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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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“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
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“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
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In the citing paper
“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
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“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
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“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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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
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
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
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
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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
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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
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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
Accelerating extrapulmonary tuberculosis diagnosis with a rapid molecular assay
Guillet-Caruba, C., Bénet, C., Jmel, H., Doucet‐Populaire, F., & Bourgeois‐Nicolaos, N. (2025) · Microbiology Spectrum · doi:10.1128/spectrum.00104-25 · Cited by 5
“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
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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
“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…”
Tian, Y., Deng, M., Wang, Y., Duan, B., Chen, Q., Fang, Z. A., Li, Q., Zhou, G., Chen, H., & Wang, Q. (2025) · Scientific Reports · doi:10.1038/s41598-025-90391-8 · Cited by 4
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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
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“However, data on its use for diagnosing extrapulmonary TB, especially TBM, are scarce [13–15].”
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“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
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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].”
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Fatal tuberculous meningitis in an infant presenting with seizures in the UK
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Diagnosing tuberculous meningitis: a testing process
Donovan, J., & Walker, T. M. (2021) · The International Journal of Tuberculosis and Lung Disease · doi:10.5588/ijtld.21.0303 · Cited by 2
Bakterielle Meningitis und Neurotuberkulose
Klein, M. (2022) · Neurologie up2date · doi:10.1055/a-1716-7500 · Cited by 1
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
Challenges and advancements in the diagnosis of central nervous system tuberculosis
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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
“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].”
Metadata
- 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
- 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 › Infectious Diseases › 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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