16S community profiling identifies proton pump inhibitor related differences in gastric, lung, and oropharyngeal microflora

Critical appraisal of how COVID-19 infection and imposed lockdowns have impacted gastroesophageal reflux: A review

Previous literature has demonstrated that COronaVIrus Disease of 2019 (COVID-19) impacts an individual gastrointestinal tract (GIT), causing symptoms like nausea, diarrhea, and loss of appetite. Severe acute respiratory syndrome coronavirus RNA has been discovered in the stool of infected individuals in earlier research. It was discovered that severe acute respiratory syndrome coronavirus was significantly expressed in the GIT, indicating that the virus can also infect the digestive system. Angiotensin-converting enzyme 2 functions as the viral receptor. The chronic illness known as gastroesophageal reflux disease (GERD) is typified by frequent reflux of stomach acid into the esophagus. By triggering the sensitized esophageal-bronchial neuronal circuit or aspirating into the airways (microaspiration), GER exacerbates respiratory diseases. Aspiration is a well-known risk to be considered when treating patients in intensive care units. Strong genetic correlations have been identified between COVID-19 infection and GERD susceptibility, suggesting a shared genetic basis for both conditions. Nonetheless, even though GERD, extraesophageal reflex, and COVID-19 have a number of significant risk factors and exhibit similar symptoms, the relationship between these illnesses has not yet been examined in depth. This review is the first of its kind to critically examine the association between the COVID-19 epidemic and GER and its associated diseases. The key objective of this work is to promote the creation of prevention plans, treatment plans, and guidelines while also enhancing and optimizing our understanding of the relationship between COVID-19 and GERs.

Recent Advances in the Genetic Pathogenesis, Diagnosis, and Management of Esophageal Atresia and Tracheoesophageal Fistula: A Review

Infants born with esophageal atresia and tracheoesophageal fistula, a complex congenital malformation occurring in 1/2500-4000 live births, may suffer threats to their cardiac, respiratory, and digestive health in addition to anomalies that may exist in the genitourinary and musculoskeletal systems. Optimal care for these patients throughout their lives is best achieved through a coordinated, multidisciplinary approach that our health care system is not always well-equipped to provide. This review, though not exhaustive, highlights the components of care that pertain to initial surgical reconstruction and subsequent diagnosis and management of the complications that are most frequently encountered. Authors from among the many specialties involved in the care of these patients summarize the current best practice with attention to the most recent advances. Assessment and improvement of quality of life and transition to adult specialists as children grow to adulthood is also reviewed.

A prospective study of extraesophageal reflux and potential microaspiration in patients hospitalized with COVID-19 in Jordan

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lung infection has represented a global challenge. Intriguingly, it has been shown that the alveolar lung epithelium expresses little Angiotensin Converting Enzyme receptor protein (ACE2), the entry receptor for SARS-CoV-2. Upper airway establishment of infection and translocation to the lung is well documented but other anatomical niches may be relevant to potentially serious lung infection. ACE2 is heavily expressed in the gastrointestinal tract and gastrointestinal symptoms support a clinical diagnosis of Coronavirus disease 2019 (COVID-19). This suggests a research question and the need to gather patient data exploring potential aerodigestive links in SARS-CoV-2 tranlocation and infection which may be relevant in the peripheral lung. This recognizes anatomical proximity and concepts of bi-directional movement between the Gastrointestinal and lung systems in normal physiology and disease. We have therefore explored the potential for gastro oesophageal reflux disease (GORD) micro aspiration and aeorodigestive pathophysiology in a novel prospective investigation of patients hospitalized with COVID-19.

METHODS

This is a prospective descriptive cohort study of 210 patients who were hospitalized with a confirmed diagnosis of COVID-19. The cohort was divided into three groups of patients based on symptom severity and radiological results. The Reflux Symptom Index (RSI) was used to evaluate the presence and severity of GOR. An RSI greater than 13 is considered to be abnormal. Patients' saliva samples were tested using enzyme-linked immunosorbent assay (ELISA) to determine the level of salivary pepsin among the cohort of patients.

RESULTS

A total of 210 patients with COVID-19 were enrolled in the study with 55.2% (116/210) classified as mildly ill, 31.9% (67/210) moderately ill and 12.9% (27/210) as severely ill. 34% (72/210) of the patients had an RSI score of over 13 and a median salivary pepsin value of 54 ± 29 ng/ml which suggested an incidence of extraesophageal reflux (EOR) in around a third of patients. The presence of respiratory comorbid conditions, an RSI score of over 13 and a salivary pepsin level of > 76ng/ml increased the risk of developing a more severe COVID-19 infection.

CONCLUSION

The study showed a high prevalence of EOR among the study cohort and provide the first prospective evidence suggesting the potential for aerodigestive pathophysiology including microaspiration in COVID-19 disease. We believe that the results of our study support the need for more extensive research.

Proton pump inhibitor use and risk of pneumonia: a self-controlled case series study

BACKGROUND

Recent research indicates that use of proton pump inhibitors (PPIs) is associated with pneumonia, but existing evidence is inconclusive because of methodological issues. This study aimed to answer whether PPI-use increases risk of pneumonia while taking the methodological concerns of previous research into account.

METHODS

This population-based and nationwide Swedish study conducted in 2005-2019 used a self-controlled case series design. Data came from national registries for medications, diagnoses, and mortality. Conditional fixed-effect Poisson regression provided incidence rate ratios (IRR) with 95% confidence intervals (CI) for pneumonia comparing PPI-exposed periods with unexposed periods in the same individuals, thus controlling for confounding. Analyses were stratified by PPI-treatment duration, sex, age, and smoking-related diseases. Use of histamine type-2 receptor antagonists (used for the same indications as PPIs) and risk of pneumonia was analysed for assessing the validity and specificity of the results for PPI-therapy and pneumonia.

RESULTS

Among 519,152 patients with at least one pneumonia episode during the study period, 307,709 periods of PPI-treatment occurred. PPI-use was followed by an overall 73% increased risk of pneumonia (IRR 1.73, 95% CI 1.71-1.75). The IRRs were increased across strata of PPI-treatment duration, sex, age, and smoking-related disease status. No such strong association was found between histamine type-2 receptor antagonist use and risk of pneumonia (IRR 1.08, 95% CI 1.02-1.14).

CONCLUSIONS

PPI-use seems to be associated with an increased risk of pneumonia. This finding highlights a need for caution in using PPIs in individuals with a history of pneumonia.

Prevalence of gastro-intestinal symptoms among COVID-19 patients and the association with disease clinical outcomes

Aim

This study examined the various manifestations of COVID-19 in people's gastro-intestinal system and how gastro-intestinal involvement relates to the progression and outcome of the disease.

Methodology

A questionnaire survey was used to collect data from 561 COVID-19 patients between February 6 and 6 April 2022. Laboratory data and clinical outcomes were obtained from the patients' medical records.

Results

39.9% of patients presented gastro-intestinal symptoms, mainly loss of appetite, nausea, vomiting and diarrhea. Gastro-intestinal symptoms were not linked to poorer outcomes such as mortality, ICU admission or length of hospital stays.

Conclusion

gastro-intestinal symptoms were common among patients and may manifest with respiratory symptoms. We recommended clinicians to watch out for gastro-intestinal symptoms as related to COVID-19 infection.

Gastroesophageal Reflux Treatment in Infancy Through Young Adulthood

Gastroesophageal reflux treatment varies greatly across the pediatric age spectrum. Infant reflux treatments rely heavily on nutritional interventions, whereas reflux in older children is treated more commonly with medications. However, because of the broad differential diagnosis, treatment nonresponse merits a re-evaluation of the diagnosis being treated and additional testing to provide a more precision-medicine approach to care.

Can Bioactive Food Substances Contribute to Cystic Fibrosis-Related Cardiovascular Disease Prevention?

Advances in cystic fibrosis (CF) care have significantly improved the quality of life and life expectancy of patients. Nutritional therapy based on a high-calorie, high-fat diet, antibiotics, as well as new therapies focused on CFTR modulators change the natural course of the disease. They do so by improving pulmonary function and growing BMI. However, the increased weight of such patients can lead to unwanted long-term cardiovascular effects. People with CF (pwCF) experience several cardiovascular risk factors. Such factors include a high-fat diet and increased dietary intake, altered lipid metabolism, a decrease in the level of fat-soluble antioxidants, heightened systemic inflammation, therapeutic interventions, and diabetes mellitus. PwCF must pay special attention to food and eating habits in order to maintain a nutritional status that is as close as possible to the proper physiological one. They also have to benefit from appropriate nutritional counseling, which is essential in the evolution and prognosis of the disease. Growing evidence collected in the last years shows that many bioactive food components, such as phytochemicals, polyunsaturated fatty acids, and antioxidants have favorable effects in the management of CF. An important positive effect is cardiovascular prevention. The possibility of preventing/reducing cardiovascular risk in CF patients enhances both quality of life and life expectancy in the long run.

Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort

BACKGROUND

The effects of proton-pump inhibitors (PPIs) on the infant microbiome remain unclear. Swedish pilot cohort study to assess the longitudinal effect of long-term PPI on the infant gut microbiome, including ten newborn infants operated for esophageal atresia exposed to PPIs (mean 57 weeks), compared to healthy one-year-old controls. All children were born vaginally and were otherwise healthy. Within- and between sample diversity of the fecal microbiome was assessed using untargeted whole genome Shotgun metagenomics which sequences all the DNA in the sample and can capture genes rather than a taxonomic fingerprint.

RESULTS

A longer duration of PPI-use was associated with considerable changes in evenness and high variation on diversity within samples compared to a shorter duration of use. The limited difference between baseline samples and controls suggests that this shift was most likely due to the drug exposure and not the underlying alterations on the microbiome. We found no associations with the number of antibiotic treatment episodes among the PPI-users.

CONCLUSION

Prolonged PPI-use may alter the early infant gut microbiome composition, especially those with the most prolonged duration of use.

Proton Pump Inhibitors in Allergy: Benefits and Risks

Proton pump inhibitors (PPIs) are widely prescribed and are indicated for the treatment of several gastrointestinal disorders. Allergists may prescribe PPIs as a result of the coincidence of gastroesophageal reflux disease with asthma or rhinitis, or when gastroesophageal reflux disease presents as chronic cough. Furthermore, long-term, high-dose PPI therapy is a recommended option for managing eosinophilic esophagitis, resulting in histologic remission in approximately 40% of patients. Here, we discuss current recommendations for PPI use, its deescalation, and its side effect profile. We review evidence supporting the epidemiologic link between the use of acid-suppressant medication and the subsequent development of allergic disorders.

A literature review on the potential clinical implications of streptococci in gastric cancer

Streptococcus is widely found in nature and the human body, and most species are not pathogenic. In recent years, studies have found that Streptococcus is associated with gastric cancer. Streptococcus was found to be enriched in the oral cavity, stomach and intestine of gastric cancer patients and found to be increased in gastric cancer tissues, suggesting that Streptococcus may be the pathogenic bacteria underlying gastric cancer. This review discusses the discovery of Streptococcus, the relationship between Streptococcus and gastric cancer, and the possible carcinogenic mechanism of Streptococcus and summarizes the progress of the research on the role of Streptococcus in gastric cancer to provide new ideas for the early detection, diagnosis and treatment of gastric cancer.

Exposure to bile and gastric juice can impact the aerodigestive microbiome in people with cystic fibrosis

Studies of microbiota reveal inter-relationships between the microbiomes of the gut and lungs. This relationship may influence the progression of lung disease, particularly in patients with cystic fibrosis (CF), who often experience extraoesophageal reflux (EOR). Despite identifying this relationship, it is not well characterised. Our hypothesis is that the gastric and lung microbiomes in CF are related, with the potential for aerodigestive pathophysiology. We evaluated gastric and sputum bacterial communities by culture and 16S rRNA gene sequencing in 13 CF patients. Impacts of varying levels of bile acids, pepsin and pH on patient isolates of Pseudomonas aeruginosa (Pa) were evaluated. Clonally related strains of Pa and NTM were identified in gastric and sputum samples from patients with symptoms of EOR. Bacterial diversity was more pronounced in sputa compared to gastric juice. Gastric and lung bile and pepsin levels were associated with Pa biofilm formation. Analysis of the aerodigestive microbiomes of CF patients with negative sputa indicates that the gut can be a reservoir of Pa and NTM. This combined with the CF patient's symptoms of reflux and potential aspiration, highlights the possibility of communication between microorganisms of the gut and the lungs. This phenomenon merits further research.

The association between chronic rhinosinusitis and proton pump inhibitor use: a nested case-control study using a health screening cohort

This study aimed to evaluate the relationship between chronic rhinosinusitis (CRS) and proton pump inhibitor (PPI) use in a Korean population. The Korea National Health Insurance Service-National Sample Cohort was assessed from 2002 to 2013. Patients with CRS (n = 7194) and control participants (n = 28,776) were matched by random order at a 1:4 ratio for age, sex, income group, region of residence, and index date. We analyzed PPI use by patients with and without CRS. ICD-10 codes defined CRS, and claim codes defined previous PPI use. Conditional logistic regression analyzed the crude and adjusted odds ratios (ORs) with 95% confidence intervals (CI). Subgroup analyses were performed according to age and sex. There was a difference in PPI prescription history and prescription duration between the CRS and control groups. The rate of CRS was higher in current (33.8% [263/778]) and past (26.3% [713/2708]) PPI users than PPI non-users (19.1% [6218/32,484], P < 0.001). The adjusted OR (aOR) of CRS with/without nasal polyps was 1.71 (95% CI 1.46–2.02, P < 0.001) and 1.28 (95% CI 1.16–1.41, P < 0.001) in current and past PPI users, respectively. Irrespective of PPI prescription days, PPI use was associated with higher CRS occurrence (aOR 1.46; 95% CI 1.26–1.69, P < 0.001) in the 30–89-day PPI user group. The subgroup analyses results were consistent. The ORs of CRS were higher in PPI users than in the controls, and consistently so in all age and sex groups.

Acid suppression duration does not alter anastomotic stricture rates after esophageal atresia with distal tracheoesophageal fistula repair: A prospective multi-institutional cohort study

INTRODUCTION

Anastomotic stricture is the most common complication after esophageal atresia (EA) repair. We sought to determine if postoperative acid suppression is associated with reduced stricture formation.

METHODS

A prospective, multi-institutional cohort study of infants undergoing primary EA repair from 2016 to 2020 was performed. Landmark analysis and multivariate Cox regression were used to explore if initial duration of acid suppression was associated with stricture formation at hospital discharge (DC), 3-, 6-, and 9-months postoperatively.

RESULTS

Of 156 patients, 79 (51%) developed strictures and 60 (76%) strictures occurred within three months following repair. Acid suppression was used in 141 patients (90%). Landmark analysis showed acid suppression was not associated with reduction in initial stricture formation at DC, 3-, 6- and 9-months, respectively (p = 0.19-0.95). Multivariate regression demonstrated use of a transanastomotic tube was significantly associated with stricture formation at DC (Hazard Ratio (HR) = 2.21 (95% CI 1.24-3.95, p<0.01) and 3-months (HR 5.31, 95% CI 1.65-17.16, p<0.01). There was no association between acid suppression duration and stricture formation.

CONCLUSION

No association between the duration of postoperative acid suppression and anastomotic stricture was observed. Transanastomotic tube use increased the risk of anastomotic strictures at hospital discharge and 3 months after repair.

Impact of Coronavirus Disease 2019 on the Pediatric Population with Aerodigestive Disease

OBJECTIVE

To determine the impact of the coronavirus disease 2019 (COVID-19) quarantine on baseline health, medication use, health anxiety, and healthcare use in pediatric patients with aerodigestive disease and to evaluate for associations of commonly prescribed medications with the risk of COVID-19 illness.

STUDY DESIGN

Prospective study of patients presenting in person to pediatric neurogastroenterology clinics between July 2020 and March 2021.

RESULTS

Of 202 recruited patients, 71.3% were seen in the aerodigestive diseases center and 28.7% in the functional abdominal pain (FAP)/motility clinic. Of all patients, 25.1% reported improved overall health during quarantine; patients with aerodigestive disease (35.3%) reported higher rates of improved overall health compared with patients with FAP/motility disorders (3.6%, P = .0001). Patients with aerodigestive disease had fewer airway symptoms (P < .05) and less medication use during quarantine (inhaled steroids, P < .05 and albuterol, P < .05). Despite objective improvement, there was significant health-related anxiety, with greater anxiety scores reported during and at the end of quarantine (P < .05), with no difference between patient groups (P > .11). Patients continued to access healthcare during quarantine. In total, 28.7% of patients were seen in the emergency department (patients with FAP more than patients with aerodigestive disease, P = .02), and 19.8% were hospitalized. COVID-19 testing was performed in 58.4% of patients and 2.0% (n = 4) of the entire cohort tested positive.

CONCLUSIONS

Patients with aerodigestive disease show improvement of airway symptoms and decreased use of medications during the pandemic, despite increased health-related anxiety. Despite complexities of accessing care due to the widespread lockdown, all patient groups continued to access healthcare.

Intestinal Inflammation and Alterations in the Gut Microbiota in Cystic Fibrosis: A Review of the Current Evidence, Pathophysiology and Future Directions

Cystic fibrosis (CF) is a life-limiting autosomal recessive multisystem disease. While its burden of morbidity and mortality is classically associated with pulmonary disease, CF also profoundly affects the gastrointestinal (GI) tract. Chronic low-grade inflammation and alterations to the gut microbiota are hallmarks of the CF intestine. The etiology of these manifestations is likely multifactorial, resulting from cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction, a high-fat CF diet, and the use of antibiotics. There may also be a bidirectional pathophysiological link between intestinal inflammation and changes to the gut microbiome. Additionally, a growing body of evidence suggests that these GI manifestations may have significant clinical associations with growth and nutrition, quality of life, and respiratory function in CF. As such, the potential utility of GI therapies and long-term GI outcomes are areas of interest in CF. Further research involving microbial modulation and multi-omics techniques may reveal novel insights. This article provides an overview of the current evidence, pathophysiology, and future research and therapeutic considerations pertaining to intestinal inflammation and alterations in the gut microbiota in CF.

Novel Advances in the Evaluation and Treatment of Children With Symptoms of Gastroesophageal Reflux Disease

Gastroesophageal reflux disease has long been implicated as a cause for multiple pediatric symptoms ranging from abdominal pain and regurgitation to cough and dental erosions. Diagnostic testing has evolved greatly over the last 20 years; initial testing with pH-metry to measure esophageal acid reflux burden has evolved into measurement of both acid and non-acid reflux and liquid and gas reflux. However, measuring reflux burden alone only tells a small part of the GERD story and many symptoms originally thought to be reflux related are, in fact, related to other disorder which mimic reflux. The current paradigm which involves empiric treatment of symptoms with acid suppression has been replaced with early testing for not only gastroesophageal reflux but also for other diagnostic masqueraders. The focus for interventions has shifted away from acid suppression toward motility interventions and includes a greater recognition of both functional and motility disorders which present with reflux symptoms.

Proton pump inhibitor use and hearing loss in patients with type 2 diabetes: evidence from a hospital-based case-control study and a population-based cohort study

OBJECTIVES

This study aimed to investigate the association between proton pump inhibitor (PPI) use and risk of sensorineural hearing loss (SNHL) or tinnitus in patients with type 2 diabetes using hospital- and population-based data.

METHODS

For the case-control study using the Asan biomedical research environment (ABLE) database, the characteristics between cases and sex-, age-, and index-year-matched controls were compared by the chi-squared test. Conditional logistic regression was used to estimate the odds ratios (ORs). For the cohort study using the Korean National Health Insurance Service-National Sample Cohort, the hazard ratios (HRs) for SNHL or tinnitus associated with PPI use were analyzed by the Cox proportional hazard regression model.

RESULTS

The case-control study included 1,379 cases and 5,512 matched controls. After adjustment, PPI use was associated with an increased risk of SNHL or tinnitus (OR: 1.61, 95% CI: 1.30-1.99). The ORs were higher for current or recent use of PPI and high average daily dose. In the cohort study including 17,233 pairs of PPI users and non-users after propensity score matching, the risk of SNHL or tinnitus increased in PPI users compared with non-users (HR: 1.50, 95% CI: 1.40-1.61). In the stratified analyses, risks remained significant, and the magnitude of association was relatively high in those of younger age, patients without gastroesophageal reflux disease, and patients not receiving histamine 2 receptor blockers.

CONCLUSIONS

Our study suggests that PPI use is associated with an increased risk of SNHL or tinnitus. Given the widespread use of PPIs, the potential ototoxic effects of PPIs remain an important concern.

Comparison of the airway microbiota in children with chronic suppurative lung disease

RATIONALE

The airway microbiota is important in chronic suppurative lung diseases, such as primary ciliary dyskinesia (PCD) and cystic fibrosis (CF). This comparison has not previously been described but is important because difference between the two diseases may relate to the differing prognoses and lead to pathological insights and potentially, new treatments.

OBJECTIVES

To compare the longitudinal development of the airway microbiota in children with PCD to that of CF and relate this to age and clinical status.

METHODS

Sixty-two age-matched children (age range 0.5-17 years) with PCD or CF (n=31 in each group) were recruited prospectively and followed for 1.1 years. Throat swabs or sputum as well as clinical information were collected at routine clinical appointments. 16S rRNA gene sequencing was performed.

MEASUREMENTS AND MAIN RESULTS

The microbiota was highly individual and more diverse in PCD and differed in community composition when compared with CF. While Streptococcus was the most abundant genus in both conditions, Pseudomonas was more abundant in CF with Haemophilus more abundant in PCD (P_adj=0.0005). In PCD only, an inverse relationship was seen in the relative abundance of Streptococcus and Haemophilus with age.

CONCLUSIONS

Bacterial community composition differs between children with PCD and those with CF. Pseudomonas is more prevalent in CF and Haemophilus in PCD, at least until infection with Pseudomonas supervenes. Interactions between organisms, particularly members of Haemophilus, Streptococcus and Pseudomonas genera appear important. Study of the interactions between these organisms may lead to new therapies or risk stratification.

Gastro-oesophageal reflux disease

Gastro-oesophageal reflux disease (GERD) is a common disorder in adults and children. The global prevalence of GERD is high and increasing. Non-erosive reflux disease is the most common phenotype of GERD. Heartburn and regurgitation are considered classic symptoms but GERD may present with various atypical and extra-oesophageal manifestations. The pathophysiology of GERD is multifactorial and different mechanisms may result in GERD symptoms, including gastric composition and motility, anti-reflux barrier, refluxate characteristics, clearance mechanisms, mucosal integrity and symptom perception. In clinical practice, the diagnosis of GERD is commonly established on the basis of response to anti-reflux treatment; however, a more accurate diagnosis requires testing that includes upper gastrointestinal tract endoscopy and reflux monitoring. New techniques and new reflux testing parameters help to better phenotype the condition. In children, the diagnosis of GERD is primarily based on history and physical examination and treatment vary with age. Treatment in adults includes a combination of lifestyle modifications with pharmacological, endoscopic or surgical intervention. In refractory GERD, optimization of proton-pump inhibitor treatment should be attempted before a series of diagnostic tests to assess the patient's phenotype.

Influence of Acid Blockade on the Aerodigestive Tract Microbiome in Children With Cystic Fibrosis

BACKGROUND

Acid blockade is commonly prescribed in patients with cystic fibrosis (CF). Growing concerns, however, exist about its possible role in the pathophysiology of pulmonary infections. We aimed to investigate if acid blockade alters esophageal and respiratory microbiota leading to dysbiosis and inflammation.

METHODS

We performed a cross sectional study of children with CF who were either prescribed acid blockade or not. Samples from the gastrointestinal and respiratory tracts were obtained and microbiome analyzed. Mixed effect models were used to compare outcomes between cohorts and across sampling sites. A random subject intercept was included to account for the multiple sampling sites per individual.

RESULTS

A cohort of 25 individuals, 44% girls with median age of 13.8 years [IQR 11.2--14.8] were enrolled. Alpha diversity, total bacterial load, and beta diversity were similar across anatomic compartments, across the upper gastrointestinal tract, and in respiratory samples. Similar alpha diversity, total bacterial load, and beta diversity results were also observed when comparing individuals on versus those off acid blockade. IL-8 was elevated in the distal versus proximal esophagus in the whole cohort (P < 0.01). IL-8 concentrations were similar in the distal esophagus in patients on and off acid blockade, but significantly greater in the proximal esophagus of subjects on treatment (P < 0.01).

CONCLUSIONS

On the basis of these data, acid blockade use does not appear to influence the microbiome of the aerodigestive tract in children with cystic fibrosis suggesting a complex interplay between these medications and the bacterial composition of the esophagus and lung.

Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome

The stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in early phase and rely principally on linear techniques for multivariate analysis. Here we disclose the importance of complementing linear dimensionality reduction techniques with nonlinear ones to unveil hidden patterns that remain unseen by linear embedding. Then, we prove the advantages to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of bacterial network re-organizations which emerge from perturbations induced by a medical treatment (PPIs) or an infectious state (H. pylori). Finally, we show how to build bacteria-metabolite multilayer networks that can deepen our understanding of the metabolite pathways significantly associated to the perturbed microbial communities.

Disturbance in the oropharyngeal microbiota in relation to antibiotic and proton pump inhibitor medication and length of hospital stay

The aim of this study was to investigate the appearance of a disturbed oropharyngeal microbiota during hospitalization and explore the patient characteristics that maybe associated with such a disturbance. Oropharyngeal swabs were collected from 134 patients at hospital admission and every 3-4 days thereafter. The samples were cultivated to determine the presence of a disturbed microbiota, which, in turn, was subcategorized into respiratory tract pathogens, gut microbiota and yeast species. Demographics, medical history data and hospitalization events were compared. The percentage of disturbed oropharyngeal microbiota increased significantly with length of stay (LOS). Receiving antibiotic treatment during the hospitalization tended to be associated with a disturbed microbiota (OR 2.75 [0.99-7.60]). Proton pump inhibitor (PPI) medication and receiving antibiotics before hospitalization were associated with the development of a disturbed oropharyngeal microbiota with colonization of gut pathogens (OR 3.49 [1.19-10.2] and OR 4.52 [1.13-18.1], respectively), while acute hospital admission was associated with a lower risk of colonization of gut pathogens (OR: 0.23 [0.074-0.72]). The risk of developing a disturbed oropharyngeal microbiota increased with LOS in hospitalized patients. PPI medication and receiving antibiotics before hospitalization were independent risk factors for developing oropharyngeal colonization of gut pathogens.

Proton pump inhibitor use is associated with a variety of infections in patients with liver cirrhosis

There is evidence that intake of proton pump inhibitors (PPI) increases the risk for spontaneous bacterial peritonitis (SBP) in patients with liver cirrhosis. However, data regarding the impact of PPI intake on occurrence of infections other than SBP are still lacking.We hypothesized that PPI use is associated with a higher rate of infections other than SBP in patients with liver cirrhosis.The current case-control study sample included patients with liver cirrhosis from the Disease Analyzer database (IQVIA), which compiles data such as risk factors, drug prescriptions and diagnoses obtained from general practitioners and specialists in Germany. In total, 2,823 patients with infections were matched with 2,823 patients without infections by propensity scores. For quantification of PPI use the prescribed quantity of PPI during the past 12 months before index date was analyzed.Frequency of PPI users was significantly higher in patients with infections than in patients without infections (47.9% vs 37.9%). In regression analysis, PPI use was significantly associated with the occurrence of infections overall (OR 1.55, 95% CI 1.39-1.72, P < .001), and associated with the occurrence of lower respiratory tract infections, urinary tract infections and infectious gastroenteritis. There was no association between PPI use and skin infections. Pantoprazole and omeprazole were the most frequently prescribed PPIs and were both independently associated with the occurrence of infections.PPI use may be associated with infections other than SBP in patients with liver cirrhosis. Prescription of PPI should be limited to patients with a clear indication.

The impact of gastrointestinal dysmotility on the aerodigestive microbiome of pediatric lung transplant recipients

BACKGROUND

Delayed gastric emptying has been associated with increased graft rejection, although the mechanism of this association is not known. This study aims to investigate the interrelationship between delays in gastrointestinal motility and the diversity and composition of gastric, oropharyngeal, and lung microbiomes in pediatric lung transplant recipients.

METHODS

We prospectively recruited 23 pediatric lung transplant recipients and 98 pediatric patients with respiratory symptoms undergoing combined endoscopy and bronchoscopy. Gastric, oropharyngeal, and bronchoalveolar lavage samples were collected for 16S sequencing. Gastric samples were also analyzed for bile composition using liquid chromatography.

RESULTS

Patients who underwent lung transplantation had significantly reduced alpha diversity in gastric and oropharyngeal sites compared with patients with respiratory symptoms. This reduction in alpha diversity was especially evident in gastric samples in patients with delayed gastric emptying defined as abnormal gastric emptying on nuclear scintigraphy or as an elevation in gastric bile concentration (p ≤ 0.05). Whereas monocolonies were seen in the lungs of patients who underwent transplantation, these were not the same microbes seen in the stomach; the microbial overlap between lung and gastric samples within patients was low, and data indicated high individual variation between lung transplant recipients. Other contributors to reduced alpha diversity included antibiotics in combination with proton pump inhibitors, especially in gastric and oropharyngeal samples.

CONCLUSIONS

Lung transplant recipients have reduced microbial diversity in gastric fluid (GF) and oropharynx compared with patients who did not undergo lung transplantation. The decreased alpha diversity in GF may be associated with dysmotility.

Clinical Significance of Changes in Gut Microbiome Associated with Use of Proton Pump Inhibitors

Proton pump inhibitors (PPIs) are commonly used for the treatment of gastric acid-related disorders, and are generally well tolerated. However, by reducing the secretion of gastric acid in the long term, PPI can increase the risk of inducing an imbalance in the gut microbiome composition. Moreover, gastric hypochlorhydria that is caused by PPIs favors the survival and migration of oral bacteria in the lower part of the gastrointestinal tract, with a possible induction of pro-inflammatory microenvironment. Therefore, gut dysbiosis that is associated with the use of PPI has been found to cause adverse infectious and inflammatory diseases. In this regard, adverse effects of the PPI-related gut dysbiosis have been reported in different observational studies, but their clinical relevance remains unclear. Therefore, the aim of this review was to explore the available data on the PPI-related gut dysbiosis in order to better understand its clinical significance.

Host-microbe cross-talk in the lung microenvironment: implications for understanding and treating chronic lung disease

Chronic respiratory diseases are highly prevalent worldwide and will continue to rise in the foreseeable future. Despite intensive efforts over recent decades, the development of novel and effective therapeutic approaches has been slow. However, there is new and increasing evidence that communities of micro-organisms in our body, the human microbiome, are crucially involved in the development and progression of chronic respiratory diseases. Understanding the detailed mechanisms underlying this cross-talk between host and microbiota is critical for development of microbiome- or host-targeted therapeutics and prevention strategies. Here we review and discuss the most recent knowledge on the continuous reciprocal interaction between the host and microbes in health and respiratory disease. Furthermore, we highlight promising developments in microbiome-based therapies and discuss the need to employ more holistic approaches of restoring both the pulmonary niche and the microbial community.

The reciprocal interaction between microbes and host in the lung is increasingly recognised as an important determinant of health. The complexity of this cross-talk needs to be taken into account when studying diseases and developing future new therapies.https://bit.ly/2VKYUfT

Characterization of Upper Gastrointestinal Motility in Infants With Persistent Distress and Non-IgE-mediated Cow's Milk Protein Allergy

BACKGROUND

Persistent crying in infancy is common and may be associated with gastroesophageal reflux disease (GERD) and/or non-IgE-mediated cow's milk protein allergy (CMPA). We aimed to document upper gastrointestinal motility events in infants with CMPA and compare these to findings in infants with functional GERD.

METHODS

Infants aged 2 to 26 weeks with persistent crying, GERD symptoms and possible CMPA were included. Symptoms were recorded by 48-hour cry-fuss chart and validated reflux questionnaire (infant GERD questionnaire [IGERDQ]). Infants underwent a blinded milk elimination-challenge sequence to diagnose CMPA. GERD parameters and mucosal integrity were assessed by 24-hour pH-impedance monitoring before and after cow's milk protein (CMP) elimination. C-octanoate breath testing for gastric emptying dynamics, dual-sugar intestinal permeability, fecal calprotectin, and serum vitamin D were also measured.

RESULTS

Fifty infants (mean age 13 ± 7 weeks; 27 boys) were enrolled. On the basis of CMP elimination-challenge outcomes, 14 (28%) were categorized as non-IgE-mediated CMPA, and 17 (34%) were not allergic to milk; 12 infants with equivocal findings, and 7 with incomplete data were excluded. There were no baseline differences in GERD parameters between infants with and without CMPA. In the CMPA group, CMP elimination resulted in a significant reduction in reflux symptoms, esophageal acid exposure (reflux index), acid clearance time, and an increase in esophageal mucosal impedance.

CONCLUSIONS

In infants with persistent crying, upper gastrointestinal motility parameters did not reliably differentiate between non-IgE-mediated CMPA and functional GERD. In the group with non-IgE-mediated CMPA, elimination of CMP significantly improved GERD symptoms, esophageal peristaltic function, and mucosal integrity.

Systematic review: the effects of proton pump inhibitors on the microbiome of the digestive tract-evidence from next-generation sequencing studies

BACKGROUND

Proton pump inhibitors (PPI) are widely used to treat acid-related disorders of the upper gastrointestinal tract. However, large observational studies have raised concerns about PPI-associated adverse events. In recent years, data from next-generation sequencing studies suggested that PPIs affect the composition of the intestinal microbiota, while a balanced gut microbiome is essential for maintaining health.

AIM

To review the available evidence from next-generation sequencing studies on the effect of PPIs on the intestinal microbiome and to discuss possible implications of PPI-induced dysbiosis in health and disease.

METHODS

A systematic review was conducted following the recommendations of the Preferred Reporting Items for Systematic reviews and Meta-Analyses statement. A PubMed query yielded 197 results. 19 publications met the prespecified eligibility criteria.

RESULTS

Twelve observational study cohorts with 708 PPI users and 11 interventional cohorts with 180 PPI users were included in the review. In most studies, PPI treatment did not affect microbiological richness and diversity, but was associated with distinct taxonomic alterations: In the upper gastrointestinal tract, PPI users showed overgrowth of orally derived bacteria, mostly Streptococcaceae (findings based on six independent cohorts with 126 PPI users). In faecal samples, PPIs increased multiple taxa from the orders Bacillales (eg, Staphylococcaceae), Lactobacillales (eg, Enterococcaceae, Lactobacillaceae, Streptococcaceae) and Actinomycetales (eg, Actinomycetaceae, Micrococcaceae), the families Pasteurellaceae and Enterobacteriaceae and the genus Veillonella. Taxa decreased by PPIs include Bifidobacteriaceae, Ruminococcaceae, Lachnospiraceae and Mollicutes (findings in faecal samples based on 19 independent cohorts with 790 PPI users).

CONCLUSION

PPI use is associated with moderate alterations to upper and distal gut microbiota. The available data suggest that PPI-induced hypochlorhydria facilitates colonization of more distal parts of the digestive tract by upper gastrointestinal microbiota.

Microbiome and Gastric Cancer

The late 1800s Louis Pasteur and Robert Koch introduced and popularized the germ theory of disease. At that time, gastric cancer was the most common cause of cancer deaths in most countries making the stomach an early site of microbial research with a focus on gastric luminal and mucosal bacteria and the role of Boas-Oppler bacillus (Lactobacillus) in the diagnosis of gastric cancer. In the 1970s, the research focus evolved to studies of the gastric microbiome in the production of nitrosamines and included development of the Correa cascade. Interest in nitrosamine production peaked in the late 1980s and was replaced by studies of the newly described Helicobacter pylori and studies of its role in gastritis, gastric atrophy, and gastric cancer. The last decade has witnessed a rebirth in interest in the gastric microbiota as part of worldwide interest in the human microbiome. Although fungi were prominent in the studies of gastric microbiology in the nineteenth century, their potential role in disease pathogenesis has yet to be addressed using modern techniques. Overall, current studies of the gastric bacterial microbiome do not provide convincing evidence to expand the role of the gastric microbiome in cancer pathogenesis beyond what is directly attributable to the oncogenic potential of H. pylori and its role in persisting acute-on-chronic inflammation.

Methods in Lung Microbiome Research

The lung microbiome is associated with host immune response and health outcomes in experimental models and patient cohorts. Lung microbiome research is increasing in volume and scope; however, there are no established guidelines for study design, conduct, and reporting of lung microbiome studies. Standardized approaches to yield reliable and reproducible data that can be synthesized across studies will ultimately improve the scientific rigor and impact of published work and greatly benefit microbiome research. In this review, we identify and address several key elements of microbiome research: conceptual modeling and hypothesis framing; study design; experimental methodology and pitfalls; data analysis; and reporting considerations. Finally, we explore possible future directions and research opportunities. Our goal is to aid investigators who are interested in this burgeoning research area and hopefully provide the foundation for formulating consensus approaches in lung microbiome research.

Systematic review: gastric microbiota in health and disease

BACKGROUND

Helicobacter pylori is the most infamous constituent of the gastric microbiota and its presence is the strongest risk factor for gastric cancer and other gastroduodenal diseases. Although historically the healthy stomach was considered a sterile organ, we now know it is colonised with a complex microbiota. However, its role in health and disease is not well understood.

AIM

To systematically explore the literature on the gastric microbiota in health and disease as well as the gut microbiota after bariatric surgery.

METHODS

A systematic search of online bibliographic databases MEDLINE/EMBASE was performed between 1966 and February 2019 with screening in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Randomised controlled trials, cohort studies and observational studies were included if they reported next-generation sequencing derived microbiota analysis on gastric aspirate/tissue or stool samples (bariatric surgical outcomes).

RESULTS

Sixty-five papers were eligible for inclusion. With the exception of H pylori-induced conditions, overarching gastric microbiota signatures of health or disease could not be determined. Gastric carcinogenesis induces a progressively altered microbiota with an enrichment of oral and intestinal taxa as well as significant changes in host gastric mucin expression. Proton pump inhibitors usage increases gastric microbiota richness. Bariatric surgery is associated with an increase in potentially pathogenic proteobacterial species in patient stool samples.

CONCLUSION

While H pylori remains the single most important risk factor for gastric disease, its capacity to shape the collective gastric microbiota remains to be fully elucidated. Further studies are needed to explore the intricate host/microbial and microbial/microbial interplay.

CYP2C19 Phenotype and Risk of Proton Pump Inhibitor-Associated Infections

OBJECTIVES

Proton pump inhibitors (PPIs) are often used in pediatrics to treat common gastrointestinal disorders, and there are growing concerns for infectious adverse events. Because CYP2C19 inactivates PPIs, genetic variants that increase CYP2C19 function may decrease PPI exposure and infections. We tested the hypothesis that CYP2C19 metabolizer phenotypes are associated with infection event rates in children exposed to PPIs.

METHODS

This retrospective biorepository cohort study included individuals aged 0 to 36 months at the time of PPI exposure. Respiratory tract and gastrointestinal tract infection events were identified by using International Classification of Diseases codes in the year after the first PPI mention. Variants defining CYP2C19 *2, *3, *4, *8, *9, and *17 were genotyped, and all individuals were classified as CYP2C19 poor or intermediate, normal metabolizers (NMs), or rapid or ultrarapid metabolizers (RM/UMs). Infection rates were compared by using univariate and multivariate analyses.

RESULTS

In all, 670 individuals were included (median age 7 months; 44% girls). CYP2C19 NMs (n = 267; 40%) had a higher infection rate than RM/UMs (n = 220; 33%; median 2 vs 1 infections per person per year; P = .03). There was no difference between poor or intermediate (n = 183; 27%) and NMs. In multivariable analysis of NMs and RM/UMs adjusting for age, sex, PPI dose, and comorbidities, CYP2C19 metabolizer status remained a significant risk factor for infection events (odds ratio 0.70 [95% confidence interval 0.50-0.97] for RM/UMs versus NMs).

CONCLUSIONS

PPI therapy is associated with higher infection rates in children with normal CYP2C19 function than in those with increased CYP2C19 function, highlighting this adverse effect of PPI therapy and the relevance of CYP2C19 genotypes to PPI therapeutic decision-making.

Short Bowel Syndrome

Purpose of Review

Short gut syndrome is life-altering and life-threatening disease resulting most often from massive small bowel resection. Recent advances in understanding of the perturbed physiology in these patients have translated into improved care and outcomes. This paper seeks to review the advances of care in SBS patients.

Recent Findings

Anatomic considerations still predominate the early care of SBS patients, including aggressive preservation of bowel and documentation of remnant bowel length and quality. Intestinal adaptation is the process by which remnant bowel changes to fit the physiologic needs of the patient. Grossly, the bowel dilates and elongates to increase intestinal weight and protein content. Architectural changes are noted, such as villus lengthening and deepening of crypts. In addition, gene expression changes occur that function to maximize nutrient uptake and fluid preservation. Management is aimed at understanding these physiologic changes and augmenting them whenever possible in an effort to gain enteral autonomy. Complication mitigation is key, including avoidance of catheter complications, bloodstream infections, cholestasis, and nutrient deficiencies.

Summary

Multidisciplinary teams working together towards intestinal rehabilitation have shown improved outcomes. Today's practioner needs a current understanding of the ever-evolving care of these patients in order to promote enteral autonomy, recognize complications, and counsel patients and families appropriately.

Association of Proton Pump Inhibitors With Hospitalization Risk in Children With Oropharyngeal Dysphagia

Importance

Proton pump inhibitors (PPI) are commonly prescribed to children with oropharyngeal dysphagia and resultant aspiration based on the assumption that these patients are at greater risk for reflux-related lung disease. There is little data to support this approach and the potential risk for increased infections in children treated with PPI may outweigh any potential benefit.

Objective

The aim of this study was to determine if there is an association between hospitalization risk in pediatric patients with oropharyngeal dysphagia and treatment with PPI.

Design, Setting, and Participants

We performed a retrospective cohort study to compare the frequency and length of hospitalizations for children who had abnormal results on videofluoroscopic swallow studies that were performed between January 1, 2015, and December 31, 2015, and who were or were not treated with PPI, with follow-up through December 31, 2016. Records were reviewed for children who presented for care at Boston Children's Hospital, a tertiary referral center. Participants included 293 children 2 years and younger with evidence of aspiration or penetration on videofluoroscopic swallow study.

Exposures

Groups were compared based on their exposure to PPI treatment.

Main Outcomes and Measures

The primary outcomes were hospital admission rate and hospital admission nights and these were measured as incident rates. Multivariable analyses were performed to determine predictors of hospitalization risk after adjusting for comorbidities. Kaplan-Meier curves were created to determine the association of PPI prescribing with time until first hospitalization.

Results

A total of 293 patients with a mean (SD) age of 8.8 (0.4) months and a mean (SD) follow-up time of 18.15 (0.20) months were included in the analysis. Patients treated with PPI had higher admission rates (Incidence rate ratio [IRR], 1.77; 95% CI, 1.16-2.68) and admission nights (IRR, 2.51; 95% CI, 1.36-4.62) even after adjustment for comorbidities. Patients with enteral tubes who were prescribed PPIs were at the highest risk for admission (hazard ratio [HR], 2.31; 95% CI, 1.24-4.31).

Conclusions and Relevance

Children with aspiration who are treated with PPI have increased risk of hospitalization compared with untreated patients. These results support growing concern about the risks of PPI use in children.

The Impact of the American Academy of Pediatrics Brief Resolved Unexplained Event Guidelines on Gastrointestinal Testing and Prescribing Practices

OBJECTIVES

To determine if hospitalization, testing, diagnosis, and management of suspected gastroesophageal reflux, and follow-up visits decreased since introduction of American Academy of Pediatrics guidelines for brief resolved unexplained events (BRUEs).

STUDY DESIGN

We performed a retrospective cohort study of infants with BRUE evaluated at Boston Children's Hospital in the year before and after guideline implementation to determine if practice patterns have changed. Outcomes included hospitalization rates, frequency of swallow assessments, other diagnostic testing, and reflux diagnoses, cost of care, and number of repeat visits. Groups were compared based on whether they presented before or after guideline implementation.

RESULTS

In total, 359 subjects (186 pre-, 173 post-guidelines) were identified. There were no significant differences in practice patterns or outcomes before or after guideline implementation. Subjects had mean age 2.53 ± 0.15 months, and 80% were hospitalized for 2.49 ± 0.26 days. Each subject had 2.47 diagnostic tests performed, and 89% were noncontributory. Despite only 13% having videofluoroscopic swallow study performed, 72% showed aspiration/penetration. No subject had gastroesophageal reflux testing, yet reflux was implicated as the cause for admission in 40% of subjects, resulting in increased odds of discharge on acid suppressing medications (OR 2.88, 95% CI 1.68-4.92, P = .0001). In follow-up, 28% of subjects had repeat hospitalizations or emergency department visits for persistent symptoms.

CONCLUSIONS

Infants with BRUE continue to undergo low-yield diagnostic testing and after admission remain symptomatic and frequently re-present to medical care. Swallow testing remains infrequent despite its high-yield, reflux continues to be implicated and children are still being discharged on acid suppression despite lack of efficacy.

Should Proton Pump Inhibitors be Systematically Prescribed in Patients With Esophageal Atresia After Surgical Repair?

OBJECTIVE

To evaluate outcomes of patients with esophageal atresia (EA) on systematic treatment with proton pump inhibitors (PPI) since the neonatal period and to determine factors associated with successful discontinuation of PPI.

STUDY DESIGN

Longitudinal cohort study with prospective data collection of 73 EA patients, over 11 years systematically treated with PPI. Outcome and predictive factors for discontinuation of PPI treatment were evaluated at study end in February 2017. The incidence of anastomotic strictures was compared with a historical cohort of 134 EA patients followed in the same institution between 1990 and 2005 before the era of systematic PPI treatment.

RESULTS

PPI treatment was discontinued definitively in 48% of patients during follow-up. Prematurity, longer initial hospitalization, moderate-to-severe tracheomalacia, anastomotic leak and anastomotic stricture had a significant negative association with PPI discontinuation on univariate analysis (P < 0.05). On adjusted multivariable Cox regression analysis, moderate-to-severe tracheomalacia and anastomotic leak were negatively associated with discontinuation of PPI treatment (hazard ratio 0.26 [95% CI 0.12-0.59]; P = 0.001 and hazard ratio 0.38 [95% CI 0.16-0.93]; P = 0.03, respectively). There was no significant difference in the incidence of anastomotic strictures in the present cohort compared with the historical cohort (44% vs 39%); (P > 0.05).

CONCLUSIONS

PPI treatment does not prevent the formation of anastomotic strictures and appears to be over-prescribed in children with airway symptoms because of tracheomalacia. This suggests that PPI treatment could be prescribed more selectively. Close monitoring and long-term follow-up, however, of these vulnerable patients in specialized multidisciplinary clinics is imperative.

Acute exacerbation of chronic fibrosing interstitial pneumonia in patients receiving antifibrotic agents: incidence and risk factors from real-world experience

Background and objective

Here, we present real-world data on the incidence and risk factors of acute exacerbation (AE) in patients with chronic fibrotic interstitial pneumonia (CFIP) treated with antifibrotic agents, which has been previously poorly documented.

Methods

We retrospectively examined clinical characteristics, incidence and risk factors of AE in a cohort of 100 patients with CFIP (n = 75, idiopathic pulmonary fibrosis [IPF]; n = 25, other conditions), all of whom received antifibrotic agents in a real-world setting.

Results

The median follow-up was 17.4 months (interquartile range [IQR], 6.6 to 26.7 months). During the follow-up periods, 21 patients experienced AE after starting antifibrotic agents. The estimated 1-, 2-, and 3-year AE incidence rates were 11.4% (95% confidence interval [95%CI], 6.2–20.3%), 32% (95%CI, 20.7–47.4%), and 36.3% (95%CI 23.5–53.1%), respectively. Decreased baseline lung function (forced vital capacity and carbon monoxide diffusing capacity of the lung), existence of pulmonary hypertension estimated from an echocardiogram, higher Interstitial Lung Disease-Gender, Age, and Physiology (ILD-GAP) score, supplementary oxygen, and concomitant corticosteroid and proton-pump inhibitor (PPI) use upon starting the antifibrotic agent were risk factors of AE. Concomitant corticosteroid and PPI use and corticosteroid dose were risk factor of AE in a multivariate Cox regression hazard model adjusting for ILD-GAP score.

Conclusion

AE of CFIP is more common in patients with physiologically and functionally advanced disease under antifibrotic agents. Prudent use of corticosteroids and PPIs when initiating antifibrotic agents may be recommended. Further studies are warranted.

Electronic supplementary material

The online version of this article (10.1186/s12890-019-0880-0) contains supplementary material, which is available to authorized users.

Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function

BACKGROUND

Children with oropharyngeal dysphagia have impaired airway protection mechanisms and are at higher risk for pneumonia and other pulmonary complications. Aspiration of gastric contents is often implicated as a cause for these pulmonary complications, despite being supported by little evidence. The goal of this study is to determine the relative contribution of oropharyngeal and gastric microbial communities to perturbations in the lung microbiome of children with and without oropharyngeal dysphagia and aspiration.

METHODS

We conducted a prospective cohort study of 220 patients consecutively recruited from a tertiary aerodigestive center undergoing simultaneous esophagogastroduodenoscopy and flexible bronchoscopy. Bronchoalveolar lavage, gastric and oropharyngeal samples were collected from all recruited patients and 16S sequencing was performed. A subset of 104 patients also underwent video fluoroscopic swallow studies to assess swallow function and were categorized as aspiration/no aspiration. To ensure the validity of the results, we compared the microbiome of these aerodigestive patients to the microbiome of pediatric patients recruited to a longitudinal cohort study of children with suspected GERD; patients recruited to this study had oropharyngeal, gastric and/or stool samples available. The relationships between microbial communities across the aerodigestive tract were described by analyzing within- and between-patient beta diversities and identifying taxa which are exchanged between aerodigestive sites within patients. These relationships were then compared in patients with and without aspiration to evaluate the effect of aspiration on the aerodigestive microbiome.

RESULTS

Within all patients, lung, oropharyngeal and gastric microbiomes overlap. The degree of similarity is the lowest between the oropharynx and lungs (median Jensen-Shannon distance (JSD) = 0.90), and as high between the stomach and lungs as between the oropharynx and stomach (median JSD = 0.56 for both; p = 0.6). Unlike the oropharyngeal microbiome, lung and gastric communities are highly variable across people and driven primarily by person rather than body site. In patients with aspiration, the lung microbiome more closely resembles oropharyngeal rather than gastric communities and there is greater prevalence of microbial exchange between the lung and oropharynx than between gastric and lung sites (p = 0.04 and 4x10-5, respectively).

CONCLUSIONS

The gastric and lung microbiomes display significant overlap in patients with intact airway protective mechanisms while the lung and oropharynx remain distinct. In patients with impaired swallow function and aspiration, the lung microbiome shifts towards oropharyngeal rather than gastric communities. This finding may explain why antireflux surgeries fail to show benefit in pediatric pulmonary outcomes.

Effect of proton pump inhibitors on the risk and prognosis of infections in patients with cirrhosis and ascites

BACKGROUND & AIMS

Many patients with cirrhosis use proton pump inhibitors. We aimed to determine their effects on the risk and prognosis of infections in patients with cirrhosis and ascites.

METHODS

We used data from three 1-year trials of satavaptan treatment of ascites (N = 1198) to compare incidence and 90-day mortality of first-time infections between users and nonusers of proton pump inhibitors. With standard and marginal structural Cox models, we adjusted for differences in gender, age, cirrhosis aetiology, Model for End-stage Liver Disease score, serum albumin, lactulose use, severity of ascites, and history of spontaneous bacterial peritonitis or variceal bleeding.

RESULTS

During the follow-up, 446 patients had an infection. At inclusion, 524 patients (44%) used proton pump inhibitors, and 645 (54%) used them at some point during the follow-up. Proton pump inhibitor use increased the rate of infections overall (adjusted hazard ratio = 1.43, 95% CI 1.18-1.74), and it also increased the rate of all specific types of infections except upper respiratory tract infections of presumably viral origin. The estimated cumulative risk of infections was 36.4% for proton pump inhibitor users vs 25.1% for nonusers at 6 months (relative risk = 1.45, 95% CI 1.22-1.73), and 45.2% vs 37.7% at 1 year (relative risk = 1.20, 95% 0.97-1.40). Use of proton pump inhibitors did not affect mortality during the 90 days following infection (adjusted hazard ratio = 0.83, 95% CI 0.53-1.31).

CONCLUSIONS

Approximately half of patients with cirrhosis and ascites use proton pump inhibitors. This use increases their risk of bacterial infections, but does not affect their prognosis after an infection occurs.

Antibiotic and acid-suppression medications during early childhood are associated with obesity

OBJECTIVE

Gut microbiota alterations are associated with obesity. Early exposure to medications, including acid suppressants and antibiotics, can alter gut biota and may increase the likelihood of developing obesity. We investigated the association of antibiotic, histamine-2 receptor antagonist (H2RA) and proton pump inhibitor (PPI) prescriptions during early childhood with a diagnosis of obesity.

DESIGN

We performed a cohort study of US Department of Defense TRICARE beneficiaries born from October 2006 to September 2013. Exposures were defined as having any dispensed prescription for antibiotic, H2RA or PPI medications in the first 2 years of life. A single event analysis of obesity was performed using Cox proportional hazards regression.

RESULTS

333 353 children met inclusion criteria, with 241 502 (72.4%) children prescribed an antibiotic, 39 488 (11.8%) an H2RA and 11 089 (3.3%) a PPI. Antibiotic prescriptions were associated with obesity (HR 1.26; 95% CI 1.23 to 1.28). This association persisted regardless of antibiotic class and strengthened with each additional class of antibiotic prescribed. H2RA and PPI prescriptions were also associated with obesity, with a stronger association for each 30-day supply prescribed. The HR increased commensurately with exposure to each additional medication group prescribed.

CONCLUSIONS

Antibiotics, acid suppressants and the combination of multiple medications in the first 2 years of life are associated with a diagnosis of childhood obesity. Microbiota-altering medications administered in early childhood may influence weight gain.

Microbial dysbiosis and mortality during mechanical ventilation: a prospective observational study

Background

Host-associated microbial communities have important roles in tissue homeostasis and overall health. Severe perturbations can occur within these microbial communities during critical illness due to underlying diseases and clinical interventions, potentially influencing patient outcomes. We sought to profile the microbial composition of critically ill mechanically ventilated patients, and to determine whether microbial diversity is associated with illness severity and mortality.

Methods

We conducted a prospective, observational study of mechanically ventilated critically ill patients with a high incidence of pneumonia in 2 intensive care units (ICUs) in Hamilton, Canada, nested within a randomized trial for the prevention of healthcare-associated infections. The microbial profiles of specimens from 3 anatomical sites (respiratory, and upper and lower gastrointestinal tracts) were characterized using 16S ribosomal RNA gene sequencing.

Results

We collected 65 specimens from 34 ICU patients enrolled in the trial (29 endotracheal aspirates, 26 gastric aspirates and 10 stool specimens). Specimens were collected at a median time of 3 days (lower respiratory tract and gastric aspirates; interquartile range [IQR] 2–4) and 6 days (stool; IQR 4.25–6.75) following ICU admission. We observed a loss of biogeographical distinction between the lower respiratory tract and gastrointestinal tract microbiota during critical illness. Moreover, microbial diversity in the respiratory tract was inversely correlated with APACHE II score (r = − 0.46, p = 0.013) and was associated with hospital mortality (Median Shannon index: Discharged alive; 1.964 vs. Deceased; 1.348, p = 0.045).

Conclusions

The composition of the host-associated microbial communities is severely perturbed during critical illness. Reduced microbial diversity reflects high illness severity and is associated with mortality. Microbial diversity may be a biomarker of prognostic value in mechanically ventilated patients.

Trial registration

ClinicalTrials.gov ID NCT01782755. Registered February 4 2013.

Electronic supplementary material

The online version of this article (10.1186/s12931-018-0950-5) contains supplementary material, which is available to authorized users.

Associations between Community-Acquired Pneumonia and Proton Pump Inhibitors in the Laryngeal/Voice-Disordered Population

OBJECTIVES

To examine the relationship between community-acquired pneumonia (CAP) and proton pump inhibitor (PPI) treatment among patients with laryngeal/voice disorders.

STUDY DESIGN

Retrospective cohort analysis.

SETTING

Large national administrative US claims database.

SUBJECTS AND METHODS

Patients were included if they were ≥18 years old; had outpatient treatment for a laryngeal/voice disorder from January 1, 2010, to December 31, 2014 (per International Classification of Diseases, Ninth Revision, Clinical Modification codes); had 12 months of continuous enrollment prior to the index date (ie, first diagnosis of laryngeal/voice disorder); had no preindex diagnosis of CAP; and had prescription claims captured from 1 year preindex to end of follow-up. Patient demographics, comorbid conditions, index laryngeal diagnosis, number of unique preindex patient encounters, and CAP diagnoses during the postindex 3 years were collected. Two models-a time-dependent Cox regression model and a propensity score-based approach with a marginal structural model-were separately performed for patients with and without pre-index date PPI prescriptions.

RESULTS

A total of 392,355 unique patients met inclusion criteria; 188,128 (47.9%) had a PPI prescription. The 3-year absolute risk for CAP was 4.0% and 5.3% among patients without and with preindex PPI use, respectively. For patients without and with pre-index date PPI use, the CAP occurrence for a person who had already received a PPI is 30% to 50% higher, respectively, than for a person who had not yet had a PPI but may receive one later.

CONCLUSIONS

Patients without and with pre-index date PPI use experienced a roughly 30% to 50% increased likelihood of CAP, respectively, as compared with patients who had not had PPI prescriptions.

Considering gut microbiota disturbance in the management of Helicobacter pylori infection

Helicobacter pylori (Hp) infection produces drastic changes in the gastric microenvironment, which, in turn, influence the gastric microbiota composition and might be correlated with large intestinal microbiota changes. This excellent perturbing actor could trigger important modifications in the homeostatic functions exerted by gut commensals leading to a new gastrointestinal balance. At the same time, the therapeutic strategies used to eradicate Hp can modulate this physiological symbiosis, but can be also conversely affected by its properties. Area covered: The purpose of this review is to explore the reciprocal interplay between Hp infection and gut microbiota and analyze how microbial changes can influence the management of Hp eradication therapies. Expert commentary: While many studies have described Hp-dependent gut microbiota alterations, their clinical implications are only partially clear, as well as the mechanism of actions that sustain these processes. This represents a clear challenge for future research projects that will also need to understand which role is exerted by viruses, parasites, and yeasts.

Acid-Suppressive Therapy and Risk of Infections: Pros and Cons

This narrative review summarises the benefits, risks and appropriate use of acid-suppressing drugs (ASDs), proton pump inhibitors and histamine-2 receptor antagonists, advocating a rationale balanced and individualised approach aimed to minimise any serious adverse consequences. It focuses on current controversies on the potential of ASDs to contribute to infections-bacterial, parasitic, fungal, protozoan and viral, particularly in the elderly, comprehensively and critically discusses the growing body of observational literature linking ASD use to a variety of enteric, respiratory, skin and systemic infectious diseases and complications (Clostridium difficile diarrhoea, pneumonia, spontaneous bacterial peritonitis, septicaemia and other). The proposed pathogenic mechanisms of ASD-associated infections (related and unrelated to the inhibition of gastric acid secretion, alterations of the gut microbiome and immunity), and drug-drug interactions are also described. Both probiotics use and correcting vitamin D status may have a significant protective effect decreasing the incidence of ASD-associated infections, especially in the elderly. Despite the limitations of the existing data, the importance of individualised therapy and caution in long-term ASD use considering the balance of benefits and potential harms, factors that may predispose to and actions that may prevent/attenuate adverse effects is evident. A six-step practical algorithm for ASD therapy based on the best available evidence is presented.

Research progress and perspectives of microscopic colitis

Microscopic colitis (MC) is a common cause of chronic diarrhea. Over the past 20 years, the prevalence of MC has been increasing rapidly, which has aroused the close attention of digestive physicians. The etiology of MC is still unknown, and immune abnormalities are the main pathogenesis, followed by some drugs. MC is clinically characterized by chronic non-bloody watery diarrhea, spastic abdominal pain, weight loss, and fatigue, but colonoscopy is often normal or roughly normal. Colonic biopsy often shows mucosal inflammation or subepithelial collagen band thickening, based on which a diagnosis can be made. At present, there has been no special treatment for MC, with steroid budesonide and immunosuppressive agents being the main treatments. As a self-limiting disease, MC has a good prognosis. Studies have found that MC has a protective effect against colorectal cancer. However, it was recently found that innate immune abnormalities may have carcinogenic effects.

Lung Microbiota and Its Impact on the Mucosal Immune Phenotype

The use of culture-independent techniques has allowed us to appreciate that the upper and lower respiratory tract contain a diverse community of microbes in health and disease. Research has only recently explored the effects of the microbiome on the host immune response. The exposure of the human body to the bacterial environment is an important factor for immunological development; thus, the interaction between the microbiome and its host is critical to understanding the pathogenesis of disease. In this article, we discuss the mechanisms that determine the composition of the airway microbiome and its effects on the host immune response. With the use of ecological principles, we have learned how the lower airways constitute a unique niche subjected to frequent microbial migration (e.g., through aspiration) and constant immunological pressure. The discussion will focus on the possible inflammatory pathways that are up- and downregulated when the immune system is challenged by dysbiosis. Identification of potential markers and microbial targets to address the modulation of inflammation in early disease, when changes may have the most effect, will be critical for future therapies.

Proton pump inhibitors and the risk of severe cognitive impairment: The role of posttraumatic stress disorder

Introduction

Proton pump inhibitors (PPIs), a common treatment for gastroesophageal reflux disease (GERD), were recently associated with increased risk of dementia. However, severe or chronic stress including, for example, posttraumatic stress disorder (PTSD) was not accounted for. This study examined whether PPI use was associated with severe cognitive impairment (SCI) and whether PTSD explained this association in a cohort of World Trade Center (WTC) responders.

Method

A prospective cohort study of 3779 WTC responders attending a university-based monitoring and treatment program. Prescriptions for PPIs and SCI determined using the Montreal Cognitive Assessment were the focus of the analysis.

Results

Overall, 1451 (38.4%) responders were dispensed PPIs, and 83 (2.2%) had SCI. Bivariable analyses revealed significant associations between being-dispensed PPIs in relation to SCI. After adjusting for PTSD, major depressive disorder, WTC exposures, age, and sex, being-dispensed PPIs were significantly associated with odds of SCI (adjusted odds ratio = 1.67 95% confidence interval = 1.054–2.643).

Conclusions

Being-dispensed PPIs were associated with SCI in this analysis of WTC responders. Results suggest that clinicians treating GERD seek to both understand patients' mental health history and monitor cognitive functioning when designing treatment routines. Overall, results confirmed that this is an important area of investigation with potential direct clinical implications.

Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies

Omic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation. Biologists and medical researchers often prefer effective methods that offer an immediate interpretation to complicated algorithms that in principle promise an improvement but in practice are difficult to be applied and interpreted. Here we present PC-corr: a simple algorithm that associates to any PCA segregation a discriminative network of features. Such network can be inspected in search of functional modules useful in the definition of combinatorial and multiscale biomarkers from multifaceted omic data in systems and precision biomedicine. We offer proofs of PC-corr efficacy on lipidomic, metagenomic, developmental genomic, population genetic, cancer promoteromic and cancer stem-cell mechanomic data. Finally, PC-corr is a general functional network inference approach that can be easily adopted for big data exploration in computer science and analysis of complex systems in physics.