Daniel E. Freedberg

Proton pump inhibitors alter the composition of the gut microbiota

Objective Proton pump inhibitors (PPIs) are drugs used to suppress gastric acid production and treat GI disorders such as peptic ulcers and gastro-oesophageal reflux. They have been considered low risk, have been widely adopted, and are often over-prescribed. Recent studies have identified an increased risk of enteric and other infections with their use. Small studies have identified possible associations between PPI use and GI microbiota, but this has yet to be carried out on a large population-based cohort. Design We investigated the association between PPI usage and the gut microbiome using 16S ribosomal RNA amplification from faecal samples of 1827 healthy twins, replicating results within unpublished data from an interventional study. Results We identified a significantly lower abundance in gut commensals and lower microbial diversity in PPI users, with an associated significant increase in the abundance of oral and upper GI tract commensals. In particular, significant increases were observed in Streptococcaceae. These associations were replicated in an independent interventional study and in a paired analysis between 70 monozygotic twin pairs who were discordant for PPI use. We propose that the observed changes result from the removal of the low pH barrier between upper GI tract bacteria and the lower gut. Conclusions Our findings describe a significant impact of PPIs on the gut microbiome and should caution over-use of PPIs, and warrant further investigation into the mechanisms and their clinical consequences.

Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial.

We conducted an open-label crossover trial to test whether proton pump inhibitors (PPIs) affect the gastrointestinal microbiome to facilitate Clostridium difficile infection (CDI). Twelve healthy volunteers each donated 2 baseline fecal samples, 4 weeks apart (at weeks 0 and 4). They then took PPIs for 4 weeks (40 mg omeprazole, twice daily) and fecal samples were collected at week 8. Six individuals took the PPIs for an additional 4 weeks (from week 8 to 12) and fecal samples were collected from all subjects at week 12. Samples were analyzed by 16S ribosomal RNA gene sequencing. We found no significant within-individual difference in microbiome diversity when we compared changes during baseline vs changes on PPIs. There were, however, significant changes during PPI use in taxa associated with CDI (increased Enterococcaceae and Streptococcaceae, decreased Clostridiales) and taxa associated with gastrointestinal bacterial overgrowth (increased Micrococcaceae and Staphylococcaceae). In a functional analysis, there were no changes in bile acids on PPIs, but there was an increase in genes involved in bacterial invasion. These alterations could provide a mechanism by which PPIs predispose to CDI. ClinicalTrials.gov ID NCT01901276.

Frequent p16-Independent Inactivation of p14ARF in Human Melanoma

BACKGROUND The tumor suppressors p14(ARF) (ARF) and p16(INK4A) (p16) are encoded by overlapping reading frames at the CDKN2A/INK4A locus on chromosome 9p21. In human melanoma, the accumulated evidence has suggested that the predominant tumor suppressor at 9p21 is p16, not ARF. However, recent observations from melanoma-prone families and murine melanoma models suggest a p16-independent tumor suppressor role for ARF. We analyzed a group of melanoma metastases and cell lines to investigate directly whether somatic alterations to the ARF gene support its role as a p16-independent tumor suppressor in human melanoma, assuming that two alterations (genetic and/or epigenetic) would be required to inactivate a gene. METHODS We examined the p16/ARF locus in 60 melanoma metastases from 58 patients and in 9 human melanoma cell lines using multiplex ligation-dependent probe amplification and multiplex polymerase chain reaction (PCR) to detect deletions, methylation-specific PCR to detect promoter methylation, direct sequencing to detect mutations affecting ARF and p16, and, in a subset of 20 tumors, immunohistochemistry to determine the effect of these alterations on p16 protein expression. All statistical tests were two-sided. RESULTS We observed two or more alterations to the ARF gene in 26/60 (43%) metastases. The p16 gene sustained two or more alterations in 13/60 (22%) metastases (P = .03). Inactivation of ARF in the presence of wild-type p16 was seen in 18/60 (30%) metastases. CONCLUSION Genetic and epigenetic analyses of the human 9p21 locus indicate that modifications of ARF occur independently of p16 inactivation in human melanoma and suggest that ARF is more frequently inactivated than p16.

Proton Pump Inhibitors and Risk for Recurrent Clostridium difficile Infection Among Inpatients

OBJECTIVES:Observational studies suggest that proton pump inhibitors (PPIs) are a risk factor for incident Clostridium difficile infection (CDI). Data also suggest an association between PPIs and recurrent CDI, although large-scale studies focusing solely on hospitalized patients are lacking. We therefore performed a retrospective cohort analysis of inpatients with incident CDI to assess receipt of PPIs as a risk factor for CDI recurrence in this population.METHODS:Using electronic medical records, we identified hospitalized adult patients between 1 December 2009 and 30 June 2012 with incident CDI, defined as a first positive stool test for C. difficile toxin B and who received appropriate treatment. Electronic records were parsed for clinical factors including receipt of PPIs, other acid suppression, non-CDI antibiotics, and comorbidities. The primary exposure was in-hospital PPIs given concurrently with C. difficile treatment. Recurrence was defined as a second positive stool test 15–90 days after the initial positive test. C. difficile recurrence rates in the PPI exposed and unexposed groups were compared with the log-rank test. Multivariable Cox proportional hazards modeling was performed to control for demographics, comorbidities, and other clinical factors.RESULTS:We identified 894 inpatients with incident CDI. The cumulative incidence of CDI recurrence in the cohort was 23%. Receipt of PPIs concurrent with CDI treatment was not associated with C. difficile recurrence (hazard ratio (HR)=0.82; 95% confidence interval (CI)=0.58–1.16). Black race (HR=1.66, 95% CI=1.05–2.63), increased age (HR=1.02, 95% CI=1.01–1.03), and increased comorbidities (HR=1.09, 95% CI=1.04–1.14) were associated with CDI recurrence. In light of a higher 90-day mortality seen among those who received PPIs (log-rank P=0.02), we also analyzed the subset of patients who survived to 90 days of follow-up. Again, there was no association between PPIs and CDI recurrence (HR=0.87; 95% CI=0.60–1.28). Finally, there was no association between recurrent CDI and increased duration or dose of PPIs.CONCLUSIONS:Among hospitalized adults with C. difficile, receipt of PPIs concurrent with C. difficile treatment was not associated with CDI recurrence. Black race, increased age, and increased comorbidities significantly predicted recurrence. Future studies should test interventions to prevent CDI recurrence among high-risk inpatients.

The impact of proton pump inhibitors on the human gastrointestinal microbiome.

Potent gastric acid suppression using proton pump inhibitors (PPIs) is common in clinical practice but may have important effects on human health that are mediated through changes in the gastrointestinal microbiome. In the esophagus, PPIs change the normal bacterial milieu to decrease distal esophageal exposure to inflammatory gram-negative bacteria. In the stomach, PPIs alter the abundance and location of gastric Helicobacter pylori and other bacteria. In the small bowel, PPIs cause polymicrobial small bowel bacterial overgrowth and have been associated with the diagnosis of celiac disease. In the colon, PPIs associate with incident but not recurrent Clostridium difficile infection.

Proton Pump Inhibitors Do Not Increase Risk for Clostridium difficile Infection in the Intensive Care Unit.

Objectives:Patients in the intensive care unit (ICU) frequently receive proton pump inhibitors (PPIs) and have high rates of Clostridium difficile infection (CDI). PPIs have been associated with CDI in hospitalized patients, but ICU patients differ fundamentally from non-ICU patients and few studies have focused on PPI use exclusively in the critical care setting. We performed a retrospective cohort study to determine the associations between PPIs and health-care facility-onset CDI in the ICU.Methods:We analyzed data from all adult ICU patients at three affiliated hospitals (14 ICUs) between 2010 and 2013. Patients were excluded if they had recent CDI or an ICU stay of <3 days. We parsed electronic medical records for ICU exposures, focusing on PPIs and other potentially modifiable exposures that occurred during ICU stays. Health-care facility-onset CDI in the ICU was defined as a newly positive PCR for the C. difficile toxin B gene from an unformed stool, with subsequent receipt of anti-CDI therapy. We analyzed PPIs and other exposures as time-varying covariates and used Cox proportional hazards models to adjust for demographics, comorbidities, and other clinical factors.Results:Of 18,134 patients who met the criteria for inclusion, 271 (1.5%) developed health-care facility-onset CDI in the ICU. Receipt of antibiotics was the strongest risk factor for CDI (adjusted HR (aHR) 2.79; 95% confidence interval (CI), 1.50–5.19). There was no significant increase in risk for CDI associated with PPIs in those who did not receive antibiotics (aHR 1.56; 95% CI, 0.72–3.35), and PPIs were actually associated with a decreased risk for CDI in those who received antibiotics (aHR 0.64; 95% CI, 0.48–0.83). There was also no evidence of increased risk for CDI in those who received higher doses of PPIs.Conclusions:Exposure to antibiotics was the most important risk factor for health-care facility-onset CDI in the ICU. PPIs did not increase risk for CDI in the ICU regardless of use of antibiotics.

Use of Acid Suppression Medication is Associated With Risk for C. difficile Infection in Infants and Children: A Population-based Study

BACKGROUND Acid suppression medication is associated with Clostridium difficile infection (CDI) in adults and is increasingly prescribed to children. This study evaluated the relationship between acid suppression medication and incident CDI in children. METHODS This was a population-based, nested case-control study. Patients were eligible if they were aged 0-17 years with 3 or more visits or 1 year or more of follow-up in the dataset. Patients were excluded if they had comorbidities that associate with CDI and might also associate with acid suppression medication. Patients with codes for CDI were matched 1:5 with control patients by age, sex, medical practice, time of entry into the dataset, and follow-up time. The primary exposure was use of acid suppression medication with proton pump inhibitors (PPIs) or histamine-2 receptor antagonists (H2RAs) within 8-90 days. RESULTS We identified 650 CDI cases and 3200 controls. The adjusted odds ratio (OR) for CDI and acid suppression medication was 7.66 (95% confidence interval [CI], 3.24-18.1). Acid suppression medication was associated with CDI in infants aged <1 year (OR, 5.24; 95% CI, 1.13-24.4) and children aged 1-17 years (OR, 9.33; 95% CI, 3.25-26.8). There was increased risk for CDI with PPIs compared with H2RAs and with recent compared with distant exposure. CONCLUSIONS Acid suppression medication associated with CDI in infants and children in the outpatient setting, with an effect based on medication timing. Increased risk for CDI should be factored into the decision to use acid suppression medication in children.

Deriving comorbidities from medical records using natural language processing

Extracting comorbidity information is crucial for phenotypic studies because of the confounding effect of comorbidities. We developed an automated method that accurately determines comorbidities from electronic medical records. Using a modified version of the Charlson comorbidity index (CCI), two physicians created a reference standard of comorbidities by manual review of 100 admission notes. We processed the notes using the MedLEE natural language processing system, and wrote queries to extract comorbidities automatically from its structured output. Interrater agreement for the reference set was very high (97.7%). Our method yielded an F1 score of 0.761 and the summed CCI score was not different from the reference standard (p=0.329, power 80.4%). In comparison, obtaining comorbidities from claims data yielded an F1 score of 0.741, due to lower sensitivity (66.1%). Because CCI has previously been validated as a predictor of mortality and readmission, our method could allow automated prediction of these outcomes.

Potential Role of the Microbiome in Barrett’s Esophagus and Esophageal Adenocarcinoma

Esophageal adenocarcinoma and its precursor Barrett’s esophagus have been rapidly increasing in incidence for half a century, for reasons not adequately explained by currently identified risk factors such as gastroesophageal reflux disease and obesity. The upper gastrointestinal microbiome may represent another potential cofactor. The distal esophagus has a distinct microbiome of predominantly oral-derived flora, which is altered in Barrett’s esophagus and reflux esophagitis. Chronic low-grade inflammation or direct carcinogenesis from this altered microbiome may combine with known risk factors to promote Barrett’s metaplasia and progression to adenocarcinoma.

Clostridium difficile infection in the community: are proton pump inhibitors to blame?

Once a nosocomial disease, Clostridium difficile infection (CDI) now appears frequently in the community in the absence of exposure to antibiotics. Prior studies have shown that patients with community-acquired CDI are younger, more likely to be female, and have fewer comorbidities compared to patients with hospital-associated CDI. Because most studies of CDI are hospital-based, comparatively little is known about community-acquired CDI. The recent study by Chitnis has received widespread attention because it used active surveillance to capture all cases of community-acquired CDI within a large population and assessed key risk factors. The authors found that low-level healthcare exposure and proton pump inhibitor use were common among those with non-antibiotics associated, community-acquired CDI. In this commentary, we discuss the changing epidemiology of community-acquired CDI and the evidence basis for the controversial association between proton pump inhibitors and community-acquired CDI.