Changes in fecal microbiota with CFTR modulator therapy: A pilot study.

Studies have demonstrated that people with CF with pancreatic insufficiency (PI) have fecal dysbioses. Evidence suggests the causes of these dysbioses are multifactorial, and that important drivers include antibiotic exposure, dietary intake, and CF gastrointestinal tract dysfunction, including nutrient malabsorption. In this pilot study, we tested whether initiation of the CFTR modulator treatments ivacaftor (in a cohort of pancreatic sufficient (PS) people with CF and an R117H CFTR variant) or lumacaftor/ivacaftor (in a cohort of PI people with CF and an F508del variant) changed fecal measures of malabsorption or fecal microbiomes. While we identified no statistically significant fecal changes with either treatment, we detected trends in the PI cohort when initiating lumacaftor/ivacaftor towards decreased fecal fat content and towards fecal microbiomes that more closely resembled the fecal microbiota of people without PI. While these findings support a model in which nutrient malabsorption resulting from CF-induced PI drives fecal dysbiosis, they must be validated in future, larger studies of fecal microbiome and malabsorption outcomes with highly effective CFTR modulator therapies.

Gut microbiome as a response marker for pancreatic enzyme replacement therapy in a porcine model of exocrine pancreas insufficiency.

BACKGROUND: Exocrine pancreatic insufficiency (EPI) is characterized by the loss of active pancreatic enzymes and a resulting severely reduced food digestion. EPI therapy requires orally applied pancreatic enzyme replacement. The gut microbiome is a known mediator of intestinal diseases and may influence the outcome of EPI and the effects of a pancreatic enzyme replacement therapy (PERT). Here, we analyzed the effects of EPI and PERT on the gut microbiome in the model of pancreatic duct ligated minipigs. RESULTS: The microbial community composition in pig feces was analyzed by next generation sequencing of 16S rRNA amplicons. The data were evaluated for α- and ß-diversity changes and changes at the different Operational Taxonomic Unit (OTU) levels by Shannon-Wiener and inverse Simpson index calculation as well as by Principal Coordinates Analysis based on Bray-Curtis dissimilarity. Microbial α-diversity was reduced after EPI induction and reverted to nearly healthy state after PERT. Analysis of microbial composition and ß-diversity showed distinctive clusters of the three study groups and a change towards a composition comparable to healthy animals upon PERT. The relative abundance of possible pathobionts like Escherichia/Shigella, Acinetobacter or Stenotrophomonas was reduced by PERT. CONCLUSION: These data demonstrate that EPI-induced dysbiosis could be reverted by PERT to a nearly healthy state. Elevated α-diversity and the reduction of bacterial overgrowth after PERT promises benefits for EPI patients. Non-invasive microbiome studies may be useful for EPI therapy monitoring and as marker for response to PERT.

The Gut Microbiome in Patients With Chronic Pancreatitis Is Characterized by Significant Dysbiosis and Overgrowth by Opportunistic Pathogens.

INTRODUCTION: Exocrine pancreatic function is a critical host factor in determining the intestinal microbiota composition. Diseases affecting the exocrine pancreas could therefore influence the gut microbiome. We investigated the changes in gut microbiota of patients with chronic pancreatitis (CP). METHODS: Patients with clinical and imaging evidence of CP (n = 51) were prospectively recruited and compared with twice the number of nonpancreatic disease controls matched for distribution in age, sex, body mass index, smoking, diabetes mellitus, and exocrine pancreatic function (stool elastase). From stool samples of these 153 subjects, DNA was extracted, and intestinal microbiota composition was determined by bacterial 16S ribosomal RNA gene sequencing. RESULTS: Patients with CP exhibited severely reduced microbial diversity (Shannon diversity index and Simpson diversity number, P < 0.001) with an increased abundance of facultative pathogenic organisms (P < 0.001) such as Enterococcus (q < 0.001), Streptococcus (q < 0.001), and Escherichia.Shigella (q = 0.002). The CP-associated changes were independent of exocrine pancreatic insufficiency. Short-chain fatty acid producers, considered protective for epithelia such as Faecalibacterium (q < 0.001), showed reduced abundance in patients with CP. Of 4 additional patients with CP previously treated with antibiotics (ceftriaxone and metronidazole), 3 patients were characterized by distinct Enterococcus overgrowth. DISCUSSION: CP is associated with marked gut microbiota dysbiosis, greatly reduced diversity, and increased abundance of opportunistic pathogens, specifically those previously isolated from infected pancreatic necrosis. Taxa with a potentially beneficial role in intestinal barrier function are depleted. These changes can increase the probability of complications from pancreatitis such as infected fluid collections or small intestinal bacterial overgrowth (see Graphical Abstract, Supplementary Digital Content 1, http://links.lww.com/CTG/A383).

Interaction among variants in the SLC gene family (SLC6A14, SLC26A9, SLC11A1, and SLC9A3) and CFTR mutations with clinical markers of cystic fibrosis.

BACKGROUND: Cystic fibrosis (CF) is due to dysfunction of the CFTR channel and function of this channel is, in turn, affected by modifier genes that can impact the clinical phenotype. In this context, we analyzed the interaction among rs3788766*SLC6A14, rs7512462*SLC26A9, rs17235416*SLC11A1, and rs17563161*SLC9A3 variants, CFTR mutations and 40 CF severity markers by the Multifactor Dimensionality Reduction (MDR) model. METHODS: A total of 164 patients with CF were included in the study. The variants in the modifier genes were identified by real-time PCR and the genotype of the CFTR gene in the diagnostic routine. Analysis of interaction between variants, CFTR mutations groupings and demographic, clinical and laboratory data were performed by the MDR. RESULTS: There were interaction between the rs3788766, rs7512462, rs17235416, and rs17563161 variants, and CFTR mutations with pancreatic insufficiency (PI), onset of digestive symptoms, and presence of mucoid Pseudomonas aeruginosa. Regarding PI, the interaction was observed for CFTR*rs17563161 (P-value = 0.015). Also, for onset of digestive symptoms the interaction was observed for CFTR*rs3788766*rs7512462*rs17235416*rs17563161 (P-value = 0.036). Considering the presence of mucoid P. aeruginosa, the interaction occurred for CFTR*rs3788766*rs7512462*rs17563161 (P-value = 0.035). CONCLUSION: Interaction between variants in the SLC family genes and the grouping for CFTR mutations were associated with PI, onset of digestive symptoms and mucoid P. aeruginosa, being important to determine one of the factors that may cause the diversity among the patients with CF.

The prevalence of small intestinal bacterial overgrowth in non-surgical patients with chronic pancreatitis and pancreatic exocrine insufficiency (PEI).

BACKGROUND: Small intestinal bacterial overgrowth (SIBO) is a condition characterised by symptoms similar to pancreatic exocrine insufficiency (PEI) in chronic pancreatitis patients. SIBO is thought to complicate chronic pancreatitis in up to 92% of cases; however, studies are heterogeneous and protocols non-standardised. SIBO may be determined by measuring lung air-expiration of either hydrogen or methane which are by-products of small bowel bacterial fermentation of intraluminal substrates such as carbohydrates. We evaluated the prevalence of SIBO among a defined cohort of non-surgical chronic pancreatitics with mild to severe PEI compared with matched healthy controls. METHODS: Thirty-five patients and 31 age-, gender- and smoking status-matched healthy controls were evaluated for SIBO by means of a fasting glucose hydrogen breath test (GHBT). The relationship between SIBO and clinical symptoms in chronic pancreatitis was evaluated. RESULTS: SIBO was present in 15% of chronic pancreatitis patients, while no healthy controls tested positive (P = 0.029). SIBO was more prevalent in those taking pancreatic enzyme replacement therapy (PERT) (P = 0.016), with proton pump inhibitor use (PPI) (P = 0.022) and in those with alcohol aetiology (P = 0.023). Patients with concurrent diabetes were more often SIBO-positive and this was statistically significant (P = 0.009). There were no statistically significant differences in reported symptoms between patients with and without SIBO, with the exception of 'weight loss', with patients reporting weight loss more likely to have SIBO (P = 0.047). CONCLUSION: The prevalence of SIBO in this study was almost 15% and consistent with other studies of SIBO in non-surgical chronic pancreatitis patients. These data support the testing of patients with clinically-relevant PEI unresolved by adequate doses of PERT, particularly in those patients with concurrent diabetes. SIBO can be easily diagnosed therefore allowing more specific and more targeted symptom treatment.

Clinafloxacin for Treatment of Burkholderia cenocepacia Infection in a Cystic Fibrosis Patient.

Respiratory infection with Burkholderia cenocepacia is associated with accelerated decline in lung function and increased mortality in cystic fibrosis (CF) patients (A. M. Jones, M. E. Dodd, J. R. W. Govan, V. Barcus, C. J. Doherty, J. Morris, and A. K. Webb, Thorax 59:948-951, 2004, http://dx.doi.org/10.1136/thx.2003.017210). B. cenocepacia often possesses innate resistance to multiple antimicrobial classes, making eradication uncommon in established infection (P. B. Davis, Am J Respir Crit Care Med 173:475-482, 2006, http://dx.doi.org/10.1164/rccm.200505-840OE). We report the use of clinafloxacin in a CF patient with advanced B. cenocepacia infection, present pharmacokinetic (PK) data, and discuss the potential therapeutic role of clinafloxacin in patients with this condition.

[Small intestine bacterial overgrowth in patients with chronic pancreatitis]. / Sobrecrecimiento bacteriano intestinal en pacientes con pancreatitis crónica.

BACKGROUND: Previous reports describe 30-40% of small intestine bacterial overgrowth (SIBO) in patients with chronic pancreatitis (CP), SIBO is a cause of persistent symptoms in this group of patients even when they are treated with pancreatic enzymes. AIM: To asses the frequency of SIBO in patients with CP. PATIENTS AND METHODS: We studied 14 patients with CP using an hydrogen breath test with lactulose to detect SIBO, a nonabsorbable carbohydrate, whose results are not influenced by the presence of exocrine insufficiency. Main symptoms and signs were bloating in 9 (64%), recurrent abdominal pain in 8 (57%), intermittent diarrhea in 5 (36%) and steatorrhea in 5 (36%). At the same time we studied a healthy control group paired by age and sex. RESULTS: SIBO was present in 13 of 14 patients with CP (92%) and in 1 of 14 controls (p<0.001). The only patient with CP and without SIBO was recently diagnosed and had minimal morphologic alterations in computed tomography and endoscopic pancreatography. CONCLUSIONS: SIBO is common in CP and may be responsible for persistent symptoms. Proper diagnosis and treatment could alleviate symptoms and improve quality of Ufe.

Sobrecrecimiento bacteriano intestinal en pacientes con pancreatitis crónica / Small intestine bacterial overgrowth in patients with chronic pancreatitis

Background: Previous reports describe 30-40 percent of small intestine bacterial overgrowth (SIBO) in patients with chronic pancreatitis (CP), SIBO is a cause of persistent symptoms in this group of patients even when they are treated with pancreatic enzymes. Aim: To asses the frequency of SIBO in patients with CP. Patients and methods: We studied 14 patients with CP using an hydrogen breath test with lactulose to detect SIBO, a nonabsorbable carbohydrate, whose results are not influenced by the presence of exocrine insufficiency. Main symptoms and signs were bloating in 9 (64 percent), recurrent abdominal pain in 8 (57 percent), intermittent diarrhea in 5 (36 percent) and steatorrhea in 5 (36 percent). At the same time we studied a healthy control group paired by age and sex. Results: SIBO was present in 13 of 14 patients with CP (92 percent) and in 1 of 14 controls (p<0.001). The only patient with CP and without SIBO was recently diagnosed and had minimal morphologic alterations in computed tomography and endoscopic pancreatography Conclusions: SIBO is common in CP and may be responsible for persistent symptoms. Proper diagnosis and treatment could alleviate symptoms and improve quality of life.

Hydrogen breath test with glucose in exocrine pancreatic insufficiency.

The present study was designed to investigate the prevalence of bacterial overgrowth in patients with exocrine pancreatic insufficiency by using the hydrogen breath test with glucose. Thus, in 30 patients with exocrine pancreatic insufficiency (in 15 due to chronic pancreatitis and in 15 associated to primary immunodeficiency), established by quantifying trypsin output before and after stimulation with cerulein using a duodenal perfusion technique, a glucose test was performed by administering 50 g of glucose and quantifying H2 in the breath by gas chromatography. The glucose test was positive in six of 15 patients with chronic pancreatitis but in only one of 15 immunodeficient patients (p < 0.05). Age, sex, etiology, time of evolution, associated diabetes, pancreatic calcifications, duodenal pH, or duodenal trypsin output did not differ between patients with and those without bacterial overgrowth. Previous gastroduodenal surgery was more common in chronic pancreatitis patients with overgrowth (six of six vs. four of nine; p < 0.05). Five patients with a positive glucose test were treated with antibiotics for 2 weeks and became negative in two of them. These results suggest that a positive glucose test indicating overgrowth is relatively common in exocrine pancreatic insufficiency due to chronic pancreatic, especially in patients with previous gastroduodenal surgery.

Effect of treatment on the jejunal and colonic bacterial flora of dogs with exocrine pancreatic insufficiency.

The bacterial flora from the jejunum and colon of 19 dogs with naturally occurring exocrine pancreatic insufficiency (EPI) was examined. In six dogs with EPI that did not receive any treatment the bacterial count in the small intestine was > 10(6) colony-forming units (CFU)/g. This was consistent with bacterial overgrowth (BOG) (control dogs: < 10(5) CFU/g). Six dogs with EPI that received pancreatic enzyme supplementation and were in good condition had bacterial counts (> 10(6) CFU/g) that were nonsignificantly different from the untreated group. The remaining seven dogs with EPI that received both pancreatic enzyme supplementation and oral antibiotic therapy (tylosin), had bacterial flora counts that were significantly lower than the values in the other two groups of EPI dogs, and did not differ significantly from those of the control group. There were no statistical differences between the number of bacteria in the colon among the different groups of dogs with EPI and the control dogs. We conclude that the prevalence of BOG in dogs with EPI is high. Pancreatic enzyme supplementation did not affect the microflora of dogs with naturally occurring EPI. Oral antibiotic therapy with tylosin, however, effectively decreased BOG in these dogs.

Effects of exocrine pancreatic insufficiency and replacement therapy on the bacterial flora of the duodenum in dogs.

The influence of pancreatic secretions on the bacterial flora of the small intestine in 6 dogs was investigated by determining effects of exocrine pancreatic insufficiency on numbers and types of bacteria in duodenal juice, and by examining the subsequent response to dietary supplementation with bovine pancreatic extract. Exocrine pancreatic insufficiency was induced by ligation of pancreatic ducts and was confirmed by indirect assessment of exocrine pancreatic function. Duct ligation was followed by large increases (P less than 0.01) in total numbers of bacteria, reflecting increased numbers particularly of Lactobacillus spp and Streptococcus spp, in 3 dogs accompanied by obligate anaerobes. Total numbers of aerobes and anaerobes decreased markedly (P less than 0.05) after supplementation with bovine pancreatic extract to values that were not significantly different from those determined before duct ligation. Exocrine pancreatic insufficiency therefore resulted in small intestinal bacterial overgrowth that was reversed by pancreatic replacement therapy, indicating that pancreatic secretions can have an important influence on the small intestinal bacterial flora of dogs.

Bacterial overgrowth in the duodenum of dogs with exocrine pancreatic insufficiency.

Bacterial overgrowth (greater than 10(5) colony-forming units/ml duodenal juice) in the duodenum was demonstrated in 8 of 11 dogs with exocrine pancreatic insufficiency (EPI). In 4 of these 8 dogs, the overgrowth included large numbers (greater than 10(4) colony-forming units/ml) of obligate anaerobic bacteria and was associated with decreased activities of several brush border marker enzymes and, in 2 dogs, with partial villous atrophy in the jejunum. Changes in the jejunal mucosa of the remaining dogs (with either no overgrowth or overgrowth of aerobic bacteria alone) were characterized by increased activities of some brush border disaccharides and of lysosomal hydrolases. One dog was euthanatized without treatment, at the owner's request. The response of 4 of the remaining 10 dogs treated with enzyme replacement alone was poor or suboptimal, and all of these 4 dogs had bacterial overgrowth. One of these dogs had an excellent clinical response when also given oxytetracycline orally for 14 days, but the other 3 dogs did not improve further in response to the same treatment. It was concluded that bacterial overgrowth in the duodenum is common in dogs with EPI and that, when such overgrowth includes large numbers of obligate anaerobes, there may be associated biochemical and morphologic abnormalities in jejunal mucosa. Functional disturbances related to abnormal intestinal microflora may be responsible for the failure of some dogs with EPI to respond fully to oral pancreatic enzyme supplementation without antibiotic therapy.