Identifying Bacterial Biomarkers Associated with Disease Progression in Cystic Fibrosis

Steck, Todd

Abstract

The evolution of pulmonary disease in cystic fibrosis (CF) usually begins during childhood when environmental and commensal bacteria get trapped in the sticky mucus of the lungs and become established as chronic infections. Inflammation and respiratory failure from these chronic infections is the primary cause of death in people with CF. While most patients at a young age experience long periods of stability, periods of acute illness, known as pulmonary exacerbations (PE)s, can occur multiple times per year and result in permanent damage to the lungs. Little is known of the shift from a period of stability to a PE but this shift is often attributed to changes in bacterial abundance prior to an elevation of patiet signs and symptoms. For many decades identifying bacteria in the CF lung was limited to only those species which could be cultured from lungs. Within the past two decades researchers have discovered a vast number of different bacterial species inhabiting the lungs by using culture-independent techniques. In a three-year study of a single CF patient, we used culture-independent analyses and sputum samples collected weekly to monitor changes to the microbiota that occurred during nine PEs. Different from most bacterial studies on CF, we performed genus-specific quantitative PCR (qPCR) on bacterial DNA from sputum and identified an overall increase in bacterial abundance over time, an increase in the abundance of Burkholderia multivorans, a CF- associated pathogen, but no increase in Pseudomonas aeruginosa, the primary pathogen, prior to the occurrence of a PE. Applying Illumina sequencing to a subset of these samples revealed a stable microbiota consisting of ~160 distinct taxa. In addition, we identified an inverse relationship with the number of different taxa and time which was likely due to repeated antibiotic exposure. We propose to utilize the innovative approach of combining both Illumina sequencing and qPCR on frequently collected sputum samples from multiple adolescent patients to identify biomarkers for PE occurrence and antibiotic efficacy by correlating changes in the microbial community with changes in patient health. Our goals for the R15, Academic Research Enhancement Award proposal are to identify changes in the lung bacterial community that reflect patient health, predict onset of an exacerbation, and reveal the in vivo effects of antibiotic treatment.

Public Health Relevance

Our group has shown that applying quantitative PCR and Illumina sequencing technology allows us to detect changes to the bacterial community in a CF lung that occur over time and prior to the onset of a pulmonary exacerbation with more accuracy than either method alone. In this Academic Research Enhancement Award (AREA) R15 proposal, we will simultaneously monitor patient health and changes to the bacterial community within CF patients over time to learn which members of the microbiota: predict onset of a PE, are affected by antibiotic therapy, and are involved in disease progression in CF patients. Our long term goal is to develop tools to allow CF patients to better manage symptoms of an exacerbation and slow the progression of irreversible lung disease.