Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study
Natasha Spottiswoode, Joshua D Bloomstein, Saharai Caldera, Abdul Sessolo, Kathryn McCauley, Patrick Byanyima, Josephine Zawedde, Katrina Kalantar, Sylvia Kaswabuli, Rachel L Rutishauser, Monica K Lieng, J Lucian Davis, Julia Moore, Amanda Jan, Shoko Iwai, Meera Shenoy, Ingvar Sanyu, Joseph L DeRisi, Susan V Lynch, William Worodria, Laurence Huang, Charles R LangelierThe Lancet, 2022Abstract:
Pneumonia is a leading cause of death worldwide and is a major health-care challenge in people living with HIV. Despite this, the causes of pneumonia in this population remain poorly understood. We aimed to assess the feasibility of metatranscriptomics for epidemiological surveillance of pneumonia in patients with HIV in Uganda. We performed a retrospective observational study in patients with HIV who were admitted to Mulago Hospital, Kampala, Uganda between Oct 1, 2009, and Dec 31, 2011. Inclusion criteria were age 18 years or older, HIV-positivity, and clinically diagnosed pneumonia. Exclusion criteria were contraindication to bronchoscopy or an existing diagnosis of tuberculosis. Bronchoalveolar lavage fluid was collected within 72 h of admission and a combination of RNA sequencing and Mycobacterium tuberculosis culture plus PCR were performed. The primary outcome was detection of an established or possible respiratory pathogen in the total study population.