Journal: medRxiv

Article Title: Microbial cell-free DNA sequencing of bronchoalveolar lavage fluid improves diagnostic yield and may add clinical utility in immunocompromised patients with severe pneumonia

doi: 10.1101/2025.11.05.25339543

Figure Lengend Snippet: Flow diagram depicting patient and sample selection for the comparison of BAL fluid mcfDNA sequencing with the Karius® test and standard of care testing.

Article Snippet: For each sample, the BAL fluid mcfDNA sequencing test report included the name of each identified organism, the number of microbial reads found for the organism, and the Karius® designation for the pathogenicity of the organism (see Definitions).

Techniques: Selection, Comparison, Sequencing

Journal: medRxiv

Article Title: Microbial cell-free DNA sequencing of bronchoalveolar lavage fluid improves diagnostic yield and may add clinical utility in immunocompromised patients with severe pneumonia

doi: 10.1101/2025.11.05.25339543

Figure Lengend Snippet: Additive diagnostic value of BAL fluid mcfDNA sequencing with the Karius® test (KT-BAL) compared to standard of care (SOC) testing in immunocompromised patients with pneumonia. A) Number of organisms across all samples identified by either SOC alone, KT-BAL alone, or both techniques, split by KT-BAL category. B) Organisms identified exclusively by KT-BAL across all samples, split by KT-BAL category.

Article Snippet: For each sample, the BAL fluid mcfDNA sequencing test report included the name of each identified organism, the number of microbial reads found for the organism, and the Karius® designation for the pathogenicity of the organism (see Definitions).

Techniques: Diagnostic Assay, Sequencing

Journal: medRxiv

Article Title: Microbial cell-free DNA sequencing of bronchoalveolar lavage fluid improves diagnostic yield and may add clinical utility in immunocompromised patients with severe pneumonia

doi: 10.1101/2025.11.05.25339543

Figure Lengend Snippet: Patients for whom BAL fluid mcfDNA testing with the Karius® test (KT-BAL) identified Category One or Two organisms missed by standard of care (SOC) had significantly more cumulative intubation days compared to patients where KT-BAL and SOC were concordant for all Category One or Two organisms. Hospital length of stay, ICU length of stay, and ICU mortality were worse in the KT-BAL only group, but these differences were not significant (Mann-Whitney U test for continuous variables, Fisher’s exact test for mortality).

Article Snippet: For each sample, the BAL fluid mcfDNA sequencing test report included the name of each identified organism, the number of microbial reads found for the organism, and the Karius® designation for the pathogenicity of the organism (see Definitions).

Techniques: MANN-WHITNEY

Journal: Open Forum Infectious Diseases

Article Title: An Observational Cohort Study of Bronchoalveolar Lavage Fluid Galactomannan and Aspergillus Culture Positivity in Patients Requiring Mechanical Ventilation

doi: 10.1093/ofid/ofaf090

Figure Lengend Snippet: Bronchoalveolar lavage (BAL) fluid galactomannan and Aspergillus growth. A , Summary on a patient level. B , Summary of BAL samples. Abbreviations: BAL, bronchoalveolar lavage; GM, galactomannan; ODI, optical density index.

Article Snippet: These samples are typically sent for cell count and differential, amylase, bacterial and fungal cultures (incubated for 4 weeks at 30 ° C on inhibitory mold agar plates with identification performed by microscopic morphology and ability to grow at 45 ° C), BAL fluid GM (Bio-Rad Platelia Aspergillus Ag), and multiplex polymerase chain reaction (PCR; both viral and bacterial), as well as other studies when indicated.

Techniques:

Journal: Open Forum Infectious Diseases

Article Title: An Observational Cohort Study of Bronchoalveolar Lavage Fluid Galactomannan and Aspergillus Culture Positivity in Patients Requiring Mechanical Ventilation

doi: 10.1093/ofid/ofaf090

Figure Lengend Snippet: A , Bronchoalveolar lavage (BAL) fluid galactomannan (GM) optical density index (ODI) is higher in patients who grow Aspergillus at least once during admission. B , BAL fluid GM ODI is higher in the BAL samples where Aspergillus grew, though sometimes also elevated in BAL samples that did not grow Aspergillus .

Article Snippet: These samples are typically sent for cell count and differential, amylase, bacterial and fungal cultures (incubated for 4 weeks at 30 ° C on inhibitory mold agar plates with identification performed by microscopic morphology and ability to grow at 45 ° C), BAL fluid GM (Bio-Rad Platelia Aspergillus Ag), and multiplex polymerase chain reaction (PCR; both viral and bacterial), as well as other studies when indicated.

Techniques:

Journal: Open Forum Infectious Diseases

Article Title: An Observational Cohort Study of Bronchoalveolar Lavage Fluid Galactomannan and Aspergillus Culture Positivity in Patients Requiring Mechanical Ventilation

doi: 10.1093/ofid/ofaf090

Figure Lengend Snippet: Example timelines of four patients ( A , B , C , D ) who grew Aspergillus on bronchoalveolar lavage (BAL) fluid culture (red square indicates Aspergillus growth, blue circle indicates no Aspergillus growth) and BAL fluid galactomannan (GM) optical density index (ODI) levels (y-axis). Patients who grew Aspergillus did not grow it consistently, even on BAL samples that had elevated BAL fluid GM ODIs. The bottom line of each graph shows antifungal therapy with anti- Aspergillus activity by intensive care unit (ICU) day (gray x marker, no antifungal therapy; green plus marker, antifungal therapy administered).

Article Snippet: These samples are typically sent for cell count and differential, amylase, bacterial and fungal cultures (incubated for 4 weeks at 30 ° C on inhibitory mold agar plates with identification performed by microscopic morphology and ability to grow at 45 ° C), BAL fluid GM (Bio-Rad Platelia Aspergillus Ag), and multiplex polymerase chain reaction (PCR; both viral and bacterial), as well as other studies when indicated.

Techniques: Activity Assay, Marker