AsPIRES (Assessing Predictors of Infant RSV Effects and Severity) - Identification of host responses to Respiratory Syncytial Virus (RSV) infection and identification of factors associated with severe disease (Walsh)
A clinical translational study in two cohorts of infants, representing the full spectrum of RSV disease severity, in which innate and adaptive immune status are comprehensively measured in association with environmental, viral, and bacteriologic factors.
Validation of Gene Array to Predict Bacterial Co-infection In Adults Hospitalized with Viral Lower Respiratory Tract Infections (LRTI) (Mariani/Fasley)
The primary goal of the current innovation project is to conduct analysis of the RNASeq data collected in DMID 13-0070, in an effort to identify gene expression variables capable of classifying, or predicting, bacterial and viral infection in adults with LRTI. The secondary goal is to perform gene expression validation of previously identified and new predictors.
Integrative Analysis of Microbiome, Host Transcriptome, Immune Biomarkers, and Clinical Outcomes in Collaboration with the Rochester Respiratory Pathogens Research Center (Glass/Liu)
We coexist with a vast number of microbes—our microbiota—that live in and on our bodies. Although much has been learned about the diversity and distribution of human-associated microbial communities, little is known about the biology of microbiota, how it interacts with the host, and how the host responds to its resident microbiota. Integrating microbiomics, host omics data, and clinical outcomes will help us identify biological risk factors that predict disease progression. In particular, we plan to conduct an integrative analysis of microbiomics, host transcriptomics, immune biomarkers, and clinical outcomes of human infants in both DMID 12-0004 and 12-0012 studies to understand the molecular correlates of disease severity.
Testing for an impaired function of cord blood T regulatory cells from preterm neonates who are predisposed to developing severe respiratory viral infection versus gestational age-matched controls (Misra)
The overall goal of the project is to provide a manuscript at the end of the study period, which describes the function of T regulatory cells from the cord blood of infants who are born preterm in the presence of inflammation of the umbilical cord and those who develop the lung disease Bronchopulomnary Dysplasia.
Testing of Sputum by Film Array for viral and atypical bacterial respiratory pathogens (Falsey)
The purpose of this project was to develop a simple method to test sputum in a fully automated PCR system. Archived samples from R01AI079446-01 were used. The work was consistent with the original intent and consent of the study to develop better tests for diagnosis of viral and bacterial infection.
Pneumococcal Colonization in Older Adults (Falsey)
Determine the cumulative incidence of pneumococcal carriage over an 8 month period of time in persons > 65 years of age. Evaluate potential variables that influence the risk of carriage. Depending on the cumulative incidence the following secondary objectives will be explored. Samples will be collected and stored in such a way to allow future testing as warranted.
H5 Influenza Vaccine Study: Gene Expression and HAI Antibody Response Analysis (Topham)
This study takes advantage of existing clinical samples (frozen PBMC) collected as part of DMID-08-0059. This study was comprised of three groups of subjects that differ in their pre-vaccination immune status. All subjects are healthy adults between the ages of 18 and 64. Samples for assessment of B cell and CD4 T cell responses were obtained on days 0, 3, 7, 14, and 28 following each dose of vaccine. In the current project, we plan to use the day 0, 3 and 7 samples after each immunization to assess host gene expression. The goal is to better understand differences in the innate immune response to vaccination that predict vaccine outcome (production of antibody).
ß-lactam antibiotic resistance in Mycobacterium abscessus (Pavelka)
We will determine the susceptibility of M. abscessus strains to various β-lactam antibiotics in the presence or absence of different β-lactamase inhibitors. We will also clone the two β-lactamase genes from M. abscessus into a plasmid for overexpression in E. coli for purification, followed by in vitro β-lactamase enzyme assays. Finally, we will construct mutant strains of M. abscessus and evaluate their antibiotic resistance profiles.
A Multiplex Label-Free Chip for Pneumococcus Serology (Miller/Nahm)
We will develop a new label-free antibody microarray for Pneumoccus serology. As part of this process, we will benchmark the performance of the new array versus the standard serologic methodology using bacterial culture supernatants. Completion of these initial studies will set the stage for an expanded development effort targeting a pneumococcus serology array incorporating antibodies to all known serotypes.
Impact of Influenza-specific Regulatory T cells on the Magnitude of Immunity of Influenza Infection and Vaccination (Fowell)
Regulatory T cells (Tregs) play a fundamental role in modulating immune responses: homeostatically to self-antigen and following infectious challenge. Originally shown to dampen immune responses to infection and limit pathogen clearance, in recent years we have begun to appreciate the beneficial role of Tregs in limiting immune pathology associated with infection. Therefore, the balance between detrimental and beneficial roles for Tregs is likely to be context dependent and pathogen specific. Critical gaps in knowledge of Tregs in influenza: CD4+Foxp3+ Tregs expand to influenza infection in mice with similar kinetics to conventional CD4+ T cells (Tconv) and some of these expanded Tregs appear to be virus-specific. Using TCR transgenic systems, antigen-specific Tregs can be shown to limit the recall response to influenza infection and control the extent of infection-induced immunopathology. However, in the absence of elevated frequencies afforded by a TCR-Tg, the role of virus-specific Tregs in shaping responses to influenza is unclear. In humans, the degree of influenza-specific Treg expansion to infection or vaccination is not known. Nor do we know if repeated exposure to influenza antigens builds a robust virus-specific Treg population that modifies responsiveness to new viral challenge.
Validation of Gene Array to predict bacterial co-infection in adults hospitalized with LRTI (Falsey)
The objective of this project is to prospectively validate 15 classifier genes previously identified as useful to differentiate viral, bacterial and mixed viral- bacterial infections in adults hospitalized with LRTI. RNA sequencing will be used to validate previous findings and explore potentially new alternative gene expression patterns. To accomplish this goal ~ 300 adults hospitalized with LRTI will be prospectively enrolled, microbiologic testing performed and RNA sequencing will be performed in those with identifiable viral and or bacterial infection.
Complement dependent lytic (CDL) and antibody dependent cellular cytotoxicity (ADCC) antibodies after influenza vaccination (Ennis)
Antibodies neutralize influenza infectivity by binding to the HA protein or by inhibiting virus release by binding to the neuraminidase protein. In addition, influenza -specific antibodies can bind to infected cells, and lyse these cells through the action of complement (complement dependent lysis- CDL) or through NK cells (antibody dependent cellular cytotoxicity-ADCC). We are planning to test serum samples collected as part of experimental human H7N9 vaccine trials in order to better understand the role that CDL and ADCC antibodies play in protection against influenza infection.