Adam Penn-Nicholson

Background: Community-based tuberculosis screening can identify asymptomatic tuberculosis, but microbiological confirmation has been sputum-dependent. We evaluated the diagnostic performance, yield, and operational characteristics of centralized qPCR testing of community-collected tongue swabs (TS). Methods: We conducted a cross-sectional study among household contacts (HHCs; ≥18 years) of individuals receiving treatment for pulmonary TB in South Africa. During household visits, health workers collected TS specimens and, where possible, sputum, which was tested in participants’ homes using Xpert MTB/RIF Ultra. TSs were transported non-refrigerated in molecular transport medium to a distant central laboratory for manual qPCR assay. The primary outcome was diagnostic performance of TS qPCR compared with sputum Xpert Ultra using paired results. Secondary outcomes were diagnostic yield by TS and operational indicators of the centralized testing workflow. Findings: 909 HHCs were enrolled; median age 39 years (IQR 28–55), 532 (58·5%) were asymptomatic, 617 (67·9%) were sputum scarce. TS were collected from 901/909 (99·1%) and sputum from 292/909 (32·1%) participants. Among 271 paired TS–sputum results, TS qPCR sensitivity was 60·9% (95% CI 38·5–80·3), specificity 95·2% (91·7–97·5), and overall agreement 92·3% (88·5–95·0). Yield increased from 1·8% (95% CI 1·0–2·8) with symptom-restricted sputum testing to 3·2% (2·1–4·5) with symptom-agnostic sputum testing and 5·9% (4·5–7·7) when TS testing was implemented among sputum-scarce individuals, identifying 25 additional HHCs with positive molecular test results (86·2% increase). Operational indicators demonstrated successful implementation, with 2·3% specimen loss and valid molecular results for 93·8% who provided a TS. Interpretation: Despite lower per-test sensitivity than sputum testing, TS may provide a scalable strategy for expanding microbiological screening beyond sputum-dependent pathways, thereby substantially increasing tuberculosis detection among HHCs. Funding: U.S. NIH; Australian Department of Foreign Affairs and Trade; UK Foreign, Commonwealth and Development Office RESEARCH IN CONTEXT: Evidence before this study: A growing body of evidence suggests that a large proportion of tuberculosis (TB) exists as asymptomatic disease, defined by the World Health Organization as a person with TB disease who does not report symptoms suggestive of TB during screening. However, TB detection strategies have traditionally relied on symptom-based screening of people with presumed disease who present to healthcare facilities for evaluation using sputum-based diagnostic pathways. We searched PubMed, Embase and Google Scholar for studies published in English from January 1, 2010, to July 7, 2026, using combinations of the terms “tuberculosis” or “TB”, “tongue swab”, “oral swab”, “community screening”, “household contacts”, “active case finding”, “sputum scarce”, “asymptomatic”, “subclinical”, “PCR”, “qPCR”, and “Xpert”. Community-based screening studies, including household contact investigations, have reported microbiologically detectable TB outside routine facility-based pathways, including among people without symptoms and among those unable to produce sputum. Previous studies and systematic reviews showed that tongue swab testing can detect Mycobacterium tuberculosis with high specificity but only moderate sensitivity, generally lower than sputum-based molecular testing and often weaker in paucibacillary and asymptomatic disease. However, the recent evaluation of the near-point-of-care Pluslife MiniDock MTB platform using sputum and tongue swabs met WHO diagnostic accuracy targets for tuberculosis detection. Recent multi-country and in-home prospective tongue swab studies suggested feasibility and diagnostic potential. However, evidence remained limited on centralized workflows, non-refrigerated transport of community-collected swabs, operational implementation indicators, and the incremental contribution of tongue swabs to microbiological case detection in sputum-scarce populations outside traditional clinic-based settings. Added value of this study: This study evaluates centralized qPCR testing of community-collected tongue swabs among adult household contacts of people receiving treatment for pulmonary TB in Eastern Cape, South Africa. Relative to paired sputum Xpert MTB/RIF Ultra, tongue-swab qPCR had sensitivity of 60.9%, specificity of 95·2%, and overall agreement of 92·3%. Across screening strategies, 64 participants were microbiologically detected with TB; 51 were identified by tongue swabs and 29 by sputum, with overlap between modalities. Incorporating tongue swab testing for sputum-scarce participants identified 25 additional people with TB beyond symptom-agnostic sputum testing alone, increasing TB detection by 86·2%. Operationally, tongue swabs were collected from 99·1% of participants, the median shipment-to-receipt time was 47·5 hours, specimen loss during transport was 2·3%, and valid molecular results were generated for 93·8% of participants that provided a tongue swab specimen. To our knowledge, no previous study has combined community-based tongue swab collection, ambient transport, centralized batch qPCR testing, diagnostic performance evaluation, diagnostic-yield comparisons, and operational implementation measures in this population. Implications of all the available evidence: The available evidence suggests that tongue swabs should be considered not only as an alternative specimen, but also as a programmatic access strategy for microbiological TB testing outside traditional health facilities. Centralized high-throughput tongue swab testing workflows could strengthen community-based screening by extending microbiological testing to asymptomatic and sputum-scarce populations who are not found in traditional health system settings and are often missed by sputum-dependent pathways. Priorities for future research include improving assay sensitivity, evaluating cost-effectiveness and health-system integration, assessing prospective effects on treatment initiation and transmission, and determining generalizability across populations, platforms, and settings.

The COVID-19 pandemic led to significantly disrupted tuberculosis case detection and management. Additionally, overlapping symptoms, radiological findings and risk factors make differentiating tuberculosis and COVID-19 disease difficult. We conducted a prospective multicentre diagnostic accuracy study to determine sensitivity, specificity and operational characteristics of the Truenat MTB Ultima/COVID-19 assay, using a combined sputum plus nasopharyngeal swab specimen, in a single multiplex molecular assay. Participants were consenting adults with presumptive tuberculosis enrolled via convenience sampling from Uganda, Peru, South Africa, and India between August 2022 and December 2023. A microbiological reference standard of sputum GeneXpert MTB/RIF Ultra and culture was used for tuberculosis, whereas national RT-PCR was used for COVID-19. Wilson’s score method was used to determine the sensitivity and specificity. Of 1,928 participants enrolled, median age was 38 years (IQR 28–50), 359/1928 (18.6%) previously had TB, and 287/1928 (14.9%) were HIV-positive. Overall prevalence of tuberculosis was 24.8% [95% CI 22.9-26.8%]. Prevalence of COVID-19 was 3.8% [3.1-4.8%] overall, and 4.7% [3.1-7.0%] in those with confirmed tuberculosis. Overall sensitivity of Truenat MTB Ultima/COVID-19 for tuberculosis was 79.8% [95% CI 76.0-83.2%]. When comparing paired samples, Truenat MTB Ultima/COVID-19 had a 9.5% [6.5-13.1%] decreased sensitivity against sputum TB culture, compared to GeneXpert Ultra; (82.8% [78.9-86.1%] vs 92.4% [89.4-94.5%]). Overall specificity of Truenat MTB Ultima/COVID-19 for tuberculosis was 98.9% [98.2-99.3%]. For COVID-19 detection, sensitivity of Truenat MTB Ultima/COVID-19 was 64.4% [52.9-74.4%], with specificity of 99.2% [98.7-99.5%]. Although optimal diagnostic performance was not demonstrated, the potential and need for rapid development of tests that integrate tuberculosis diagnosis with detection of other relevant respiratory infections is highlighted. The study was registered on ClinicalTrials.gov (NCT05405296).

Tuberculosis (TB) is a global health threat complicated by increasing INH resistance (INH-R) and rifampicin resistance (RIF-R), including RIF-R due to rpoB Ile491Phe (I491F) mutations, which are not detected by current molecular resistance tests. We developed a low‐complexity automated nucleic acid amplification test MDRmDx, designed to operate on the 10-color GeneXpert instrument, which detects Mycobacterium tuberculosis (MTB), and RIF-R in both the rifampicin resistance determining region (RRDR) and the I491F allele, and INH-R due to mutations in katG , fabG1 , and the inhA promoter directly from sputum. In an analytic study, the limit of detection (LoD) for detecting MTB in sputum was 21.6 CFU/mL (95% confidence interval [CI]: 14.9–28.3) for the MDRmDx assay, versus 19.1 CFU/mL (95% CI: 14.0–24.1) for the Xpert MTB/RIF Ultra assay (Ultra). The LoD for rifampicin susceptibility (RIF-S) detection was 108.8 CFU/mL (95% CI: 77.4–140.2) versus 100.9 CFU/mL (95% CI: 67.3–134.5) for MDRmDx versus Ultra. The LoD for INH susceptibility detection was 92.2 CFU/mL (95% CI: 65.3–119.1). MDRmDx identified all rpoB mutations with a ≥0.5% global prevalence, including several not detected by Ultra. MDRmDx was 100% specific. Testing frozen sputum enriched for smear-negative, RIF-R, and INH-R samples, MDRmDx sensitivity was 91.3% (95% CI: 85.6–94.8) for MTB detection, 100% (95% CI: 95.1–100) for RIF resistance, and 98.7% (95% CI: 93.0–99.8) for INH resistance, with a specificity of 98.0% (95% CI: 89.3–99.6) for MTB detection, 93.8% (95% CI: 83.2–97.9) for RIF resistance, performance comparable to Ultra. MDRmDx specificity for INH-R was 100% (95% CI: 90.8–100). IMPORTANCE: The Xpert MTB/RIF Ultra assay (Ultra) is a gold standard test for rapidly diagnosing tuberculosis (TB) as well as resistance to rifampicin directly from sputum samples. However, the Ultra assay does not detect certain rifampicin resistance mutations, which are observed clinically and cannot detect resistance to isoniazid, another key drug against TB. We modified the Ultra assay, creating a prototype MDRmDx assay designed for 10-color instruments that detects isoniazid resistance, which can be a precursor of potential rifampicin resistance and has improved ability to detect rifampicin resistance. In both analytic and retrospectively collected clinical sputum samples, we found that the MDRmDx assay performed at least as well as the Ultra assay with the additional advantage of detecting isoniazid resistance and rpoB I491F mutations with high sensitivity and specificity. The MDRmDx assay's improved performance should improve detection of drug-resistant TB and facilitate the selection of effective treatment.

Background: Identifying risk factors for Mycobacterium tuberculosis (Mtb) sensitization (defined as interferon-gamma release assays [IGRA]-positive) and progression to tuberculosis (TB) disease is critical to guide targeted prevention strategies. Methods: We analyzed data from a prospective cohort of adults (18–60 years) without HIV, enrolled at five high-incidence South African sites. Participants underwent testing for Mtb sensitization and microbiologically confirmed TB at baseline, and during 15 months follow-up. Multivariable logistic and Cox regression models were used to assess factors associated with Mtb sensitization and TB progression. Sampling weights were applied to reflect the screened population. Results: Among 2912 participants with valid IGRA results, 63.4% (n = 1895) were Mtb-sensitized. Prevalent TB was detected in 1.81% (62/1895) of Mtb-sensitized vs 0.62% (12/1017) of Mtb-unsensitized individuals (P = .01). During follow-up of participants without prevalent TB, 2.01% (48/1833) Mtb-sensitized and 0.53% (8/1005) Mtb-unsensitized individuals developed TB (P = .01). Factors associated with Mtb sensitization included increasing age (adjusted odds ratio [aOR] = 1.02, 95% CI 1.01–1.03), male sex (aOR = 1.34, 95% CI 1.08–1.67), smoking (aOR = 1.31, 95% CI 1.05–1.64), prior TB (aOR = 2.20, 95% CI 1.40–3.47), and TB contact history (aOR = 1.40, 95% CI 1.08–1.83). Risk factors for progression to TB were Mtb sensitization (adjusted hazard ratio [aHR] = 3.05, 95% CI 1.14–8.18), smoking history (aHR = 2.34, 95% CI 1.03–5.31), and lower body mass index (BMI) (aHR = 0.89, 95% CI .82–.97). Conclusions: Mtb-sensitized individuals had a 3-fold higher risk of prevalent TB and progressing to TB compared to Mtb-unsensitized individuals. In high-prevalence settings, identifying individuals at greatest risk—such as those recently infected, with a history of smoking, or low BMI—could help refine TB prevention efforts and reduce community-level transmission.

Background: Household contact investigation for tuberculosis (TB) is limited by referral for clinic-based testing services. We evaluated the performance of in-home tongue swab (TS) testing among symptom-agnostic household contacts (HCC) to inform HCI screening strategies. Methods: We conducted a prospective cohort study among HHC of TB patients in Eastern Cape, South Africa. In-home testing of sputum and TSs, with TSs pooled from up to three HHCs, was performed using Xpert Ultra on portable GeneExpert devices. Outcomes included diagnostic performance of TS testing relative to sputum and linkage-to-care outcomes. Findings: Between June 2021 and October 2024, 909 HHC were enrolled; 99·1% provided s TS, 31·6% provided sputum. Overall sensitivity and specificity of TS testing was 61·9% (95% CI: 38·4%–81·9%) and 100% (98·9%–100%), respectively; sensitivity was 100% (47·8%–100%) for individually tested swabs. Among two-swab and three-swab pools where ³1 individual was sputum positive, 55·6% (21·2%–86·3%) and 42·9% (9·9%–81·6%) tested positive, respectively; TS sensitivity declined with decreasing sputum Ultra semi-quantitative category. 27 of 439 (6·2%) households had an indictation of secondary TB; 13 (3·0%) by sputum and TS, 11 (2·5%) by sputum only, 3 (0·7%) by TS only. Sputum testing identified 29 HHC with TB (yield=3·2%); 25/29 (86·2%) linked to care (median 1 day [IQR 1–2]). Interpretation: While in-home molecular testing of sputum supported rapid linkage-to-care, and TSs enabled near-universal testing of symptom-agnostic HHCs, efficiency gains through pooled TS testing must be balance against sensitivity trade-offs.

The COVID-19 pandemic led to significantly disrupted tuberculosis case detection and management. Additionally, overlapping symptoms, radiological findings and risk factors make differentiating tuberculosis and COVID-19 disease difficult. We conducted a prospective multicentre diagnostic accuracy study to determine sensitivity, specificity and operational characteristics of the Truenat MTB Ultima/COVID-19 assay, using a combined sputum plus nasopharyngeal swab specimen, in a single multiplex molecular assay. Participants were consenting adults with presumptive tuberculosis enrolled via convenience sampling from Uganda, Peru, South Africa, and India between August 2022 and December 2023. A microbiological reference standard of sputum GeneXpert MTB/RIF Ultra and culture was used for tuberculosis, whereas national RT-PCR was used for COVID-19. Wilson’s score method was used to determine the sensitivity and specificity. Of 1928 participants enrolled, median age was 38 years (IQR 28-50), 359/1928 (18.6%) previously had TB, and 287/1928 (14.9%) were HIV-positive. Overall prevalence of tuberculosis was 24.8% [95% CI 22.9-26.8%]. Prevalence of COVID-19 was 3.8% [3.1-4.8%] overall, and 4.7% [3.1-7.0%] in those with confirmed tuberculosis. Overall sensitivity of Truenat MTB Ultima/COVID-19 for tuberculosis was 79.8% [95% CI 76.0-83.2%]. When comparing paired samples, Truenat MTB Ultima/COVID-19 had a 9.5% [6.5-13.1%] decreased sensitivity against sputum TB culture, compared to GeneXpert Ultra; (82.8% [ 78.9-86.1%] vs 92.4% [89.4-94.5%]). Overall specificity of Truenat MTB Ultima/COVID-19 for tuberculosis was 98.9% [98.2-99.3%]. For COVID-19 detection, sensitivity of Truenat MTB Ultima/COVID-19 was 64.4% [52.9-74.4%], with specificity of 99.2% [98.7-99.5%]. Although optimal diagnostic performance was not demonstrated, the potential and need for rapid development of tests that integrate tuberculosis diagnosis with detection of other relevant respiratory infections is highlighted. The study was registered on ClinicalTrials.gov ( NCT05405296 ).

Background: Delayed and missed diagnoses are a persistent barrier to tuberculosis (TB) control, driven by difficulties collecting sputum and an unmet need for decentralized testing. Household contact investigation with point-of-care (POC) testing of noninvasive specimens may offer a cost-effective solution to strengthen active case finding. Methods: In-home molecular POC testing was conducted using sputum and tongue specimens collected from household contacts of people with confirmed TB residing in South Africa. A health economic assessment was executed to estimate and compare the cost and cost-effectiveness of different in-home POC testing strategies against centralized sputum testing (standard of care) from a provider's perspective. The primary cost-effectiveness outcome was measured as the incremental cost per additional household contact with TB detected and linked to treatment. Decision analytic modeling was used to estimate and compare incremental cost-effectiveness ratios across strategies. Results: The total implementation cost of delivering the standard of care to 300 households over a 2-year period was $85 188. Strategies that integrated in-home POC testing ranged from $88 672 to $97 271. The cost per test for in-home POC sputum testing was the highest at $20.08. Two strategies, POC sputum testing and POC combined sputum and individual tongue swab testing, were the most cost-effective with incremental cost-effectiveness ratios of $641 and $775, respectively, both below a $2760 willingness-to-pay threshold. Conclusions: In-home POC molecular TB testing strategies that use combination testing of tongue swabs and sputum specimens can meaningfully improve the number of people tested, diagnosed, and notified during household contact investigation while being cost-effective.

Background: Tuberculosis (TB) remains a major public health problem globally, as reflected in persistently high morbidity and mortality rates. Current control efforts have been further complicated by the ongoing SARS-CoV-2 (COVID-19) pandemic. Rapid molecular diagnostics remain crucial to identifying the millions of people with undiagnosed TB.Objectives: The study aimed to determine the diagnostic accuracy of Truenat MTB Ultima/COVID-19 for the detection of COVID-19 and TB among presumptive TB participants, using a microbiological reference standard (MRS) and a country-approved real-time reverse transcription polymerase chain reaction (RT-PCR) COVID-19 assay.Methods: This prospective cohort study assessed the diagnostic accuracy of the Truenat MTB Ultima/COVID-19 multiplex test among adults with presumptive TB, enrolled from healthcare facilities in four countries, aiming to reach 270 confirmed TB cases. The inclusion criteria were as follows: adults who self-reported at least one symptom suggestive of pulmonary TB, were willing to return for a day 2 visit, and agreed to provide oral swab samples for bio-banking. Patients were excluded from enrolment in the study if they had started anti-TB treatment within 60 days or TB preventive therapy within 6 months prior to enrolment or if they were unable to provide 3 mL of sputum or nasopharyngeal (NP) and tongue swab samples.Expected outcome: This study expected to obtain point estimates of the sensitivity and specificity of the Truenat MTB Ultima/COVID-19 multiplex test for TB and COVID-19 detection, compared to Xpert Ultra, among presumptive TB participants using an MRS and pre-defined COVID-19 assay.