Imperial College London

ProfessorRobertWilkinson

Faculty of MedicineDepartment of Infectious Disease

Professor in Infectious Diseases
 
 
 
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Contact

 

r.j.wilkinson Website

 
 
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Location

 

Commonwealth BuildingHammersmith Campus

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Summary

 

Publications

Publication Type
Year
to

441 results found

Coppolla M, Lai R, Wilkinson RJ, Ottenhoff THMet al., 2021, The in vivo transcriptomic blueprint of Mycobacterium tuberculosis in the lung, Frontiers in Immunology, ISSN: 1664-3224

Journal article

Lai RP-J, Cortes T, Marais S, Rockwood N, Burke M, Garza-Garcia A, Horswell S, Sesay AK, O'Garra A, Young DB, Wilkinson RJet al., 2021, Transcriptomic characterization of tuberculous sputum reveals a host Warburg effect and microbial cholesterol catabolism, mBio, ISSN: 2150-7511

Journal article

Gupte A, Kumar P, Araújo-Pereira M, Kulkarni V, Paradkar M, Pradhan N, Menon P, Darasini P, Hanna L-E, Shivakumar SVBY, Rockwood NS, Du Bruyn E, Karyakarte R, Gaikwad S, Bollinger R, Golub J, Gupte N, Viswanathan V, Wilkinson RJ, Mave V, Babu S, Kornfeld H, Andrade BB, Gupta Aet al., 2021, Baseline IL-6 is a biomarker for unfavorable tuberculosis treatment outcomes: a multi-site discovery and validation study, European Respiratory Journal, ISSN: 0903-1936

Background: Biomarkers of unfavorable tuberculosis treatment outcomes are needed to accelerate new drug and regimen development. Whether plasma cytokine levels can predict unfavorable tuberculosis treatment outcomes is unclear. Methods: We identified and internally validated the association between 20 a-priori selected plasma inflammatory markers and unfavorable treatment outcomes of failure, recurrence and all-cause mortality among adults with drug-sensitive pulmonary tuberculosis in India. We externally validated these findings in two independent cohorts of predominantly diabetic and HIV coinfected tuberculosis patients in India and South Africa, respectively. Results: Pre-treatment IFN-γ, IL-13 and IL-6 were associated with treatment failure in the discovery analysis. Internal validation confirmed higher pre-treatment IL-6 concentrations among failure cases compared to controls. External validation among predominantly diabetic tuberculosis patients found an association between pre59 treatment IL-6 concentrations and subsequent recurrence and death. Similarly, external validation among predominantly HIV coinfected tuberculosis patients found an association between pre-treatment IL-6 concentrations and subsequent treatment failure and death. In a pooled analysis of 363 tuberculosis cases from the Indian and South African validation cohorts, high pre-treatment IL-6 concentrations were associated with higher risk of failure (adjusted odds ratio [aOR]=2.16, 95%CI 1.08-4.33, p=0.02), recurrence (aOR=5.36, 95%CI 2.48-11.57, p<0.001) and death (aOR=4.62, 95%CI 1.95-10.95, p<0.001). Adding baseline IL-6 to a risk-prediction model comprising of low BMI, high smear grade and cavitation improved model performance by 15 percent (C-statistic of 0.66 versus 0.76, p=0.02). Conclusion: Pre-treatment IL-6 is a biomarker for unfavorable tuberculosis treatment outcomes. Future studies should identify optimal IL-6 concentrations for point-of-care risk prediction.

Journal article

Fendler A, Au L, Shepherd STC, Byrne F, Cerrone M, Boos LA, Rzeniewicz K, Gordon W, Shum B, Gerard CL, Ward B, Xie W, Schmitt AM, Joharatnam-Hogan N, Cornish GH, Pule M, Mekkaoui L, Ng KW, Carlyle E, Edmonds K, Rosario LD, Sarker S, Lingard K, Mangwende M, Holt L, Ahmod H, Stone R, Gomes C, Flynn HR, Agua-Doce A, Hobson P, Caidan S, Howell M, Wu M, Goldstone R, Crawford M, Cubitt L, Patel H, Gavrielides M, Nye E, Snijders AP, MacRae JI, Nicod J, Gronthoud F, Shea RL, Messiou C, Cunningham D, Chau I, Starling N, Turner N, Welsh L, van As N, Jones RL, Droney J, Banerjee S, Tatham KC, Jhanji S, OBrien M, Curtis O, Harrington K, Bhide S, Bazin J, Robinson A, Stephenson C, Slattery T, Khan Y, Tippu Z, Leslie I, Gennatas S, Okines A, Reid A, Young K, Furness AJS, Pickering L, Gandhi S, Gamblin S, Swanton C, Flynn HR, Caidan S, Howell M, Wu M, Goldstone R, Crawford M, Cubitt L, Nicod J, Nicholson E, Kumar S, Yousaf N, Wilkinson KA, Swerdlow A, Harvey R, Kassiotis G, Larkin J, Wilkinson RJ, Turajlic S, Wilkinson KA, Swerdlow A, Wilkinson RJet al., 2021, Functional antibody and T cell immunity following SARS-CoV-2 infection, including by variants of concern, in patients with cancer: the CAPTURE study, Nature Cancer

<jats:title>Abstract</jats:title><jats:p>Patients with cancer have higher COVID-19 morbidity and mortality. Here we present the prospective CAPTURE study, integrating longitudinal immune profiling with clinical annotation. Of 357 patients with cancer, 118 were SARS-CoV-2 positive, 94 were symptomatic and 2 died of COVID-19. In this cohort, 83% patients had S1-reactive antibodies and 82% had neutralizing antibodies against wild type SARS-CoV-2, whereas neutralizing antibody titers against the Alpha, Beta and Delta variants were substantially reduced. S1-reactive antibody levels decreased in 13% of patients, whereas neutralizing antibody titers remained stable for up to 329 days. Patients also had detectable SARS-CoV-2-specific T cells and CD4<jats:sup>+</jats:sup> responses correlating with S1-reactive antibody levels, although patients with hematological malignancies had impaired immune responses that were disease and treatment specific, but presented compensatory cellular responses, further supported by clinical recovery in all but one patient. Overall, these findings advance the understanding of the nature and duration of the immune response to SARS-CoV-2 in patients with cancer.</jats:p>

Journal article

Fendler A, Shepherd STC, Au L, Wilkinson KA, Wu M, Byrne F, Cerrone M, Schmitt AM, Joharatnam-Hogan N, Shum B, Tippu Z, Rzeniewicz K, Boos LA, Harvey R, Carlyle E, Edmonds K, Del Rosario L, Sarker S, Lingard K, Mangwende M, Holt L, Ahmod H, Korteweg J, Foley T, Bazin J, Gordon W, Barber T, Emslie-Henry A, Xie W, Gerard CL, Deng D, Wall EC, Agua-Doce A, Namjou S, Caidan S, Gavrielides M, MacRae J, Kelly G, Peat K, Kelly D, Murra A, Kelly K, O'Flaherty M, Dowdie L, Ash N, Gronthoud F, Shea RL, Gardner G, Murray D, Kinnaird F, Cui W, Pascual J, Rodney S, Mencel J, Curtis O, Stephenson C, Robinson A, Oza B, Farag S, Leslie I, Rogiers A, Iyengar S, Ethell M, Messiou C, Cunningham D, Chau I, Starling N, Turner N, Welsh L, van As N, Jones RL, Droney J, Banerjee S, Tatham KC, O'Brien M, Harrington K, Bhide S, Okines A, Reid A, Young K, Furness AJS, Pickering L, Swanton C, Gandhi S, Gamblin S, Bauer DL, Kassiotis G, Kumar S, Yousaf N, Jhanji S, Nicholson E, Howell M, Walker S, Wilkinson RJ, Larkin J, Turajlic Set al., 2021, Adaptive immunity and neutralizing antibodies against SARS-CoV-2 variants of concern following vaccination in patients with cancer: the CAPTURE study, Nature Cancer, ISSN: 2662-1347

Coronavirus disease 2019 (COVID-19) antiviral response in a pan-tumor immune monitoring (CAPTURE) (NCT03226886) is a prospective cohort study of COVID-19 immunity in patients with cancer. Here we evaluated 585 patients following administration of two doses of BNT162b2 or AZD1222 vaccines, administered 12 weeks apart. Seroconversion rates after two doses were 85% and 59% in patients with solid and hematological malignancies, respectively. A lower proportion of patients had detectable titers of neutralizing antibodies (NAbT) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) versus wild-type (WT) SARS-CoV-2. Patients with hematological malignancies were more likely to have undetectable NAbT and had lower median NAbT than those with solid cancers against both SARS-CoV-2 WT and VOC. By comparison with individuals without cancer, patients with hematological, but not solid, malignancies had reduced neutralizing antibody (NAb) responses. Seroconversion showed poor concordance with NAbT against VOC. Previous SARS-CoV-2 infection boosted the NAb response including against VOC, and anti-CD20 treatment was associated with undetectable NAbT. Vaccine-induced T cell responses were detected in 80% of patients and were comparable between vaccines or cancer types. Our results have implications for the management of patients with cancer during the ongoing COVID-19 pandemic.

Journal article

Fendler A, Au L, Shepherd STC, Byrne F, Cerrone M, Boos LA, Rzeniewicz K, Gordon W, Shum B, Gerard CL, Ward B, Xie W, Schmitt AM, Joharatnam-Hogan N, Cornish GH, Pule M, Mekkaoui L, Ng KW, Carlyle E, Edmonds K, Del Rosario L, Sarker S, Lingard K, Mangwende M, Holt L, Ahmod H, Stone R, Gomes C, Flynn HR, Agua-Doce A, Hobson P, Caidan S, Howell M, Wu M, Goldstone R, Crawford M, Cubitt L, Patel H, Gavrielides M, Nye E, Snijders AP, MacRae J, Nicod J, Gronthoud F, Shea RL, Messiou C, Cunningham D, Chau I, Starling N, Turner N, Welsh L, van As N, Jones RL, Droney J, Banerjee S, Tatham KC, Jhanji S, O'Brien M, Curtis O, Harrington K, Bhide S, Bazin J, Robinson A, Stephenson C, Slattery T, Khan Y, Tippu Z, Leslie I, Gennatas S, Okines A, Reid A, Young K, Furness AJS, Pickering L, Gandhi S, Gamblin S, Swanton C, Nicholson E, Kumar S, Yousaf N, Wilkinson KA, Swerdlow A, Harvey R, Kassiotis G, Larkin J, Wilkinson RJ, Turajlic Set al., 2021, Functional antibody and T cell immunity following SARS-CoV-2 infection, including by variants of concern, in patients with cancer: the CAPTURE study, NATURE CANCER

Journal article

Bohrer AC, Castro E, Hu Z, Queiroz ATL, Tocheny CE, Assmann M, Sakai S, Nelson C, Baker PJ, Ma H, Wang L, Zilu W, du Bruyn E, Riou C, Kauffman KD, Moore IN, Del Nonno F, Petrone L, Goletti D, Martineau AR, Lowe DM, Cronan MR, Wilkinson RJ, Barry CE, Via LE, Barber DL, Klion AD, Andrade BB, Song Y, Wong K-W, Mayer-Barber KDet al., 2021, Eosinophils are part of the granulocyte response in tuberculosis and promote host resistance in mice, JOURNAL OF EXPERIMENTAL MEDICINE, Vol: 218, ISSN: 0022-1007

Journal article

Chen RY, Yu X, Smith B, Liu X, Gao J, Diacon AH, Dawson R, Tameris M, Zhu H, Qu Y, Zhang R, Pan S, Jin X, Goldfeder LC, Cai Y, Arora K, Wang J, Vincent J, Malherbe S, Thienemann F, Wilkinson RJ, Walzl G, Barry CEet al., 2021, Radiological and functional evidence of the bronchial spread of tuberculosis: an observational analysis, The Lancet Microbe, Vol: 2, Pages: E518-E526, ISSN: 2666-5247

BackgroundDirect bronchial spread of tuberculosis was extensively described in pre-antibiotic human pathology literature but this description has been overlooked in the post-antibiotic era, in which most pathology data come from animal models that emphasise the granuloma. Modern techniques, such as [18F]2-fluoro-2-deoxy-D-glucose (FDG) PET-CT scans, might provide further insight. Our aim was to understand normal early tuberculosis resolution patterns on pulmonary PET-CT scans in treated patients with tuberculosis who were subsequently cured.MethodsIn this observational analysis, we analysed data from PredictTB, an ongoing, prospective, randomised clinical trial that examined sequential baseline and week 4 FDG-PET-CT scans from participants successfully treated (sputum culture negative 18 months after enrolment) for drug-susceptible pulmonary tuberculosis in South Africa and China. Participants who were aged 18–75 years, GeneXpert MTB/RIF positive for tuberculosis and negative for rifampicin resistance, had not yet started tuberculosis treatment, had not been treated for active tuberculosis within the previous 3 years, and met basic safety laboratory criteria were included and participants with diabetes, HIV infection, or with extrapulmonary tuberculosis including pleural tuberculosis were excluded. Scans were assessed by two readers for the location of tuberculosis lesions (eg, cavities and consolidations), bronchial thickening patterns, and changes from baseline to week 4 of treatment.FindingsAmong the first 124 participants (enrolled from June 22, 2017, to Sept 27, 2018) who were successfully treated, 161 primarily apical cavitary lesions were identified at baseline. Bronchial thickening and inflammation linking non-cavitary consolidative lesions to cavities were observed in 121 (98%) of 124 participants' baseline PET-CT scans. After 4 weeks of treatment, 21 (17%) of 124 participants had new or expanding lesions linked to cavities via bronchial inflammation

Journal article

Barr DA, Omollo C, Mason M, Koch A, Wilkinson RJ, Lalloo D, Meintjes GA, Mizrahi V, Warner D, Davies Get al., 2021, Flow cytometry method for absolute counting and single-cell phenotyping of mycobacteria, Scientific Reports, Vol: 11, Pages: 1-17, ISSN: 2045-2322

Detection and accurate quantitation of viable Mycobacterium tuberculosis is fundamental to understanding mycobacterial pathogenicity, tuberculosis (TB) disease progression and outcomes; TB transmission; drug action, efficacy and drug resistance. Despite this importance, methods for determining numbers of viable bacilli are limited in accuracy and precision owing to inherent characteristics of mycobacterial cell biology – including the tendency to clump, and “differential” culturability – and technical challenges consequent on handling an infectious pathogen under biosafe conditions. We developed an absolute counting method for mycobacteria in liquid cultures using a bench-top flow cytometer, and the low-cost fluorescent dyes Calcein-AM (CA) and SYBR-gold (SG). During exponential growth CA+ cell counts are highly correlated with CFU counts and can be used as a real-time alternative to simplify the accurate standardisation of inocula for experiments. In contrast to CFU counting, this method can detect and enumerate cell aggregates in samples, which we show are a potential source of variance and bias when using established methods. We show that CFUs comprise a sub-population of intact, metabolically active mycobacterial cells in liquid cultures, with CFU proportion varying by growth conditions. A pharmacodynamic application of the flow cytometry method, exploring kinetics of fluorescent probe defined subpopulations compared to CFU is demonstrated. Flow cytometry derived Mycobacterium bovis bacillus Calmette-Guérin (BCG) time-kill curves differ for rifampicin and kanamycin versus isoniazid and ethambutol, as do the relative dynamics of discrete morphologically-distinct subpopulations of bacilli revealed by this high-throughput single-cell technique.

Journal article

Burke RM, Rickman HM, Singh V, Kalua T, Labhardt N, Hosseinipour M, Wilkinson RJ, MacPherson Pet al., 2021, Same-day antiretroviral therapy initiation in people living with HIV who have tuberculosis symptoms: a systematic review, HIV Medicine, ISSN: 1464-2662

ObjectivesTuberculosis symptoms are very common among people living with HIV (PLHIV) initiatingantiretroviral therapy (ART), are not specific for tuberculosis disease and may result indelayed ART start. The risks and benefits of same-day ART initiation in PLHIV with tuberculosissymptoms are unknown.MethodsWe systematically reviewed nine databases on 12 March 2020 to identify studies thatinvestigated same-day ART initiation among PLHIV with tuberculosis symptoms and reportedboth their approach to TB screening and clinical outcomes. We extracted and summariseddata about TB screening, numbers of people starting same-day ART and outcomes.ResultsWe included four studies. Two studies deferred ART for everyone with any tuberculosissymptoms (one or more of cough, fever, night sweats or weight loss) and substantial numbersof people had deferred ART start (28% and 39% did not start same-day ART). Two studiespermitted some people with tuberculosis symptoms to start same-day ART, and fewer peopledeferred ART (2% and 16% did not start same-day). Two of the four studies were conductedsequentially; proven viral load suppression at eight months was 31% when everyone withtuberculosis symptoms had ART deferred, and 44% when algorithm was changed so thatsome people with tuberculosis symptoms could start same-day ART.ConclusionsAlthough tuberculosissymptoms are very common in people starting ART, there is insufficientevidence about whether presence of tuberculosis symptoms should lead to ART start beingdeferred or not. Research to inform clear guidelines would help maximise benefits of sameday ART.

Journal article

Roy HA, Cascini N, Ajay B, Mukherjee S, MCGAVIN L, Inman A, Martin AJ, Wilkinson RJ, Whitfield PCet al., 2021, Intracranial tuberculoma and the challenges of global neurosurgery, Advances in Clinical Neuroscience and Rehabilitation, ISSN: 1473-9348

In a world of increasing globalisation, neurosurgeons need to be able to diagnose and treat neurosurgical conditions which may not be common to the local population. To illustrate this, we describe the case of an intracranial tuberculoma presenting in the post-partum period. Tuberculosis (TB) is a widely recognised mimic of other conditions, including high grade gliomas, which can result in diagnostic delays.We highlight clinical features that should increase the index of suspicion for TB and create a low threshold fortrial of empirical treatment. We also discuss educational partnership strategies that may help facilitate global perspectives in neurosurgical training.

Journal article

Bunjun R, Omondi FMA, Makatsa MS, Keeton R, Wendoh JM, Muller TL, Prentice CSL, Wilkinson RJ, Riou C, Burgers WAet al., 2021, Th22 cells are a major contributor to the mycobacterial 1 CD4+ T cell 2 response and are depleted during HIV infection, Journal of Immunology, ISSN: 0022-1767

HIV-1 infection substantially increases the risk of developing tuberculosis (TB). Mechanisms such as defects in the Th1 response to Mycobacterium tuberculosis (M.tb) in HIV-infected persons have been widely reported. However, Th1-independent mechanisms also contribute to protection against TB. To identify a broader spectrum of defects in TB immunity during HIV infection, we examined IL-17A and IL-22 production in response to mycobacterial antigens in peripheral blood of persons with latent TB infection (LTBI) and HIV co-infection. Upon stimulating with mycobacterial antigens, we observed a distinct CD4+ T helper lineage producing IL-22 in the absence of IL-17A and IFN-g. Mycobacteria-specific Th22 cells were present at high frequencies in blood and contributed up to 50% to the CD4+ T cell response to mycobacteria, comparable in magnitude to the IFN-g Th1 response (median 0.91% and 0.55%, respectively). Phenotypic characterization of Th22 cells revealed that their memory differentiation was similar to M.tb-specific Th1 cells (i.e. predominantly early-differentiated CD45RO+CD27+ phenotype). Moreover, CCR6 and CXCR3 expression profiles of Th22 cells were similar to Th17 cells, while their CCR4 and CCR10 expression patterns displayed an intermediate phenotype between Th1 and Th17 cells. Strikingly, mycobacterial IL-22 responses were three-fold lower in HIV-infected persons compared to uninfected persons, and the magnitude of responses correlated inversely with HIV viral load. These data provide important insights into mycobacteria-specific T helper subsets in humans and suggest a potential role for IL-22 in protection against TB during HIV infection. Further studies are needed to fully elucidate the role of IL-22 in protective TB immunity

Journal article

Au L, Fendler A, Shepherd STC, Rzeniewicz K, Cerrone M, Byrne F, Carlyle E, Edmonds K, Del Rosario L, Shon J, Haynes WA, Ward B, Shum B, Gordon W, Gerard CL, Xie W, Joharatnam-Hogan N, Young K, Pickering L, Furness AJS, Larkin J, Harvey R, Kassiotis G, Gandhi S, Swanton C, Fribbens C, Wilkinson KA, Wilkinson RJ, Lau DK, Banerjee S, Starling N, Chau I, Turajlic Set al., 2021, Cytokine release syndrome in a patient with colorectal cancer after vaccination with BNT162b2, Nature Medicine, Vol: 27, Pages: 1362-1366, ISSN: 1078-8956

Patients with cancer are currently prioritized in coronavirus disease 2019 (COVID-19) vaccination programs globally, which includes administration of mRNA vaccines. Cytokine release syndrome (CRS) has not been reported with mRNA vaccines and is an extremely rare immune-related adverse event of immune checkpoint inhibitors. We present a case of CRS that occurred 5 d after vaccination with BTN162b2 (tozinameran)—the Pfizer-BioNTech mRNA COVID-19 vaccine—in a patient with colorectal cancer on long-standing anti-PD-1 monotherapy. The CRS was evidenced by raised inflammatory markers, thrombocytopenia, elevated cytokine levels (IFN-γ/IL-2R/IL-18/IL-16/IL-10) and steroid responsiveness. The close temporal association of vaccination and diagnosis of CRS in this case suggests that CRS was a vaccine-related adverse event; with anti-PD1 blockade as a potential contributor. Overall, further prospective pharmacovigillence data are needed in patients with cancer, but the benefit–risk profile remains strongly in favor of COVID-19 vaccination in this population.

Journal article

Du Bruyn E, Fukutani KF, Rockwood N, Schutz C, Meintjes G, Arriaga MB, Cubillos-Angulo JM, Tibúrcio R, Sher A, Riou C, Wilkinson KA, Andrade BB, Wilkinson RJet al., 2021, Inflammatory profile of patients with tuberculosis with or without HIV-1 co-infection: a prospective cohort study and immunological network analysis, The Lancet Microbe, Vol: 2, Pages: e375-e385, ISSN: 2666-5247

BackgroundHIV-1 mediated dysregulation of the immune response to tuberculosis and its effect on the response to antitubercular therapy (ATT) is incompletely understood. We aimed to analyse the inflammatory profile of patients with tuberculosis with or without HIV-1 co-infection undergoing ATT, with specific focus on the effect of ART and HIV-1 viraemia in those co-infected with HIV-1.MethodsIn this prospective cohort study and immunological network analysis, a panel of 38 inflammatory markers were measured in the plasma of a prospective patient cohort undergoing ATT at Khayelitsha Site B clinic, Cape Town, South Africa. We recruited patients with sputum Xpert MTB/RIF-positive rifampicin-susceptible pulmonary tuberculosis. Patients were excluded from the primary discovery cohort if they were younger than 18 years, unable to commence ATT for any reason, pregnant, had unknown HIV-1 status, were unable to consent to study participation, were unable to provide baseline sputum samples, had more than three doses of ATT, or were being re-treated for tuberculosis within 6 months of their previous ATT regimen. Plasma samples were collected at baseline (1–5 days after commencing ATT), week 8, and week 20 of ATT. We applied network and multivariate analysis to investigate the dynamic inflammatory profile of these patients in relation to ATT and by HIV status. In addition to the discovery cohort, a validation cohort of patients with HIV-1 admitted to hospital with CD4 counts less than 350 cells per μL and a high clinical suspicion of new tuberculosis were recruited.FindingsBetween March 1, 2013, and July 31, 2014, we assessed a cohort of 129 participants (55 [43%] female and 74 [57%] male, median age 35·1 years [IQR 30·1–43·7]) and 76 were co-infected with HIV-1. HIV-1 status markedly influenced the inflammatory profile regardless of ATT duration. HIV-1 viral load emerged as a major factor driving differential inflammatory marker expression an

Journal article

Altmann MC, Rinchai D, Baldwin N, Toufiq M, Whalen E, Garand M, Kabeer BSA, Alfaki M, Presnell S, Khaenam P, Benitez AA, Mougin F, Thébault P, Chiche L, Jourde-Chiche N, Phillips JT, Klintmalm G, O'Garra A, Berry M, Bloom C, Wilkinson RJ, Graham CM, Lipman M, Lertmemongkolchai G, Bedognetti D, Thiebaut R, Kheradmand F, Mejias A, Ramilo O, Palucka K, Pascual V, Banchereau J, Chaussabel Det al., 2021, Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data, Nature Communications, Vol: 12, Pages: 1-19, ISSN: 2041-1723

As the capacity for generating large-scale molecular profiling data continues to grow, the ability to extract meaningful biological knowledge from it remains a limitation. Here, we describe the development of a new fixed repertoire of transcriptional modules, BloodGen3, that is designed to serve as a stable reusable framework for the analysis and interpretation of blood transcriptome data. The construction of this repertoire is based on co-clustering patterns observed across sixteen immunological and physiological states encompassing 985 blood transcriptome profiles. Interpretation is supported by customized resources, including module-level analysis workflows, fingerprint grid plot visualizations, interactive web applications and an extensive annotation framework comprising functional profiling reports and reference transcriptional profiles. Taken together, this well-characterized and well-supported transcriptional module repertoire can be employed for the interpretation and benchmarking of blood transcriptome profiles within and across patient cohorts. Blood transcriptome fingerprints for the 16 reference cohorts can be accessed interactively via: https://drinchai.shinyapps.io/BloodGen3Module/.

Journal article

Wasserman S, Davis AG, Stek C, Chirehwa M, Botha S, Daroowala R, Bremer M, Maxebengula M, Koekemoer S, Goliath RT, Jackson A, Crede T, Naude J, Szymanski P, Vallie Y, Moosa MS, Wiesner L, Black J, Meintjes G, Maartens G, Wilkinson RJet al., 2021, Plasma pharmacokinetics of high dose oral versus intravenous rifampicin in patients with tuberculous meningitis: a randomized controlled trial, Antimicrobial Agents and Chemotherapy, Vol: 65, Pages: 1-12, ISSN: 0066-4804

BackgroundHigher doses of intravenous rifampicin may improve outcomes in tuberculous meningitis but is impractical in high burden settings. We hypothesized that plasma rifampicin exposures would be similar between oral 35 mg/kg and intravenous 20 mg/kg, which has been proposed for efficacy trials in tuberculous meningitis.Materials and methodsWe performed a randomized parallel group pharmacokinetic study nested within a clinical trial of intensified antimicrobial therapy for tuberculous meningitis. HIV-positive participants with tuberculous meningitis were recruited from South African hospitals and randomized to one of three rifampicin dosing groups: standard (oral 10 mg/kg), high dose (oral 35 mg/kg), and intravenous (intravenous 20 mg/kg). Intensive pharmacokinetic sampling was done on day 3. Data were described using non-compartmental analysis and exposures compared by geometric mean ratio (GMR).ResultsForty-six participants underwent pharmacokinetic sampling (standard dose, n = 17; high dose oral, n= 15; intravenous, n = 14). Median CD4 count was 130 cells/mm3 (IQR 66 - 253). Rifampicin geometric mean AUC0-24 was 42.9 μg·h/mL (95% CI, 24.5 – 75.0) for standard dose; 295.2 μg·h/mL (95% CI, 189.9 – 458.8) for high dose oral; and 206.5 μg·h/mL (95% CI, 154.6 – 275.8) for intravenous administration. Rifampicin AUC0-24 GMR was 1.44 (90% CI, 0.84 - 2.21) and Cmax GMR was 0.89 (90% CI, 0.63 – 1.23) for high dose oral with respect to intravenous dosing.ConclusionsPlasma rifampicin AUC0-24 was higher after an oral 35 mg/kg dose compared with intravenous administration at 20 mg/kg dose over the first few days of TB treatment. Findings support oral rifampicin dosing in future tuberculous meningitis trials.

Journal article

Davis A, Donovan J, Bremer M, Van Toorn R, Schoeman J, Dadabhoy A, Lai RPJ, Cresswell F, Boulware D, Wilkinson R, Thuong NTT, Thwaites G, Bahr N, Tuberculous Meningitis International Research Consortiumet al., 2021, Host directed therapies for tuberculous meningitis [version 2; peer review: 1 approved, 1 approved with reservations], Wellcome Open Research, Vol: 5, ISSN: 2398-502X

A dysregulated host immune response significantly contributes to morbidity and mortality in tuberculous meningitis (TBM). Effective host directed therapies (HDTs) are critical to improve survival and clinical outcomes. Currently only one HDT, dexamethasone, is proven to improve mortality. However, there is no evidence dexamethasone reduces morbidity, how it reduces mortality is uncertain, and it has no proven benefit in HIV co-infected individuals. Further research on these aspects of its use, as well as alternative HDTs such as aspirin, thalidomide and other immunomodulatory drugs is needed. Based on new knowledge from pathogenesis studies, repurposed therapeutics which act upon small molecule drug targets may also have a role in TBM. Here we review existing literature investigating HDTs in TBM, and propose new rationale for the use of novel and repurposed drugs. We also discuss host variable responses and evidence to support a personalised approach to HDTs in TBM.

Journal article

Burke RM, Rickman HM, Singh V, Corbett EL, Ayles H, Jahn A, Hosseinipour M, Wilkinson RJ, MacPherson Pet al., 2021, What is the optimum time to start antiretroviral therapy in people with HIV and tuberculosis coinfection? A systematic review and meta-analysis, Journal of the International AIDS Society, Vol: 24, Pages: 1-16, ISSN: 1758-2652

Background: HIV and tuberculosis are frequently diagnosed concurrently. In March 2021, World Health Organization recommended that antiretroviral therapy (ART) should be started within two weeks of tuberculosis treatment start, at any CD4 count. We aimed to assess whether earlier ART improved outcomes in people with newly diagnosed HIV and tuberculosis.Methods: We did a systematic review by searching nine database for for trials that compared earlier ART to later ART initiation in people with HIV and tuberculosis. We included studied published from database inception to 12 March 2021. We compared ART within four weeks vs. ART more than four weeks after TB treatment, and ART within two weeks vs. ART between two and eight weeks, and stratified analysis by CD4 count. The main outcome was death; secondary outcomes included IRIS and AIDS-defining events. We used random effects meta-analysis to pool effect estimates.Results: 2468 abstracts were screened, from which we identified nine trials. Among people with all CD4 counts, there was no difference in mortality by earlier ART (≤ 4 week) vs. later ART (> 4 week) (risk difference [RD] 0%; 95% confidence interval [CI] -2% to +1%). Among people with CD4 count ≤50 cells/mm3, earlier ART (≤4 weeks) reduced risk of death (RD -6%; -10% to -1%). Among people with all CD4 counts earlier ART (≤4 weeks) increased the risk of IRIS (RD +6%, 95% CI +2% to +10%) and reduced the incidence of AIDS defining events (RD -2%, 95% CI -4% to 0%). Results were similar when trials were restricted to the five trials which permitted comparison of ART within two weeks to ART between two and eight weeks.Discussion: Earlier ART did not alter risk of death overall among people living with HIV who had TB disease. Trials were conducted between 2004 and 2014, before recommendations to treat HIV at any CD4 count or to rapidly start ART in people without TB. No trials included children or pregnant women. No trials included integrase in

Journal article

Bunjun R, Soares AP, Thawer N, Müller TL, Kiravu A, Ginbot Z, Corleis B, Murugan BD, Kwon DS, Groote-Bidlingmaier FV, Riou C, Wilkinson RJ, Walzl G, Burgers Wet al., 2021, Dysregulation of the immune environment in the airways during HIV infection, Frontiers in Immunology, Vol: 12, Pages: 1-12, ISSN: 1664-3224

HIV-1 increases susceptibility to pulmonary infection and disease, suggesting pathogenesis in the lung. However, the lung immune environment during HIV infection remains poorly characterized. This study examined T cell activation and the cytokine milieu in paired bronchoalveolar lavage (BAL) and blood from 36 HIV-uninfected and 32 HIV-infected participants. Concentrations of 27 cytokines were measured by Luminex, and T cells were phenotyped by flow cytometry. Blood and BAL had distinct cytokine profiles (p=0.001). In plasma, concentrations of inflammatory cytokines like IFN-γ (p=0.004) and TNF-α (p=0.004) were elevated during HIV infection, as expected. Conversely, BAL cytokine concentrations were similar in HIV-infected and uninfected individuals, despite high BAL viral loads (VL; median 48,000 copies/ml epithelial lining fluid). HIV-infected individuals had greater numbers of T cells in BAL compared to uninfected individuals (p=0.007); and BAL VL positively associated with CD4+ and CD8+ T cell numbers (p=0.006 and p=0.0002, respectively) and CXCL10 concentrations (p=0.02). BAL T cells were highly activated in HIV-infected individuals, with nearly 2-3 fold greater frequencies of CD4+CD38+ (1.8-fold; p=0.007), CD4+CD38+HLA-DR+ (1.9-fold; p=0.0006), CD8+CD38+ (2.8-fold; p=0.0006), CD8+HLA-DR+ (2-fold; p=0.022) and CD8+CD38+HLA-DR+ (3.6-fold; p<0.0001) cells compared to HIV-uninfected individuals. Overall, this study demonstrates a clear disruption of the pulmonary immune environment during HIV infection, with readily detectable virus and activated T lymphocytes, which may be driven to accumulate by local chemokines.

Journal article

Bohrer A, Castro E, Hu Z, Queiroz ATL, Tocheny CE, Assmann M, Sakai S, Nelson C, Baker PJ, Ma H, Wang L, Zilu W, du Bruyn E, Riou C, Kauffman KD, Moore IM, Del Nonno F, Petrone L, Goletti D, Martineau AR, Cronan MR, Wilkinson RJ, Barry III CE, Via LE, Barber DL, Klion AD, Andrade BB, Song Y, Wong W-W, Lowe DM, Mayer-Barber Ket al., 2021, Eosinophils are an integral component of the pulmonary granulocyte response in Tuberculosis and promote host resistance in mice, Journal of Experimental Medicine, ISSN: 0022-1007

Host resistance to Mycobacterium tuberculosis infection requires the activities of multipleleukocyte subsets, yet the roles of the different innate effector cells during tuberculosis areincompletely understood. Here we uncover an unexpected association between eosinophils andMtb infection. In humans, eosinophils are decreased in the blood but enriched in resected humantuberculosis lung lesions and autopsy granulomas. Influx of eosinophils is also evident in infectedzebrafish, mice, and nonhuman primate granulomas, where they are functionally activated anddegranulate. Importantly, employing complementary genetic models of eosinophil deficiency, wedemonstrate that, in mice, eosinophils are required for optimal pulmonary bacterial control andhost survival after Mtb infection. Collectively, our findings uncover an unexpected recruitment ofeosinophils to the infected lung tissue and a protective role for these cells in the control of Mtbinfection in mice.

Journal article

Bremer M, Kadernani Y, Wasserman S, Wilkinson RJ, Davis AGet al., 2021, Strategies for the diagnosis and management of meningitis in HIV-infected adults in resource limited settings, Expert Opinion on Pharmacotherapy, Vol: 22, Pages: 2053-2070, ISSN: 1465-6566

Introduction:The incidence of human immunodeficiency virus-1 (HIV-1) associated meningitis has been declining in the post-combination antiretroviral treatment (ART) era, although survival rates remain low for the common causes like tuberculosis and cryptococcal disease. Diagnosis and treatment of meningitis in HIV-1 is complicated by atypical clinical presentations, limited accuracy of diagnostic tests, access to diagnostic tests, and therapeutic agents in low- and middle-income countries (LMIC) and immune reconstitution inflammatory syndrome (IRIS).Areas covered:We provide an overview of the common etiologies of meningitis in HIV-1-infected adults, suggest a diagnostic approach based on readily available tests, and review specific chemotherapeutic agents, host-directed therapies, supportive care, timing of ART initiation, and considerations in the management of IRIS with a focus on resource-limited settings. They identify key knowledge gaps and suggest areas for future research.Expert opinion:Evidence-based management of HIV-1-associated meningitis is sparse for common etiologies. More readily available and sensitive diagnostic tests as well as standardized investigation strategies are required in LMIC. There is a lack of availability of recommended drugs in areas of high HIV-1 prevalence and a limited pipeline of novel chemotherapeutic agents. Host-directed therapies have been inadequately studied.

Journal article

Riou C, Schafer G, du Bruyn E, Goliath RT, Stek C, Mou H, Hung D, Wilkinson KA, Wilkinson Ret al., 2021, Rapid, simplified whole blood-based multiparameter assay to quantify and phenotype SARS-CoV-2 specific T cells, European Respiratory Journal, ISSN: 0903-1936

Rapid tests to evaluate SARS-CoV-2-specific T cell responses are urgently needed to decipher protective immunity and aid monitoring vaccine-induced immunity. Using a rapid whole blood assay requiring minimal amount of blood, we measured qualitatively and quantitatively SARS-38CoV-2-specific CD4 T cell responses in 31 healthcare workers, using flow cytometry. 100% of COVID-19 convalescent participants displayed a detectable SARS-CoV-2-specific CD4 T cell response. SARS-CoV-2-responding cells were also detected in 40.9% of participants with no COVID-19-associated symptoms or who tested PCR negative. Phenotypic assessment indicated that, in COVID-19 convalescent participants, SARS-CoV-2 CD4 responses displayed an early differentiated memory phenotype with limited capacity to produce IFNɣ. Conversely, in participants with no reported symptoms, SARS-CoV-2 CD4 responses were enriched in late differentiated cells, co-expressing IFNɣ and TNFα and also Granzyme B. This proof-of-concept study presents a scalable alternative to PBMC-based assays to enumerate and phenotype SARS-CoV-2-responding T cells, thus representing a practical tool to monitor adaptive immunity due to natural infection or vaccine trials.

Journal article

Davis AG, Wasserman S, Maxebengula M, Stek C, Bremer M, Daroowala R, Aziz S, Goliath R, Stegmann S, Koekemoer S, Jackson A, Lai Sai L, Kadernani Y, Sihoyiya T, Liang CJ, Dodd L, Denti P, Crede T, Naude J, Szymanski P, Vallie Y, Banderker I, Moosa S, Raubenheimer P, Lai RPJ, Joska J, Nightingale S, Dreyer A, Wahl G, Offiah C, Vorster I, Candy S, Robertson F, Meintjes E, Maartens G, Black J, Meintjes G, Wilkinson RJet al., 2021, Study protocol for a phase 2A trial of the safety and tolerability of increased dose rifampicin and adjunctive linezolid, with or without aspirin, for HIV-associated tuberculous meningitis [LASER-TBM], Wellcome Open Research, Vol: 6, ISSN: 2398-502X

Background: Tuberculous meningitis (TBM) is the most lethal form of tuberculosis with a mortality of ~50% in those co-infected with HIV-1. Current antibiotic regimens are based on those known to be effective in pulmonary TB and do not account for the differing ability of the drugs to penetrate the central nervous system (CNS). The host immune response drives pathology in TBM, yet effective host-directed therapies are scarce. There is sufficient data to suggest that higher doses of rifampicin (RIF), additional linezolid (LZD) and adjunctive aspirin (ASA) will be beneficial in TBM yet rigorous investigation of the safety of these interventions in the context of HIV associated TBM is required. We hypothesise that increased dose RIF, LZD and ASA used in combination and in addition to standard of care for the first 56 days of treatment with be safe and tolerated in HIV-1 infected people with TBM. Methods: In an open-label randomised parallel study, up to 100 participants will receive either; i) standard of care (n=40, control arm), ii) standard of care plus increased dose RIF (35mg/kg) and LZD (1200mg OD for 28 days, 600mg OD for 28 days) (n=30, experimental arm 1), or iii) as per experimental arm 1 plus additional ASA 1000mg OD (n=30, experimental arm 2). After 56 days participants will continue standard treatment as per national guidelines. The primary endpoint is death and the occurrence of solicited treatment-related adverse events at 56 days. In a planned pharmacokinetic (PK) sub-study we aim to assess PK/pharmacodynamic (PD) of oral vs IV rifampicin, describe LZD and RIF PK and cerebrospinal fluid concentrations, explore PK/PD relationships, and investigate drug-drug interactions between LZD and RIF. Safety and pharmacokinetic data from this study will inform a planned phase III study of intensified therapy in TBM. Clinicaltrials.gov registration: NCT03927313 (25/04/2019).

Journal article

Davis AG, Wasserman S, Maxebengula M, Stek C, Bremer M, Daroowala R, Aziz S, Goliath R, Stegmann S, Koekemoer S, Jackson A, Lai Sai L, Kadernani Y, Sihoyiya T, Liang CJ, Dodd L, Denti P, Crede T, Naude J, Szymanski P, Vallie Y, Banderker I, Moosa S, Raubenheimer P, Lai RPJ, Joska J, Nightingale S, Dreyer A, Wahl G, Offiah C, Vorster I, Candy S, Robertson F, Meintjes E, Maartens G, Black J, Meintjes G, Wilkinson RJet al., 2021, Study protocol for a phase 2A trial of the safety and tolerability of increased dose rifampicin and adjunctive linezolid, with or without aspirin, for HIV-associated tuberculous meningitis [LASER-TBM], Publisher: F1000 Research Ltd

Background: Tuberculous meningitis (TBM) is the most lethal form of tuberculosis with a mortality of ~50% in those co-infected with HIV-1. Current antibiotic regimens are based on those known to be effective in pulmonary TB and do not account for the differing ability of the drugs to penetrate the central nervous system (CNS). The host immune response drives pathology in TBM, yet effective host-directed therapies are scarce. There is sufficient data to suggest that higher doses of rifampicin (RIF), additional linezolid (LZD) and adjunctive aspirin (ASA) will be beneficial in TBM yet rigorous investigation of the safety of these interventions in the context of HIV associated TBM is required. We hypothesise that increased dose RIF, LZD and ASA used in combination and in addition to standard of care for the first 56 days of treatment with be safe and tolerated in HIV-1 infected people with TBM.Methods: In an open-label randomised parallel study, up to 100 participants will receive either; i) standard of care (n=40, control arm), ii) standard of care plus increased dose RIF (35mg/kg) and LZD (1200mg OD for 28 days, 600mg OD for 28 days) (n=30, experimental arm 1), or iii) as per experimental arm 1 plus additional ASA 1000mg OD (n=30, experimental arm 2). After 56 days participants will continue standard treatment as per national guidelines. The primary endpoint is death and the occurrence of solicited treatment-related adverse events at 56 days. In a planned pharmacokinetic (PK) sub-study we aim to assess PK/pharmacodynamic (PD) of oral vs IV rifampicin, describe LZD and RIF PK and cerebrospinal fluid concentrations, explore PK/PD relationships, and investigate drug-drug interactions between LZD and RIF. Safety and pharmacokinetic data from this study will inform a planned phase III study of intensified therapy in TBM.Clinicaltrials.gov registration: NCT03927313 (25/04/2019)

Working paper

du Bruyn E, Stek C, Daroowala R, Said-Hartley Q, Hsiao M, Goliath R, Abrahams F, Jackson A, Wasserman S, Allwood B, Davis A, Lai RP-J, Coussens A, Wilkinson K, de Vries J, Tiffin N, Cerrone M, Ntusi N, Riou C, Wilkinson R, Aziz S, Bangani N, Black J, Bremer M, Burgers W, Ciko Z, Esmail H, Gordon S, Harley Y, Lakay F, Martinez-Estrada F-O, Meintjes G, Mendelson M, Papavarnavas T, Proust A, Ruzive S, Schafer G, Serole K, Whitaker C, Zvinairo Ket al., 2021, Communicable and non-communicable co-morbidities and the presentation of COVID-19 in an African setting of high HIV-1 and tuberculosis prevalence, Publisher: Cold Spring Harbor Laboratory

Objectives To describe the presentation and outcome of SARS-CoV2 infection in an African setting of high non-communicable co-morbidity and also HIV-1 and tuberculosis prevalence.Design Case control analysis with cases stratified by HIV-1 and tuberculosis status.Setting A single-centre observational case-control study of adults admitted to a South African hospital with proven SARS-CoV-2 infection or alternative diagnosis.Participants 104 adults with RT-PCR-proven SARS-CoV2 infection of which 55 (52.9%) were male and 31 (29.8%) HIV-1 co-infected. 40 adults (35.7% male, 30.9% HIV-1 co-infected) admitted during the same period with no RT-PCR or serological evidence of SARS-CoV2 infection and assigned alternative diagnoses. Additional in vitro data from prior studies of 72 healthy controls and 118 HIV-1 uninfected and infected persons participants enrolled to a prior study with either immune evidence of tuberculosis sensitization but no symptoms or microbiologically confirmed pulmonary tuberculosis.Results Two or more co-morbidities were present in 57.7% of 104 RT-PCR proven COVID-19 presentations, the commonest being hypertension (48%), type 2 diabetes mellitus (39%), obesity (31%) but also HIV-1 (30%) and active tuberculosis (14%). Amongst patients dually infected by tuberculosis and SARS-CoV-2, clinical features could be dominated by either SARS-CoV-2 or tuberculosis: lymphopenia was exacerbated, and some markers of inflammation (D-dimer and ferritin) elevated in singly SARS-CoV-2 infected patients were even further elevated (p < 0.05). HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, with those in the lowest peripheral CD4 percentage strata exhibiting absent or lower antibody responses against SARS-CoV2. Death occurred in 30/104 (29%) of all COVID-19 patients and in 6/15 (40%) of patients with coincident SARS-CoV-2 and tuberculosis.Conclusions In this South African setting, HIV-1 and tuberculosis are common co-m

Working paper

Riou C, Du Bruyn E, Stek C, Daroowala R, Goliath RT, Abrahams F, Said-Hartley Q, Allwood BW, Hsiao N-Y, Wilkinson KA, Lindestam Arlehamn CS, Sette A, Wasserman S, Wilkinson RJet al., 2021, Relationship of SARS-CoV-2-specific CD4 response to COVID-19 severity and impact of HIV-1 and Tuberculosis co-infection, Journal of Clinical Investigation

Journal article

Davis AG, Wilkinson RJ, 2021, Aspirin in tuberculous meningitis, EClinicalMedicine, Vol: 35, ISSN: 2589-5370

Journal article

Barr DA, Omollo CO, Mason M, Koch A, Wilkinson R, Lalloo D, Meintjes G, Mizrahi V, Warner DF, Davies Get al., 2021, Flow cytometry method for absolute counting and single-cell phenotyping of mycobacteria, Publisher: Cold Spring Harbor Laboratory

Detection and accurate quantitation of viable Mycobacterium tuberculosis is fundamental to understanding mycobacterial pathogenicity, tuberculosis (TB) disease progression and outcomes; TB transmission; drug action, efficacy and drug resistance. Despite this importance, methods for determining numbers of viable bacilli are limited in accuracy and precision owing to inherent characteristics of mycobacterial cell biology - including the tendency to clump, and "differential" culturability - and technical challenges consequent on handling an infectious pathogen under biosafe conditions. We developed an absolute counting method for mycobacteria in liquid cultures using a bench-top flow cytometer, and the low-cost fluorescent dyes Calcein-AM (CA) and SYBR-gold (SG). During exponential growth CA+ cell counts are highly correlated with CFU counts and can be used as a real-time alternative to simplify the accurate standardisation of inocula for experiments. In contrast to CFU counting, this method can detect and enumerate cell aggregates in samples, which we show are a potential source of variance and bias when using established methods. We show that CFUs comprise a sub-population of intact, metabolically active mycobacterial cells in liquid cultures, with CFU-proportion varying by growth conditions. A pharmacodynamic application of the flow cytometry method, exploring kinetics of fluorescent probe defined subpopulations compared to CFU is demonstrated. Flow cytometry derived Mycobacterium bovis BCG time-kill curves differ for rifampicin and kanamycin versus isoniazid and ethambutol, as do the relative dynamics of discrete morphologically-distinct subpopulations of bacilli revealed by this high-throughput single-cell technique.

Working paper

Stek C, Buyze J, Menten J, Schutz C, Tinman F, Blumenthal L, Maartens G, Boyles T, Wilkinson RJ, Meintjes G, Lynen Let al., 2021, Diagnostic accuracy of the INSHI consensus case definition for the diagnosis of paradoxical tuberculosis-IRIS, JAIDS: Journal of Acquired Immune Deficiency Syndromes, Vol: 86, Pages: 587-592, ISSN: 1525-4135

BackgroundThe diagnosis of paradoxical tuberculosis-associated immune reconstitution inflammatorysyndrome (TB-IRIS) relies on characteristic clinical features synthesized as the InternationalNetwork for the Study of HIV-associated IRIS (INSHI) case definition. There is noconfirmatory laboratory test.SettingSite B HIV-TB clinic in Khayelitsha, Cape Town, South Africa.MethodsUsing data of participants with HIV-associated tuberculosis starting antiretroviral treatmentfrom a prospective trial evaluating prednisone for TB-IRIS prevention, we applied latentclass analysis to model a gold standard for TB-IRIS.The model-predicted probability of TB-IRIS for each participant was used to assess theperformance of the INSHI case definition and compare its diagnostic accuracy with severaladapted case definitions.ResultsData for this analysis were complete for 217 participants; 41% developed TB-IRIS. Our latentclass model included the following parameters: respiratory symptoms, night sweats, INSHImajor criteria 1, 2, and 4, maximum CRP >90 mg/l, maximum heart rate >120/min,maximum temperature >37.7 0C, and pre-ART CD4 count <50 cells/μl. The model estimateda TB-IRIS incidence of 43% and had optimal goodness of fit (Χ2=337, p=1.0). The INSHI casedefinition displayed a sensitivity of 0.77 and a specificity of 0.86. Replacing all the minorINSHI criteria with objectives measures (CRP elevation, fever, and/or tachycardia) resultedin a definition with better diagnostic accuracy, with a sensitivity of 0.89 and a specificity of0.88.ConclusionThe INSHI case definition identifies TB-IRIS with reasonable accuracy. Amending the casedefinition by replacing INSHI minor criteria with objective variables improved sensitivitywithout loss of specificity.

Journal article

Allie T, Jackson A, Ambler J, Johnston K, Du Bruyn E, Schultz C, Boloko L, Wasserman S, Davis A, Meintjes G, Wilkinson RJ, Tiffin Net al., 2021, TBDBT: A TB DataBase Template for collection of harmonized TB clinical research data in REDCap, facilitating data standardisation for inter-study comparison and meta-analyses, PLoS One, Vol: 16, ISSN: 1932-6203

Clinical tuberculosis research, both within research groups and across research ecosystems, is often undertaken in isolation using bespoke data collection platforms and applying differing data conventions. This failure to harmonise clinical phenotype data or apply standardised data collection and storage standards in turn limits the opportunity to undertake meta-analyses using data generated across multiple research projects for the same research domain. We have developed the Tuberculosis DataBase Template (TBDBT), a template for the well-supported, free and commonly deployed clinical databasing platform, REDCap. This template can be used to set up a new tuberculosis research database with a built-in set of standardised data conventions, to ensure standardised data capture across research projects and programs. A modular design enables researchers to implement only the modules of the database template that are appropriate for their particular study. The template includes core modules for informed consent data, participant demographics, clinical symptoms and presentation, diagnostic imaging and laboratory tests. Optional modules have been designed for visit scheduling and calendar functionality, clinical trial randomisation, study logistics and operations, and pharmacokinetic data. Additional fields can be added as needed. This REDCap template can facilitate collection of high-quality data for tuberculosis research, providing a tool to ensure better data harmonisation, analysis and meta-analysis.

Journal article

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