Characteristics and outcomes of patients admitted to a tertiary academic hospital in Pretoria with HIV and severe pneumonia : a retrospective cohort study

BACKGROUND : Human immunodeficiency virus (HIV) contributes significantly to morbidity and mortality in South Africa. Pneumonia and opportunistic infections remain a major cause for hospital admission among those living with HIV, even in the era of the widespread availability of antiretroviral therapy. METHODS : In this retrospective cohort study, the records of patients admitted with HIV and severe pneumonia, requiring high care/intensive care admission, during a period of 12 months (February 2018 to January 2019) were reviewed. Demographic details, antiretroviral use, HIV viral load, CD4 count, sputum culture results and radiological imaging of patients were recorded. Data was analysed to determine variables associated with mortality. RESULTS : One hundred and seventeen patient records were reviewed for this study. The patients were young (mean age 38.3 years), had advanced disease with low CD4 counts (mean 120.2 cells/mm3) and high HIV viral loads (mean 594,973.7 copies/mL). Only 36.9% (42/117) were on highly active antiretroviral therapy (HAART) on presentation to the hospital. Mycobacterium tuberculosis (M. tuberculosis) was found to be the cause for pneumonia in 35% (41/117), whilst Pneumocystis jirovecii (P. jirovecii) was found in 21.4% (25/117). Bacterial pneumonia was the cause in 17.1% (20/117) of patients while no specific aetiology was found in 26.6% (31/117) of patients in the cohort. Mortality among the cohort studied was high (40.1%) and the average length of stay in hospital in excess of two weeks. The need for ICU admission, ventilation and CMV viremia was associated with increased mortality. Chest X-ray findings did not correlate with the aetiology of pneumonia, but multiple B-lines on lung ultrasound correlated with P. jirovecii as an aetiology and there was a signal that pleural effusion with fibrin stranding predicts tuberculosis. CONCLUSIONS : Patients studied presented with advanced HIV and were often naïve to antiretroviral therapy. Mortality in this cohort of young patients was high, which emphasis the need for earlier diagnosis and treatment of HIV at a primary care level. Lung ultrasound may have clinical utility in the management of patients with HIV and pneumonia, particularly to diagnose P. jirovecii as an aetiology.http://www.biomedcentral.com/bmcinfectdisam2023Internal MedicineMedical Microbiolog

The lung microbiome in HIV‑positive patients with active pulmonary tuberculosis

Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection. Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN, Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for 16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared to the HIV-positive control cohort. Microbial community structure was also distinct from the control cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter, Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIVpositive control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the HIV-positive control cohort without PTB, with an associated loss of microbial diversity.DATA AVAILABILITY : The datasets generated and analysed during the current study are available in the University of Pretoria data repository and can be accessed at https://doi.org/10.25403/UPresearchdata.19491317.v1.The Infectious diseases Research Fund.http://www.nature.com/scientificreportsam2023BiochemistryGeneticsInternal MedicineMedical MicrobiologyMicrobiology and Plant Patholog