(P. aeruginosa aggregates in CF Patient Sample)
Microbial evolution in the CF airway (Cooper, Myerburg, Bomberger): Dr. Cooper is an evolutionary microbiologist and is interested in the evolution that occurs during human infections, particularly in the airway of cystic fibrosis patients. He has developed laboratory models of this process. His laboratory has identified evolved mutations with the Illumina NextSeq platform and their comprehensive bioinformatic analytical capacity, fueling collaborations with dozens of laboratories at the University of Pittsburgh and worldwide. In collaboration with Dr. Myerburg, the Cooper lab is focused on adaptations to antibiotics and to biofilm formation in P. aeruginosa, the B. cepacia complex and S. aureus in CF. Dr. Cooper’s model of the biofilm life cycle has revealed that many mutations selected during chronic CF infections can be explained by biofilm-related selection alone. The Cooper lab, in collaboration with Dr. Bomberger and the Infection & Immunity (I&I) Core (Core C), has adapted his in vitro biofilm evolution model with organotypic lung cultures (Core A) to examine the impact of the host on bacterial evolution in CF.
Viral-bacterial interactions in the lung (Bomberger, Williams, Corcoran, Lee, Methé, Lakdawala): Clinical observations link respiratory virus infection and Pseudomonas aeruginosa colonization in CF(25-28), yet little is known about viral-bacterial interactions in the CF respiratory tract. Dr. Bomberger’s recent study provides compelling evidence that respiratory viral infections, and the antiviral immune response to them, drive P. aeruginosa to transition from acute to chronic infection, with biofilm biogenesis. Dr. Bomberger is examining the mechanisms by which antiviral signaling promote bacterial biofilm growth and assessing the genes in the antiviral immune response that facilitate biofilm biogenesis, with support of a Vertex Research Innovation Award. Using a mixed species biotic biofilm model with the two most common CF pathogens, P. aeruginosa and S. aureus, these investigators have exciting preliminary data showing that P. aeruginosa outcompetes S. aureus in co-culture on HBE cells (Core A) only in the presence of a virus co-infection. Using metatranscriptomic sequencing, with Core C, the impact of virus infection on S. aureus and P. aeruginosa biofilm populations is being investigated. Polymicrobial in vitro model systems provide an unparalleled ability to model microbial interactions and predict shifts in the communities. This is vital because dominance of a species in mixed microbial communities often correlates with poor patient outcomes in CF. Understanding these microbial interactions as they relate to MCC is also of interest to Dr. Corcoran and has spurred a new collaborative effort.
Translating in vitro studies to examine viral-bacterial interactions in the CF respiratory tract (Bomberger, Cooper, S. Lee, Pilewski, Williams, Morris, Methé): With the goal of translating bench science to the bedside, a collaborative team is studying viral-bacterial interactions in the upper respiratory tract (paranasal sinuses) and airways. Investigators are examining how viral exacerbations in CF patients alter the microbial composition of the upper and lower respiratory tract, examining both overall community diversity and diversity within the P. aeruginosa population in longitudinal sinonasal and sputum samples from patients at the Adult Cystic Fibrosis Clinic, UPMC (Core D). Metagenomics and metatranscriptomics will be used to define the overall genus and species abundance, distribution and function in the upper and lower respiratory tract (Core C). To measure the composition of the dominant P. aeruginosa population, whole genome sequencing of P. aeruginosa present in both upper and lower respiratory tract will be performed. This is important because bacterial burden rarely changes during exacerbation in CF, leading many to hypothesize that a common cause for exacerbations is respiratory viral infection and/or the shift in dominance of a bacterial mutant that leads to worsened pulmonary function. Dr. Methé’s team is integrating all study data (Core C), including demographics, pulmonary function values, sinonasal symptoms, quality of life measures, 16S microbial profiles, viral panels, and whole genome sequencing data for P. aeruginosa, to develop a model that can be used for hypothesis testing and ultimately to predict those patients whose lung function may worsen (vs. remain stable) following viral infection.
Identification of P. aeruginosa biofilm inhibitors (Zemke, Pilewski, Bomberger, Gladwin, Di): Due to the lack of small animal models that suitably recapitulate P. aeruginosa biofilm growth in the human respiratory tract, the in vitro biotic biofilm models of primary airway (Core A) or organotypic respiratory epithelial cultures used by the Bomberger lab and I&I Core are the first of their kind to support the study of bacterial biofilm development in the lung. In addition to the iron chelation clinical study in development (described above), they are also utilizing in vitro studies to develop new antibiofilm therapeutic approaches. Drs. Bomberger and Montelaro recently reported that an engineered antimicrobial peptide (WLBU2) disrupts extremely antibiotic resistant bacterial biofilms grown during a viral co-infection while concurrently reducing viral burden. This is the first synthetic antimicrobial peptide with activity across kingdoms, targeting both viral and bacterial pathogens during a polymicrobial infection. These studies on WLBU2 generated significant interest in the therapeutic development of this compound and spurred the founding of a startup company (Peptilogics) to support its clinical development. Dr. Di is continuing to study WLBU2 applications to pulmonary infections, using in vivo pneumonia models and D-amino acid analogs to improve stability for clinical applications.
Sodium nitrite as an antibiofilm therapy: A collaborative series of studies with Drs. Zemke, Gladwin, Bomberger and Pilewski described the antibiofilm properties of sodium nitrite and its mechanism of action. Sodium nitrite has broad antimicrobial properties and has been tolerated as a nebulized compound at high concentrations in human subjects; however, its effects have not been evaluated on biotic biofilms or in combination with other clinically useful antibiotics. Using the unique resources in Core A, members of the research team determined that nitrite alone prevented 99% of biofilm growth of P. aeruginosa on the apical surface of primary human airway epithelial cells. In testing interactions with existing antibiotics, they identified significant cooperative inhibitory effects of nitrite and polymyxins, which resulted in an additional log increase of bacterial growth inhibition compared to treating with either agent alone. As described in Core D, Phase I/ IIA clinical studies of sodium nitrite in patients with CF are underway at our center (supported by a CFF Clinical Research Grant). Importantly, these studies have supported Dr. Zemke, a pulmonary and critical care physician scientist in the Bomberger laboratory (Harry Swachman Clinical Investigator Award from the Cystic Fibrosis Foundation and NIH K23 awardee) in her transition to her own independent research program. Dr. Zemke is participating in the clinical trial to assess the safety and antibiofilm properties of sodium nitrite, highlighting our ability to translate our studies at the bench to the bedside.