Xpert MTB/RIF Ultra for the diagnosis of HIV-associated tuberculous meningitis: a prospective validation study
Open accessAbstract
INTRODUCTION: Tuberculous meningitis accounts for 1-5% of tuberculosis cases. Diagnostic delay contributes to poor outcomes. We evaluated the performance of the new Xpert MTB/RIF Ultra (Xpert Ultra) for tuberculous meningitis diagnosis. METHODS: In this prospective validation study, we tested the cerebrospinal fluid (CSF) of adults presenting with suspected meningitis (ie, headache or altered mental status with clinical signs of meningism) to the Mulago National Referral Hospital and Mbarara Regional Referral Hospital in Uganda. We centrifuged the CSF, resuspended the cell pellet in 2 mL CSF, and tested 0·5 mL aliquots with Xpert Ultra, Xpert MTB/RIF (Xpert), and mycobacterial growth indicator tube (MGIT) culture. We quantified diagnostic performance against the uniform case definition of probable or definite tuberculous meningitis and a composite microbiological reference standard. FINDINGS: From Nov 25, 2016, to Jan 24, 2019, we screened 466 adults with suspected meningitis and tested 204 for tuberculous meningitis. Uniform clinical case definition classified 51 participants as having probable or definite tuberculous meningitis. Against this uniform case definition, Xpert Ultra had 76·5% sensitivity (95% CI 62·5-87·2; 39 of 51 patients) and a negative predictive value of 92·7% (87·6-96·2; 153 of 165), compared with 55·6% sensitivity (44·0-70·4; 25 of 45; p=0·0010) and a negative predictive value of 85·8% (78·9-91·1; 121 of 141) for Xpert and 61·4% sensitivity (45·5-75·6; 27 of 44; p=0·020) and negative predictive value of 85·2% (77·4-91·1; 98 of 115) for MGIT culture. Against the composite microbiological reference standard, Xpert Ultra had sensitivity of 92·9% (80·5-98·5; 39 of 42), higher than Xpert at 65·8% (48·6-80·4; 25 of 38; p=0·0063) and MGIT culture at 72·2% (55·9-86·2; 27 of 37; p=0·092). Xpert Ultra detected nine tuberculous meningitis cases missed by Xpert and MGIT culture. INTERPRETATION: Xpert Ultra detected tuberculous meningitis with higher sensitivity than Xpert and MGIT culture in this HIV-positive population. However, with a negative predictive value of 93%, Xpert Ultra cannot be used as a rule-out test. Clinical judgment and novel highly sensitive point-of-care tests are still required. FUNDING: Wellcome Trust, National Institute of Health, National Institute of Neurologic Diseases and Stroke, Fogarty International Center, and National Institute of Allergy and Infectious Diseases.
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In people living with HIV, Xpert MTB/RIF sensitivity in Cresswell 2020 was 70% (95% CI 50 to 86).
“Sensitivity (95% CI) was 90% (55 to 100) (Bahr 2017) and 89% (71 to 98) (Cresswell 2020) for Xpert Ultra and 60% (26 to 88) (Bahr 2017) and 70% (50 to 86) (Cresswell 2020) for Xpert MTB/RIF.”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Cresswell 2020
The Results section (Diagnostic performance; page unavailable) reports Xpert MTB/RIF sensitivity of 56% against the uniform case definition and 66% against the composite microbiological reference standard, not 70%. The cited 95% CI of 50–86 is not given in the passages from our copy. (LLM, conf=0.88)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredIn people living with HIV, Xpert Ultra sensitivity in Cresswell 2020 was 89% (95% CI 71 to 98).
“Sensitivity (95% CI) was 90% (55 to 100) (Bahr 2017) and 89% (71 to 98) (Cresswell 2020) for Xpert Ultra and 60% (26 to 88) (Bahr 2017) and 70% (50 to 86) (Cresswell 2020) for Xpert MTB/RIF.”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Cresswell 2020
The Results section (Diagnostic performance; page unavailable) reports Xpert Ultra sensitivity of 76% against the uniform clinical case definition and 93% against the composite microbiological reference standard in this HIV-positive cohort. It does not report the attributed 89% (95% CI 71–98) for either reference standard. (LLM, conf=0.86)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredIn people living with HIV, Xpert MTB/RIF specificity in Cresswell 2020 was 97% (95% CI 93 to 99).
“Specificity (95% CI) was 90% (83 to 95) (Bahr 2017) and 92% (86 to 95) (Cresswell 2020) for Xpert Ultra and 97% (95% CI 92 to 99) (Bahr 2017) and 97% (93 to 99) (Cresswell 2020) for Xpert MTB/RIF; Figure 11.”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Cresswell 2020
The Results, under Diagnostic performance (page unavailable), report Xpert MTB/RIF sensitivity but give no Xpert specificity estimate or confidence interval. A search for specificity found 100% specificity for Ultra in the Negative controls section, not the claimed 97% (95% CI 93–99) for Xpert. Our copy therefore does not verify the attributed figure. (LLM, conf=0.73)
Experimental — accuracy not yet measuredIn people living with HIV, Xpert Ultra specificity in Cresswell 2020 was 92% (95% CI 86 to 95).
“Specificity (95% CI) was 90% (83 to 95) (Bahr 2017) and 92% (86 to 95) (Cresswell 2020) for Xpert Ultra and 97% (95% CI 92 to 99) (Bahr 2017) and 97% (93 to 99) (Cresswell 2020) for Xpert MTB/RIF; Figure 11.”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Cresswell 2020
The Results’ Diagnostic performance section reports sensitivity and negative predictive value, but not the claimed 92% specificity or its 95% CI. A separate Negative controls section reports 100% specificity among 45 participants with cryptococcal meningitis; that subgroup result does not establish or contradict the claimed estimate. Searches for “specificity” and “86-95” found no matching estimate in our copy. (LLM, conf=0.72)
Experimental — accuracy not yet measured
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“The rapid molecular test, Xpert Mycobacterium tuberculosis/rifampicin (MTB/ RIF), is an important diagnostic test for all forms of TB, and next-generation Xpert MTB/RIF Ultra (Xpert Ultra) has a sensitivity of 44% to 77% and specificity approaching 100% in CSF of adults with TB meningitis [40, 41].”
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Diagnostic and therapeutic approach to chronic meningitis in Brazil: a narrative review
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Advances in tuberculous meningitis diagnosis
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Value of next-generation sequencing in early diagnosis of patients with tuberculous meningitis
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Efficacy of Xpert MTB/RIF Ultra in diagnosing tuberculosis meningitis
Shen, Y., Yu, G., Zhao, W., & Lang, Y. (2021) · Medicine · doi:10.1097/md.0000000000026778 · Cited by 19 · see citing works
“Most of the studies agreed that the Xpert Ultra is more sensitive than the Xpert statistically,([21,28,29]) but another study reported otherwise.”
BackgroundResultTuberculosis of the spinal cord
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CSF Metabolomics of Tuberculous Meningitis: A Review
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New management approaches to tuberculosis in people living with HIV
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Extremely high levels of central nervous system involvement in miliary tuberculosis
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“Patients underwent lumbar puncture as part of the screening process for three clinical trials (34–36) and an observational cohort focused on meningitis diagnostics (9).”
BackgroundMethodDiagnostic Accuracy of T-SPOT.TB Assay for Tuberculous Meningitis: An Updated Meta-Analysis
Luo, Y., Xue, Y., Guo, X., Lin, Q., Mao, L., Tang, G., Song, H., Wang, F., & Sun, Z. (2020) · Frontiers in Neurology · doi:10.3389/fneur.2020.00866 · Cited by 15 · see citing works
Diagnostic tests for tuberculous meningitis
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“The improved sensitivity is crucial in settings with a high prevalence of HIV co-infection [23].”
Martyn, E. M., Bangdiwala, A. S., Kagimu, E., Rutakingirwa, M. K., Kasibante, J., Okirwoth, M., Stead, G., Wadda, V., Pullen, M. F., Bold, T. D., et al. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa1444 · Cited by 14 · see citing works
“We have recently shown that the Xpert Ultra semi-quantitative category correlates with days to CSF culture positivity [8].”
BackgroundCao, W.-F., Leng, E.-L., Liu, S., Zhou, Y.-L., Luo, C.-Q., Xiang, Z.-B., Cai, W., Rao, W., Hu, F., Zhang, P., et al. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1202752 · Cited by 13 · see citing works
“Results are quick, with a turn-around time within 2 h compared to 2–3 weeks with culture methods (Kohli et al., 2018; Cresswell et al., 2020).”
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Milburn, J., Suresh, R., Doyle, R., & Jarvis, J. N. (2024) · Expert Review of Molecular Diagnostics · doi:10.1080/14737159.2024.2317414 · Cited by 12 · see citing works
“Tuberculous meningitis (TBM) is the most severe form of tuberculosis (TB) and is a leading cause of meningitis in resource-limited, high HIV-prevalence settings [4,17,38,39].”
BackgroundMethodResultInfluentialRahman, S. M. M., Nasrin, R., Kabir, S., Kabir, F., Rahman, M. A., Uddin, M. K. M., Islam, A. S. M. I., Khatun, R., Ahmed, S., Mondal, M. B. A., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-97664-2 · Cited by 9 · see citing works
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Krishnakumariamma, K., Ellappan, K., Muthuraj, M., Tamilarasu, K., Kumar, S. V., & Joseph, N. M. (2023) · Indian Journal of Medical Microbiology · doi:10.1016/j.ijmmb.2022.12.012 · Cited by 8 · see citing works
Sharma, K., Sharma, M., Modi, M., Goyal, M., Sharma, A., & Ray, P. (2020) · Molecular and Cellular Probes · doi:10.1016/j.mcp.2020.101595 · Cited by 8 · see citing works
Lin, Y., Zhang, W., Xiong, Y., Wang, Y., Yu, Q., Ma, Y., & Xie, Y. (2023) · Diagnostic Microbiology and Infectious Disease · doi:10.1016/j.diagmicrobio.2023.116025 · Cited by 10 · see citing works
Advancing Diagnosis and Treatment in People Living with HIV and Tuberculosis Meningitis
Kimuda, S., Kasozi, D., Namombwe, S., Gakuru, J., Mugabi, T., Kagimu, E., Rutakingirwa, M. K., Leon, K. E., Chow, F. C., Wasserman, S. A., et al. (2023) · Current HIV/AIDS Reports · doi:10.1007/s11904-023-00678-6 · Cited by 7 · see citing works
Bresges, C., Wilson, D., Fielding, K., Corbett, E. L., Del-Greco, F., Grint, D. J., Peters, J. A., & Gupta‐Wright, A. (2021) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofab162 · Cited by 7 · see citing works
Neurocognitive outcomes of HIV-associated tuberculous meningitis
Quinn, C. M., Kasibante, J., Namudde, A., Bangdiwala, A. S., Kabahubya, M., Nakasujja, N., Lofgren, S. M., Elliott, A. M., Boulware, D. R., Meya, D. B., et al. (2021) · Wellcome Open Research · doi:10.12688/wellcomeopenres.16967.1 · Cited by 7 · see citing works
Kohli, M., Inbaraj, L. R., Salomon, A., Scandrett, K., Korobitsyn, A., Ismail, N. A., Srinivasalu, V. A., Daniel, J., Steingart, K. R., & Takwoingi, Y. (2025) · Cochrane Database of Systematic Reviews · doi:10.1002/14651858.cd012768.pub4 · Cited by 6 · see citing works
Sporothrix brasiliensis meningitis in an immunocompetent patient
Lima, M. A., Vallier, R., & Silva, M. M. (2021) · Practical Neurology · doi:10.1136/practneurol-2020-002915 · Cited by 6 · see citing works
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Recent Developments in Tuberculous Meningitis Pathogenesis and Diagnostics
Cresswell, F. V., Davis, A., Sharma, K., Roy, R. B., Ganiem, A. R., Kagimu, E., Solomons, R., Wilkinson, R. J., Bahr, N. C., & Thương, N. T. T. (2020) · Wellcome Open Research · doi:10.12688/wellcomeopenres.15506.2 · Cited by 7 · see citing works
Accelerating extrapulmonary tuberculosis diagnosis with a rapid molecular assay
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“Invalid results were considered and classified negative (17, 18).”
CSF carnitine is a potential biomarker in paediatric tuberculous meningitis
Plaatjie, O. N., van Furth, A. M., Solomons, R., van der Kuip, M., & Mason, S. (2025) · Scientific Reports · doi:10.1038/s41598-025-15000-0 · Cited by 5 · see citing works
Ellis, J. P., Dai, B., Kabahubya, M., Hale, G., Mande, E., Katende, G., Kagimu, E., Gakuru, J., Ndyetukira, J. F., Tukundane, A., et al. (2025) · AIDS · doi:10.1097/qad.0000000000004213 · Cited by 5 · see citing works
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Neurocognitive outcomes of tuberculous meningitis in a primarily HIV-positive Ugandan cohort
Quinn, C. M., Kasibante, J., Namudde, A., Bangdiwala, A. S., Kabahubya, M., Nakasujja, N., Lofgren, S. M., Elliott, A. M., Boulware, D. R., Meya, D. B., et al. (2022) · Wellcome Open Research · doi:10.12688/wellcomeopenres.16967.2 · Cited by 4 · see citing works
“Patients were enrolled in the parent trial between January 14 and December 17, 2019, at Kiruddu National Referral Hospital in Kampala, Uganda and Mbarara Regional Refer-ral Hospital in Mbarara, Uganda, based on detection of TB in the cerebrospinal fluid (CSF) by Xpert MTB/RIF Ultra (Cepheid, Sunnyvale, CA) 26 , or pre…”
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Cerebrospinal fluid lactate as a predictive biomarker for tuberculous meningitis diagnosis
de Almeida, S. M., Kussen, G. M. B., Cogo, L. L., & Nogueira, K. D. S. (2022) · Diagnosis · doi:10.1515/dx-2022-0102 · Cited by 4 · see citing works
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“However, data on its use for diagnosing extrapulmonary TB, especially TBM, are scarce [13–15].”
BackgroundNakao, J., Fujita, K., Ishii, K., Akutsu, Y., Hara, T., Kamezaki, T., & Ishikawa, E. (2022) · Acute Medicine & Surgery · doi:10.1002/ams2.727 · Cited by 3 · see citing works
Li, M., Yang, X., Zhou, Q., Wang, J., Wang, X., & Mao, L. (2024) · IDCases · doi:10.1016/j.idcr.2024.e02096 · Cited by 3 · see citing works
Ariza, E., Ello, F., Andriamamonjisoa, H., Machault, V., González-Martín, J., Calvo-Cortes, M.-C., Eholié, S. P., Tchabert, G. A., Ouassa, T., Raberahona, M., et al. (2022) · Infectious Diseases and Therapy · doi:10.1007/s40121-022-00667-z · Cited by 3 · see citing works
“sensitive Ultra version [14], and drug susceptibility testing (DST) for pyrazinamide was introduced.”
BackgroundAn autopsy case of tuberculous meningitis undiagnosed by nested-PCR of CSF samples and brain biopsy
Kitazaki, Y., Ikawa, M., Enomoto, S., Shirafuji, N., Hayashi, K., Yamamura, O., Yamada, S., Arishima, H., Noriki, S., Nakamoto, Y., et al. (2020) · Journal of the Neurological Sciences · doi:10.1016/j.jns.2020.116968 · Cited by 3 · see citing works
Mitha, M., Pillay, M., Moodley, J., Balakrishna, Y., Abbai, N. S., Bhagwan, S., Dangor, Z., & Bhigjee, A. I. (2020) · Southern African Journal of Infectious Diseases · doi:10.4102/sajid.v35i1.135 · Cited by 3 · see citing works
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Pathophysiology of intracranial hypertension in cryptococcal meningoencephalitis
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“For comparison, reported tuberculous meningitis bacillary counts in CSF are lower, approximately 10 2 –10 3 CFU/mL, while bacterial meningitis spans a wide range (~10 3 –10 9 CFU/mL), though the cells are smaller (44, 45).”
Tuberculous meningitis in Bhubaneswar, Odisha, during 2016 to 2022
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“%) of Xpert Ultra results where DNA was detected in CSF were trace readouts (and only 6 of the 14 trace readouts were positive by culture) [28].”
Wang, C., Sun, L., Li, Q., & Lu, H. (2022) · Drug Discoveries & Therapeutics · doi:10.5582/ddt.2022.01082 · Cited by 2 · see citing works
Fatal tuberculous meningitis in an infant presenting with seizures in the UK
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Diagnosing tuberculous meningitis: a testing process
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Bakterielle Meningitis und Neurotuberkulose
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Diagnostic Prediction Model for Tuberculous Meningitis: An Individual Participant Data Meta-Analysis
Stadelman, A., Tiffin, N., Ellis, J. P., Cresswell, F. V., Ssebambulidde, K., Nuwagira, E., Richards, L., Lutje, V., Hristea, A., Jipa, R. E., et al. (2024) · American Journal of Tropical Medicine and Hygiene · doi:10.4269/ajtmh.23-0789 · Cited by 3 · see citing works
Challenges and advancements in the diagnosis of central nervous system tuberculosis
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Liang, L., Su, S., Peng, L., Zhuang, H., Chen, Y., & Cao, Y. (2026) · Microbial Pathogenesis · doi:10.1016/j.micpath.2026.108408 · Cited by 1 · see citing works
Boschung, K. F., Wong, P. H. P., Werry, D., Sekirov, I., Turvey, S. L., Cook, V. J., Johnston, J. C., & Connors, W. J. A. (2026) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofag046 · Cited by 1 · see citing works
“Importantly, while CSF culture is often the reference standard for TBM diagnosis, Xpert Ultra can detect MTB in culture-negative cases, with 1 study noting that 6 of 21 Xpert Ultra-positive TBM cases were CSF culture negative [12, 14].”
- Authors
- Cresswell, F. V., Tugume, L., Bahr, N. C., Kwizera, R., Bangdiwala, A. S., Musubire, A. K., Rutakingirwa, M., Kagimu, E., Nuwagira, E., Mpoza, E., Rhein, J., Williams, D. A., Muzoora, C., Grint, D., Elliott, A. M., Meya, D. B., & Boulware, D. R.
- Affiliations
- London School of Hygiene & Tropical Medicine (GB)
- Infectious Diseases Institute (UG)
- University of Kansas (US)
- University of Minnesota (US)
- Mbarara University of Science and Technology (UG)
- Corresponding author
- Cresswell, Fiona V
- ORCID
- Venue
- The Lancet Infectious Diseases
- Publisher
- Elsevier BV
- Published
- 2020-03
- Volume
- 20
- Issue
- 3
- Pages
- 308-317
- ISSN
- 1473-3099 (ISSN-L)
- PMC
- PMC7045085
- OpenAlex
- W2998865775
- Cited by
- 124
- References
- 26
- Citations by year
- 2026: 12 · 2025: 14 · 2024: 11 · 2023: 16 · 2022: 22 · 2021: 22 · 2020: 26 · 2019: 1
- FWCI
- 19.64
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- The Lancet Infectious Diseases (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
- Funders
- National Institute of Allergy and Infectious Diseases (T32AI055433)
- Fogarty International Center (K01TW010268, K43TW010718)
- National Institute of Neurological Disorders and Stroke (K23NS110470, R01NS086312)
- Wellcome Trust (210772/Z/18/Z)
- European Commission
- European and Developing Countries Clinical Trials Partnership
- African Academy of Sciences
- Medical Research Council
- Department for International Development, UK Government
- Topics
- Health Sciences › Medicine › Surgery › Infectious Diseases and Tuberculosis
- Health Sciences › Medicine › Infectious Diseases › Tuberculosis Research and Epidemiology
- Life Sciences › Immunology and Microbiology › Microbiology › Bacterial Infections and Vaccines
- Keywords
- tuberculous meningitis, HIV-associated tuberculosis, Xpert MTB/RIF Ultra, Xpert MTB/RIF, cerebrospinal fluid, sensitivity and specificity, molecular diagnosis, delayed diagnosis, Uganda, meningitis diagnosis, case definition, negative predictive value, resource-limited settings
- MeSH terms
- Cerebrospinal Fluid, Hospitals, Humans, Mycobacterium tuberculosis, Predictive Value of Tests, Sensitivity and Specificity, Tuberculosis, Meningeal, Uganda, HIV Infections, Tuberculosis, Multidrug-Resistant, Molecular Diagnostic Techniques
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