Xpert MTB/RIF for diagnosis of tuberculosis : performance variability and impact on patient-important outcomes

Accurate diagnosis and early treatment are key in achieving global targets to end tuberculosis (TB). Between 2000 and 2017, nearly 54 million deaths were averted due to timely diagnosis and treatment initiation. Xpert MTB/RIF (“Xpert”¸Cepheid, Sunnyvale, CA, US) is a molecular diagnostic test with integration of an automated sample processing system and hemi-nested real time polymerase chain reaction (PCR) in a single cartridge. It provides results within two hours and can be used at point-of-care. Xpert was endorsed by WHO in 2010 and currently is strongly recommended for adults and children suspected for MDR-TB or HIV and conditionally for all suspected with TB, should resources allow. By 2016, approximately 34 million Xpert cartridges were procured globally. Despite considerable development in evaluation and roll out of Xpert, important questions still remain to be addressed. Xpert has shown varibility in performance and it remains a question whether the observed variability is entirely explained by differences in populations and epidemiological burden or methodological differences in how Xpert is being evaluated such as effect of time to positivity (TTP) on a reference standard (culture) on sensitivity and how previous history of TB affects the specificity of Xpert. Accurate TTP can only be determined in automated systems such as MGIT culture system. Furthermore, studies that have assessed patient-important outcomes have shown inconsistent results. This doctoral thesis provides evidence on the overall population level pooled effect of Xpert on important patient outcomes based on the Cochrane review and evidence on effect of TTP and history of TB on sensitivity and specificity Xpert, respectively. This thesis is based on three manuscripts: Manuscript 1: Effect of time to culture positivity as a reference standard on Xpert MTB/RIF sensitivity for diagnosis of pulmonary tuberculosis This manuscript shows the effect of TTP on the sensitivity of Xpert based on the analysis of data from a database of 16 different studies that evaluated Xpert with a total of 11,870 participants from ten different countries. The TTP was divided up in categories of five days up to 42 days. In all culture positive, sensitivity of Xpert in categories up to 15 days were: ≤ 5, 99.3% , (95% CI: 95-100, N=351) , >5≤10, 99.3 % (95%CI, 98.4-99.7, N=2231) and >10≤15, 96.8% (95%CI,94-98.3,N=1885). In smear negative-culture positive: ≤ 5, 99%, (95% CI: 62-100, N=37) , >5≤10, 98% (95%CI, 80-100, N=237) and >10≤15, 92% (95%CI,83-96 ,N=413). In HIV positive: ≤ 5, 96% , (95% CI: 63-100, N=51) , >5≤10, 98% (95%CI, 90-100, N=199) and >10≤15, 94% (95%CI,82-98 ,N=168) The sensitivity of Xpert in the first fifteen days was high in all three groups of analysis: all culture positive, smear positive-culture positive and smear negative-culture positive and irrespective of HIV status. A significant drop in sensitivity of Xpert when TTP of more than 15 days were assessd across all groups of analysis. Xpert sensitivity decreased with increasing TTP. This may explain some of the variation seen across different studies published on the diagnostic performance of Xpert. In settings with better TB control efforts, it is expected that patients are diagnosed earlier and TTP will be increased. Thus, reporting TTP of MGIT culture is important to ensure comparability of studies on Xpert as a diagnostic TB test. Manuscript 2: Effect of a previous history of tuberculosis on the specificity of Xpert MTB/RIF This manuscript shows the effect of history of TB based on the analysis of data from a database of 16 different studies that evaluated Xpert with a total of 11,870 participants. A total of 1,630 participants had a history of TB. The median time since previous TB treatment was 3 years (Interquartile range (IQR), 0.0-6). Among the 803 patients with a TB episode within two years of testing, the specificity of Xpert was 92.2% (95% CI 81-97). The specificity increased with time since previous TB. Between two and five years (373 participants), the specificity was 99.0% (95% CI; 86-100) and above five years (454 participants), 98.6% (95% CI; 85.4-99.8).This manuscript shows that a history of TB negatively affects Xpert specificity, and this effect is increased among those with TB in the last two years. This implies for a need of algorithms in patients with history of TB and positive Xpert to guide interpretation and management. The use of chest X-ray and clinical judgement remain relevant. Manuscript 3: Impact of the diagnostic test Xpert MTB/RIF® on health outcomes for tuberculosis This manuscript is based on a Cochrane review and summarizes the effect of Xpert on patient-important outcomes. The review included ten studies, seven of which were randomized controlled trials and three pre-post intervention studies. In the domains of the Cochrane risk of bias tool, most randomized studies had a low risk of bias. There was evidence of a positive effect of Xpert on tuberculosis confirmation in treated patients (RR 1.29 95%CI 1.11, 1.51 in the randomized trials) and reduction in pre-treatment loss to follow up (RR 0.59 95% CI 0.42-0.84). Overall there was a reduction on all-cause mortality of 12% (RR 0.88 (95% CI 0.73, 1.05) and 24% (RR 0.76 95% CI 0.58-1.00) among HIV positive participants. There was evidence that Xpert lead to an increase in the overall proportion of patients treated for TB (RR 1.10 95%CI 0.98, 1.23), the likelihood of being cured (OR 1.09 95% CI 1.02, 1.16), and that the proportion of those treated who were not microbiologically confirmed was reduced (RR 0.59 95%CI 0.41 0.85. This manuscript shows that compared with smear microscopy, Xpert reduces all-cause mortality by 12% although uncertainty around the effect estimate was high and the data was also compatible with reduction of up to 27% and an increase of up to 5%. The mechanisms by which Xpert could affect mortality is likely at least in part related to the reduction in pre-treatment loss to follow-up as well as the increase in the proportion of patients cured. Further studies should assess the role of empirical treatment on the impact of Xpert on patient outcomes

A Bundle of Services Increased Ascertainment of Tuberculosis among HIV-Infected Individuals Enrolled in a HIV Cohort in Rural Sub-Saharan Africa

OBJECTIVES: To report on trends of tuberculosis ascertainment among HIV patients in a rural HIV cohort in Tanzania, and assessing the impact of a bundle of services implemented in December 2012, consisting of three components:(i)integration of HIV and tuberculosis services; (ii)GeneXpert for tuberculosis diagnosis; and (iii)electronic data collection. DESIGN: Retrospective cohort study of patients enrolled in the Kilombero Ulanga Antiretroviral Cohort (KIULARCO), Tanzania.). METHODS: HIV patients without prior history of tuberculosis enrolled in the KIULARCO cohort between 2005 and 2013 were included.Cox proportional hazard models were used to estimate rates and predictors of tuberculosis ascertainment. RESULTS: Of 7114 HIV positive patients enrolled, 5123(72%) had no history of tuberculosis. Of these, 66% were female, median age was 38 years, median baseline CD4+ cell count was 243 cells/microl, and 43% had WHO clinical stage 3 or 4. During follow-up, 421 incident tuberculosis cases were notified with an estimated incidence of 3.6 per 100 person-years(p-y)[95% confidence interval(CI)3.26-3.97]. The incidence rate varied over time and increased significantly from 2.96 to 43.98 cases per 100 p-y after the introduction of the bundle of services in December 2012. Four independent predictors of tuberculosis ascertainment were identified:poor clinical condition at baseline (Hazard Ratio (HR) 3.89, 95% CI 2.87-5.28), WHO clinical stage 3 or 4 (HR 2.48, 95% CI 1.88-3.26), being antiretroviralnaive (HR 2.97, 95% CI 2.25-3.94), and registration in 2013(HR 6.07, 95% CI 4.39-8.38). CONCLUSION: The integration of tuberculosis and HIV services together with comprehensive electronic data collection and use of GeneXpert increased dramatically the ascertainment of tuberculosis in this rural African HIV cohort

Chronic airflow obstruction in Tanzania - a cross-sectional study

Chronic obstructive pulmonary disease is a global problem and available data from sub-Saharan Africa is very limited.; A cross-sectional facility-based pilot study among patients and visitors to an urban and a rural primary healthcare facility was conducted in coastal Tanzania. The primary outcome was the prevalence of chronic airflow obstruction.; The final analysis included 598 participants with valid post-bronchodilator spirometry. Applying ATS/ERS spirometric criteria, chronic airflow obstruction was found in n = 24 (4%, CI95 2.7-5.9) participants and in n = 30 (5%, CI95 3.5-7.1) applying GOLD spirometric criteria. To analyse risk factors for chronic airflow obstruction including those not meeting ATS/ERS or GOLD criteria, FEF25-75 and FEV1% predicted was analysed in participants without evidence of pulmonary restriction among those exposed or not exposed to risk factors (n = 552). FEV1% predicted, but in particular FEF25-75 decreased with increasing symptom severity of shortness of breath as well as limitations in daily activities of participants. Cooking in general and cooking with biomass fuels vs. gas or electricity was associated with significantly lower FEF25-75, but not with lower FEV1% predicted. Participants having refrained from taking a job because of shortness of breath exhibited lower FEF25-75 (p < 0.01). A history of prior active TB was the most relevant risk factor associated with a decrease in FEF25-75 as well as FEV1% predicted.; This study demonstrated a relevant prevalence of chronic airflow obstruction in primary healthcare attendants and healthy visitors of a Tanzanian hospital. Using the baseline data provided, larger and population-based studies are needed to validate these findings. TB may have more impact on development of chronic airway obstruction than smoking in Africa. Due to the influence of age on the GOLD definition of chronic airflow obstruction, studies should report results using both ATS/ERS and GOLD definitions and include age-stratified analysis. Analysis of FEV1 and in particular FEF25-75 may yield additional information on risk factors and earlier stages of chronic airflow obstruction

Xpert MTB/RIF Ultra assay for the diagnosis of pulmonary tuberculosis in children: a multicentre comparative accuracy study

We evaluated the diagnostic performance of the novel next-generation Xpert MTB/RIF Ultra (Xpert Ultra) in comparison to Xpert MTB/RIF (Xpert) assay for the detection of paediatric pulmonary tuberculosis in high burden settings.; From May 2011 to September 2012, children with suspected pulmonary tuberculosis were enrolled at two Tanzanian sites and sputum samples were examined using sputum smear, Xpert and culture. Xpert Ultra was tested between January and June 2017 using sputum pellets, which had been stored at -80°C. The diagnostic accuracy of Ultra versus Xpert was determined using well-defined case definitions as reference standard.; In total, 215 children were included. The median age was 5.4 years, the HIV prevalence was 52% and 13% had culture-confirmed pulmonary tuberculosis. When only the first available sample of each patient was analysed, the sensitivity of Xpert Ultra was 64.3 % (95% CI: 44.1 to 81.4) while that of Xpert was 53.6% (95%CI: 33.9 to 72.5). The specificity of Xpert Ultra based on analysis of all available samples was 98.1% (95%CI: 93.4 to 99.7), that of Xpert was 100%.; Xpert Ultra was found to have a higher sensitivity, but slightly reduced specificity compared to Xpert in detecting pulmonary tuberculosis in children

Xpert Ultra versus Xpert MTB/RIF for pulmonary tuberculosis and rifampicin resistance in adults with presumptive pulmonary tuberculosis

Background Xpert MTB/RIF and Xpert MTB/RIF Ultra (Xpert Ultra) are World Health Organization (WHO)‐recommended rapid tests that simultaneously detect tuberculosis and rifampicin resistance in people with signs and symptoms of tuberculosis. This review builds on our recent extensive Cochrane Review of Xpert MTB/RIF accuracy. Objectives To compare the diagnostic accuracy of Xpert Ultra and Xpert MTB/RIF for the detection of pulmonary tuberculosis and detection of rifampicin resistance in adults with presumptive pulmonary tuberculosis. For pulmonary tuberculosis and rifampicin resistance, we also investigated potential sources of heterogeneity. We also summarized the frequency of Xpert Ultra trace‐positive results, and estimated the accuracy of Xpert Ultra after repeat testing in those with trace‐positive results. Search methods We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, LILACS, Scopus, the WHO ICTRP, the ISRCTN registry, and ProQuest to 28 January 2020 with no language restriction. Selection criteria We included diagnostic accuracy studies using respiratory specimens in adults with presumptive pulmonary tuberculosis that directly compared the index tests. For pulmonary tuberculosis detection, the reference standards were culture and a composite reference standard. For rifampicin resistance, the reference standards were culture‐based drug susceptibility testing and line probe assays. Data collection and analysis Two review authors independently extracted data using a standardized form, including data by smear and HIV status. We assessed risk of bias using QUADAS‐2 and QUADAS‐C. We performed meta‐analyses comparing pooled sensitivities and specificities, separately for pulmonary tuberculosis detection and rifampicin resistance detection, and separately by reference standard. Most analyses used a bivariate random‐effects model. For tuberculosis detection, we estimated accuracy in studies in participants who were not selected based on prior microscopy testing or history of tuberculosis. We performed subgroup analyses by smear status, HIV status, and history of tuberculosis. We summarized Xpert Ultra trace results. Main results We identified nine studies (3500 participants): seven had unselected participants (2834 participants). All compared Xpert Ultra and Xpert MTB/RIF for pulmonary tuberculosis detection; seven studies used a paired comparative accuracy design, and two studies used a randomized design. Five studies compared Xpert Ultra and Xpert MTB/RIF for rifampicin resistance detection; four studies used a paired design, and one study used a randomized design. Of the nine included studies, seven (78%) were mainly or exclusively in high tuberculosis burden countries. For pulmonary tuberculosis detection, most studies had low risk of bias in all domains. Pulmonary tuberculosis detection Xpert Ultra pooled sensitivity and specificity (95% credible interval) against culture were 90.9% (86.2 to 94.7) and 95.6% (93.0 to 97.4) (7 studies, 2834 participants; high‐certainty evidence) versus Xpert MTB/RIF pooled sensitivity and specificity of 84.7% (78.6 to 89.9) and 98.4% (97.0 to 99.3) (7 studies, 2835 participants; high‐certainty evidence). The difference in the accuracy of Xpert Ultra minus Xpert MTB/RIF was estimated at 6.3% (0.1 to 12.8) for sensitivity and −2.7% (−5.7 to −0.5) for specificity. If the point estimates for Xpert Ultra and Xpert MTB/RIF are applied to a hypothetical cohort of 1000 patients, where 10% of those presenting with symptoms have pulmonary tuberculosis, Xpert Ultra will miss 9 cases, and Xpert MTB/RIF will miss 15 cases. The number of people wrongly diagnosed with pulmonary tuberculosis would be 40 with Xpert Ultra and 14 with Xpert MTB/RIF. In smear‐negative, culture‐positive participants, pooled sensitivity was 77.5% (67.6 to 85.6) for Xpert Ultra versus 60.6% (48.4 to 71.7) for Xpert MTB/RIF; pooled specificity was 95.8% (92.9 to 97.7) for Xpert Ultra versus 98.8% (97.7 to 99.5) for Xpert MTB/RIF (6 studies). In people living with HIV, pooled sensitivity was 87.6% (75.4 to 94.1) for Xpert Ultra versus 74.9% (58.7 to 86.2) for Xpert MTB/RIF; pooled specificity was 92.8% (82.3 to 97.0) for Xpert Ultra versus 99.7% (98.6 to 100.0) for Xpert MTB/RIF (3 studies). In participants with a history of tuberculosis, pooled sensitivity was 84.2% (72.5 to 91.7) for Xpert Ultra versus 81.8% (68.7 to 90.0) for Xpert MTB/RIF; pooled specificity was 88.2% (70.5 to 96.6) for Xpert Ultra versus 97.4% (91.7 to 99.5) for Xpert MTB/RIF (4 studies). The proportion of Ultra trace‐positive results ranged from 3.0% to 30.4%. Data were insufficient to estimate the accuracy of Xpert Ultra repeat testing in individuals with initial trace‐positive results. Rifampicin resistance detection Pooled sensitivity and specificity were 94.9% (88.9 to 97.9) and 99.1% (97.7 to 99.8) (5 studies, 921 participants; high‐certainty evidence) for Xpert Ultra versus 95.3% (90.0 to 98.1) and 98.8% (97.2 to 99.6) (5 studies, 930 participants; high‐certainty evidence) for Xpert MTB/RIF. The difference in the accuracy of Xpert Ultra minus Xpert MTB/RIF was estimated at −0.3% (−6.9 to 5.7) for sensitivity and 0.3% (−1.2 to 2.0) for specificity. If the point estimates for Xpert Ultra and Xpert MTB/RIF are applied to a hypothetical cohort of 1000 patients, where 10% of those presenting with symptoms have rifampicin resistance, Xpert Ultra will miss 5 cases, and Xpert MTB/RIF will miss 5 cases. The number of people wrongly diagnosed with rifampicin resistance would be 8 with Xpert Ultra and 11 with Xpert MTB/RIF. We identified a higher number of rifampicin resistance indeterminate results with Xpert Ultra, pooled proportion 7.6% (2.4 to 21.0) compared to Xpert MTB/RIF pooled proportion 0.8% (0.2 to 2.4). The estimated difference in the pooled proportion of indeterminate rifampicin resistance results for Xpert Ultra versus Xpert MTB/RIF was 6.7% (1.4 to 20.1). Authors' conclusions Xpert Ultra has higher sensitivity and lower specificity than Xpert MTB/RIF for pulmonary tuberculosis, especially in smear‐negative participants and people living with HIV. Xpert Ultra specificity was lower than that of Xpert MTB/RIF in participants with a history of tuberculosis. The sensitivity and specificity trade‐off would be expected to vary by setting. For detection of rifampicin resistance, Xpert Ultra and Xpert MTB/RIF had similar sensitivity and specificity. Ultra trace‐positive results were common. Xpert Ultra and Xpert MTB/RIF provide accurate results and can allow rapid initiation of treatment for rifampicin‐resistant and multidrug‐resistant tuberculosis

Maturation and mip-1β production of cytomegalovirus-specific T cell responses in Tanzanian children, adolescents and adults : impact by HIV and Mycobacterium tuberculosis co-infections

It is well accepted that aging and HIV infection are associated with quantitative and functional changes of CMV-specific T cell responses. We studied here the expression of Mip-1β and the T cell maturation marker CD27 within CMVpp65-specific CD4+ and CD8+ T cells in relation to age, HIV and active Tuberculosis (TB) co-infection in a cohort of Tanzanian volunteers (≤16 years of age, n = 108 and ≥18 years, n = 79). Independent of HIV co-infection, IFNγ+ CMVpp65-specific CD4+ T cell frequencies increased with age. In adults, HIV co-infection further increased the frequencies of these cells. A high capacity for Mip-1β production together with a CD27low phenotype was characteristic for these cells in children and adults. Interestingly, in addition to HIV co-infection active TB disease was linked to further down regulation of CD27 and increased capacity of Mip-1β production in CMVpp65-specific CD4+ T cells. These phenotypic and functional changes of CMVpp65-specific CD4 T cells observed during HIV infection and active TB could be associated with increased CMV reactivation rates

Limited value of whole blood Xpert(®) MTB/RIF for diagnosing tuberculosis in children

We evaluated the ability of the Xpert(®) MTB/RIF assay to detect Mycobacterium tuberculosis in whole blood of children with tuberculosis in tuberculosis endemic settings with high rates of HIV infection.; From June 2011 to September 2012 we prospectively enrolled children with symptoms or signs suggestive of tuberculosis at three research centres in Tanzania and Uganda. After clinical assessment, respiratory specimens were collected for microscopy and culture, as well as whole blood for Xpert(®) MTB/RIF. Children were classified according to standardised case definitions.; A total of 232 children were evaluated; 14 (6.0%) had culture-confirmed tuberculosis. The Xpert(®) MTB/RIF assay detected M. tuberculosis in 5/232 (2.2%) blood samples with 1 (0.4%) error reading and presumably 1 (0.4%) false-positive result. The sensitivity of the assay in children with culture-confirmed (1/14) versus no tuberculosis (1/117) was 7.1% (95% CI, 1.3-31.5). Three of the five Xpert(®) MTB/RIF positive patients had negative cultures, but were classified as probable tuberculosis cases. Assay sensitivity against a composite reference standard (culture-confirmed, highly probable or probable tuberculosis) was 5.4% (95% CI, 2.1-13.1).; Whole blood Xpert(®) MTB/RIF demonstrated very poor sensitivity, although it may enhance the diagnostic yield in select cases, with culture-negative tuberculosis

Summary of the baseline characteristics of study participants.

<p>Percentages exclude missing values: Chronic diseases include arterial hypertension, diabetes mellitus and cancer. KIULARCO: Kilombero Ulanga Antiretroviral Cohort; IQR: Interquartile range; WHO: World Health Organization, ART: Antiretroviral treatment</p><p>Summary of the baseline characteristics of study participants.</p

Flow diagram of the study population.

<p>Flow diagram of the study population.</p