Added Diagnostic Utility Of Clinical Metagenomics For The Diagnosis Of Pneumonia In Immunocompromised Adults.

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In the evaluation of community-acquired pneumonia, 30-60% of cases remain undiagnosed, despite extensive conventional microbiologic testing (CMT). Clinical metagenomics (CM) is an unbiased pathogen detection method that can increase diagnostic yield.Does adding clinical metagenomics to conventional microbiologic testing improve the diagnostic yield for pneumonia in immunocompromised adults?We performed a non-interventional prospective study of immunocompromised adults with pneumonia who underwent bronchoscopy and bronchoalveolar lavage (BAL) over 2-years. CMT was performed per standard of care. A commercial CM test (Explify™ Respiratory) was performed on residual BAL fluid. Final microbiologic diagnoses were based on CMT vs. CMT + CM. Final clinical diagnoses were made based on laboratory results in conjunction with clinical and radiological findings and interpreted using CMT vs. CMT+CM. Hypothetical impact of CMT+CM on management and antimicrobial stewardship was also assessed.A total of 30 immunocompromised adult patients (31 episodes of pneumonia) were included. Final microbiologic diagnoses were made in 11 cases (35%) using CMT and in 18 cases (58%) using CMT+CM. Bacterial pneumonia was diagnosed in 5 cases (16%) by CMT and in 13 cases (42%) by CMT+CM, fungal pneumonia in 6 cases (19%) by CMT and in 7 cases (23%) by CMT+CM and viral pneumonia in 2 cases (6%) by CMT and in 5 cases (16%) by CMT+CM. The hypothetical impact of CMT+CM on management was deemed probable in 1 case, possible in 8 and unlikely in 2 whereas the impact on antimicrobial stewardship was possible in 13 cases and unlikely in 7. Final clinical diagnoses were made in 20/31 cases (65%) based on CMT and in 23/31 cases (74%) based on CMT+CM.CMT+CM increased diagnostic yield in immunocompromised adults with pneumonia from 35% to 58%, mostly by detecting additional bacterial etiologies but was less useful for fungal pneumonia.

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