Improving diagnosis of brain infections in Indonesia using novel and established molecular diagnostic tools.

Brain infections, such as meningitis and encephalitis, are a significant cause of morbidity and mortality in Indonesia, as elsewhere, with considerable costs to families, health care and society.

The key step in early patient management is to distinguish bacterial causes, which need immediate antibiotic treatment, from the many clinical mimics, such as viral meningitis, which do not. The gold standard for distinguishing the two is lumbar puncture, followed by microscopy and culture of the cerebrospinal fluid (CSF). However, culture results are often delayed, or inconclusive. Many patients are therefore treated with unnecessary antibiotics until a diagnosis of bacterial meningitis is excluded, contributing to the burden of antimicrobial resistance.

In Liverpool, we have developed the TRanscripts to Identify bacterial Meningitis (TRIM) test. It is a host transcript-based diagnostic blood test. We have shown it exhibits high sensitivity (100%), specificity (90%) and negative predictive value (100%) in distinguishing adult bacterial meningitis from mimics (viral meningitis or meningism [where patients have clinical symptoms of meningitis but the number of white blood cells in the CSF is not raised]). A key advantage of the TRIM test is that results can be rapidly available (in under four hours) from sample arrival in the laboratory.
As a rapid, accurate and low cost (target cost under £10 per patient) blood test, the TRIM test offers improved rule-out of bacterial brain infections, enhancing patient management and promoting cessation of unnecessary antimicrobial use. In partnership with Universitas Gadjah Mada (UGM), Indonesia, preliminary work assessing the TRIM assay at UGM indicate it maintains high accuracy (100%) in distinguishing bacterial infection from mimics among child and adult Indonesian patients with symptoms/signs of meningitis or encephalitis.

Our second diagnostic approach is to use pathogen-specific polymerase chain reaction (PCR) and antibody tests; through these we have increased pathogen detection among children with suspected meningo-encephalitis at UGM by over 30 percent (from 11% to 42%), through a pilot of systematic testing of CSF.

In this three year study, we will assess the accuracy of the TRIM test in a larger cohort of Indonesian patients with suspected meningo-encephalitis, recruited through hospitals linked to UGM and Universitas of Indonesia. Alongside, we will increase pathogen detection through pathogen-specific PCR and antibody testing at these sites.

To improve our pathogen-specific PCR panel, we will perform next generation sequencing, at the Eijkman Institute, Indonesia, on CSF samples where no pathogen has been detected. Sequence information from identified pathogens will be used to inform PCR test design.

Linking with the University of Warwick, we will evaluate the cost-effectiveness of introducing these diagnostic tools into routine clinical care for suspected brain infection patients in Indonesian hospitals.

This study will assess and implement novel and established diagnostic tools among Indonesian brain infection patients. In the longer-term, these tools will support more appropriate treatment of brain infections among Indonesian patients, strengthen local research capacity and collaboration between UK and Indonesia.

Brain infections, such as meningitis and encephalitis, remain a significant cause of morbidity and mortality in Indonesia and the UK, with considerable costs to families, health care and society.
In Liverpool, we have developed a novel host-transcript based blood test: TRanscripts to Identify bacterial Meningitis or TRIM test. It uses host transcripts in the blood. The test exhibits high sensitivity (100%), specificity (90%) in distinguishing patients with bacterial meningitis from the mimics (meningism or viral meningitis). The test offers to help clinicians' rule-out bacterial infection and decide appropriate treatment.

In partnership with Universitas Gadjah Mada (UGM), Indonesia, our preliminary results indicate the TRIM test maintains high accuracy (100%) in distinguishing bacterial meningo-encephalitis from clinical mimics among child and adult patients. In addition, at UGM, we have increased pathogen detection among suspected meningo-encephalitis cases by 31% (from 11 to 42%) via introduction of systematic testing of cerebrospinal fluid (CSF) using pathogen-specific PCR and pathogen directed antibody ELISA testing.

In this three year study, we will validate TRIM test accuracy in a large number of suspected Indonesian meningo-encephalitis patients (n=694), recruited through hospitals linked to UGM and Universitas of Indonesia (UI). Alongside, we will continue systematic CSF testing at UGM, and extend to patients recruited through UI. To further improve pathogen detection, we will perform next-generation sequencing on PCR negative CSF samples, at the Eijkman Institute. Identified pathogen sequences will be used to refine pathogen-specific PCR.

This study will assess and implement novel and established diagnostic tools among Indonesian brain infection patients. In the longer-term, these tools will support more appropriate treatment of these patients, strengthen local research capacity and collaboration between UK and Indonesia.

This proposal we will validate TRIM test accuracy in distinguishing bacterial meningo-encephalitis from clinical mimics in child and adult Indonesian patients (objective 1). Assuming target accuracy is achieved this will stimulate translation of the TRIM test multiplex assay into a diagnostic test ready for clinical use in Indonesia.
Longer term, successful application of the TRIM test in Indonesian child and adult populations will promote further assessment of the TRIM test in paediatric populations (including the UK), different Asian populations and lower and middle income countries.
Implementation of systematic pathogen testing (pathogen specific PCR and antibody testing) and next generation sequencing (objectives 2+5) will improve knowledge on the causes of CNS infection in two large regional hospitals in Indonesia. In turn, this knowledge will inform clinical management of CNS infections in these hospitals.
Cost-effectiveness analysis, combined with a model of the potential increase in quality adjusted life years gained by clinicians acting on the test results (objective 3), will provide valuable information to health-care stakeholders to consider introduction of these tests for routine use in local hospitals. It will also stimulate further research on how to encourage uptake and adoption of new diagnostics in health settings.
Development and assessment of an extended TRIM test that distinguishes tuberculous meningitis (TBM) from other bacterial causes of meningitis among an Indonesian population (objective 4), will extend the diagnostic capability of the TRIM test. Assuming target accuracy is achieved, this data will stimulate translation of the extended set of TRIM markers into multiplex assays. Longer term, successful validation of the extended TRIM test will stimulate its development into a diagnostic test ready for clinical use for Indonesia and other populations with a high TBM prevalence.
Longer-term, clinical use of molecular tools to rule-out bacterial CNS infection (i.e. the TRIM test) or identify the causative pathogen (pathogen specific PCR) will facilitate more targeted patient treatment, reduce use of antibiotics and improve patient care.
Improved knowledge of etiology, availability of diagnostics and clinical experience of successful targeted treatment will promote a culture of more appropriate treatment of CNS infections. Direct dissemination of this knowledge through academic meetings involving partner and local Institutes during this study and indirectly through academic and clinical staff rotation through these large hospitals, will lead to improved treatment strategies for CNS infection across Indonesia.
Better etiology data on CNS infection will inform future Indonesian health-care, public health and vaccination strategies, for the benefit of the country. For example, identification of further paediatric cases of TBM will stimulate review of availability of GeneXpert testing for Mycobacterium tuberculosis in meningitis cases and in children. Currently, GeneXpert is available for testing pulmonary tuberculosis In Indonesia, and only in a few specific hospitals for testing for TBM in adults. Similarly, identification of further cases of meningitis due to Haemophilus influenzae by pathogen-specific PCR (we have already identified 2 cases) will stimulate review of hospital laboratory microbiological culture protocols and vaccination policies. Haemophilus is not detected by standard culture techniques used in the majority of Indonesian hospitals.
Finally, establishing a robust local research infrastructure and long-standing partnerships will provide a spring-board for a portfolio of clinical and basic science CNS infection studies for the mutual benefit of all research partners, child and adult patients with CNS infections and ultimately through improved health-care Indonesian society.