The impact of GeneXpert cerebrospinal fluid testing on tuberculous meningitis diagnosis in routine care in Botswana

Introduction Tuberculous meningitis (TBM) disproportionately impacts high-HIV prevalence, resource-limited settings where diagnosis is challenging. The GeneXpert platform has utility in TBM diagnosis but uptake remains limited. In Botswana, prior to the introduction of GeneXpert, TB testing was only available through mycobacterial culture at the National TB Reference Laboratory. Data describing routine use of Xpert MTB/RIF for CSF testing in resource-limited settings are scarce. Methods Electronic records for patients with CSF tested in government facilities in Botswana between 2016-2022 were obtained from a central online repository as part of ongoing national meningitis surveillance. Samples were excluded from one site where Xpert MTB/RIF is performed universally. The proportion receiving TB-specific investigation on CSF and the number positive for Mycobacterium tuberculosis following increased Xpert MTB/RIF capacity were determined. Results The proportion of CSF samples receiving TB-specific investigation increased from 4.5% (58/1288) in 2016 to 29.0% (201/693) in 2022, primarily due to increased analysis with Xpert MTB/RIF from 0.9% (11/1288) to 23.2% (161/693). There was an overall decline in the annual number of CSF samples analysed but the proportion with microbiologically-confirmed TBM increased from 0.4% to 1.2%. The proportion of samples tested for TB that were collected from healthcare facilities >100km from the National TB Reference Laboratory increased with Xpert MTB/RIF rollout from 65.9% (87/132) to 78.0% (494/633). Discussion In Botswana access to TB culture is challenging in remote populations; more accessible near-patient testing using Xpert MTB/RIF increased the number of patients receiving TB-specific testing on CSF and the number of confirmed TBM cases.