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

Lead Research Organisation: University of Liverpool
Department Name: Institute of Infection and Global Health

Abstract

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.

Technical Summary

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.

Planned Impact

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.

Publications

10 25 50
 
Description Brain infections are a devastating illness. This is particularly true in Indonesia. Prior to our intervention, less than 5% of brain infection patients had an infectious aetiology identified. As a consequence of limited diagnostic support, treatment by clinicians was empiric and variable. 28% of brain infection patients (45% of adults) died, 74% of survivors (87% of children) suffered neurological impairment, with 32% suffering severe long-term disability.
As part of our study, we have introduced new diagnostic tests (such as pathogen specific PCR) to expand methods of detecting infection in patient samples. We have supported training/education for these tests to be clinically available in local hospital laboratories. These new tests have been used by local clinical teams to mange patients with suspected meningitis. Results from these tests have been provided to the clinicians. The results have been used to guide clinical care among their patients. Improvements in care fed back by the local research team include reports increased case detection, particularly for TBM and Cryptococcus meningitis, prescribing more appropriate antibiotic treatment, such as anti-tuberculous drugs, for patients diagnosed (by the new tests) with tuberculous meningitis.
However, the study was paused due to COVID in 2020. We received a limited no-cost extension, but this did not fully compensate for the time/activity lost during COVID. The MRC has advised we are able to continue work on the award beyond the end date of the grant. We continue to work with local research and clinical staff to evaluate and confirm the impact of the increased hospital testing availability introduced during the study on downstream economic outputs, clinical behaviour and patient care.
Exploitation Route The epidemiological data from this study will increase knowledge in Indonesia and beyond about common identified causes of brain infection among children and adults. It will also provide information on the clinical outcome for patients experiencing these infections in this setting.
Knowledge on common pathogens causing brain infection, will indirectly, help guide empiric treatment and clinical management of brain infections in Indonesia.
The knowledge and technology transfer on performing and interpreting an expanded range of diagnostics tests that has occurred during the study, will help encourage local laboratories to continue to undertake and offer these tests, and clinicians to request and utilise the results.
Post COVID we have been able to undertake further consolidatory training of hospital laboratory staff to perform pathogen specific PCR , and further work with hospital staff (managers/clinicians) to promote request for and use of GeneXprt for Mtb testing in CSF. Testing for Mtb in suspected TBM using GenXprt is now performed more regularly. We are still working with the clinical staff to evaluate the impact of this testing. This work will continue beyond the end of the grant.
Sectors Healthcare

 
Description As part of this study, diagnostic tests (particularly for Tuberculous (TB) and Crytococcal meningitis) have been translated from research use into clinical use. These tests were offered as routine clinical care prior to study pause in April 2020 (pause due to COVID pandemic) Preliminary reports indicated these tests were being requested by local clinicians. The tests were providing new detection of pathogens causing meningo-encephalitis. However, since our study was paused , and the local hospital laboratories have focussed on delivery of COVID diagnostics, our changes in care have been more difficult to sustain. Since COVID, we have undertaken workshops with laboratory staff from regional and hospital microbiology laboratories. We have undertaken refresher training in undertaking nucleic acid extraction from clinical samples (CSF/blood) and undertaken pathogen specific PCR on the resultant nucleic acid. We have also given training in maintaining quality assurance (documentation / use of positive / negative controls) when performing these procedures. The regional microbiology staff now have the consumables and training to undertake pathogen specific PCR for a range of pathogens, including Mtb, Strep. pneumoniae, Haemophilus. Similarly hospital laboratory staff also now have consumables and training to undertake pathogen-specific PCR. One highlight, is that hospital laboratory staff can now successfully perform PCR for Mtb on CSF. We have also done further work with the laboratory managers and clinical teams to promote use of GeneXprt for testing of CSF for Mtb. Both paedaitric and adult clinicians can now request, through liaison with the respiratory teams, to undertake GeneXprt testing for Tuberculous Meningitis, in suspected patients. Feedback indicates this shift in testing has enabled new TBM cases to be identified. We are now working with the clinical teams to evaluate the impact of this change in testing. The local teams have funding to continue this work. This evaluation will continue beyond the end of the grant.
First Year Of Impact 2020
Sector Healthcare
Impact Types Policy & public services

 
Description I am an invited member of a WHO expert group on meningitis diagnostics, aiding development of a target product profile for a multi-pathogen meningitis diagnostic.
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
URL https://www.who.int/docs/default-source/documents/health-topics/meningitis/in-vitro-diagnostics-test...
 
Description I am consultant for PATH (global non-profit organisation promoting public health) on 'case use for meningitis testing '. I advise on clinical and economic value of different approaches to clinical testing of suspected meningitis
Geographic Reach Multiple continents/international 
Policy Influence Type Contribution to a national consultation/review
URL https://www.who.int/docs/default-source/documents/health-topics/meningitis/in-vitro-diagnostics-test...
 
Description Introduced use of more accurate laboratory testing for pathogens in local laboratory
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Influenced training of practitioners or researchers
Impact The tests are being requested by local hospital clinicians for investigation of in-patients (adult and paediatric) with suspected meningitis. This has resulted in detection of new cases of TBM and cryptoccocal meningitis. Feedback from clinical staff suggests more appropriate clinical management of these hospital cases, e.g. via more targeted use of anti-tuberculous and anti-fungal treatments. Local hospital managers have adapted GeneXpert protocols for routine use and locally sourcing CRAG rapid antigen tests for use in their departments This change in testing behaviour although first initiated in 2019 has continued to be promoted and occur over the last 4 years (up to 2023). CSF testing for Mtb via GenXprt is now requested by clinicians managing cases of suspected TBM. This is done in discussion with the clinical respiratory teams (who are still the gate-keeper to GenXprt testing and access to anti-tuberculous drugs). Prior to the DIME study regional testing of CSF for Mtb did not occur.
 
Description Invited consultant to the World Health Organisation. I contributed to development of their road map for 'Defeating Meningitis by 2030'
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
URL http://www.who.int/publications/m/item/defeating-meningitis-by-2030-a-global-road-map.
 
Guideline Title Meningitis (bacterial) and meningococcal disease: recognition, diagnosis and management
Description Invited member for the National Institute for Clinical Excellence guideline committee on Meningitis and meningococcal septicaemia: recognition, diagnosis and management.
Geographic Reach National 
Policy Influence Type Citation in clinical guidelines
URL https://www.nice.org.uk/guidance/ng240
 
Description Participation in development of the "Meningitis Progress Tracker"
Geographic Reach Multiple continents/international 
Policy Influence Type Contribution to a national consultation/review
URL https://www.meningitis.org/mpt?msclkid=824bd7efa5da11ec89ffb0be0cf394af
 
Description NIHR Global Health Research Group on Improving the Management of Acute Brain Infections at University of Liverpool - Supplement
Amount £237,075 (GBP)
Funding ID 17/63/110 supplement 
Organisation National Institute for Health Research 
Sector Public
Country United Kingdom
Start 03/2021 
End 03/2022
 
Title Assessment of prototype TRIM assay among Indonesian patients. 
Description We have undertaken knowledge exchange and technology transfer between UoL and local Indonesian research teams, to enable them to perform and assess the prototype TRIM assay in their local laboratories. The TRIM assay has been run on Paxgene samples recruited from local hospital in-patients admitted with suspected meningo-encephalitis. In 2023 we have also carried out knowledge exchange between UoL and local Indonesian research teams to enable them to perform and assess a modified version of the TRIM assay in their local lab. The modified version includes additional markers that help distinguish TBM from pyogenic bacterial meningitis. The assay has again been run on locally recruited samples. Evaluation of the performance of the modified TRIM assay by the local research team is ongoing. 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? Yes  
Impact The TRIM assay has been able to discriminate bacterial and/or mycobacterial tuberculosis (MTB) causes of meningitis from viral cases of meningitis. This information is feedback into the Indonesian and TRIM studies to enable refinement of the prototype TRIM assay to begin to develop the markers to discriminate between pyogenic bacterial pathogens (e.g. S.Pneumoniae) from MTB. The feedback from local research staff while performing the TRIM assay at 'field' sites in Indonesia, is also being used to support development of the TRIM test system and associated instruction manual/protocol. 
 
Title Development of pathogen specific PCR for detection of pathogens associated with meningo-encephlitis in Indonesia 
Description Working with local Indonesian researchers we have identified/and assessed a series of sensitive and specific PCR primers. The best performing primers have bene taken forward and included in a series of protocols and quality control procedures to perform accurate real-time PCR assays for detection of pathogens associated with meningo-encephalitis among CSF and blood samples from Indonesian hospital patients admitted with suspected brain infection. Pathogens specific PCR the local laboratories are now able to detect includes: Strep.Pneumo, N.Meningitidis, H.Influenzae, E.Coli, Enterovirus. 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? Yes  
Impact The pathogen specific primers have been used to to detect pathogens among Indonesian samples from patients with suspected meningitis. The approach has been able to confirm infection with specific pathogens among cases, that were undiagnosed, by local standard microbiological techiques (typically culture). 
 
Title Introduction of pathogen specific PCR for mycobacterium tuberculosis to research and hospital laboratories in Indonesia 
Description As part of our Indonesia award we have introduced local molecular training and protocols to undertake pathogen specific PCR testing for Mycobacterium Tuberculosis among patient samples from patients with suspected TB meningitis. We have supported the local research and hospital laboratories to perform pathogen specific PCR for MTB on CSF and blood (using their own primers). We have also supported them to adapt the hospital and regional protocols for GeneXpert TB assay for use with CSF. 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? Yes  
Impact The tests are being requested by local hospital clinicians for investigation of in-patients (adult and paediatric) with suspected TB meningitis (TBM). This has resulted in detection of new cases of TBM and more appropriate clinical management of these hospital cases. Local hospital managers are adapting the GeneXpert protocols for routine use in their departments. 
 
Title Local introduction of Cryptococcal Antigen testing 
Description The local hospital laboratories in Yogyakarta tend to use India ink stain to test for cryptococcus in CSF among suspected CNS infection patients. As part of the research protocol we introduced use of a commercial Crytococcal Antigen (CRAg) lateral flow rapid antigen test. Locally we have shown the CRAg test has higher specificity than India ink (the latter does not distinguish between candida and cryptococcal fungal species). Following training, the microbiology laboratory linked to the GMU is now able to perform CRAg rapid tests. The test was initially only performed as part of the research protocol. However, the local microbiology staff having been further engaged in the study, are now using the test in their clinical work. 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? Yes  
Impact Initially this test was only applied as part of our research study. However, following engagement and involvement of the local Indonesian hospital laboratory teams in the study, the CRAG test has become available as a routine test for order by clinicians suspecting cryptoccocal meningitis among hospital patients. 
 
Title Pathogen Specific PCR development in Fiocruz, Recife, Brazil 
Description Building on our Brazilian research links developed during our Zika Grant and the activities undertaken in our Indonesia award, we are working with the Virology unit, within Fiocruz, Recife, Brazil top broaden their Pathogen Specific PCR diagnostics, to detect a range of viruses and bacteria associated with central nervous system infections (meningitis/encephalitis). The methods being introduced in Fiocruz are based on the protocols developed as part of our Indonesia award. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? No  
Impact Once established the tool will be available to clinicians based in Brazilian hospitals to help guide management of suspected meningo-encephalitis 
 
Title Dataset with diagnostic and epidemiological information from Indonesian adults and children admitted to hospital with suspected meningo-encephalitis 
Description Unique collection of data from >500 Indonesian patients (children and adults) with suspected meningo-encephalitis. Clinical data is being linked with laboratory data on pathogens identified and associated parameters (e.g. CSF white cell count). Pathogen data is acquired from hospital laboratories and results from new diagnostic methods introduced and undertaken on samples collected as part of the study. New diagnostic assays were performed by our research team and results were appended into database. Relevant patient outcomes have also included (where available) This database is currently accessible to the research team. We aim to continue to develop this into a more accessible online database for local laboratory, research and clinical groups to support knowledge gain in epidemiology of suspected meningo-encephalitis in Indonesia. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? No  
Impact Dataset has been used to support the research team to select which pathogens to focus on when developing new diagnostic approaches in the local laborartories. The dataset has also helped support education of local clinicians on the relative frequency of different pathogens causing meningo-encephalitis within the local hospitals 
 
Description Collaboration with Eijkman Institute 
Organisation Eijkman Institute
Country Indonesia 
Sector Public 
PI Contribution Our team contributed in providing advice in setting up and conducting the laboratory research attached to this study. We also provided support in advising options for molecular and antibody testing.
Collaborator Contribution The local team is developing a molecular and and pathogen directed antibody testing strategy for pathogen detection among a sub-set of samples collected through the clinical arm of the study. Study activity has been paused during the COVID pandemic. The Institute is leading national COVID diagnostic and sequencing provision.
Impact Sharing of expertise between Institutions
Start Year 2019
 
Description Collaboration with General Hospital Dr. Sardjito, Yogyakarta 
Organisation Central General Hospital Dr. Sardjito
Country Indonesia 
Sector Hospitals 
PI Contribution Our team contributed in providing advice in setting up and conducting the clinical diagnostic interventional study in Yogyakarta region, Indonesia. We provided training in molecular and antigen testing for pathogens in the clinical hospital Microbiology laboratories. This included remote and hands on training (at the local site) in safe extraction of nucleic acid from clinical samples (cerebro-spinal fluid and blood; then running real-time PCR using pathogen specific primers on the nucleic acid. It also included examples of troubleshooting the results and the importance of including control panel in the PCR run to check for contamination and accurate detection. We also provided training in performing antigen testing (via ELISAs) and rapid tests. This training and engagement has enabled some of the tests initially undertaken as RUO to be translated for use in the clinical setting. As part of the study, new diagnostic tests have made available for clinical care, The results have been used to guide clinical care among patients with suspected meningo-encephalitis. We have provided clinical and laboratory consumables. Lab. consumables include nucleic acid extraction kits, pathogen specific primers, control samples and laboratory plastics (e.g. PCR plates, sealers, cryovials, ELISAs for pathogen (antigen) testing and Rapid LFA tests for Cryptococcal Antigen testing) In addition, our team contributed in providing advice in setting up and conducting the clinical interventional study within the adult neurology and paediatric departments at the hospital. We also shared advice in performing LP's among the potential recruits and about the value of conducting targeted pathogen testing among patients with suspected CNS infection. We also supply clinical consumables - such as sample collection tubes and LP equipment (such as CSF manometers).
Collaborator Contribution The hospital Neurology and Paediatric clinical teams have supported engagement with hospital laboratories and promoted the translation of new diagnostic tests into clinical care. They have also supported education of fellow clinicians / hospital staff to request / utilise the test results in their care of patients with suspected meningo-encehalitis. The hospital Neurology and Paediatric clinical teams work with the study team to identify and facilitate recruitment of patients into the interventional study and engagement of the clinical team. There was a break in the study during COVID 2020-2021. However, patient study recruitment re-started in September 2021.
Impact Introduction and local undertaking of clinical pathogen detection tests not previously employed by the hospital laboratories. Translation of these tests into clinical care. Request and result utilising of the new tests by the clinical teams when managing patients with suspected meningitis. Feedback from clinical team that new test results are diagnosing new cases of confirmed pathogen infection among meningitis cases and that the results are helping guide clinicians to provide more targeted treatments. Gain in local knowledge in laboratory and clinical staff on the benefits/use of targeted pathogen testing. Knowledge exchange between local and UK Institutions and Departments.
Start Year 2019
 
Description Collaboration with Universitas Indonesia 
Organisation Universitas Indonesia
Country Indonesia 
Sector Academic/University 
PI Contribution Our team contributed in providing advice in designing the local research protocol and setting up the clinical research study in the Child Health Sciences Division of the University and the Paediatric department of the linked hospital RSUPN Cipto Mangunkusumo. We have also provided advice in developing the ethical approval applications and the legal agreements between study partners.
Collaborator Contribution The Universitas of Indonesia (UI) research team has recruited a local study coordinator. They have developed a research protocol , applied for local ethics and applied for local agreements for sharing data (and samples) between UI , RSUPN Cipto Mangunkusumo Hospital, Eijkman Institute and Gadjah Mada University. They have also applied for an agreement between UI and the University of Liverpool. Study progress was paused during COVID pandemic. Study activity was re-starting February 2022.
Impact Development of links and knowledge exchange between collaborating Institutions. Gain in local research expertise in developing a multi-centre clinical and laboratory study.
Start Year 2019
 
Description Collaboration with University of Sydney, 
Organisation University of Sydney
Country Australia 
Sector Academic/University 
PI Contribution Collaboration with the Centre for Infectious Diseases, University of Sydney. Mutual research interests in Meningitis and working in CNS infections in Indonesia Scoping areas of research for joint work
Collaborator Contribution Scoping areas of research for joint work and formulating an agreement
Impact n/a
Start Year 2024
 
Description Partnership with Gadjah Mada University (GMU) 
Organisation Gadjah Mada University
Country Indonesia 
Sector Academic/University 
PI Contribution Our team provided support in setting up and conducting the clinical diagnostic interventional study in Yogyakarta region, Indonesia. We also provided training in molecular and antigen testing for pathogens in the research and linked clinical Microbiology laboratories. This included remote and hands on training (at the local site) in safe extraction of nucleic acid from clinical samples (cerebro-spinal fluid and blood; then running real-time PCR using pathogen specific primers on the nucleic acid. It also included examples of troubleshooting the results and the importance of including control panel in the PCR run to check for contamination and accurate detection. We also provided training in performing antigen testing (via ELISAs) and rapid tests. We have provided clinical and laboratory consumables. Lab. consumables include nucleic acid extraction kits, pathogen specific primers, control samples and laboratory plastics (e.g. PCR plates, sealers, cryovials, ELISAs for pathogen (antigen) testing and Rapid LFA tests for Cryptococcal Antigen testing) We have also supported training and provided consumables to enable the local research team to perform the TRIM assay and work with us to assess the performance of the assay using samples recruited from Indonesian patients (children and adults) with suspected meningitis.
Collaborator Contribution The research team have set-up the clinical study at their linked hospital (working with their clinical colleagues) and successfully obtained local ethical and MTA permissions. They have advertised and recruited a research team - including support staff for clinical, laboratory and administrative roles in the study. They have successfully started the study and recruiting patients. They have collected clinical and laboratory research data. They have collected and stored appropriate clinical samples. The laboratory has also commenced sample processing and undertaken nucleic extraction from a sub-set of the collected patient samples. The laboratory is conducting pathogen antigen detection tests, such as testing for Cryptococcus pathogen using rapid antigen tests. The research team has also collaborated with their hospital laboratory team and supported training and promoted translation of diagnostic tests (such as GenXpert MTB and CRAG rapid antigen tests ) to being clinically available and utilised for assisting diagnoses and management of hospital in-patients with suspected meningitis.
Impact Gain in local expertise / experience in conducting a clinical trial Gain in local expertise / experience in performing laboratory based molecular and antigen testing Local recruitment of patients with suspected CNS infection Local collection of patient samples from recruited / consenting patients with suspected CNS infection Local processing of patient samples for molecular pathogen testing. Introduction and local undertaking of clinical sample testing for pathogens using rapid antigen tests and pathogen specific PCR in hospital laboratories to support clinical diagnosis and management of patients with suspected meningitis. These tests/approaches were not previously employed by the local hospital laboratories.
Start Year 2019
 
Title Assessment of Pathogen Specific PCR to improve diagnosis and management of Indonesian patients with suspected meningo-encephalitis 
Description Assessment of Pathogen Specific PCR (series of multiplex probes), TB PCR testing and use of CRAG implemented via real-time PCR and rapid antigen tests on CSF and blood. Local staff trained and components of the tests supplied to the local research and hospital laboratories. Initial transfer of protocols to local laboratory and clinical team and assessment has been undertaken. Evaluation aspect of the study has been paused March 2020 due to COVID. Clinical patient recruitment has re-started. Laboratory capacity is now available to re-start evaluation. Preliminary feedback reported improvement in patient diagnosis and more appropriate clinical management (based on available diagnoses) Supported by this study. Evaluation of impact is ongoing and likely to extend beyond the end of the award. 
Type Diagnostic Tool - Non-Imaging
Current Stage Of Development Initial development
Year Development Stage Completed 2020
Development Status Under active development/distribution
Clinical Trial? Yes
UKCRN/ISCTN Identifier NA
Impact Uptake of research diagnostic tools, particularly TB PCR (GenXpert) and CRAG tests, by local hospital laboratories These tests have been made available for routine investigation of local hospital patients with suspected meningo-encephalitis. In turn, local clinicians have requested these tests, and they have reported more targeted clinical management of patient treatment based on results of these tests. One example, has been increased clinical awareness of adult and paediatric TBM cases, with increased testing of CSF for Myocbacterium tuberculosis and reports of increased prescribing of anti-tuberculous treatment. 
 
Title Meningitis Progress Tracker 
Description Currently, data on the global meningitis burden are hard to interpret. This is due in part to there being multiple causes, and because the data comes from many different sources. The aim of the "Meningitis Progress Tracker" (MPT), is a online tool that combines multiple information sources to enable tracking of UK national and global progress toward defeating the disease. I am invited member of an international group of clinical and research and policy experts to advise on development and further refinement of the outputs provided by the MPT. Again our experiences/findings from the ongoing Indonesia study have contributed to criteria/outputs that will support knowledge exchange on improved diagnosis and management of meningitis across the globe Contributing to development Meningitis Progress Tracker (MPT), 
Type Of Technology Webtool/Application 
Year Produced 2022 
Open Source License? Yes  
Impact Website is providing easier to access unified information on the incidence and impact of meningitis for countries across the globe, for clinicians, researchers, policy advisors. 
URL https://www.meningitis.org/mpt?msclkid=824bd7efa5da11ec89ffb0be0cf394af
 
Description Local Laboratory training workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Our research team has undertaken a series of workshops with laboratory staff and clinicians in academic, regional microbiology, and hospital laboratory settings.
We have given education on the value of improved diagnostics for patients with suspected CNS infection.
We have provided education on different molecular tools (antigen, PCR, NGS) that can be used to support diagnosis of CNS infection.
We provided practical hands-on training on sample preparation and performing pathogen specific PCR in hospital laboratories.
We have worked through examples of successful and unsuccessful cases of PCR testing and provided a QA framework for laboratory staff/managers to review the quality of their work.
We have highlighted the benefit of molecular detection being performed during the study, and used these examples to encourage more sustained change in clinical requests and testing procedures in the hospital labs. These sessions have involved staff managers involved in local / regional policy making on procedures for hospital microbiological diagnostic testing.
Year(s) Of Engagement Activity 2022,2023