Clinical and molecular epidemiology of central nervous system infections in the Philippines

Title of PhD project

Clinical and molecular epidemiology of central nervous system infections in the Philippines

Supervisory team

Nagasaki University

Lead: Chris Smith (

Koya Ariyoshi (

Annavi Villanueva (


Martin Hibberd (Faculty of Infectious and Tropical Diseases,

Brief description of project

The aetiology of Central Nervous System (CNS) infection at San Lazaro Hospital, Manila, Philippines is poorly understood, with a definitive diagnosis not being made in a substantial proportion of cases. This study aims to utilize molecular methods to generate updated information on the clinical and molecular epidemiology of CNS infections in Metro Manila, Philippines. 

Multiplex real-time PCR systems for the detection of 163 human viruses (47 DNA and 116 RNA viruses) (Katano et al., 2011), and 68 bacterial and 9 fungal species (Fukumoto et al., 2015) in various clinical specimen have been developed and validated in the National Institute of Infectious Diseases in Tokyo, Japan. These protocols, together with metagenomic approaches, will be employed in the Philippines in this study.

The student will modify the above multiplex PCR for the context of the Philippines, considering suspected but currently undiagnosed pathogens such as Japanese encephalitis, and then design and implement a prospective study, recruiting individuals attending with suspected CNS infection (e.g. those with fever, headache, loss of consciousness etc) who require a lumbar puncture. 

Metagenomic approaches will be used to explore the completeness of the multiplex PCR findings and aid the selection of assays to be used. By comparing the diagnostic reliability of molecular methods to the traditional tests, the results from this study will guide diagnostic laboratories in deciding which tests to adapt for diagnosing CNS infections. 
Results from this study will address some of the knowledge gap on CNS infections in the Philippines. It will be useful for clinicians, epidemiologists, researchers, and public health officials in working to prevent and improve the management of CNS infections among Filipinos.

The role of LSHTM and NU in this collaborative project

NU: support for fieldwork in the Philippines including PCR, clinical tropical medicine 
LSHTM: lead on metagenomic sequencing, phylogenetic analyses

Particular prior educational requirements for a student undertaking this project

Master's degree in related field.

Skills we expect a student to develop/acquire whilst pursuing this project

Sequencing, bioinformatics, molecular epidemiology.