Pneumonia Surveillance in Ugandans with HIV Through the Lens of Culture-Independent Metatranscriptomics: A Cross Sectional Study

Background: Pneumonia is a leading cause of death worldwide and is a major healthcare challenge for HIV-infected persons. Despite this, the etiology of pneumonia in this population remains poorly understood. Methods: We employed a combination of bulk RNA sequencing of bronchoalveolar lavage fluid and standard culture- and PCR-based diagnostics to survey the landscape of transcriptionally active respiratory pathogens in 217 Ugandan patients with HIV who were hospitalized for pneumonia. Findings: A microbiologic diagnosis was obtained in 211 (97.2%) of individuals, with at least one microorganism of established respiratory pathogenicity identified in 113 (52.1%) of patients, and a microbe of possible pathogenicity identified in 94 (47.9%) of patients. Mycobacterium tuberculosis (MTB) was the most commonly identified established pathogen in 35 (16.1%) of the patients and bacterial or viral co-infections were found in 13 (37.2%) of MTB-positive individuals. Streptococcus mitis, not previously reported as a cause of pneumonia in patients with HIV, was the most commonly identified bacterial organism (n=37, 17.1% of patients), and Hemophilus influenzae was the most commonly identified established bacterial pathogen (n=20, 9.2% of patients). Pneumocystis jirovecii, Hemophilus influenza, human rhinovirus, Streptococcus species and Veillonella species were more prevalent in patients with a CD4 T-cell count of <200 cells/mL. Streptococcus species, human herpes virus 4, and Veillonella species were associated with increased 70-day mortality. Interpretation:  We advance understanding of the microbiologic landscape of lower respiratory tract infections in the vulnerable demographic of persons living with HIV in a representative and understudied sub-Saharan African region. Funding: This study was funded by NIH U01 HL098964, R01 HL090335, R01 HL143998, R01 HL128156 (LH) and NHLBI K23HL138461-01A1 (CL). Declaration of Interests: L. H. reports NIH grants. S.I. is employed by Second Genome, Inc. from S.L. reports fees from Siolta Therapeutics outside the submitted work. All other authors have nothing to declare. Ethics Approval Statement: This study was approved by the Mulago Hospital Institutional Review Board (IRB) under protocol number 2006-0174, and the University of California San Francisco IRB under protocol number 10-02633.