Evaluation of New Biomarker-based Approaches for Improving the Diagnosis of Childhood Tuberculous Meningitis

Brief Title

Evaluation of New Biomarker-based Approaches for Improving the Diagnosis of Childhood Tuberculous Meningitis

Official Title

Evaluation of New Biomarker-based Approaches for Improving the Diagnosis of Childhood Tuberculous Meningitis

Brief Summary

      The rapid diagnosis of tuberculosis (TB) in children remains a serious challenge owing to
      limitations in the existing diagnostic tests. TB meningitis (TBM), an extrapulmonary form of
      TB, is the most severe manifestation of paediatric TB. TBM results in high morbidity and
      mortality in children, despite the availability of chemotherapy, mainly due to diagnostic
      delay. Most tests required for proper TBM diagnosis including analysis of cerebrospinal fluid
      (CSF) and brain imaging are not available in resource-limited settings e.g., in most of
      Africa including South Africa. New tests for TBM are urgently needed. The main goal of this
      proposal is to develop a point-of-care (POC) diagnostic test for TBM, based on CSF and

      Aim 1: Evaluate the diagnostic potentials of 51 host inflammatory biomarkers that the
      investigators recently identified in CSF and blood samples from children with suspected
      meningitis in a repository of 100 stored CSF and serum samples using a multiplex platform.
      After statistical analysis including multi-marker modelling by linear discriminant analysis,
      random forest, and other modelling techniques, the investigators will select the best
      combination of up to four biomarkers for incorporation into the prototype diagnostic test
      (Aim 2).

      Aim 2: Incorporate the best performing CSF and serum biomarkers into a novel, patented
      biosensor-based POC diagnostic test. The investigators will develop a multi-biomarker
      prototype test for detecting up to 4 biomarkers in serum or CSF.

      Aim 3: Evaluate the newly developed POC test on 300 children prospectively. This will be done
      at the Tygerberg Academic Hospital. The diagnostic yield of the POC test will be compared to
      the routine diagnostic tests.

Detailed Description

      IMPORTANCE AND RELEVANCE TO EDCTP2 Despite considerable ongoing efforts in the development of
      tools to combat tuberculosis (TB), the disease was responsible for approximately 1.6 million
      deaths, with 10 million people developing the disease worldwide in 2017 (1). An estimated one
      million children became ill with TB in 2017 (1, 2). Eight countries in Africa or Asia
      including South Africa, Nigeria, India, China, Indonesia, Philippines, Pakistan and
      Bangladesh accounted for two-thirds of the world's total burden of TB (1). The TB incidence
      in South Africa rose from 301 new cases/100,000 in 1990 to 948/100,000 in 2007 (3). The TB
      burden is worsened by the HIV pandemic, which is rampant in South Africa and other African
      countries. Tuberculous meningitis (TBM) is the most severe form of TB, occurs mostly during
      early childhood and has high morbidity and mortality, due to the delayed diagnosis and
      initiation of appropriate therapy (4). TBM is the most common type of bacterial meningitis in
      the Western Cape Province of South Africa (5).

      New TBM diagnostic tests are needed. Despite ongoing research, early and cost-effective
      diagnostic tools for TBM are lacking (6). The detection of Mycobacterium tuberculosis (Mtb)
      in cerebrospinal fluid (CSF) is the gold standard for diagnosing TBM. Unfortunately the
      sensitivity of both smear microscopy and culture for TBM is low (7, 8). Depending on the
      reference standard employed, the sensitivity of the GeneXpert test (Cepheid Inc, USA) for TBM
      is approximately 50-60%, and improved to 72% when centrifuged CSF was used in one study (9).
      In a more recently published study conducted on HIV positive adults, however, the GeneXpert
      performed with a sensitivity of 43% or 45%, compared to 43% or 45% for culture and 70% or 95%
      for the GeneXpert Ultra, depending on which of the two reference standards were used (10).
      Despite the relatively high roll-out of the GeneXpert test across South Africa, the test is
      currently mostly offered at centralised laboratories. The availability of the test in other
      African countries is limited. The diagnosis of TB relies on the poorly sensitive symptom
      screening and smear microscopy, especially at rural health centres. Mtb culture facilities
      are often only available at referral level laboratories and results might take up to 42 days.
      The need for multiple health care visits leads to loss of follow-up and delayed diagnosis,
      fuelling the spread of TB and advanced lung damage. In the case of TBM in particular, proper
      diagnosis is only made upon admission in a tertiary level referral center. In routine
      clinical practice, diagnosis is mostly based on a combination of clinical findings, multiple
      laboratory tests on the CSF, imaging findings and the exclusion of common differential
      diagnoses (11). Most of these techniques are unavailable in many high-burden, but
      resource-constrained settings in most of sub-Saharan Africa. Children seen at primary and
      secondary healthcare facilities often have multiple missed opportunities, up to six visits,
      before eventual diagnosis of TBM is made in a relatively well-resourced setting in South
      Africa (12). Findings from the CSF can be highly variable (13). Recently, international
      experts have proposed new uniform case definitions that should be employed in future research
      (14, 15) to replace the many different definitions in the literature (7, 8, 13, 16, 17). New
      tests are therefore urgently needed for the diagnosis of TBM.

      Point-of-care (POC) or bedside diagnostic tools are needed in Sub-Saharan Africa. Any new
      tests for TBM must be rapid, easy to perform at the POC or bedside, and suitable for use in
      resource-poor settings in African countries. Such tests should, therefore, preferably not use
      laboratory instruments that require specialists to operate. They should use portable battery-
      or solar-operated hand-held devices, suitable for use by nurses and community health workers
      (18). Diagnostics based on the human immune response may provide important additions, which
      are easily converted to POC or bedside diagnostic tools.

      Host CSF protein signatures as diagnostic candidates for TBM. The investigators investigated
      the potential of host markers detected in CSF samples from children suspected of having TBM
      as diagnostic candidates for TBM (19). The investigators evaluated the levels of the host
      biomarkers present in a standard BioPlex 27plex multiplex cytokine kit (Bio Rad Laboratories)
      and other protein biomarkers in CSF and serum samples. An unsupervised hierarchical
      clustering and principal component analysis, using the Glucore Omics explorer, revealed
      significant clustering of patients with TBM by the biomarkers detected in the CSF.

      A 3-marker host protein biosignature comprising vascular endothelial growth factor (VEGF),
      interleukin (IL)-13 and the antibacterial peptide cathelicidin, LL-37, showed potential as a
      diagnostic biosignature for TBM (international patent application: PCT/IB2015/052751) (19),
      diagnosing TBM with an area under the receiver operator characteristics curve (AUC) of 0.91,
      with sensitivity of 52%, but with good specificity of 95%. Since the publication of this
      biosignature, the investigators have evaluated the diagnostic potential of >70 host
      biomarkers in serum and plasma samples from adults suspected of having active pulmonary TB in
      5 different African countries (South Africa, Namibia, Malawi, Uganda and Ethiopia) in an
      EDCTP-funded trial (AE-TBC). The investigators identified, patented (PCT/IB2015/051435 and
      PCT/IB2017/052142), and published 6- and 7-marker protein biosignatures with strong
      diagnostic potential for TB (20, 21).

      In a more recent study (South African Provisional Patent application; Manyelo et al 2019, in
      press), the investigators hypothesized that at least some of the host biomarkers comprising
      our adult protein biosignatures may be useful for TBM diagnostics. Funded by the South
      African Technology Innovation Agency (PI: Chegou), the investigators prospectively enrolled a
      new cohort of children suspected of having TBM at the Tygerberg Academic Hospital, Western
      Cape, and determined the concentrations of 66 host biomarkers, in CSF samples from these
      children. The investigators also included the 3 biomarkers that comprised our previous CSF
      biosignature for TBM (VEGF, IL-13 and cathelicidin LL-37) (19) for validation purposes in
      this new study; a total of 69 host protein biomarkers.

      With the exception of VEGF (AUC of 0.81), the accuracy of the individual markers in the
      previous 3-marker signature was poor (AUCs of 0.58 and 0.55, respectively, for IL-13 and
      LL-37) but when used in combination the discrimination between TBM and no-TBM by the 3-marker
      model was confirmed [AUC of 0.67 (95% CI: 0.52-0.83); sensitivity of 75% and specificity of
      65%]. Forty-seven of the additional markers showed significant differences between the TBM
      and no TBM groups (Mann Whitney U test), with 28 showing strong diagnostic potential, even as
      individual markers (AUC ≥ 0.80). These markers include interferon (IFN)-γ, CCL18(MIP-4),
      CXCL9, CCL1, CCL5(RANTES), IL-6, tumour necrosis factor (TNF)-α, myeloperoxidase (MPO),
      matrix metalloproteinase 9 (MMP), MMP-8, complement C2 (CC2), IL-10, total plasminogen
      activator inhibitor 1 (PAI-1), CXCL8, IL-1β, alpha-2-antitrypsin(A1AT), CXCL10, granulocyte
      colony stimulating factor (G-CSF), CC4, CC4b, granulocyte-macrophage colony stimulating
      factor (GM-CSF), platelet-derived growth factor (PDGF)-AB/BB, apolipoprotein A1 (apoA1),
      mannose-binding lectin (MBL), ferritin, CC5a, serum amyloid P (SAP), and CC5.

      Combinations of these biomarkers were investigated and using Linear Discriminant Analysis
      (LDA) models. A 4-marker CSF biosignature comprising soluble intracellular adhesion molecule
      (sICAM)-1, MPO, CXCL8 and IFN-γ diagnosed TBM with an AUC of 0.97 (95% CI: 0.92-1.00), with a
      sensitivity of 87% (20/23) and specificity of 95.8% (23/24). After leave-one-out cross
      validation, there was no change in the sensitivity and specificity of the 4-marker
      biosignature. Further optimization of the 4-marker biosignature by the selection of better
      cut-off values resulted in a sensitivity and specificity of 96% and 96%, respectively.

      As VEGF performed well in single-marker analyses (19), the investigators evaluated the
      potential accuracy of other biosignatures that included VEGF. A 3-marker model comprising
      VEGF, IFN-γ and MPO discriminated with high accuracy between the children with and without
      TBM. In leave-one-out cross validation and optimizations of best cut-off values, the
      sensitivity and specificity of the 3-marker VEGF-based signature were 92% and 100%,

      Serum host protein signatures as diagnostic candidates for TBM. All 69 host markers
      investigated in CSF samples were also investigated on serum samples using the Luminex
      multiplex platform. The median serum levels of 17 analytes [sVCAM1, CCL2, IL-4, TNF-α, CCL4,
      adipsin, SAP, CC5, CFH, G-CSF, IL-10, Apo-CIII, IL-17A, PAI-1(total), PDGF AB/BB, MBL and
      NCAM1] were significantly different (p<0.05; Mann Whitney U test) between children with and
      without TBM. When the diagnostic potential of individual serum biomarkers was assessed by ROC
      curve analysis, 13 of the markers had promising AUC ≥ 0.70. LDA demonstrated that optimal
      diagnosis of TBM was achieved using 3 markers. The most accurate 3-marker serum biosignature
      for the diagnosis of TBM [adipsin (complement factor D), Ab42 and IL-10] diagnosed TBM with
      an AUC of 0.84 (95% CI: 0.73-0.96), a sensitivity of 82.6% (19/23) and specificity of 75%
      (18/24). In leave-one-out cross validation, the sensitivity remained 82.6% (19/23) with the
      specificity decreasing to 70.3% (17/24). Further optimisation of the biosignature by
      selection of better cut-off values resulted in an improved sensitivity and specificity of 83%
      and 83%, respectively.

      Biosensor-based diagnostic platform. The best performing CSF and serum biomarkers for TBM
      will be incorporated into a novel POC diagnostic platform to be developed at the Engineering
      Faculty, SU. The investigators have developed a prototype piezoelectric sensor using ZnO
      nanowires, as well as a resistive sensing element based on an electrospun nanofiber mesh
      (22). The device successfully detected E. coli (23). The investigators have also used this
      technique to detect small quantities of the protein LC3, a biomarker for autophagy activity
      and as part of a recent masters project, the platform was capable of detecting IFN-γ, a key
      TB biomarker in fg/ml ranges, thus demonstrating its potential high sensitivity.

      We will use a similar approach to develop a multi-biomarker based prototype test that is
      capable of detecting up to 4 biomarkers in serum or CSF, and prospectively evaluate the test
      on 300 newly recruited children with suspected TBM (Aim 3).

      OVERALL OBJECTIVE The main objective is to validate previously identified host serum and CSF
      biomarkers and to develop a biosensor-based POC test for the diagnosis of TBM, based on these

      The investigators propose to identify a panel of correlated biomarkers that showed potential
      in previous studies. This will be done to identify biomarkers which can be substituted with
      each other as the transition from a laboratory-based technological platform such as Luminex
      to a POC test using a biosensor-based technology is likely to be faced by the loss of some of
      the markers due to technical reasons or due to unavailability of some of the markers due to
      antibody ownership or cost issues. Highly correlated markers can then substitute such
      markers. The investigators will test which set of biomarkers works best in the POC diagnostic
      test platform. Finally, the investigators will evaluate the prototype test prospectively in a
      new cohort of 300 study participants with suspected TBM as described below.

      The prototype test will be based on the best biosignature of CSF or serum biomarkers,
      depending on which performs best. However, developing the test based on serum biomarkers may
      be advantageous as CSF samples are difficult to collect. Furthermore, a test based on serum
      biomarkers may be easily converted to a fingerprick based test, which will be much easier to
      implement in resource-constrained settings. The investigators are currently evaluating a
      fingerprick screening test for adult TB based on host biomarkers discovered and validated in
      serum samples as part of an EDCTP2-funded consortium (www.screen-tb.eu).


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Study Type


Primary Outcome

Identify CSF or blood-based biosignatures for the diagnosis of TBM in children


Tuberculous Meningitis

Study Arms / Comparison Groups

 Children with suspected meningitis
Description:  Patients must have a clinical diagnosis of meningitis including one or more of the following symptoms: headache, irritability, vomiting, fever and neck stiffness (Table 1). The diagnosis of probable or possible TBM is based on 1) clinical findings 2) CSF results 3) neuroimaging findings 4) evidence for TB outside the central nervous system and 5) additional laboratory criteria. A scoring system then determines whether a patient falls in the probable or possible TBM category. Points are allocated for a positive finding in each of the categories, with a maximum score for each category. A total score of at least 10 is compatible with probable TBM, while a total score of at least 6 equates with a possible TBM diagnosis.


* Includes publications given by the data provider as well as publications identified by National Clinical Trials Identifier (NCT ID) in Medline.

Recruitment Information

Estimated Enrollment


Start Date

April 1, 2020

Completion Date

October 31, 2024

Primary Completion Date

July 30, 2024

Eligibility Criteria

        Inclusion Criteria:

          -  Children between the ages of 3 months and 13 years with suspected meningitis, and who
             require CSF examination for routine diagnostic purposes at Tygerberg Children's

          -  Written informed consent will be obtained from parents for inclusion of children 3
             months to 7 years old in the study.

          -  If possible, assent will be obtained in those children older than 7 years who have a
             normal level of consciousness, i.e. a Glasgow Coma Score (GCS) of 15/15.

        Exclusion Criteria:

          -  Children 13 years and older will be excluded from the study.

          -  Failure to obtain written consent will also exclude children from the study.




3 Months - 13 Years

Accepts Healthy Volunteers



Novel Chegou, Prof, +27219389786, [email protected]

Location Countries

South Africa

Location Countries

South Africa

Administrative Informations



Organization ID


Responsible Party

Principal Investigator

Study Sponsor

University of Stellenbosch

Study Sponsor

Novel Chegou, Prof, Principal Investigator, University of Stellenbosch

Verification Date

January 2021