This is a randomized, open-label pilot study to assess whether treatment with chlorhexidine mouthwash can alter the esophageal and gastric cardia microbiome

Patients scheduled for upper endoscopy for clinical indications will be randomized to 3 weeks of either no treatment or use of twice daily chlorhexidine mouthwash leading up to the endoscopy. There will be 2-3 study visits, at Day 0 and Day 21, and for those subjects in the mouthwash arm, a final visit 1-2 weeks following the Day 21 visit. Subjects will be required to fast overnight prior to the visits on Days 0 and 21.

Inclusion Criteria:

• Age >18
• Scheduled for upper endoscopy for clinical indications
• No allergy or other contraindication to chlorhexidine

Exclusion Criteria:

• Use of proton pump inhibitors or H2 receptor antagonists within 1 month of enrollment. Acid suppressant medications raise the gastric pH and can dramatically alter the gastric and esophageal microbiome.
• History of upper gastrointestinal cancer
• History of histologically proven Barrett's esophagus
• History of antireflux or bariatric surgery, or other gastric or esophageal surgery
• Use of antimicrobial mouthwash within 1 month of enrollment
• Use of antibiotics or immunosuppressant medications within 3 months of enrollment
• Use of steroid inhalers or nasal sprays within 1 month of enrollment
• HIV or other immunosuppressed states or conditions (e.g. active malignancy)
• Pregnant or breast feeding
• Inability to give informed consent

21 days

Participants were instructed to report any side effects of chlorhexidine. Tooth discoloration (a possible side effect of chlorhexidine use) was assessed by a dentist using photographs. The dentist was blinded to whether the images were from pre- or post-treatment.

There were no indications for repeated endoscopies, so the analysis of the esophagus was limited to a single point in time; relatively small sample size.