Protocol for identifying Mycobacterium tuberculosis infection status through airway microbiome profiling.

This protocol describes the steps to determine an airway microbiome signature for identifying Mycobacterium tuberculosis infection status. We outline procedures for processing microbiome data, calculating diversity measures, and fitting Dirichlet multinomial mixture models. Additionally, we provide steps for analyzing taxonomic relative and differential abundances, as well as identifying potential biomarkers associated with infection status.

Airway microbiome signature accurately discriminates infection status.

remains one of the deadliest infectious agents globally. Amidst efforts to control TB, long treatment duration, drug toxicity, and resistance underscore the need for novel therapeutic strategies. Despite advances in understanding the interplay between microbiome and disease in humans, the specific role of the microbiome in predicting disease susceptibility and discriminating infection status in tuberculosis still needs to be fully investigated.

Characteristics and phenotypes of a COPD cohort from referral hospital clinics in Uganda.

Introduction: Chronic obstructive pulmonary disease (COPD) is a heterogeneous condition with varied clinical and pathophysiological characteristics. Although there is increasing evidence that COPD in low-income and middle-income countries may have different clinical characteristics from that in high-income countries, little is known about COPD phenotypes in these settings. We describe the clinical characteristics and risk factor profile of a COPD population in Uganda.

The Neutrophil-to-Lymphocyte Ratio as a Predictor of Acute Exacerbations Among Patients With COPD in Uganda.

Background: The neutrophil-to-lymphocyte ratio (NLR) is an inexpensive biomarker that potentially predicts acute exacerbations of chronic obstructive pulmonary disease (AECOPDs). We evaluated the association of baseline NLR and respiratory hospitalization risk within one year among chronic obstructive pulmonary disease (COPD) patients in Uganda, a low- and middle-income country.

Methods: A total of 312 COPD patients were followed for one year.

Alcohol Consumption Modifies Susceptibility to HIV-1 Entry in Cervical Mucosa-Derived CD4+ T cells of Women Resident in a Fishing Community of Lake Victoria, Uganda.

Background: A significant overlap exists in the burden of Alcohol Use Disorders (AUDs) and the HIV epidemic in Sub-Saharan Africa. Over 60% of HIV infections occur in women, mostly through the cervical mucosa. Absorption and systemic circulation of alcohol induces global physiological and immune effects, including at the genital mucosa.

Mechanisms of lung damage in tuberculosis: implications for chronic obstructive pulmonary disease.

Pulmonary tuberculosis is increasingly recognized as a risk factor for COPD. Severe lung function impairment has been reported in post-TB patients. Despite increasing evidence to support the association between TB and COPD, only a few studies describe the immunological basis of COPD among TB patients following successful treatment completion.

Reduced CCR5 expression among Uganda HIV controllers.

Background: Several mechanisms including reduced CCR5 expression, protective HLA, viral restriction factors, broadly neutralizing antibodies, and more efficient T-cell responses, have been reported to account for HIV control among HIV controllers. However, no one mechanism universally accounts for HIV control among all controllers. In this study we determined whether reduced CCR5 expression accounts for HIV control among Ugandan HIV controllers.

Prioritising primary care respiratory research needs: results from the 2020 International Primary Care Respiratory Group (IPCRG) global e-Delphi exercise.

Respiratory diseases remain a significant cause of global morbidity and mortality and primary care plays a central role in their prevention, diagnosis and management. An e-Delphi process was employed to identify and prioritise the current respiratory research needs of primary care health professionals worldwide. One hundred and twelve community-based physicians, nurses and other healthcare professionals from 27 high-, middle- and low-income countries suggested 608 initial research questions, reduced after evidence review by 27 academic experts to 176 questions covering diagnosis, management, monitoring, self-management and prognosis of asthma, COPD and other respiratory conditions (including infections, lung cancer, tobacco control, sleep apnoea).

The rural Uganda non-communicable disease (RUNCD) study: prevalence and risk factors of self-reported NCDs from a cross sectional survey.

Background: Non-communicable diseases (NCDs) are an increasing global concern, with morbidity and mortality largely occurring in low- and middle-income settings. We established the prospective Rural Uganda Non-Communicable Disease (RUNCD) cohort to longitudinally characterize the NCD prevalence, progression, and complications in rural Africa.

Methods: We conducted a population-based census for NCD research.

Efficacy of convalescent plasma for treatment of COVID-19 in Uganda.

Rationale: Convalescent plasma (CCP) has been studied as a potential therapy for COVID-19, but data on its efficacy in Africa are limited.

Objective: In this trial we set out to determine the efficacy of CCP for treatment of COVID-19 in Uganda.

Measurements: Patients with a positive SARS-CoV-2 reverse transcriptase (RT)-PCR test irrespective of disease severity were hospitalised and randomised to receive either COVID-19 CCP plus standard of care (SOC) or SOC alone.

Feasibility of collecting and processing of COVID-19 convalescent plasma for treatment of COVID-19 in Uganda.

Introduction: Evidence that supports the use of COVID-19 convalescent plasma (CCP) for treatment of COVID-19 is increasingly emerging. However, very few African countries have undertaken the collection and processing of CCP. The aim of this study was to assess the feasibility of collecting and processing of CCP, in preparation for a randomized clinical trial of CCP for treatment of COVID-19 in Uganda.

24-hour ambulatory blood pressure monitoring and hypertension related risk among HIV-positive and HIV-negative individuals: cross sectional study findings from rural Uganda.

Hypertension is diagnosed and treated based on blood pressure (BP) readings obtained in the clinic setting. Positive HIV status is associated with a higher prevalence of abnormal diurnal BP patterns, diagnosed with ambulatory BP monitoring rather than the conventional method of BP measurement. Little is known about ambulatory BP profiles in people living with HIV (PLHIV) in low-income countries, especially within sub-Saharan Africa.

Association between Blood Pressure and HIV Status in Rural Uganda: Results of Cross-Sectional Analysis.

Introduction: The association between HIV status and hypertension is not well described within sub-Saharan Africa. We examined prevalence and risk factors for hypertension among HIV positive and negative individuals living in a rural district of Uganda.

Methods: We conducted a cross-sectional analysis in two concurrent cohorts of 600 HIV negative and 721 HIV seropositive individuals aged ≥35 years.

Characteristics and outcomes of admitted patients infected with SARS-CoV-2 in Uganda.

Rationale: Detailed data on the characteristics and outcomes of patients with COVID-19 in sub-Saharan Africa are limited.

Objective: We determined the clinical characteristics and treatment outcomes of patients diagnosed with COVID-19 in Uganda.

Measurements: As of the 16 May 2020, a total of 203 cases had been confirmed.

Variations in Trim5α and Cyclophilin A genes among HIV-1 elite controllers and non controllers in Uganda: a laboratory-based cross-sectional study.

Background: Tripartite Motif Containing 5 alpha (TRIM5α), a restriction factor produced ubiquitously in cells and tissues of the body plays an important role in the immune response against HIV. TRIM5α targets the HIV capsid for proteosomal destruction. Cyclophilin A, an intracellular protein has also been reported to influence HIV infectivity in a cell-specific manner.

Chronic Obstructive Pulmonary Disease Prevalence and Associated Factors in a Setting of Well-Controlled HIV, A Cross-Sectional Study.

In Sub-Saharan Africa, COPD remains prevalent but its association with HIV is not well characterized especially in rural settings. We assessed for COPD prevalence, associated factors and lung function profile among HIV-infected individuals attending ART clinics in rural Nakaseke district of Uganda. We enrolled HIV-positive participants from four HIV treatment centers in rural Uganda.

The role of epigenetics in respiratory health in urban populations in low and middle-income countries.

As urbanization increases in low- and middle-income countries (LMICs), urban populations will be increasingly exposed to a range of environmental risk factors for non-communicable diseases. Inadequate living conditions in urban settings may influence mechanisms that regulate gene expression, leading to the development of non-communicable respiratory diseases. We conducted a systematic review of the literature to assess the relationship between respiratory health and epigenetic factors to urban environmental exposures observed in LMICs using MEDLINE, PubMed, EMBASE, and Google Scholar searching a combination of the terms: epigenetics, chronic respiratory diseases (CRDs), lung development, chronic obstructive airway disease, and asthma.

Knowledge and use of family planning among men in rural Uganda.

Background: Unmet need for family planning exceeds 33% in Uganda. One approach to decreasing unmet need is promoting male involvement in family planning. Male disapproval of use of family planning by their female partners and misconceptions about side effects are barriers to family planning globally and in Uganda in particular.

Brief Report: Identification of Elite and Viremic Controllers From a Large Urban HIV Ambulatory Center in Kampala, Uganda.

Background: Throughout the world, there are antiretroviral therapy-naive HIV+ individuals who maintain elevated peripheral CD4 T-cell counts, historically referred to as long-term nonprogressors (LTNPs). With recent improvements in viral load (VL) detection methods to levels as low as 20 copies per milliliter, 2 subsets of LTNPs have been defined: elite controllers (ECs), with undetectable VLs for at least 6-12 months, and viremic controllers (VCs), with VLs between 200 and 2000 copies per milliliter. ECs and VCs have been extensively studied in the developed world to determine underlying mechanisms responsible for virologic control.

Trends and level of control of hypertension among adults attending an ambulatory HIV clinic in Kampala, Uganda: a retrospective study.

Background: With an ageing HIV-positive population, sub-Saharan Africa is now facing a dual epidemic of communicable and non-communicable diseases (NCDs). This study aimed to assess trends in the prevalence of hypertension and factors associated with hypertension, among adults attending an ambulatory HIV clinic in Kampala, Uganda.

Methods: We conducted a retrospective chart review to identify patients with hypertension.