Effect of Acid Blockade on Microbiota and Inflammation in Cystic Fibrosis (CF)

Patients with cystic fibrosis (CF) have significant morbidity and mortality due to airway
infections. These infections are related to the deficiency of mucociliary clearance due to
thick dehydrated secretions. Thus, considerable effort is spent managing airway infections.
This includes therapies to improve mucus clearance and antibiotic treatments that target
important pathogens. Understanding the source of airway microbiota, increased risk of
infection, and exacerbation is critical to improve management of airway infection. A large
proportion of CF patients are also treated with anti-acid medications. These medications
decrease symptoms associated with gastroesophageal reflux disease (GERD), and improve the
efficacy of enzyme replacement therapies. Critical for this proposal is the fact that
aspiration may represent a potential route for airway infection from microorganisms in the
upper gastrointestinal (GI) tract, and anti-acid treatments shift the GI microbiota. In
preliminary studies we have identified a strong alteration of the esophageal microbiota in
subjects using acid blocking medications. Thus, these treatments may have a significant
effect on the bacterial communities present in the upper GI tract and may play a role in
infection and exacerbation in CF. Traditionally, access to the upper GI tract has required
endoscopy to acquire biopsy tissue, which is an invasive procedure and not routinely
performed in CF. To circumvent the invasive sampling required for study of the esophagus we
have recently shown that a minimally invasive test, the esophageal string test (EST), is
capable of sampling the upper GI tract, and has performance comparable to biopsy for a number
of measurements including assessment of the esophageal microbiota.

The primary hypothesis for this proposal is that acid blockade medication alters the
esophageal microbiota in CF, increasing the presence of pathogenic bacteria and inflammation.
To test this hypothesis we propose three Specific Aims:

Specific aim 1: Determine whether esophageal microbial composition in children with CF
changes after withdrawal of acid blockade

1. Comparison of esophageal bacterial load by 16S qPCR in subjects on acid blockade and
after withdrawal

2. Examine the stability of the esophageal bacterial communities based on longitudinal
collection of the esophageal string test (EST) prior to withdrawal of acid blockade
treatment.

3. Determine if there are changes after withdrawal of acid blockade in both sputum
microbiota composition and esophageal microbiota (including presence of pathogenic
bacteria) and whether the changes are correlated across the two sample types.

Specific aim 2: Determine whether esophageal microbiota in children with CF changes after
initiation of acid blockade in patients started for clinical indications

1. Comparison of esophageal bacterial load by 16S qPCR of the esophageal bacteria in
subjects pre and post acid blockade treatment.

2. Examine the stability of the esophageal bacterial communities based on longitudinal
collection of the esophageal string test (EST) prior to acid blockade treatment
initiation.

3. Determine if there are changes after initiation of acid blockade in both sputum
microbiota composition and esophageal microbiota (including presence of pathogenic
bacteria) and whether the changes are correlated across the two sample types.

Specific aim3: Examine the relation between acid blockade medication and inflammation in
association with bacterial communities in subjects from aim 1 and 2

1. CompareIL-8 in the esophagus in subjects with and without acid blockade

2. Compare IL-8 in the sputum in subjects with and without acid blockade and determine
relation between inflammation and association with shifts in the bacterial communities.

Together, these aims will provide novel information regarding the impact of acid blockade
treatment on the esophageal and lung microbiota that may impact management of respiratory
disease in CF. We anticipate similar effects of acid blockade on the esophageal bacterial
communities as we observed in non-CF pediatric and adult subjects, but acknowledge that
treatment burden in CF, particularly antibiotics, may affect the expected outcome. These data
will provide critical information to evaluate the effect of acid blockade on infection risk,
which could affect therapeutic choices for patients with CF. The long-term goal of these
studies, is to improve patient care by assessing the effect of acid blocker therapy on the
microbiota and inflammation.

Inclusion Criteria:

1. Ages 10-21 years

2. Known diagnosis of CF based on sweat chloride > 60 mEq/L or identification of two
known Cystic fibrosis transmembrane conductance regulator (CFTR) mutations

3. Clinically stable pulmonary disease defined by

1. clinical impression of patient's primary CF provider,

2. no newly prescribed antibiotic treatments in the 30 days prior to enrollment, and

3. relativly stable lung function with a forced expiratory volume in 1 second (FEV1)
within 10% of baseline.

4. Male and female

5. Willing to participate in and comply with all study procedures, and

6. Willingness of the subject, parent or legally authorized representative to provide
written informed consent.

7. Body Mass Index (BMI) >25%

8. >40% FEV1.

9. Willing to stop acid blockade medication for 6 weeks for aim 1.

10. Not on acid blockade for 6 weeks for aim 2.

Exclusion Criteria:

1. FEV1 less than 40% predicted

2. History of meconium ileus, distal intestinal obstructive syndrome, gastrointestinal
surgery, or intestinal stricture.

3. CF liver disease with cirrhosis, gastric or esophageal varices.

4. Unwilling to participate in and comply with the study procedures.

5. Unwillingness of the subject, parent or legally authorized representative to provide
written informed consent.

6. Unwilling or unable to swallow the capsule with the esophageal string test (EST).

7. Gelatin allergy.

8. History of esophageal surgery including fundoplication, or

9. Presence of a gastrostomy tube.

10. Confirmed or suspected diagnosis of Gastroesophageal Reflux Disease (GERD)

11. BMI < 25%