Browsing by Subject "Tuberculosis"

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    A comparison of the conditional inference survival forest model to random survival forests based on a simulation study as well as on two applications with time-to-event data
    (2017) Nasejje, Justine B; Mwambi, Henry; Sabur, Natasha F; Lesosky, Maia
    Abstract Background Random survival forest (RSF) models have been identified as alternative methods to the Cox proportional hazards model in analysing time-to-event data. These methods, however, have been criticised for the bias that results from favouring covariates with many split-points and hence conditional inference forests for time-to-event data have been suggested. Conditional inference forests (CIF) are known to correct the bias in RSF models by separating the procedure for the best covariate to split on from that of the best split point search for the selected covariate. Methods In this study, we compare the random survival forest model to the conditional inference model (CIF) using twenty-two simulated time-to-event datasets. We also analysed two real time-to-event datasets. The first dataset is based on the survival of children under-five years of age in Uganda and it consists of categorical covariates with most of them having more than two levels (many split-points). The second dataset is based on the survival of patients with extremely drug resistant tuberculosis (XDR TB) which consists of mainly categorical covariates with two levels (few split-points). Results The study findings indicate that the conditional inference forest model is superior to random survival forest models in analysing time-to-event data that consists of covariates with many split-points based on the values of the bootstrap cross-validated estimates for integrated Brier scores. However, conditional inference forests perform comparably similar to random survival forests models in analysing time-to-event data consisting of covariates with fewer split-points. Conclusion Although survival forests are promising methods in analysing time-to-event data, it is important to identify the best forest model for analysis based on the nature of covariates of the dataset in question.
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    A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic
    (2020-02-04) Klopper, Marisa; Heupink, Tim H; Hill-Cawthorne, Grant; Streicher, Elizabeth M; Dippenaar, Anzaan; de Vos, Margaretha; Abdallah, Abdallah M; Limberis, Jason; Merker, Matthias; Burns, Scott; Niemann, Stefan; Dheda, Keertan; Posey, James; Pain, Arnab; Warren, Robin M
    Abstract Background Atypical Beijing genotype Mycobacterium tuberculosis strains are widespread in South Africa and have acquired resistance to up to 13 drugs on multiple occasions. It is puzzling that these strains have retained fitness and transmissibility despite the potential fitness cost associated with drug resistance mutations. Methods We conducted Illumina sequencing of 211 Beijing genotype M. tuberculosis isolates to facilitate the detection of genomic features that may promote acquisition of drug resistance and restore fitness in highly resistant atypical Beijing forms. Phylogenetic and comparative genomic analysis was done to determine changes that are unique to the resistant strains that also transmit well. Minimum inhibitory concentration (MIC) determination for streptomycin and bedaquiline was done for a limited number of isolates to demonstrate a difference in MIC between isolates with and without certain variants. Results Phylogenetic analysis confirmed that two clades of atypical Beijing strains have independently developed resistance to virtually all the potent drugs included in standard (pre-bedaquiline) drug-resistant TB treatment regimens. We show that undetected drug resistance in a progenitor strain was likely instrumental in this resistance acquisition. In this cohort, ethionamide (ethA A381P) resistance would be missed in first-line drug-susceptible isolates, and streptomycin (gidB L79S) resistance may be missed due to an MIC close to the critical concentration. Subsequent inadequate treatment historically led to amplification of resistance and facilitated spread of the strains. Bedaquiline resistance was found in a small number of isolates, despite lack of exposure to the drug. The highly resistant clades also carry inhA promoter mutations, which arose after ethA and katG mutations. In these isolates, inhA promoter mutations do not alter drug resistance, suggesting a possible alternative role. Conclusion The presence of the ethA mutation in otherwise susceptible isolates from ethionamide-naïve patients demonstrates that known exposure is not an adequate indicator of drug susceptibility. Similarly, it is demonstrated that bedaquiline resistance can occur without exposure to the drug. Inappropriate treatment regimens, due to missed resistance, leads to amplification of resistance, and transmission. We put these results into the context of current WHO treatment regimens, underscoring the risks of treatment without knowledge of the full drug resistance profile.
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    A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic
    (2020-02-21) Klopper, Marisa; Heupink, Tim H; Hill-Cawthorne, Grant; Streicher, Elizabeth M; Dippenaar, Anzaan; de Vos, Margaretha; Abdallah, Abdallah M; Limberis, Jason; Merker, Matthias; Burns, Scott; Niemann, Stefan; Dheda, Keertan; Posey, James; Pain, Arnab; Warren, Robin M
    Abstract Background Atypical Beijing genotype Mycobacterium tuberculosis strains are widespread in South Africa and have acquired resistance to up to 13 drugs on multiple occasions. It is puzzling that these strains have retained fitness and transmissibility despite the potential fitness cost associated with drug resistance mutations. Methods We conducted Illumina sequencing of 211 Beijing genotype M. tuberculosis isolates to facilitate the detection of genomic features that may promote acquisition of drug resistance and restore fitness in highly resistant atypical Beijing forms. Phylogenetic and comparative genomic analysis was done to determine changes that are unique to the resistant strains that also transmit well. Minimum inhibitory concentration (MIC) determination for streptomycin and bedaquiline was done for a limited number of isolates to demonstrate a difference in MIC between isolates with and without certain variants. Results Phylogenetic analysis confirmed that two clades of atypical Beijing strains have independently developed resistance to virtually all the potent drugs included in standard (pre-bedaquiline) drug-resistant TB treatment regimens. We show that undetected drug resistance in a progenitor strain was likely instrumental in this resistance acquisition. In this cohort, ethionamide (ethA A381P) resistance would be missed in first-line drug-susceptible isolates, and streptomycin (gidB L79S) resistance may be missed due to an MIC close to the critical concentration. Subsequent inadequate treatment historically led to amplification of resistance and facilitated spread of the strains. Bedaquiline resistance was found in a small number of isolates, despite lack of exposure to the drug. The highly resistant clades also carry inhA promoter mutations, which arose after ethA and katG mutations. In these isolates, inhA promoter mutations do not alter drug resistance, suggesting a possible alternative role. Conclusion The presence of the ethA mutation in otherwise susceptible isolates from ethionamide-naïve patients demonstrates that known exposure is not an adequate indicator of drug susceptibility. Similarly, it is demonstrated that bedaquiline resistance can occur without exposure to the drug. Inappropriate treatment regimens, due to missed resistance, leads to amplification of resistance, and transmission. We put these results into the context of current WHO treatment regimens, underscoring the risks of treatment without knowledge of the full drug resistance profile.
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    A novel cough aerosol sampling device for sputum-scarce individuals with tuberculosis
    (2025) Ismail, Ra'eesah; Sivarasu, Sudesh; Dheda, Keertan
    Introduction In 2021, there were 10.6 million tuberculosis cases worldwide, with 1.6 million deaths. Bacterial infection occurs when aerosol droplets enter the respiratory tract and travel to the lungs, causing pulmonary disease. If untreated, the disease has a 50% mortality rate. TB diagnostics require a sputum sample to conduct tests to confirm the presence of Mtb but more than 15% of patients have difficulty producing this sample. A cough aerosol sampling system (CASS) can collect aerosol droplet samples for testing when sputum sampling is not possible. These systems rely on inertial impaction whereby particles are sorted based on their diameter. Thus, CASS also offers information regarding the infectivity of the patient based on their expelled aerosol sizes. This is because smaller respiratory droplets can travel to the smallest structures of the lung and are more likely to cause infection. CASS is a useful technology in field sampling in place of sputum sampling. However current systems are bulky, heavy and not optimised for field testing in resource limited settings – which this project aims to address. Methods & Materials The methodology included designing and developing a physical prototype of a novel miniaturised cough aerosol sampling system (Mini CASS). This device was designed in subsystems, namely the impaction cascade, pump system, mask part and casing. All subsystems followed a rapid prototyping approach characterised by multiple design iterations. The impaction cascade design was guided by Marple and Liu's methodology (1976). This included testing various impaction substrates. Furthermore, it was optimised by computational fluid dynamics. The entire design was evaluated against a set of predefined needs criteria developed through identification of inadequacies in current devices. Verification testing at the Medical Devices Lab (University of Cape Town) included confirmation of the aerosol size fractionation capacity of the cascade impactor. Validation testing was conducted at the Centre for Lung Infection and Immunity (Groote Schuur Hospital) to confirm the ability of Mini CASS to collect culturable bioaerosols (M. smegmatis). Results & Discussion A partially disposable, portable and miniaturised CASS was built with a weight and size of less than 1 kg & 40 cm2 respectively. Results of in-silico and verification testing have confirmed the ability of the device to perform size fractionation with atleast a 30% efficiency per stage. The device successfully collected nebulised M. smegmatis & M. bovis. Culture confirmation of the bacteria proves this as a viable impactor with atleast 3 colony forming units on each stage, comparable to current CASS systems. Conclusion The final Mini CASS prototype exhibited favourable characteristics of being lightweight and easily portable. It fared well in tests conducted to assess viability, proving its capability to collect bioaerosol samples for culture from coughing. It exhibited the ability to fractionate aerosol samples to provide a semi-quantitative measure of infectiousness with known particle sizes and efficiencies. This proof-of-concept device shows CASS technology can be optimised for use in the clinical setting, thereby enabling it to become a more powerful sampling and research tool. The lightweight, easy to use technology has the potential for use at home or temporary sampling sites.
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    A quantitative characterization of tuberculin skin test indurations using hyperspectral imaging to enable automated latent tuberculosis screening
    (2025) Oladokun, Ajibola Samson; Malila, Bessie; Mutsvangwa, Tinashe
    An estimated two billion people globally are believed to harbour latent tuberculosis infection (LTBI), which is a precursor to active tuberculosis (TB). Immunocompromising conditions, such as human immunodeficiency virus (HIV) infection, diabetes, chronic renal failure, and chemotherapy, are associated with the risk of progression from LTBI to active TB. People with LTBI represent a major reservoir for new active TB cases. Thus, the detection and management of LTBI is key to the world health organisation (WHO) goal to reduce TB incidence globally by 90% by the year 2035. The tuberculin skin test (TST) is the most widely used test for LTBI in low- and middle-income countries (LMICs). It involves the injection of tuberculin into the forearm skin of a participant. An induration – a subdermal lump – forms at the injection site 48 – 72 hours after the test. Using the Mantoux reading method, diagnosis is obtained using a pen and a ruler to measure the induration diameter and comparing it with consensus thresholds. Mantoux readings are subject to inter- and intra-observer subjective variations in readings. The manual nature of this method precludes any repeat analysis or validation after the 72-hour expiry of an induration. Furthermore, the Mantoux method does not provide any significant insight on the pathophysiology of indurations which could improve current understanding of LTBI. Recent applications of hyperspectral imaging (HSI) in other dermatological applications provides evidence of its viability in addressing the shortcomings of the TST. Thus, the aim of this research was to develop and validate an HSI-based approach for quantitative characterisation of TST indurations that can aid the diagnosis of LTBI. This aim was achieved through three objectives. The first objective was to develop and validate an HSI protocol for reliable and reproducible acquisition of spectral signatures of TST injection sites. An enclosure was designed to implement and validate the developed protocol. The validation was done using a range of light source types and ten participants with a wide range of skin tones. The effect of light source type on skin spectral signature was investigated to reveal factors that impact spectral reproducibility. The validated imaging protocol was utilized in the second objective to reliably capture the hyperspectral images of 70 participants (38 from South Africa and 32 from Vietnam). The objective was to develop and validate an HSI-model that can generate precise diameter estimations of TST indurations that are comparable to traditional Mantoux readings. Principal component analysis was utilized to transform the hyperspectral images (or hypercubes) into principal components and generate induration segmentation masks. Precise induration diameter estimations, which were comparable to corresponding Mantoux readings, were generated from the masks. An intraclass correlation coefficient score of 0.80, a median difference in reading of 0.29 mm, and a Pearson's correlation of 0.664 (p<0.001), was achieved between the HSI-based diameter estimations and corresponding Mantoux readings. This metrics surpassed the performance of similar studies. This is evidence that HSI can mitigate the subjectivity of the Mantoux method by generating comparable but more precise diameter estimations of TST indurations. The induration hypercubes and segmentation masks were utilized in the third objective to develop and validate an HSI framework capable of identifying biomarkers that accurately and consistently characterise TST indurations. The framework enabled the generation of chromophore maps from induration hypercubes. Radiomics was applied on the chromophore maps to generate a set of features. The features were used, in conjunction with a support vector machine model, to rank the ability of the generated chromophore maps to predict LTBI. Ferritin, water, and oxyhaemoglobin maps were identified as the most predictive chromophore maps for LTBI. The predictive accuracies for TST diagnosis using these chromophores were 90.0% across all participants, and 96.0% and 96.7% for the South African and Vietnamese participants. This is evidence that HSI can noninvasively facilitate the generation of chromophore biomarkers to characters TST indurations – a first of its kind in literature. These findings present HSI as a potential modality for mitigating the subjectivity of the Mantoux method and identifying digital biomarkers that noninvasively offer insights into induration pathophysiology. The potential impact of this research is improved health outcome for at-risk TBgroups via enhanced LTBI screening accuracy and precision.
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    A semi-automatic technique to quantify complex tuberculous lung lesions on 18F-fluorodeoxyglucose positron emission tomography/computerised tomography images
    (Springer Berlin Heidelberg, 2018-06-25) Malherbe, Stephanus T; Dupont, Patrick; Kant, Ilse; Ahlers, Petri; Kriel, Magdalena; Loxton, André G; Chen, Ray Y; Via, Laura E; Thienemann, Friedrich; Wilkinson, Robert J; Barry, Clifton E; Griffith-Richards, Stephanie; Ellman, Annare; Ronacher, Katharina; Winter, Jill; Walzl, Gerhard; Warwick, James M
    Background There is a growing interest in the use of 18F-FDG PET-CT to monitor tuberculosis (TB) treatment response. However, TB causes complex and widespread pathology, which is challenging to segment and quantify in a reproducible manner. To address this, we developed a technique to standardise uptake (Z-score), segment and quantify tuberculous lung lesions on PET and CT concurrently, in order to track changes over time. We used open source tools and created a MATLAB script. The technique was optimised on a training set of five pulmonary tuberculosis (PTB) cases after standard TB therapy and 15 control patients with lesion-free lungs. Results We compared the proposed method to a fixed threshold (SUV > 1) and manual segmentation by two readers and piloted the technique successfully on scans of five control patients and five PTB cases (four cured and one failed treatment case), at diagnosis and after 1 and 6 months of treatment. There was a better correlation between the Z-score-based segmentation and manual segmentation than SUV > 1 and manual segmentation in terms of overall spatial overlap (measured in Dice similarity coefficient) and specificity (1 minus false positive volume fraction). However, SUV > 1 segmentation appeared more sensitive. Both the Z-score and SUV > 1 showed very low variability when measuring change over time. In addition, total glycolytic activity, calculated using segmentation by Z-score and lesion-to-background ratio, correlated well with traditional total glycolytic activity calculations. The technique quantified various PET and CT parameters, including the total glycolytic activity index, metabolic lesion volume, lesion volumes at different CT densities and combined PET and CT parameters. The quantified metrics showed a marked decrease in the cured cases, with changes already apparent at month one, but remained largely unchanged in the failed treatment case. Conclusions Our technique is promising to segment and quantify the lung scans of pulmonary tuberculosis patients in a semi-automatic manner, appropriate for measuring treatment response. Further validation is required in larger cohorts.
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    Addressing challenges in the treatment of tuberculosis and tuberculosis meningitis: a pharmacometric approach
    (2025) Abdelgawad, Noha; Denti, Paolo; Gausi, Kamunkhwala
    Tuberculosis (TB) is the primary cause of death from a single infectious agent worldwide. During the coronavirus disease (COVID-19) pandemic, TB briefly fell to second place, but it has now regained its position as the top infectious killer. It is caused by Mycobacterium tuberculosis and mainly targets the lungs, but it can spread to other tissues, which can result in TBM, a more severe and often fatal form that affects the central nervous system (CNS), particularly the meninges. In South Africa, TB and TBM burdens are particularly high due to factors such as high HIV prevalence. The treatment of TB and TBM presents significant challenges. Firstly, it typically involves numerous antibiotics taken over several months that may cause serious adverse effects, leading to poor adherence, which can result in treatment failure or the development of drug resistance. Secondly, TB management in hospitalised patients becomes more difficult since they often face more advanced stages of the infection, as well as physiological changes that could impact the pharmacokinetics of anti-TB drugs. Lastly, TBM treatment is further complicated by limited antitubercular drug penetration into the CNS due to its protective barriers, disease-related physiological changes to these barriers and neurological complications. A further challenge is the treatment of special populations, such as children, where unique pharmacokinetic and formulation considerations may complicate management. In this thesis, we use pharmacometric modelling and simulation approaches to tackle some of the obstacles encountered in TB and TBM treatment. Firstly, we demonstrate how pharmacometric approaches can x be useful in monitoring adherence to TB drugs. Secondly, we investigated the differences in the pharmacokinetics of rifampicin, isoniazid, and pyrazinamide in hospitalised patients, who are more severely ill, compared to outpatients. Although we found slower rifampicin absorption and higher between-subject variability in pyrazinamide clearance in hospitalised patients compared to outpatients, we did not identify any changes in pharmacokinetics that are expected to be of clinical significance. It is reassuring that hospitalized patients do not seem to have lower antitubercular drug exposures than outpatients. Thirdly, in South African children diagnosed with definite or probable TBM, we estimated the extent of rifampicin's lumbar and ventricular cerebrospinal fluid (CSF) penetration to be ~5% of plasma. We were also able to use the microdialysis technique to obtain brain extracellular fluid samples to present a proof-of-concept that rifampicin enters the brain tissue. These results show that the microdialysis technique is a promising way to study site-of-disease pharmacokinetics in TBM and pave the way for optimisation of TBM regimens. Lastly, in South African adults with TBM/HIV, we described the plasma and CSF pharmacokinetics of standard and high-dose (10 and 35 mg/kg) rifampicin and linezolid. We estimated lumbar CSF penetration of rifampicin to be ~5%, which is in line with the results of our study in children. Linezolid CSF penetration increased with higher CSF total protein levels, peaking at 37%. Neither the duration of rifampicin co treatment nor the dose level (standard 10 mg/kg vs high 35 mg/kg) was found to affect xi linezolid pharmacokinetics. Our findings endorse the continued evaluation of high dose rifampicin (35 mg/kg) and linezolid for optimizing TBM treatment regimens. To conclude, thanks to pharmacometric approaches, we could address some of the challenges encountered in TB treatment, namely, using modelling and simulation to monitor drug adherence, understanding the pharmacokinetics of the first-line anti TB drugs in hospitalised TB patients, and investigating CNS pharmacokinetics of rifampicin and linezolid in TBM patients.
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    Adenosine Deaminase Acting on RNA-1 (ADAR1) Inhibits HIV-1 Replication in Human Alveolar Macrophages
    (Public Library of Science, 2014) Weiden, Michael D; Hoshino, Satomi; Levy, David N; Li, Yonghua; Kumar, Rajnish; Burke, Sean A; Dawson, Rodney; Hioe, Catarina E; Borkowsky, William; Rom, William N; Hoshino, Yoshihiko
    While exploring the effects of aerosol IFN-γ treatment in HIV-1/tuberculosis co-infected patients, we observed A to G mutations in HIV-1 envelope sequences derived from bronchoalveolar lavage (BAL) of aerosol IFN-γ-treated patients and induction of adenosine deaminase acting on RNA 1 (ADAR1) in the BAL cells. IFN-γ induced ADAR1 expression in monocyte-derived macrophages (MDM) but not T cells. ADAR1 siRNA knockdown induced HIV-1 expression in BAL cells of four HIV-1 infected patients on antiretroviral therapy. Similar results were obtained in MDM that were HIV-1 infected in vitro . Over-expression of ADAR1 in transformed macrophages inhibited HIV-1 viral replication but not viral transcription measured by nuclear run-on, suggesting that ADAR1 acts post-transcriptionally. The A to G hyper-mutation pattern observed in ADAR1 over-expressing cells in vitro was similar to that found in the lungs of HIV-1 infected patients treated with aerosol IFN-γ suggesting the model accurately represented alveolar macrophages. Together, these results indicate that ADAR1 restricts HIV-1 replication post-transcriptionally in macrophages harboring HIV-1 provirus. ADAR1 may therefore contribute to viral latency in macrophages.
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    Adherence to isoniazid prophylaxis among HIV-infected children: a randomized controlled trial comparing two dosing schedules
    (BioMed Central Ltd, 2009) le Roux, Stanzi; Cotton, Mark; Golub, Jonathan; le Roux, David; Workman, Lesley; Zar, Heather
    BACKGROUND:Tuberculosis contributes significantly to morbidity and mortality among HIV-infected children in sub-Saharan Africa. Isoniazid prophylaxis can reduce tuberculosis incidence in this population. However, for the treatment to be effective, adherence to the medication must be optimized. We investigated adherence to isoniazid prophylaxis administered daily, compared to three times a week, and predictors of adherence amongst HIV-infected children. METHODS: We investigated adherence to study medication in a two centre, randomized trial comparing daily to three times a week dosing of isoniazid. The study was conducted at two tertiary paediatric care centres in Cape Town, South Africa. Over a 5 year period, we followed 324 HIV-infected children aged [greater than or equal to] 8 weeks. Adherence information based on pill counts was available for 276 children. Percentage adherence was calculated by counting the number of pills returned. Adherence [greater than or equal to] 90% was considered to be optimal. Analysis was done using summary and repeated measures, comparing adherence to the two dosing schedules. Mean percentage adherence (per child during follow-up time) was used to compare the mean of each group as well as the proportion of children achieving an adherence of [greater than or equal to] 90% in each group. For repeated measures, percentage adherence (per child per visit) was dichotomized at 90%. A logistic regression model with generalized estimating equations, to account for within-individual correlation, was used to evaluate the impact of the dosing schedule. Adjustments were made for potential confounders and we assessed potential baseline and time-varying adherence determinants. RESULTS: The overall adherence to isoniazid was excellent, with a mean adherence of 94.7% (95% confidence interval [CI] 93.5-95.9); similar mean adherence was achieved by the group taking daily medication (93.8%; 95% CI 92.1-95.6) and by the three times a week group (95.5%; 95% CI 93.8-97.2). Two-hundred and seventeen (78.6%) children achieved a mean adherence of [greater than or equal to] 90%. Adherence was similar for daily and three times a week dosing schedules in univariate (odds ratio [OR] 0.88; 95% CI 0.66-1.17; P = 0.38) and multivariate (adjusted OR 0.85; 95% CI 0.64-1.11; P = 0.23) models. Children from overcrowded homes were less adherent (adjusted OR 0.71; 95% CI 0.54-0.95; P = 0.02). Age at study visit was predictive of adherence, with better adherence achieved in children older than 4 years (adjusted OR 1.96; 95% CI 1.16-3.32; P = 0.01). CONCLUSION: Adherence to isoniazid was excellent regardless of the dosing schedule used. Intermittent dosing of isoniazid prophylaxis can be considered as an alternative to daily dosing, without compromising adherence or efficacy.TRIAL REGISTRATION:Clinical Trials NCT00330304
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    Adult meningitis in a setting of high HIV and TB prevalence: findings from 4961 suspected cases
    (BioMed Central Ltd, 2010) Jarvis, Joseph; Meintjes, Graeme; Williams, Anthony; Brown, Yolande; Crede, Tom; Harrison, Thomas
    BACKGROUND: The presentation and causes of adult meningitis in South Africa have changed substantially as a result of HIV. Knowledge of aetiology and laboratory findings in patients presenting with meningitis are important in guiding management. We performed a retrospective study to determine these findings in a setting of high HIV and TB prevalence in Cape Town. METHODS: Patients undergoing lumbar punctures between 1st January 2006 and 31st December 2008 at a public sector referral hospital were studied. Cases were classified by microbiological diagnosis, or in the absence of definitive microbiology as 1) normal CSF (neutrophils [less than or equal to] 1 x 106/L, lymphocytes [less than or equal to] 5 x 106/L, protein [less than or equal to] 0.5 g/dL, glucose [greater than or equal to]1.5 mmol/L), 2) minor abnormalities (neutrophils 2-5, lymphocytes 6-20, protein 0.51-1.0, glucose 1.0-1.49) or 3) markedly abnormal (neutrophils>5, lymphocytes>20, protein>1.0, glucose<1.0). RESULTS: 5578 LPs were performed on 4549 patients, representing 4961 clinical episodes. Of these, 2293 had normal CSF and 931 had minor abnormalities and no aetiology identified. Of the remaining 1737, microbiological diagnoses were obtained in 820 (47%). Cryptococcus accounted for 63% (514) of microbiological diagnoses, TB for 28% (227), bacterial meningitis for 8% (68). Of the remaining 917 who had marked abnormalities, the majority (59%) had a sterile lymphocytic CSF. Of note 16% (81) patients with confirmed Cryptococcus, 5% (12) with TB and 4% (3) with bacterial meningitis had normal CSF cell-counts and biochemistry. CONCLUSIONS: Cryptococcal and tuberculous meningitis are now the commonest causes of adult meningitis in this setting. TB meningitis is probably underdiagnosed by laboratory investigation, as evidence by the large numbers presenting with sterile lymphocytic markedly abnormal CSFs.
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    Altered ratio of IFN-γ/IL-10 in patients with drug resistant Mycobacterium tuberculosis and HIV-tuberculosis immune reconstitution inflammatory syndrome
    (Public Library of Science, 2012) Skolimowska, Keira H; Rangaka, Molebogeng X; Meintjes, Graeme; Pepper, Dominique J; Seldon, Ronnett; Matthews, Kerryn; Wilkinson, Robert J; Wilkinson, Katalin A
    We have described a clinical relationship between HIV-Tuberculosis Immune Reconstitution Inflammatory Syndrome (TB-IRIS) and anti-tubercular drug resistance. Here we studied the immune response of TB-IRIS patients from whom a drug-resistant (n = 11) or drug-susceptible (n = 25) Mycobacterium tuberculosis (MTB) strain was isolated after presenting with TB-IRIS. ELISpot analysis and multiplex cytokine analysis of the supernatant collected from peripheral blood mononuclear cells stimulated overnight with the heat-killed H37Rv MTB laboratory strain was used. Although there was no statistical difference in IFN-gamma ELISpot responses between the two groups, the results point towards higher bacterial load in the drug-resistant patients, possibly due to failed therapy. The ratio between secreted IFN-gamma/IL-10 and IL-2/IL-10 was significantly lower in TB-IRIS patients in whom the cause of TB was a drug-resistant strain compared to those with a fully sensitive strain (p = 0.02). Since host immune responses are dependent on the bacterial load, we hypothesise that the impaired cytokine balance is likely to be caused by the poorly controlled bacterial growth in these patients.
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    An approach to the patient with suspected pericardial disease
    (2016) Kyriakakis, Charles G; Mayosi, Bongani M; de Vries, Elma; Isaacs, Abdul; Doubell, Anton F
    Diseases of the pericardium commonly manifest in one of three ways: acute pericarditis, pericardial effusion and constrictive pericarditis. In the developed world, the most common cause of acute pericarditis is viral or idiopathic disease, while in the developing world tuberculous aetiology, particularly in sub-Saharan Africa, is commonplace owing to the high prevalence of HIV. This article provides an approach to the diagnosis, investigation and management of these patients.
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    Antiretroviral therapy for prevention of tuberculosis in adults with HIV: a systematic review and meta-analysis
    (Public Library of Science, 2012) Suthar, Amitabh B; Lawn, Stephen D; Del Amo, Julia; Getahun, Haileyesus; Dye, Christopher; Sculier, Delphine; Sterling, Timothy R; Chaisson, Richard E; Williams, Brian G; Harries, Anthony D
    In a systematic review and meta-analysis, Amitabh Suthar and colleagues investigate the association between antiretroviral therapy and the reduction in the incidence of tuberculosis in adults with HIV infection.
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    Antiretroviral treatment cohort analysis using time-updated CD4 counts: assessment of bias with different analytic methods
    (Public Library of Science, 2011) Kranzer, Katharina; Lewis, James J; White, Richard G; Glynn, Judith R; Lawn, Stephen D; Middelkoop, Keren; Bekker, Linda-Gail; Wood, Robin
    BACKGROUND: Survival analysis using time-updated CD4+ counts during antiretroviral therapy is frequently employed to determine risk of clinical events. The time-point when the CD4+ count is assumed to change potentially biases effect estimates but methods used to estimate this are infrequently reported. METHODS: This study examined the effect of three different estimation methods: assuming i) a constant CD4+ count from date of measurement until the date of next measurement, ii) a constant CD4+ count from the midpoint of the preceding interval until the midpoint of the subsequent interval and iii) a linear interpolation between consecutive CD4+ measurements to provide additional midpoint measurements. Person-time, tuberculosis rates and hazard ratios by CD4+ stratum were compared using all available CD4+ counts (measurement frequency 1-3 months) and 6 monthly measurements from a clinical cohort. Simulated data were used to compare the extent of bias introduced by these methods. RESULTS: The midpoint method gave the closest fit to person-time spent with low CD4+ counts and for hazard ratios for outcomes both in the clinical dataset and the simulated data. CONCLUSION: The midpoint method presents a simple option to reduce bias in time-updated CD4+ analysis, particularly at low CD4 cell counts and rapidly increasing counts after ART initiation.
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    Are the effects of isoniaid preventive therapy and highly active antiretroviral therapy additive in preventing HIV-associated tuberculosis
    (2009) Wood, Robin; Lawn, Stephen D; Bekker, Linda-Gail
    Golub et al. [1] recently reported a retrospective analysis of rates of incident tuberculosis (TB) in a large observational cohort of 2778 patients accessing HIV care in rural and urban South Africa. The TB incidence rate was highest [7.1/100 person-years; 95% confidence interval (CI)¼ 6.2–8.2] during the period of care when patients did not receive isoniazid preventive therapy (IPT) or highly active antiretroviral therapy (HAART). The rates were lower during person-time that accrued throughout follow-up after initiation of IPT (5.2/100 person-years; 95% CI¼ 3.4–7.8) and throughout follow-up on HAART alone (4.6/100 person-years, 95% CI¼ 3.4– 6.2). The rate was lower still (1.1/100 person-years 95% CI¼ 0.2–7.6) during person-time accrued during sequential IPT and HAART (IPTþ HAART). The authors concluded that TB risk was significantly reduced by IPT in HAART-treated adults. It was further concluded that ‘the dramatic reduction in TB risk’ demonstrated in this study together with supportive data from a similarly analysed study from Brazil [2] indicates that widespread use 1444 AIDS 2009, Vol 23 No 11 Fig. 1. T2-weighted flair image demonstrating enhancing lesion in the right precentral gyrus. Copyright © Lippincott Williams & Wilkins. Unauthorized reproduction of this article is prohibited. of IPT should be implemented in conjunction with the roll-out of HAART.
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    Are the effects of isoniaid preventive therapy and highly active antiretroviral therapy additive in preventing HIV-associated tuberculosis
    (2009) Wood, Robin; Lawn, Stephen D; Bekker, Linda-Gail
    Golub et al. [1] recently reported a retrospective analysis of rates of incident tuberculosis (TB) in a large observational cohort of 2778 patients accessing HIV care in rural and urban South Africa. The TB incidence rate was highest [7.1/100 person-years; 95% confidence interval (CI)¼ 6.2–8.2] during the period of care when patients did not receive isoniazid preventive therapy (IPT) or highly active antiretroviral therapy (HAART). The rates were lower during person-time that accrued throughout follow-up after initiation of IPT (5.2/100 person-years; 95% CI¼ 3.4–7.8) and throughout follow-up on HAART alone (4.6/100 person-years, 95% CI¼ 3.4– 6.2). The rate was lower still (1.1/100 person-years 95% CI¼ 0.2–7.6) during person-time accrued during sequential IPT and HAART (IPTþ HAART). The authors concluded that TB risk was significantly reduced by IPT in HAART-treated adults. It was further concluded that 'the dramatic reduction in TB risk' demonstrated in this study together with supportive data from a similarly analysed study from Brazil [2] indicates that widespread use 1444 AIDS 2009, Vol 23 No 11 Fig. 1. T2-weighted flair image demonstrating enhancing lesion in the right precentral gyrus. Copyright © Lippincott Williams & Wilkins. Unauthorized reproduction of this article is prohibited. of IPT should be implemented in conjunction with the roll-out of HAART.
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    Assessment at antiretroviral clinics during TB treatment reduces loss to follow-up among HIV-infected patients
    (Public Library of Science, 2012) Pepper, Dominique J; Marais, Suzaan; Bhaijee, Feriyl; Wilkinson, Robert J; De Azevedo, Virginia; Meintjes, Graeme
    Setting: A South African township clinic where loss to follow-up during TB treatment may prevent HIV-infected TB patients from receiving life-saving ART. Objective: To determine factors associated with loss to follow-up during TB treatment. Design: Regression analyses of a cohort of ART-eligible TB patients who commenced TB treatment and were followed for 24 weeks. RESULTS: Of 111 ART-eligible TB patients, 15 (14%) died in the ensuing 24 weeks. Of the remaining 96 TB patients, 11 (11%) were lost to follow-up. All TB patients lost to follow-up did not initiate ART. Of 85 TB patients in follow-up, 62 (73%) initiated ART 56 days after TB diagnosis (median, IQR 33-77 days) and 31 days after initial assessment at an ART clinic (median, IQR: 18-55 days). The median duration from TB diagnosis to initial assessment at an ART clinic was 19 days (IQR: 7-48 days). At 24 weeks, 6 of 85 (7%) TB patients who presented to an ART clinic for assessment were lost to follow-up, compared to 5 of 11 (45%) TB patients who did not present to an ART clinic for assessment. Logistic regression analysis (adjusted odds ratio  = 0.1, 95% confidence interval [95% CI]: 0.03-0.66) and our Cox proportional hazards model (hazard ratio  = 0.2, 95% CI: 0.04-0.68) confirmed that assessment at an ART clinic during TB treatment reduced loss to follow-up. CONCLUSION: Assessment at antiretroviral clinics for HIV care by trained health-care providers reduces loss to follow-up among HIV-infected patients with TB.
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    Association of human TLR1 and TLR6 deficiency with altered immune responses to BCG vaccination in South African infants
    (Public Library of Science, 2011) Randhawa, April Kaur; Shey, Muki S; Keyser, Alana; Peixoto, Blas; Wells, Richard D; de Kock, Marwou; Lerumo, Lesedi; Hughes, Jane; Hussey, Gregory; Hawkridge, Anthony; Kaplan, Gilla; Hanekom, Willem A; Hawn, Thomas R
    The development of effective immunoprophylaxis against tuberculosis (TB) remains a global priority, but is hampered by a partially protective Bacillus Calmette-Guérin (BCG) vaccine and an incomplete understanding of the mechanisms of immunity to Mycobacterium tuberculosis. Although host genetic factors may be a primary reason for BCG's variable and inadequate efficacy, this possibility has not been intensively examined. We hypothesized that Toll-like receptor (TLR) variation is associated with altered in vivo immune responses to BCG. We examined whether functionally defined TLR pathway polymorphisms were associated with T cell cytokine responses in whole blood stimulated ex vivo with BCG 10 weeks after newborn BCG vaccination of South African infants. In the primary analysis, polymorphism TLR6_C745T (P249S) was associated with increased BCG-induced IFN-γ in both discovery (n = 240) and validation (n = 240) cohorts. In secondary analyses of the combined cohort, TLR1_T1805G (I602S) and TLR6_G1083C (synonymous) were associated with increased IFN-γ, TLR6_G1083C and TLR6_C745T were associated with increased IL-2, and TLR1_A1188T was associated with increased IFN-γ and IL-2. For each of these polymorphisms, the hypo-responsive allele, as defined by innate immunity signaling assays, was associated with increased production of TH1-type T cell cytokines (IFN-γ or IL-2). After stimulation with TLR1/6 lipopeptide ligands, PBMCs from TLR1/6-deficient individuals (stratified by TLR1_T1805G and TLR6_C745T hyporesponsive genotypes) secreted lower amounts of IL-6 and IL-10 compared to those with responsive TLR1/6 genotypes. In contrast, no IL-12p70 was secreted by PBMCs or monocytes. These data support a mechanism where TLR1/6 polymorphisms modulate TH1 T-cell polarization through genetic regulation of monocyte IL-10 secretion in the absence of IL-12. These studies provide evidence that functionally defined innate immune gene variants are associated with the development of adaptive immune responses after in vivo vaccination against a bacterial pathogen in humans. These findings could potentially guide novel adjuvant vaccine strategies as well as have implications for IFN-γ-based diagnostic testing for TB.
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    Bacterial loads measured by the Xpert MTB/RIF assay as markers of culture conversion and bacteriological cure in pulmonary TB
    (Public Library of Science, 2016) Shenai, Shubhada; Ronacher, Katharina; Malherbe, Stefanus; Stanley, Kim; Kriel, Magdalena; Winter, Jill; Peppard, Thomas; Barry, Charles E; Wang, Jing; Dodd, Lori E; Via, Laura E; Walzl, Gerhard; Alland, David
    Introduction Biomarkers are needed to monitor tuberculosis (TB) treatment and predict treatment outcomes. We evaluated the Xpert MTB/RIF (Xpert) assay as a biomarker for TB treatment during and at the end of the 24 weeks therapy. METHODS: Sputum from 108 HIV-negative, culture-positive pulmonary TB patients was analyzed using Xpert at time points before and during anti-TB therapy. Results were compared against culture. Direct Xpert cycle-threshold (Ct), a change in the Ct (delta Ct), or a novel "percent closing of baseline Ct deficit" (percent closing) were evaluated as classifiers of same-day and end-of-treatment culture and therapeutic outcomes. RESULTS: Xpert was positive in 29/95 (30.5%) of subjects at week 24; and positive one year after treatment in 8/64 (12.5%) successfully-treated patients who remained free of tuberculosis. We identified a relationship between initial bacterial load measured by baseline Xpert Ct and time to culture conversion (hazard ratio 1.06, p = 0.0023), and to the likelihood of being among the 8 treatment failures at week 24 (AUC = 72.8%). Xpert Ct was even more strongly associated with culture conversion on the day the test was performed with AUCs 96.7%, 99.2%, 86.0% and 90.2%, at Day 7, Week 4, 8 and 24, respectively. Compared to baseline Ct measures alone, a combined measure of baseline Ct plus either Delta Ct or percent closing improved the classification of treatment failure status to a 75% sensitivity and 88.9% specificity. CONCLUSIONS: Genome loads measured by Xpert provide a potentially-useful biomarker for classifying same day culture status and predicting response to therapy.