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Understanding pneumococcal transmission patterns in Vietnam via phylogenetic inference

Supervisory team
LSHTM: Stéphane Hué, Stefan Flasche
Nagasaki University (Pasteur Institute Nha Trang): Lay Mint Yoshida

The transmission of S. pneumonae, particularly to infants, is not well understood. However, it is at the core of the highly topical debate around relying on herd protection from pneumococcal vaccines in order to reduce unsustainably high vaccine costs in low- and middle-income countries.

In Nha Trang, Vietnam, we have collected pneumococcal carriage samples from about 70% of the total infant and toddler population and their mothers in 2016 and 2018. All samples will have been deep-sequenced by 2019. This allows for a word-wide unique opportunity to study pneumococcal transmission among young children and their mothers, to identify prominent routes of transmission and characterise factors promoting on-going paediatric infections.

The PhD candidate will use this data to develop, test and implement a robust methodology to infer pneumococcal transmission from genomic data and distinguish transmission events from close genomic proximity for other reasons (including an indirect transmission link via an intermediary), investigate who infects infants and toddlers with pneumococci using those techniques and will investigate the role of sub-dominantly carried serotypes for transmission.

As this project is at the forefront of research on the use of phylogenetics for pneumococcal transmission, a high degree of personal motivation is essential. Expertise in computer programming, ideally in R or Python as well as good command in English is required. Prior knowledge of molecular evolution and statistical proficiency are also desirable.

The student will learn about state-of-the art pneumococcal epidemiology and vaccinology, pathogen molecular evolution, genomic sequence analyses and phylogenetic inference.

If you are interested please get in touch directly (and soon) with Stephane Hue ( and/or Stefan Flasche (

PhD position
LSHTM / Nagasaki University
London / Nagasaki / Nha Trang
UK / Japan / Vietnam
Closing date
January 31st, 2019
Posted on
January 10th, 2019 22:13
Last updated
January 11th, 2019 15:29