 784 |
| Language: | English |
| DOI: | 10.1093/cid/ciad599 |
| PROVIDER: | EBSCOhost |
| PROVIDER: | cinahl plus with full text |
| PMCID: | PMC10954333 |
| PUBMED: | 37815489 |
| DOI/URL: | |
| Notes: | Accession Number: 176151670 -- Entry Date: 20240327 -- Revision Date: 20240327 -- Publication Type: Journal Article; research; tables/charts -- Journal Subset: Biomedical -- Grant Information: This study was funded by Karius Inc, Redwood City, California, USA., and Duke ClinicalResearch Institute.. -- Source: CINAHL Plus with Full Text |
