Tony Hawkridge

A blood RNA signature for tuberculosis disease risk: a prospective cohort study

BACKGROUND Identification of blood biomarkers that prospectively predict progression of Mycobacterium tuberculosis infection to tuberculosis disease might lead to interventions that combat the tuberculosis epidemic. We aimed to assess whether global gene expression measured in whole blood of healthy people allowed identification of prospective signatures of risk of active tuberculosis disease. METHODS In this prospective cohort study, we followed up healthy, South African adolescents aged 12-18 years from the adolescent cohort study (ACS) who were infected with M tuberculosis for 2 years. We collected blood samples from study participants every 6 months and monitored the adolescents for progression to tuberculosis disease. A prospective signature of risk was derived from whole blood RNA sequencing data by comparing participants who developed active tuberculosis disease (progressors) with those who remained healthy (matched controls). After adaptation to multiplex quantitative real-time PCR (qRT-PCR), the signature was used to predict tuberculosis disease in untouched adolescent samples and in samples from independent cohorts of South African and Gambian adult progressors and controls. Participants of the independent cohorts were household contacts of adults with active pulmonary tuberculosis disease. FINDINGS Between July 6, 2005, and April 23, 2007, we enrolled 6363 participants from the ACS study and 4466 from independent South African and Gambian cohorts. 46 progressors and 107 matched controls were identified in the ACS cohort. A 16 gene signature of risk was identified. The signature predicted tuberculosis progression with a sensitivity of 66·1% (95% CI 63·2-68·9) and a specificity of 80·6% (79·2-82·0) in the 12 months preceding tuberculosis diagnosis. The risk signature was validated in an untouched group of adolescents (p=0·018 for RNA sequencing and p=0·0095 for qRT-PCR) and in the independent South African and Gambian cohorts (p values <0·0001 by qRT-PCR) with a sensitivity of 53·7% (42·6-64·3) and a specificity of 82·8% (76·7-86) in the 12 months preceding tuberculosis. INTERPRETATION The whole blood tuberculosis risk signature prospectively identified people at risk of developing active tuberculosis, opening the possibility for targeted intervention to prevent the disease. FUNDING Bill & Melinda Gates Foundation, the National Institutes of Health, Aeras, the European Union, and the South African Medical Research Council.Background Identification of blood biomarkers that prospectively predict progression of Mycobacterium tuberculosis infection to tuberculosis disease may lead to interventions that impact the epidemic. Methods Healthy, M. tuberculosis infected South African adolescents were followed for 2 years; blood was collected every 6 months. A prospective signature of risk was derived from whole blood RNA-Sequencing data by comparing participants who ultimately developed active tuberculosis disease (progressors) with those who remained healthy (matched controls). After adaptation to multiplex qRT-PCR, the signature was used to predict tuberculosis disease in untouched adolescent samples and in samples from independent cohorts of South African and Gambian adult progressors and controls. The latter participants were household contacts of adults with active pulmonary tuberculosis disease. Findings Of 6,363 adolescents screened, 46 progressors and 107 matched controls were identified. A 16 gene signature of risk was identified. The signature predicted tuberculosis progression with a sensitivity of 66·1% (95% confidence interval, 63·2–68·9) and a specificity of 80·6% (79·2–82·0) in the 12 months preceding tuberculosis diagnosis. The risk signature was validated in an untouched group of adolescents (p=0·018 for RNA-Seq and p=0·0095 for qRT-PCR) and in the independent South African and Gambian cohorts (p values <0·0001 by qRT-PCR) with a sensitivity of 53·7% (42·6–64·3) and a specificity of 82·8% (76·7–86) in 12 months preceding tuberculosis. Interpretation The whole blood tuberculosis risk signature prospectively identified persons at risk of developing active tuberculosis, opening the possibility for targeted intervention to prevent the disease. Funding Bill and Melinda Gates Foundation, the National Institutes of Health, Aeras, the European Union and the South African Medical Research Council (detail at end of text).

The tuberculin skin test versus QuantiFERON TB Gold® in predicting tuberculosis disease in an adolescent cohort study in South Africa.

Setting This study was conducted in a high tuberculosis (TB) burden area in Worcester, South Africa, with a notified all TB incidence rate of 1,400/100,000. Main Objective To compare the predictive value of a baseline tuberculin skin test (TST) with that of the QuantiFERON TB Gold (In-tube) assay (QFT) for subsequent microbiologically confirmed TB disease among adolescents. Methods Adolescents aged 12–18 years were recruited from high schools in the study area. At baseline, blood was drawn for QFT and a TST administered. Participants were followed up for up to 3.8 years for incident TB disease (median 2.4 years). Results After exclusions, 5244 (82.4%) of 6,363 adolescents enrolled, were analysed. The TB incidence rate was 0.60 cases per 100 person years (pyrs) (95% CI 0.43–0.82) for baseline TST positive (≥5 mm) participants and 0.64 cases per 100 pyrs (95% CI 0.45–0.87) for baseline QFT positive participants. TB incidence rates were 0.22 per 100 pyrs (0.11–0.39) and 0.22 per 100 pyrs (0.12–0.38) among those with a negative baseline TST and QFT respectively. Sensitivity for incident TB disease was 76.9% for TST and 75.0% for QFT (p = 0.81). Positive predictive value was 1.4% for TST and 1.5% for QFT. Conclusion Positive TST and QFT tests were moderately sensitive predictors of progression to microbiologically confirmed TB disease. There was no significant difference in the predictive ability of these tests for TB disease amongst adolescents in this high burden setting. Therefore, these findings do not support use of QFT in preference to TST to predict the risk of TB disease in this study population.

Induced sputum or gastric lavage for community-based diagnosis of childhood pulmonary tuberculosis?

Objectives: To compare the diagnostic yield of Mycobacterium tuberculosis from induced sputum (IS) and gastric lavage (GL) among children in a community setting. Methods: Specimen-collection methods for bacteriological confirmation of pulmonary tuberculosis (PTB) were compared during a tuberculosis vaccine trial near Cape Town, South Africa (2001–2006). Children with a tuberculosis contact or compatible symptoms were investigated for suspected PTB. Diagnostic yields from 764 paired IS and GL specimens were compared in 191 culture-confirmed cases. Measurements and main results: The crude yield of M tuberculosis was 10.4%, n = 108 by IS (5.8%) and n = 127 by GL (6.8%), from a total of 194 cases, of which three had incomplete IS/GL specimen pairs. Agreement between IS and GL was poor (κ = 0.31). The comparative yield of a single IS sample (38%) was equivalent to a single GL sample (42%), with a difference in yield of −4% (95% CI −15% to +7%). The combined yield of same-day IS and GL specimens (67%) was equivalent to two consecutive GL specimens (66%), with a difference in yield of 1% (95% CI −9% to 11%), but significantly greater than two consecutive IS specimens (55%), with a difference in yield of 12% (95% CI 2% to 21%). The adjusted odds of a M tuberculosis culture were increased by a positive tuberculin skin test or chest radiograph compatible with PTB. Conclusions: In this community setting, the diagnostic yield of a single IS sample was equivalent to that of a single GL sample. The optimal diagnostic yield may be obtained from paired IS and GL specimens taken on a single day or two GL specimens taken on consecutive days.

Structured approaches for the screening and diagnosis of childhood tuberculosis in a high prevalence region of South Africa

OBJECTIVE To measure agreement between nine structured approaches for diagnosing childhood tuberculosis; to quantify differences in the number of tuberculosis cases diagnosed with the different approaches, and to determine the distribution of cases in different categories of diagnostic certainty. METHODS We investigated 1445 children aged < 2 years during a vaccine trial (2001-2006) in a rural South African community. Clinical, radiological and microbiological data were collected prospectively. Tuberculosis case status was determined using each of the nine diagnostic approaches. We calculated differences in case frequency and categorical agreement for binary (tuberculosis/not tuberculosis) outcomes using McNemars test (with 95% confidence intervals, CIs) and Cohens kappa coefficient (Kappa). FINDINGS Tuberculosis case frequency ranged from 6.9% to 89.2% (median: 41.7). Significant differences in case frequency (P < 0.05) occurred in 34 of the 36 pair-wise comparisons between structured diagnostic approaches (range of absolute differences: 1.5-82.3%). Kappa ranged from 0.02 to 0.71 (median: 0.18). The two systems that yielded the highest case frequencies (89.2% and 70.0%) showed fair agreement (Kappa: 0.33); the two that yielded the lowest case frequencies (6.9% and 10.0%) showed slight agreement (Kappa: 0.18). CONCLUSION There is only slight agreement between structured approaches for the screening and diagnosis of childhood tuberculosis and high variability between them in terms of case yield. Diagnostic systems that yield similarly low case frequencies may be identifying different subpopulations of children. The study findings do not support the routine clinical use of structured approaches for the definitive diagnosis of childhood tuberculosis, although high-yielding systems may be useful screening tools.

Evaluation of the quality of informed consent in a vaccine field trial in a developing country setting

BackgroundInformed consent is an ethical and legal requirement for research involving human participants. However, few studies have evaluated the process, particularly in Africa.Participants in a case control study designed to identify correlates of immune protection against tuberculosis (TB) in South Africa. This study was in turn nested in a large TB vaccine efficacy trial.The aim of the study was to evaluate the quality of consent in the case control study, and to identify factors that may influence the quality of consent.Cross-sectional study conducted over a 4 month period.MethodsConsent was obtained from parents of trial participants. These parents were asked to complete a questionnaire that contained questions about the key elements of informed consent (voluntary participation, confidentiality, the main risks and benefits, etc.). The recall (success in selecting the correct answers) and understanding (correctness of interpretation of statements presented) were measured.ResultsThe majority of the 192 subjects interviewed obtained scores greater than 75% for both the recall and understanding sections. The median score for recall was 66%; interquartile range (IQR) = 55%–77% and for understanding 75% (IQR = 50%–87%). Most (79%) were aware of the risks and 64% knew that they participated voluntarily. Participants who had completed Grade 7 at school and higher were more likely (OR = 4.94; 95% CI = 1.57 – 15.55) to obtain scores greater than 75% for recall than those who did not. Participants who were consented by professional nurses who had worked for more than two years in research were also more likely (OR = 2.62; 95% CI = 1.35–5.07) to obtain such scores for recall than those who were not.ConclusionNotwithstanding the constraints in a developing country, in a population with low levels of literacy and education, the quality of informed consent found in this study could be considered as building blocks for establishing acceptable standards for public health research. Education level of respondents and experience of research staff taking the consent were associated with good quality informed consent.

New Vaccines Against Tuberculosis

The only currently licensed tuberculosis (TB) vaccine, bacille Calmette Guérin, confers incomplete protection against tuberculosis, and is not safe in infants infected with the human immunodeficiency virus. A new, safe vaccine regimen, which better protects against lung disease, is urgently needed to control TB in high-burden countries. Multiple candidate vaccines have shown promise in preclinical studies, and are now entering phase 1 to 2B clinical trials. This article discusses progress in the field and issues surrounding safety, reactogenicity, immunogenicity, and efficacy testing of new TB vaccines.

TB Incidence in an Adolescent Cohort in South Africa

Background Tuberculosis (TB) is a major public health problem globally. Little is known about TB incidence in adolescents who are a proposed target group for new TB vaccines. We conducted a study to determine the TB incidence rates and risk factors for TB disease in a cohort of school-going adolescents in a high TB burden area in South Africa. Methods We recruited adolescents aged 12 to 18 years from high schools in Worcester, South Africa. Demographic and clinical information was collected, a tuberculin skin test (TST) performed and blood drawn for a QuantiFERON TB Gold assay at baseline. Screening for TB cases occurred at follow up visits and by surveillance of registers at public sector TB clinics over a period of up to 3.8 years after enrolment. Results A total of 6,363 adolescents were enrolled (58% of the school population targeted). During follow up, 67 cases of bacteriologically confirmed TB were detected giving an overall incidence rate of 0.45 per 100 person years (95% confidence interval 0.29–0.72). Black or mixed race, maternal education of primary school or less or unknown, a positive baseline QuantiFERON assay and a positive baseline TST were significant predictors of TB disease on adjusted analysis. Conclusion The adolescent TB incidence found in a high burden setting will help TB vaccine developers plan clinical trials in this population. Latent TB infection and low socio-economic status were predictors of TB disease.

Prospects for a new, safer, and more effective TB vaccine

Tuberculosis in infants and young children remains an all too common cause of morbidity and mortality in high burden countries, despite the fact that the majority of these children receive vaccination with BCG in infancy. BCG confers incomplete and variable protection against pulmonary tuberculosis [PTB] and is unsafe in HIV positive persons. Newer TB vaccines, which, it is hoped, will either replace or complement BCG are being developed and a number of these have reached the stage of clinical trials, with two booster vaccines going into Phase IIB trials in 2009. Prospects for at least one new licensed TB vaccine within the next 5-10 years appear reasonable. This article explores some of the issues around the development of new vaccines against TB and details the leading candidates.

The Impact of a Change in Bacille Calmette-guérin Vaccine Policy on Tuberculosis Incidence in Children in Cape Town, South Africa

Background: A decision by the South African National Department of Health to change the route of administration and strain of bacille Calmette-Guérin (BCG) vaccine was implemented in Cape Town, South Africa, between July and December 2000. This provided an opportunity to compare the incidence of tuberculosis and proportion with disseminated disease in children less than 2 years old before and after the changeover from percutaneous (PC) Tokyo 172 BCG to intradermal (ID) 1331 Danish BCG immunization. Methods: Clinical records of all tuberculosis patients aged less than 2 years at diagnosis and born between January 1, 1999, and June 30, 2000 (PC cohort) and between January 1, 2001, and June 30, 2002 (ID cohort) were collected. All cases were reviewed for likelihood of TB, its severity and disease dissemination. Results: The number of reported patients with tuberculosis in the PC cohort was 1369 and in the ID cohort 1397, giving incidence rates of 866 (95% confidence interval [CI], 821–913) and 858 (95% CI, 814–904) per 100,000 person-years, respectively. The proportion who had disseminated disease (meningitis and/or miliary spread) was significantly lower in the ID cohort (4.7%) than in the PC cohort (8.6%) (relative risk, 0.54; 95% CI, 0.40–0.72). Those not vaccinated had a significantly higher proportion of disseminated disease cases (29.2%) than the PC and ID groups combined (6.6%) (relative risk, 4.4; 95% CI, 2.7–6.7). Conclusion: A program using Danish 1331 BCG given intradermally did not prevent more tuberculosis cases in children overall as compared with a program using Tokyo 172 BCG given percutaneously but reduced the proportion with disseminated disease.

Phenotypic variability in childhood TB: implications for diagnostic endpoints in tuberculosis vaccine trials.

The endpoint definition for infant tuberculosis (TB) vaccine trials should match the TB disease phenotype expected in the control arm of the study population. Our aim was to analyse selected combinations of the clinical, radiological, and microbiological features of pulmonary TB among children investigated under vaccine trial conditions, in order to estimate case frequency for a range of expected TB phenotypes. Two thousand one hundred and eighty five South African children were investigated over a nine-year period (2001-2009). Evidence of TB exposure and classical symptoms were several times more common than chest radiography (CXR) compatible with TB, or positive Mycobacterium tuberculosis culture. Discordance between clinical, radiological, and microbiological features was common in individual children. Up to one third of children with compatible CXR, and up to half the children who were M. tuberculosis culture positive, were asymptomatic. The culture positive rate fell over time, although rates of TB exposure and compatible chest radiography increased. Consequently, the annual incidence of diagnostic combinations that included M. tuberculosis culture fell to <0.2%. However, in this study population (children <2 years of age), annual incidence of the TB disease phenotype that included the triad of TB exposure, symptoms, and compatible CXR, approached 1% (n=848 per 100,000). These findings allow modelling of expected TB case frequency in multi-centre infant TB vaccine trials, based upon benchmarking of diagnostic data against the key indicator variables that constitute the building blocks of a trial endpoint.