Vaccination and the Pediatric Microbiome

Vaccination and the Pediatric Microbiome: Funded by Washington University | 2010 – 2015


This is a multi-country multi-center study, taking place in Bangladesh, Philippines, The Gambia and South Africa. The aim of this exploratory study is to elucidate the pediatric NP microbiome by sampling the NP of newborns monthly in their first year of life and analyzing these specimens with meta-genomic DNA sequencing techniques.The sequencing is being done at Washington University and the J. Craig Venter institute, both of which have experience as US Human Microbiome Project Genetic Centers. In Bangladesh, samples are being collected from the Kumidini population-based site.


Pneumococcal pneumonia is the leading vaccine preventable cause of death in children, killing up to a million children a year. Ninety percent of these deaths occur in the developing part of the world. The Pneumococcal Conjugate Vaccine was introduced in the United States in 2000 and is now being introduced in many developing countries. PCV7 has been shown to have been more than 95% effective at reducing incidence of invasive pneumococcal disease (IPD).

Pneumococcus is also a major component of the human nasopharyngeal microbiome. The nasopharynx contains many microorganisms that begin colonizing soon after birth and they interact extensively with the human host without provoking human defense responses. However, microbes from the NP, like pneumococcus, can also cause diseases. Little is known about the detailed structure of the NP microbiome and how it is formed in newborns and what contributions do family and environment have in determining its composition. Understanding this would allow risk factors to be recognized and provide opportunities to prevent disease. Understanding the dynamics of the microbiome can help decipher the consequences of pneumococcal conjugate vaccine (PCV) introduction.


Child Health Research Foundation is the center in Bangladesh in this study. Subjects are recruited from a rural population in Mirzapur surrounding CHRF’s Kumudini sentinel site, 63 kms from the capital Dhaka. CHRF has a close relationship with the community and the study is being implemented htrough community health workers from the same village. The site has a population of 116,919 with 12,464 under five children and a birth cohort of 2,500. This study is leveraging WHO’s ongoing Invasive Bacterial Diseases (IBD) study already taking place there. CHWs visit the households every month and collect information about the expected date of delivery of babies. Newborns are visited within first 7 to 12 days and monthly afterwards. After NP samples are collected, the samples are sent to CHRF’s laboratory in Dhaka Shishu Hospital for microbiological analyses and DNA extraction. The extracted DNA is finally sent to Washington University.

Samples being collected now will help form the picture of the microbiome prior to vaccine introduction. After vaccine introduction next year, another round of enrollment will follow a new group of newborns to understand the composition microbiome after vaccine introduction and the differences between the two.


As of August 2013, 129 newborns have been enrolled and are being visited monthly.