Bacterial Gene Profiling to Predict Antibiotic Resistance During Cystic Fibrosis Pulmonary Exacerbations

Study Overview
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Brief Summary
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Pulmonary exacerbations (PEx) are key events that lead to a decline in health status among CF patients, with many never recovering to baseline health. With the advancement of new CFTR modulators and other therapies increasing the lifespan of those living with CF, it will become increasingly important to have better strategies to manage PEx in order to have better outcomes following treatment. PEx treatment decisions will need to take into consideration the increasing frequency of antimicrobial resistance bacteria and the need to treat multiple types of bacteria at once. The purpose of this study is to analyze sputum samples from CF subjects at the time of PEx in order to identify markers of antimicrobial resistant bacteria and see how those relate to treatment responses. CF patients will be recruited from patients followed by the Adult CF Program at National Jewish Health. Within 48 hours of admission to the hospital for treatment of a PEx, subjects will be enrolled and sputum will be collected. The sputum will be processed and analyzed for the presence of antimicrobial resistant bacteria. These results will be compared to clinical data, such as spirometry and frequency of hospitalizations.

Official Title
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Bacterial Gene Profiling to Predict Antibiotic Resistance During Cystic Fibrosis Pulmonary Exacerbations

Conditions
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Cystic Fibrosis

Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: CF patients 18 years or older who are hospitalized for IV treatment of an acute PEx Chronically infected with Pseudomonas aeruginosa and/or Staphylococcus aureus Can produce sputum Can provide written consent Willing to comply with study procedure Exclusion Criteria: Subjects who are not colonized with Pseudomonas aeruginosa and/or Staphylococcus aureus The presence of a condition or abnormality that, in the opinion of the Principal Investigator, would compromise the safety of the patient or the quality of the data

Ages Eligible for Study
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Minimum Age: 18 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Targeted amplicon sequencing of sputum | Results from CF specific amplicon panel; this may include number and identity of bacterial species, presence or absence of AMR genes, frequencies of strain types, and AMR genes per total bacteria | Within 48 hours of initiation of IV antibiotic treatment for CF pulmonary exacerbation | 
| Sputum microbiology | Traditional sputum microbiology results; this may include quantitative culture data for each pathogen, antimicrobial susceptibilities, and minimum inhibitory concentration (MIC) | Within 48 hours of initiation of IV antibiotic treatment for CF pulmonary exacerbation | 
| Change in lung function | Change in lung function as measured by FEV1, % predicted. | At initiation of IV antibiotic treatment and after one week of IV antibiotic treatment | 

Secondary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Changes in hospitalizations | Changes in frequency/number of hospitalizations for treatment of CF pulmonary exacerbation | 12 months prior to enrollment to 12 months after enrollment | 
| Antimicrobial regimens | Type/total number of IV antibiotic doses delivered | Throughout course of hospitalization, on average 14 days |