This is a competing renewal application for a grant that has provided 10 years of support for studies of the interaction between host immunity, evolution and epidemiology of Streptococcus pneumoniae (pneumococcus) using approaches including molecular genetics and immunology, molecular and classical epidemiology, and mathematical modeling. Pneumococcus serves as a model system for understanding how natural and vaccine-induced immunity create selection pressure on pathogens to diversify antigenic molecules or otherwise escape host immune responses. This application focuses on a genome-wide understanding of antigenic variability in protein antigens, i.e. virtually all important antigens other than the polysaccharide capsule.
The first aim uses age- structured, transmission-dynamic modeling of selection pressures from allele-specific immunity within a host population to assess what patterns one would expect to see in genes encoding antigens targeted by such immune responses. These include patterns of sequence polymorphism, presence/absence polymorphism, and differences in bacterial populations in older (more immune) vs. younger (less immune) hosts.
This aim will formalize the expectations of what sorts of patterns are expected in pneumococcal populations (Aim 2). The output is a proposed "signature" of antigenic diversifying selection that is expected to be observed in bacterial genomes sampled from human hosts.
In Aim 2, we will validate and apply the model using novel population genomic data. We will perform whole genome sequencing of 800 pneumococcal isolates from a defined population (Navajo and Apache in the US Southwest) and apply the measures defined in Aim 1 to assess the evidence that each gene in the genome is under diversifying selection, and test these predictions against mechanistically defined lists of antigens.
Aim 3 will test in vitro whether allelic variation of putative antigens (two pre- defined proteins, PspC and RrgB, and 2-3 others identified in Aim 2) permits escape from two functions of antibody action: opsonization and blocking of attachment This work will bring new precision to the study of how host immunity leads to diversification of pathogens, developing concepts with application beyond the pneumococcus.

Public Health Relevance

This project studies how the immune responses of humans lead to natural selection on bacteria (here, the pathogen Streptococcus pneumoniae) to escape these immune responses by diversifying or losing the genes that code for the antigens that are the targets of such responses. Approaches include experimental studies, mathematical modeling, and whole-genome sequencing and evolutionary analysis of a collection of 800 S. pneumoniae strains

National Institute of Health (NIH)
Research Project (R01)
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Genetic Variation and Evolution Study Section (GVE)
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Taylor, Christopher E,
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Harvard University
Public Health & Prev Medicine
Schools of Public Health
United States
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Li, Yuan; Thompson, Claudette M; Lipsitch, Marc (2014) A modified Janus cassette (Sweet Janus) to improve allelic replacement efficiency by high-stringency negative selection in Streptococcus pneumoniae. PLoS One 9:e100510
Li, Yuan; Weinberger, Daniel M; Thompson, Claudette M et al. (2013) Surface charge of Streptococcus pneumoniae predicts serotype distribution. Infect Immun 81:4519-24
Cobey, Sarah; Lipsitch, Marc (2013) Pathogen diversity and hidden regimes of apparent competition. Am Nat 181:12-24
Hyams, Catherine; Trzcinski, Krzysztof; Camberlein, Emilie et al. (2013) Streptococcus pneumoniae capsular serotype invasiveness correlates with the degree of factor H binding and opsonization with C3b/iC3b. Infect Immun 81:354-63
Li, Yuan; Thompson, Claudette M; Trzcinski, Krzysztof et al. (2013) Within-host selection is limited by an effective population of Streptococcus pneumoniae during nasopharyngeal colonization. Infect Immun 81:4534-43
Weinberger, Daniel M; Bruden, Dana T; Grant, Lindsay R et al. (2013) Using pneumococcal carriage data to monitor postvaccination changes in invasive disease. Am J Epidemiol 178:1488-95
Lipsitch, Marc; Abdullahi, Osman; DýýAmour, Alexander et al. (2012) Estimating rates of carriage acquisition and clearance and competitive ability for pneumococcal serotypes in Kenya with a Markov transition model. Epidemiology 23:510-9
Cobey, Sarah; Lipsitch, Marc (2012) Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes. Science 335:1376-80
Weinberger, Daniel M; Malley, Richard; Lipsitch, Marc (2011) Serotype replacement in disease after pneumococcal vaccination. Lancet 378:1962-73
Weinberger, Daniel M; Harboe, Zitta B; Flasche, Stefan et al. (2011) Prediction of serotypes causing invasive pneumococcal disease in unvaccinated and vaccinated populations. Epidemiology 22:199-207

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