Background Incorrect inhaler use is associated with poorer health outcomes, reduced quality of life, and higher healthcare utilisation in patients with asthma and COPD. Method We performed an observational study of pressurized metered-dose inhaler technique in patients with asthma or COPD. Patients were assessed using a six-point inhaler checklist to identify common critical inhaler technique errors. An inadequate inhaler technique was defined as the presence of one or more critical errors. A multivariate logistic regression model was used to determine the odds of an inadequate inhaler technique. Results During the 14-month study period, 357 patients were enrolled. At least one critical error was executed by 66.7% of participants, and 24.9% made four or more critical errors. The most common errors were: failure to exhale completely prior to pMDI activation and inhalation (49.6%), failure to perform a slow, deep inhalation following device activation (48.7%), and failure to perform a breathhold at the end of inspiration (47.3%). The risk of a critical error was higher in COPD patients (aOR 2.25, 95%CI 1.13 – 4.47). Prior training reduced error risk specifically when trained by a doctor (aOR 0.08, 95% CI 0.1 – 0.57) or a pharmacist (aOR 0.02, 95% CI 0.01 – 0.26) compared to those with no training. Previous clinical trial participation significantly reduced error risk and rate:< 3 trials (aOR 0.35, 95% CI 0.19 – 0.66) and ≥3 trials (aOR 0.17, 95% CI 0.07 – 0.42). The rate of critical errors was not significantly associated with age, sex, or prior pMDI experience. Conclusion This study found a high rate of critical inhaler technique errors in a mixed population of asthma and COPD patients; however, prior training and in particular, multiple previous clinical trial participation significantly reduced the risk of errors.

Childhood respiratory disease remains a major contributor of morbidity and mortality globally and both paediatric and adult chronic respiratory illness is increasing in prevalence worldwide. This burden of respiratory disease is heaviest in low-middle income countries (LMIC), areas that have a high prevalence of known risk factors for respiratory disease, such us overcrowding, poverty and environmental air pollution. Much chronic respiratory illness has its origin in early life; further low lung function in infancy is associated with later respiratory illness. However, there is limited data on lung function in African infants despite a high prevalence of respiratory disease. Understanding the determinants of infant lung function will improve our understanding of prevention and management of respiratory disease. This thesis aimed to describe lung function in South African infants from six weeks to one year and to investigate the impact of prenatal and early environmental exposures on lung function in infancy. Infants enrolled in the Drakenstein Child Health Study, a multidisciplinary birth cohort study investigating the aetiology and outcome of early life lower respiratory tract infections (LRTI), were included. Seven hundred and forty one infants were enrolled from June 2012 to February 2015. Infants had lung function measured at six (4-10) weeks of age and one year (11-14 months). Measurements, made with the infant breathing via a facemask during natural sleep, included tidal breathing, exhaled nitric oxide, sulphur hexafluoride multiple breath washout and the forced oscillation technique. Information on antenatal exposures was collected using questionnaires and urine cotinine. Household benzene was measured antenatally. The chapters of the thesis are presented as published manuscripts that describe the establishment of infant lung function for the first time in South Africa and the development of normative lung function in the first year of life. The final chapters investigate the impact of early life exposures, most notably LRTI, on lung function at six weeks and one year. The thesis concludes that infant lung function testing is feasible in a community setting in 11 a LMIC like South Africa. Size, gender and ethnicity are important determinants of lung function. Lung function of South African infants is not well predicted by European reference equations, highlighting the importance of using population specific reference data when interpreting lung function tests. The study identifies several factors including maternal smoking, maternal alcohol and household benzene exposure during pregnancy, associated with altered early lung function. In addition tracking of lung function in the first year of life is described in this cohort of African infants living in a high respiratory disease burden setting. The study identifies risk factors for impaired lung function at one year independent of low baseline lung function: LRTI, household smoke exposure and infant nutrition, factors amenable to public health intervention. Given the fact that infant lung function tracks into later life and plays a role in chronic respiratory disease, preventing respiratory illness in young children, reducing exposure to environmental tobacco and maximising nutrition are key priorities in the strengthening of child respiratory health. Long-term study of lung function and respiratory disease in these infants is a priority in order to develop new strategies to strengthen child health.

middleincome countries (LMIC) and a major reason for health care visits and hospitalisation. Environmental exposures to indoor air pollution (IAP) or tobacco smoke are important risk factors for childhood respiratory disease. Despite increased electrification, many communities in LMIC rely on alternate fuel sources for household cooking or heating. The impact of antenatal or postnatal exposures on early childhood respiratory disease has not been comprehensively studied in LMIC especially in Africa. The aim of this work was to investigate the impact of IAP and environmental tobacco smoke (ETS) exposure on child health and early-life respiratory disease in the Drakenstein Child Health Study (DCHS), a South African birth cohort study. The DCHS investigates the epidemiology and impact of early-life exposures on child health including lung disease. The study is set in a peri-urban poor community in the Western Cape, South Africa. Pregnant women were enrolled from two public primary healthcare clinics, Mbekweni (serving a predominantly black African population) and Newman (predominantly mixed-ancestry population) and 1000 mother-infant pairs longitudinally followed from birth through 1 year of life. The thesis chapters are presented as published manuscripts that describe IAP and ETS exposure in the 2 communities in the DCHS cohort from the antenatal period and the impact of these exposure on child health and lung diseases, LRTI and wheezing illness in the first year of life. To measure exposures comprehensively, two home visits, one in the antenatal period (third trimester) and the second postnatally (between 4 and 6 months of the infant’s life), were conducted to assess the home environment and to measure the most common indoor air pollutants and by-products of combustion. Devices placed in participants’ homes measured exposure to particulate matter (PM10), carbon monoxide (CO), nitrogen dioxide (NO2), sulphur dioxide (SO2) and volatile organic compounds (VOC). Maternal and infant urine cotinine measures were used to validate self-reported tobacco smoking and exposure. Study staff trained in recognition of LRTI or wheeze documented all episodes, which were categorised according to WHO case definition criteria. Exposure to IAP was comprehensively assessed in over 800 homes antenatally and postnatally providing important South African data on IAP and potential sources of exposure. Tobacco smoke exposure was assessed longitdunially by maternal self-report using validated scales and by measurement of urine cotinine in mothers and infants. Tobacco smoke exposure was found to be highly prevalent with a smoking prevalence of >50% in mixedancestry mothers. Alarmingly, 18% of infants were born with urine cotinine levels in keeping with active smoking, while a further 30% had levels indicating passive smoke exposure. Key findings were despite 92% of homes reporting access to electricity, there was still a reliance on cheaper alternate fuels. Tobacco smoking prevalence amongst pregnant women was high (32%), as was household exposure to tobacco smoke (44%). ETS exposure was associated with low birth weight and antenatal IAP or ETS exposure was significantly associated with increased LRTI. ETS exposure was also associated with wheezing illnesses. A novel finding was that antenatal exposure to toluene, a volatile organic compound, was associated with severe LRTI and hospitalisation. The timing of environmental exposures on the subsequent development of LRTI in infancy has not been well described. An important finding was that antenatal exposures were the main risk factors associated with LRTI, with maternal smoking in pregnancy or PM10 exposure most strongly associated with LRTI. Wheezing illness was associated with both antenatal and postnatal maternal smoking and antenatal maternal smoke exposure and postnatal household member smoking. Both IAP and ETS exposure impacted on both maternal and infant nasopharyngeal bacterial carriage which may be a precursor to the development of LRTI. Environmental exposures therefore had a substantial impact on child health and on LRTI and wheezing illness. The effect on LRTI of antenatal compared with postnatal exposure suggests an in utero developmental lung effect. This study highlights antenatal and early life as a critical period for lung development. Urgent and effective smoking cessation programmes targeting women of child bearing age as well as public health interventions to reduce IAP are required. Woman of childbearing age, pregnant women and children in poor communities represent vulnerable populations at risk for long-term health effects of these exposures.

BACKGROUND: Tuberculosis (TB) remains out of control globally. Recent promising vaccine candidates have failed in clinical trials and host immunity in the lung remains poorly understood. Pathogenesis of pulmonary cavitation, the basis of TB transmission, is poorly understood. The degree of heteroresistance in the human lung remains unclear. METHODOLOGY: Multi- and extensively drug-resistant TB (MDR- and XDR-TB) patients scheduled for therapeutic lung resection surgery in Cape Town were prospectively recruited. Biopsies were obtained from specific positions in and around cavities. Drug-susceptibility testing, strain-type determination, whole-genome sequencing, and whole-transcriptome shotgun sequencing was conducted. RESULTS: Samples were obtained from 2 MDR-TB, 1 pre-XDR-TB and 12 XDR-TB patients, and 10 non- TB controls. There was considerable heterogeneity between sputum and the cavity with respect to genomic and phenotypic profiles of several drugs including ethambutol, moxifloxacin and paraaminosalicylic acid. An anatomically distinct whole-transcriptome-based pathophysiological map of TB cavities was constructed. RNA sequence reads, of which 31% were splice variants, mapped to 19,049 annotated human genes. In peri-cavitary normal-appearing tissue only 33% of pathways showed significant expression change, despite having a similar bacillary burden to diseased tissue. However, in the cavity wall 72% of pathways showed high-intensity increased expression. By contrast, in the cavity center with a high bacillary burden, 53% of these pathways were massively downregulated, differing from airways and sputum. In particular, several neuroendocrine pathways (dopamine, glutamate, synaptic long-term signalling) were significantly downregulated together with those encoding for calcium, retinoic acid-inducible gene-1, and other pathogen-recognition receptors. However, genes encoding for eukaryotic initiation factor-2, triggering receptor expressed on myeloid cell-1 and peroxisome proliferator activated receptor gamma-signalling, amongst others, were upregulated. CONCLUSION: Heterogeneity in genomic and phenotypic profiles within different parts of the cavity and sputum suggests dynamic responses of mycobacterial populations, likely, under the selective pressure of treatment, which has implications for the interpretation and development of TB-specific diagnostic tests. These data may also have important implications for understanding the pathogenesis of failed host immunity and have uncovered several, hitherto, unrecognized pathways and targets that may be useful for the design of vaccines, host-directed therapies, and transmission prevention.

Includes bibliographical references. / The Practical Aproach to Lung Health in South Africa (P ALSA) initiative aims to improve the diagnosis and management of patients with respiratory diseases in primary care. An algorithm-based syndromic guideline integrating common respiratory diseases for nurses was developed after review of a generic respiratory guideline, medical literature, local policies, and qualitative research.

Background: Current tools for TB diagnosis have suboptimal accuracy, perform poorly in diagnosing extra-pulmonary TB, and are not point of care; hence results have a slow turn-around time. Objective: This project evaluated the diagnostic accuracy of the promising novel loop mediated isothermal amplification (LAMP) assay on sputum, and that of the semi-automated Xpert MTB/RIF (Xpert) test on non-sputum specimens (bronchoalveolar lavage fluid [BALF], tracheal aspirates, and cerebrospinal fluid [CSF]) from South African patients with suspected TB (the accuracy of Xpert using these fluids was unknown at the time this work was performed). Methodology: Biological samples (sputum, tracheal aspirates, BALF, or CSF) were collected from patients with suspected TB. Liquid culture served as the reference standard for the diagnosis of definite TB. Accuracy was evaluated according to HIV and smear microscopy status, where appropriate. The relationship between test performance and bacterial load (culture time-to-positivity [TTP]) was also compared. For the evaluation of LAMP, 2 spot sputa of approximately 4 ml were collected from 301 patients (60 μl of sputum was used for the assay). For the evaluation of Xpert on BALF, 152 patients who were sputum scarce or smear-negative were recruited (1 ml of the BALF aliquot or a re-suspended pellet from 10 ml BALF was used). For the evaluation of Xpert on tracheal aspirates, 120 tracheal aspirates from patients enrolled in the intensive care unit (ICU) were tested. For the evaluation of Xpert on CSF, 235 patients with suspected TBM had a lumbar puncture with 1 ml of CSF or where available a re-suspended pellet from 3 ml of CSF evaluated using Xpert.

Background and objective: To describe the clinical-radiological-pathological characteristics and treatment outcomes of childhood exogenous lipoid pneumonia (ELP) and elucidate oil administration practices. Methods: A retrospective study of children with histologically-confirmed ELP at Red Cross Children’s Hospital, South Africa. Caregivers were interviewed to understand oil administration practices. Results: Twelve children of Zimbabwean heritage aged 2.1-10.8 months were identified between 2012 and 2017. Repeated oral administration of plant-based oil for cultural reasons was reported by 10/11 caregivers. Cough (12/12), tachypnea (11/12), hypoxia (9/12) and diffuse alveolar infiltrates on chest radiography (12/12) were common at presentation. Chest computed tomography revealed ground glass opacification with lower zone predominance (9/9) and interlobular septal thickening (8/9). All bronchoalveolar lavage specimens appeared cloudy/milky, with abundant lipid laden macrophages and extracellular lipid on Oil-Red-O staining and documented polymicrobial (6/12) and Mycobacterium abscessus (2/12) co-infection. Antibiotics, systemic corticosteroids and therapeutic partial lung lavage were interventions in all, 8 and 5 patients respectively. Median time to clinical resolution was 1.1 months IQR (0.5-8.0) with radiological resolution only in 2/12 cases. Conclusions: Paediatric ELP resembles pulmonary alveolar proteinosis. Health workers should explicitly probe for a history of oil administration in children with non-resolving pneumonia and consider the diagnosis of ELP in settings where this is a common practice.

Introduction: There is limited literature on chronic obstructive airway disease in the paediatric age group. Post-infectious bronchiolitis obliterans (PIBO) is a cause of obstructive airway disease children, with limited data in African children. Aim: To describe the clinical spectrum, aetiology, and disease progression of children with post-infectious bronchiolitis obliterans. Methodology: This is a cross sectional descriptive study included all patients aged 6 months to 15 years with PIBO attending a tertiary paediatric pulmonology service in Cape Town, South Africa over period of one year (November 2019 to October 2020). Results: Fifty-one patients with PIBO were enrolled, 78% were males, median age 60 months (IQR 33-107). The median age at disease presentation was 6 months (IQR 3-12), 80% initially presented with cough. Ninety-four percent of patients required hospital admission, 76% were admitted to ICU, 92% required supplemental oxygen therapy and 75% required ventilatory support. Reported cigarette smoke exposure was high (47%). Adenovirus was the most common cause of initial infection 59%. Lung hyperinflation (84%) and air trapping (78%) were the most common current chest radiographic findings; bronchiectasis in 45% of patients. Spirometry showed mixed (41.4%) or obstructive (27%) patterns, mean (SD) FEV1 z-score - 3.3(±1.4), FVC z-scores -2.4(±1.6) and FEV1/FVC z-score -3.1(±2.4). Corticosteroids were used during initial presentation in 92% of patients. Seventy six percent of patients required two or more hospital admissions. Cough (43%) and wheeze (39%) were the commonest reported current symptoms. Lung function impairment was associated with younger age at first presentation and recurrent hospital admissions. Children with higher BMI at presentation had higher FEV1/FVC z-score in later life. Improvement of symptoms over time was reported among 82% of patients. Conclusion: PIBO is a relatively common cause of chronic lung disease in South African children, with adenovirus being the commonest preceding illness. Symptoms of airway obstruction persist over time, but showed improvement with treatment, which included corticosteroids.

Background Cystic fibrosis (CF) is described more commonly in Caucasian populations in whom p.Phe508del is the most common mutation. There is a paucity of data of CF in black African children. The aim of this study was to describe and compare the presentation and outcomes of black African children with CF to those with p.Phe508del genotype. Methods A retrospective case-controlled study was conducted from January 2000 – March 2018 of children with CF attending two CF centres in South Africa. Presentation, genotype, nutrition and pulmonary function outcomes of black African children were compared to matched controls with the p.Phe508del mutation. Results Thirty-four black African children (cases) with median age of diagnosis (5.5 months, IQR 2.0- 15.0) were matched to 34 controls. Among cases, 3120+1G->A CFTR mutation was most commonly identified; homozygous n=22 (64.7%) and heterozygous=7(20.5%). Compared to controls, cases at diagnosis were more malnourished and fewer presented with neonatal bowel obstruction [cases n=2 (5.9%) vs. controls n=10 (29.4%); p = 0.03]. Nutrition and pulmonary function (FEV1 in children ≥ 6 years) outcomes and changes over time from ages 3-16 years were similar in both groups; median FEV1 z-score at age 6,10 and 14 years was -0.9 (±1.5), -1.8 (±2.0) and -1.8 (±1.9) respectively for all patients. Deaths were recorded in three cases (8.8%) and one control (2.9%) (p = 0.6). Conclusion Black African children with CF were more malnourished at diagnosis, and fewer presented with neonatal bowel obstruction. Cases and controls had comparable nutritional, pulmonary function and early mortality outcomes.

Includes bibliographical references. / Tuberculosis (TB) and HIV are dual epidemics and a public health crisis in Southern Africa. An estimated 2.5 million children are living with HIV, of which 2.3 million live in Sub-Saharan Africa, with an estimated 230 000 child deaths from AIDS. In 2010 there were an estimated 8 million incident cases of tuberculosis (TB) globally, 1.2 million amongst people living with HIV. Over 1 million TB related deaths occurred, a third of which occurred amongst people living with HIV.[4] The African region accounts for 26% of the global TB burden and 82% of the TB cases among people living with HIV. TB and HIV are a deleterious combination. TB is a common cause of acute and chronic respiratory disease and a leading cause of death amongst HIV infected children in TB endemic areas.