Malherbe ST, Shenai S, Ronacher K, Loxton AG, Dolganov G, Kriel M, Van T, Chen RY, Warwick J, Via LE, Song T, Lee M, Schoolnik G, Tromp G, Alland D, Barry CE, Winter J, Walzl G, Lucas L, Spuy GVD, Stanley K, Theart L, Smith B, Burger N, Beltran CGG, Maasdorp E, Ellmann A, Choi H, Joh J, Dodd LE, Allwood B, Kogelenberg C, Vorster M, Griffith-Richards S

Nature Medicine

2016-08-20

Sutherland, Jayne S van der Spuy, Gian Gindeh, Awa Thuong, Nguyen Thuy Thuong Namuganga, AnnRitah Owolabi, Olumuyiwa Mayanja-Kizza, Harriet Nsereko, Mary Thwaites, Guy Winter, Jill Dockrell, Hazel M Scriba, Thomas J Geluk, Annemieke Corstjens, Paul Stanley, Kim Richardson, Tracy Shaw, Jane A Smith, Bronwyn Malherbe, Stephanus T Walzl, Gerhard Sutherland, Jayne Owolabi, Olumuyiwa Secka, Amie Daffeh, Georgetta Gindeh, Awa Mendy, Joseph Sarr, Binta Riley, Abi-Janet Jobe, Alhaji Davies, Monica Kanyi, Kairaba Jallow, Momodou Barry, Salieu Cham, Ousainou Nkereuwem, Esin Walzl, Gerhard Malherbe, Stephanus Smith, Bronwyn van der Spuy, Gian Stanley, Kim Shaw, Jane Chetram, Alicia Richardson, Tracy Finn, Marika Hiemstra, Andriette Chegou, Novel Kuivaniemi, Helena Tromp, Gerard Tonsing, Susanne Smit, Elizma Carstens, Balie Mayanja-Kizza, Harriet Nsereko, Mary Namuganga, AnnRitah Nalukwago, Sophie Akol, Joseph Lamunu, Dorcas Ordie, Michael Thwaites, Guy Nguyen, Thuong Le, Van Vo Thanh, Son Thi, Hau Nguyen Thi Ngoc, Ha Vu Le Hong, Ngoc Belisle, John Dobos, Karen Dockrell, Hazel Scriba, Thomas Hatherill, Mark Hadley, Kate Shenje, Justin Kimbung, Stanley Mulenga, Humphrey Oelofse, Rachel Bilek, Nicole van Rooyen, Elma Mabwe, Simba Corstjens, Paul Geluk, Annemieke Kon Fat, Elisa Tjon Pierneef, Louise van Hooij, Anouk Winter, Jill Ruhwald, Morten Moreau, Emmanuel Penn-Nicholson, Adam Schacht, Claudia Büech, Julia Streitz, Malte

Clinical Infectious Disaeses

(HR)-Prototype), which generates a ‘TB score’ based on mRNA expression of 3 genes. Here we describe the first prospective findings of the MTB-HR prototype.Fingerstick blood from adults presenting with symptoms compatible with TB in South Africa, The Gambia, Uganda and Vietnam was analysed using the Cepheid GeneXpert MTB-HR prototype. Accuracy of the Xpert MTB-HR cartridge was determined in relation to GeneXpert Ultra results and a composite microbiological score (GeneXpert Ultra and liquid culture) with patients classified as having TB or other respiratory diseases (ORD).When data from all sites (n=75 TB, 120 ORD) were analysed, the TB score discriminated between TB and ORD with an AUC of 0·94 (CI, 0·91-0·97), sensitivity of 87% (CI, 77-93%) and specificity of 94% (88-97%). When sensitivity was set at 90% for a triage test, specificity was 86% (CI, 75-97%). These results were not influenced by HIV status or geographical location. When evaluated against a composite microbiological score (n=80 TB, 111 ORD), the TB score was able to discriminate between TB and ORD with an AUC of 0·88 (CI, 0·83-0·94), 80% sensitivity (CI, 76-85%) and 94% specificity (CI, 91-96%).Our interim data indicate the Cepheid MTB-HR cartridge reaches the minimal target product profile for a point of care triage test for TB using fingerstick blood, regardless of geographic area or HIV infection status.

2021-12-12

ST Malherbe et al

European Journal of Nuclear Medicine and Molecular Imaging

Abstract
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.

2018-02-01

Young, Carly Ahlers, Petri Hiemstra, Andriette M Loxton, Andre G Gutschmidt, Andrea Malherbe, Stephanus T

Translational Medicine Communications

Background: Tuberculosis (TB) remains a debilitating, deadly disease that warrants innovative research tools to fully understand the pathogenesis and host immune responses, particularly at the site of infection and disease. In this regard, bronchoscopies with bronchoalveolar lavage (BAL) serve as a valuable technique for site of disease sample retrieval for further clinical- and basic research. Here we investigate the feasibility of research bronchoscopies in a low/middle-income area, where TB remains rife, and assess the value of retrieved BAL cells (BALC) for downstream fluorescent-based cellular evaluations. Methods: Using quantitative and qualitative methods, we evaluate the outcomes, safety, tolerability, participant -perception and -experience, while also providing insight into participant recruitment and screening processes of our study. Using light microscopy differential counting for BALC analysis, we evaluate the cellular composition of BAL fluid (BALF) from TB patients, healthy community controls and patients with other lung diseases. We also use flow cytometry to describe the challenges associated with fluorescence-based phenotypic analysis of autofluorescent BALC. Results: Our findings suggest that research bronchoscopies are safe, acceptable procedures for research participants and are indeed a feasible technique for future study design. We also suggest that the majority of participants are receptive to the proposition of a second research bronchoscopy. This poses an important avenue for research entailing follow-up investigations of the same study participant. Furthermore, our results show that smoking is characterized by retrieval of BALC containing particulate matter, that interferes with fluorescence-based flow cytometry data analysis. Based on light microscopy differential cell counting, our findings suggest that there are differences in the cell yields and cellular composition of the BALF between TB patients, healthy community controls and patients with other lung diseases. We also report on subject characteristics and demographic factors, namely gender and age, that have the potential to affect cell yields and cellular data of BALF.

Conclusions: These findings will serve as a valuable reference for appropriate planning and design of studies involving clinical bronchoscopies for TB and lung disease research.
 

2019-06-05

Malherbe, Stephanus T. Chen, Ray Y. Dupont, Patrick Kant, Ilse Kriel, Magdalena Loxton, André G. Smith, Bronwyn Beltran, Caroline G.G. van Zyl, Susan McAnda, Shirely Abrahams, Charmaine Maasdorp, Elizna Doruyter, Alex Via, Laura E. Barry, Clifton E. Alland, David Richards, Stephanie Griffith Ellman, Annare Peppard, Thomas Belisle, John Tromp, Gerard Ronacher, Katharina Warwick, James M. Winter, Jill Walzl, Gerhard

EJNMMI Research

Background: There is a growing interest in the use of F-18 FDG PET-CT to monitor tuberculosis (TB) treatment response. Tuberculosis lung lesions are often complex and diffuse, with dynamic changes during treatment and persisting metabolic activity after apparent clinical cure. This poses a challenge in quantifying scan-based markers of burden of disease and disease activity. We used semi-automated, whole lung quantification of lung lesions to analyse serial FDG PET-CT scans from the Catalysis TB Treatment Response Cohort to identify characteristics that best correlated with clinical and microbiological outcomes. Results: Quantified scan metrics were already associated with clinical outcomes at diagnosis and 1 month after treatment, with further improved accuracy to differentiate clinical outcomes after standard treatment duration (month 6). A high cavity volume showed the strongest association with a risk of treatment failure (AUC 0.81 to predict failure at diagnosis), while a suboptimal reduction of the total glycolytic activity in lung lesions during treatment had the strongest association with recurrent disease (AUC 0.8 to predict pooled unfavourable outcomes). During the first year after TB treatment lesion burden reduced; but for many patients, there were continued dynamic changes of individual lesions. Conclusions: Quantification of FDG PET-CT images better characterised TB treatment outcomes than qualitative scan patterns and robustly measured the burden of disease. In future, validated metrics may be used to stratify patients and help evaluate the effectiveness of TB treatment modalities.

2020-01-09

B Alisjahbana et al.

Trans R Soc Trop Med Hyg

Diabetes mellitus (DM) patients are three times more likely to develop tuberculosis (TB) than the general population. Active TB screening in people with DM is part of a bidirectional approach. The aim of this study was to conduct pragmatic active TB screening among DM patients in four countries to inform policy.DM patients were recruited in Indonesia (n=809), Peru (n=600), Romania (n=603) and South Africa (n=51). TB cases were diagnosed using an algorithm including clinical symptoms and chest X-ray. Presumptive TB patients were examined with sputum smear and culture.A total of 171 (8.3%) individuals reported ever having had TB (South Africa, 26%; Indonesia, 12%; Peru, 7%; Romania, 4%), 15 of whom were already on TB treatment. Overall, 14 (0.73% [95% confidence interval 0.40 to 1.23]) TB cases were identified from screening. Poor glucose control, smoking, lower body mass index, education and socio-economic status were associated with newly diagnosed/current TB. Thirteen of the 14 TB cases diagnosed from this screening would have been found using a symptom-based approach.These data support the World Health Organization recommendation for routine symptom-based screening for TB in known DM patients in high TB-burden countries. DM patients with any symptoms consistent with TB should be investigated and diagnostic tools should be easily accessible.

2021-06-01