Funded Research

Mechanisms of Capsular Diversity in Streptococcus Pneumoniae
This grant funds experimental, mathematical modeling, and epidemiological work on S. pneumoniae and is the primary support for the wet lab of Dr. Lipsitch.  Current emphasis is on characterizing the biological differences between pneumococcal serotypes (through epidemiologic and experimental studies), experimental studies of immune responses to pneumococcal carriage, and synthesis of these findings into an understanding of how capsular diversity is maintained in S. pneumoniae and is perturbed by serotype-specific vaccines.  See this publication for the synthesis and for citations to prior work. (PI: Lipsitch)

Conjugate vaccine impact on pneumococcal carriage, disease, and population genetics
This study aims: 1. To examine trends in pneumococcal colonizing and invasive disease isolates, with regard to serotype and antibiotic resistance, host risk factors, and invasive potential, before and after introduction of PCV13. 2. To assess shifts in pneumococcal population structure (by MLST) and evaluate potential factors associated with successful spread of pneumococcal clones in Massachusetts in the context of PCV13 introduction. 3. To use whole genome sequencing to identify potential genetic determinants associated with serotype switching and invasiveness among clones that have emerged under selective vaccine pressure.   An innovative aspect of this work is the inclusion of substantial whole genome sequencing and analysis to address epidemiologic and biological questions (Lipsitch, Hanage; PI: Jonathan Finkelstein)

Pediatric HIV/AIDS Cohort Study (PHACS) Data and Operations Center, and Strategic Leadership Group
This center serves as the collaborative nexus for analysis of perinatally-acquired HIV infection among adolescents and pre-adolescents, and the consequences of fetal and neonatal exposure to HIV and antiretroviral chemotherapy. The SLG will serve as the scientific leadership for the PHACS study. (Seage)

Epidemiology and Transmission Dynamics of MDR/XDR Tuberculosis
The aim of this project is to conduct a series of linked interdisciplinary research projects focused on the emergence and transmission of multidrug and extensively drug resistant tuberculosis: a cohort study of host and microbial factors associated with MDR and XDR TB in Lima, Peru; a study characterizing M. tuberculosis strain diversity and its contribution to the emergence and spread of MDR; and a study using epidemic and individual predictive models to support public health policy and clinical decision-making for MDR and XDR TB. (Murray)

Optimizing HIV care in less developed countries
This study will assess the clinical impact, cost, and cost-effectiveness of alternative strategies for HIV management in South Africa, India, and Cote d’Ivoire. (Lipsitch, Seage; PI: Sue Goldie)

Post-PCV pneumococcal population genetics and resistance
This study aims to assess changes in patterns of colonization and serotype-specific antimicrobial resistance among pneumococcal isolates; to enhance our understanding of the biological processes which underlie apparent shifts in community carriage and resistance; and to re-assess risk factors for colonization and transmission of S. pneumoniae in the decades following universal PCV7 immunization. (Lipsitch, PI: Jonathan Finkelstein)

Evaluating the link between HIV prevention and treatment
This project aims to evaluate the cost-effectiveness of HIV screening on treatment and prevention. (Seage, PI: David Paltiel)

Statistical/Data Management Center-Pediatric AIDS Clinical Trials Group
This project is provides epidemiologic design and analytic support for pediatric HIV trials in the PACTG. (Seage, PI: Terry Fenton)

Cost-effectiveness of Preventing HIV complications (CEPAC)
This is a study to evaluate the cost-effectiveness of preventing HIV complications in the era of highly effective antiretroviral therapies (ART). (Seage, PI: Kenneth Freedberg)

Identification of GyrA/B Mutations that Predict Fluoroquinolone Resistant TB
The aim of this project is to evaluate the correlation between newly-developed molecular genetic probes that can detect mutations in the gryA and gryB genes of tuberculosis which may render them more resistant to first and later generation quinolones. (Murray, PI: Maha Farhat)