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Helicobacter pylori ( H. pylori ) infect nearly half of the global population, contributing to upper digestive tract diseases. This 2019 cross-sectional study included 3,867 patients undergoing esophagogastroduodenoscopy (EGD) and 2,875 undergoing both colonoscopy and EGD. Subjects were categorized into H. pylori positive and negative groups by rapid urease test (RUT). In addition to exploring the relationship between H. pylori infection and upper gastrointestinal diseases, this study further revealed that H. pylori infection was closely related to lower digestive tract diseases, including colorectal polyp (63.28%) and colorectal cancer (75.76%), as well as upper and lower gastrointestinal comorbidities, including chronic atrophic gastritis with colorectal polyp (79.85%), peptic ulcer with colorectal polyp (79.72%), gastric polyp with colorectal polyp (66.24%), and chronic atrophic gastritis with colorectal cancer (92.86%). Besides, a univariate logistic regression analysis was conducted to compare the differences between the two groups (including gender, nationality, marital status, smoking history, drinking history, living area, age, BMI, glycosylated hemoglobin, fasting blood glucose, total cholesterol, and triglyceride levels), the results identified marital status and age as independent risk factors for H. pylori infection (OR, 1.435; 95% CI, 1.042 to 1.977; OR, 1.007; 95% CI, 1.001 to 1.013). Further clarification of the correlation between the prevalence of gastrointestinal diseases and H. pylori infection will be important for H. pylori infection management strategies and the treatment and prevention of gastrointestinal diseases.

Growing evidences of recent studies have shown that gut microbrome are causally related to digestive system diseases (DSDs). However, causal relationships between the gut microbiota and the risk of DSDs still remain unclear. We utilized identified gut microbiota based on class, family, genus, order and phylum information and digestive system diseases genome-wide association study (GWAS) dataset for two-sample Mendelian randomization (MR) analysis. The inverse variance weighted (IVW) method was used to evaluate causal relationships between gut microbiota and 7 DSDs, including chronic gastritis, colorectal cancer, Crohn's disease, gastric cancer, gastric ulcer, irritable bowel syndrome and esophageal cancer. Finally, we verified the robustness of MR results based on heterogeneity and pleiotropy analysis. We discovered 15 causal associations with genetic liabilities in the gut microbiota and DSDs, such as genus Victivallis, genus RuminococcaceaeUCG005, genus Ruminococcusgauvreauiigroup, genus Oxalobacter and so on. Our MR analysis revealed that the gut microbiota is causally associated with DSDs. Further researches of the gut microbiota and the pathogenesis of DSDs are still significant and provide new methods for the prevention and treatment of DSDs., Competing Interests: The authors have no conflicts of interest to disclose., (Copyright © 2024 the Author(s). Published by Wolters Kluwer Health, Inc.)

The human gastrointestinal (GI) tract hosts trillions of microbial inhabitants involved in maintaining intestinal homeostasis, dysbiosis of which provokes a motley of pathogenic and autoimmune disorders. While the mechanisms by which the microbiota modulates human health are manifold, their liberated metabolites from ingested dietary supplements play a crucial role by bidirectionally regulating the expression of micro-ribonucleic acids (miRNAs). miRNAs are small endogenous non-coding RNAs (ncRNAs) that have been confirmed to be involved in an interplay with microbiota to regulate host gene expression. This comprehensive review focuses on key principles of miRNAs, their regulation, and crosstalk with gut microbiota to influence host gene expression in various human disorders, by bringing together important recent findings centric around miRNA-microbiota interactions in diseases along various axis of the gut with other organs. We also attempt to lay emphasis on exploiting the avenues of gut-directed miRNA therapeutics using rudimentary dietary supplements to regulate abnormal host gene expression in diseases, opening doors to an accessible and economical therapeutic strategy.

Age is the dominant risk factor for infectious diseases, but the mechanisms linking age to infectious disease risk are incompletely understood. Age-related mosaic chromosomal alterations (mCAs) detected from genotyping of blood-derived DNA, are structural somatic variants indicative of clonal hematopoiesis, and are associated with aberrant leukocyte cell counts, hematological malignancy, and mortality. Here, we show that mCAs predispose to diverse types of infections. We analyzed mCAs from 768,762 individuals without hematological cancer at the time of DNA acquisition across five biobanks. Expanded autosomal mCAs were associated with diverse incident infections (hazard ratio (HR) 1.25; 95% confidence interval (CI) = 1.15-1.36; P = 1.8 × 10 -7 ), including sepsis (HR 2.68; 95% CI = 2.25-3.19; P = 3.1 × 10 -28 ), pneumonia (HR 1.76; 95% CI = 1.53-2.03; P = 2.3 × 10 -15 ), digestive system infections (HR 1.51; 95% CI = 1.32-1.73; P = 2.2 × 10 -9 ) and genitourinary infections (HR 1.25; 95% CI = 1.11-1.41; P = 3.7 × 10 -4 ). A genome-wide association study of expanded mCAs identified 63 loci, which were enriched at transcriptional regulatory sites for immune cells. These results suggest that mCAs are a marker of impaired immunity and confer increased predisposition to infections.

The diversity of probiotic products makes choosing an appropriate probiotic challenging. One unanswered question is whether single-strain probiotics are more effective than multi-strain mixtures. The aim of this review is to account for both disease and strain specificity to determine whether single strains or multiple strains are equivalent or more effective. This literature review of randomized controlled trials from 1973 to 2019 was used to compare the pooled efficacy of trials with a single strain versus the probiotic mixture with same matched strain within the same type of disease indication. A total of 65 RCTs were included (41 with single strains, 22 multi-strain mixtures and 2 comparing single strain to mixture arms) for eight different disease indications (N = 10,863). Only three strains (L. rhamnosus GG, L. helveticus R52 and B. lactis Bb12) had corresponding trials with matching mixtures. Use of L. rhamnosus GG only was significantly more protective for necrotizing enterocolitis compared to two mixtures also containing different strains of B. lactis. The mixture of L. rhamnosus GG and B. lactis Bb12 was significantly more effective than L. rhamnosus GG alone for the eradication of H. pylori. In most cases, single strains were equivalent to mixtures. Choice of an appropriate probiotic should be based, not on the number of strains in the product, rather based on evidence-based trials of efficacy. In most cases, multi-strain mixtures were not significantly more effective than single-strain probiotics.

Background: The purpose of this study was to assess the prevalence of Helicobacter pylori infection in Algerian patients with peptic disorders and evaluate the impact of different epidemiological factors (age, sex, sampling site, presence or absence of H. pylori , and type of pathology related to this bacterium)., Methods: We undertook a retrospective and descriptive study on a series of 735 symptomatic patients identified in the laboratory of pathological anatomy at Hassani Abdelkader University Hospital Center of Sidi Bel Abbes, Algeria, over a period of 16 years from January 2002 to December 2017. All patients had benefited from a high gastroscopic fibroscopy and the diagnosis was made by histological examination (hematoxylin-eosin staining). The epidemiological factors, as well as the main gastric diseases related to this bacterium, were studied., Results: The prevalence of H. pylori infection was 66.12%. The infection was more important in the age group 60-69 years (71.43%). The prevalence of H. pylori infection was statistically higher in women than in men (69.3% vs. 60.7%, p < 0.01).The antral region was most colonized by H. pylori (71.73%). In addition, the infection was associated mainly with atrophic gastritis (69.65%)., Conclusion: In this context, the identification of epidemiological data would be of great value in guiding strategies to control the spread of this bacterium., Competing Interests: The authors declare they have no conflicts of interest., (© 2020 Atlantis Press International B.V.)

Background: The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases., Methods: Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes., Results: The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases., Trial Registration: NCT04391426. Registered 18 May 2020, https://clinicaltrials.gov/ct2/show/NCT04391426., Competing Interests: The authors have declared that no competing interests exist.

Gut microbiota dysbiosis has been repeatedly observed in obesity and type 2 diabetes mellitus, two metabolic diseases strongly intertwined with non-alcoholic fatty liver disease (NAFLD). Animal studies have demonstrated a potential causal role of gut microbiota in NAFLD. Human studies have started to describe microbiota alterations in NAFLD and have found a few consistent microbiome signatures discriminating healthy individuals from those with NAFLD, non-alcoholic steatohepatitis or cirrhosis. However, patients with NAFLD often present with obesity and/or insulin resistance and type 2 diabetes mellitus, and these metabolic confounding factors for dysbiosis have not always been considered. Patients with different NAFLD severity stages often present with heterogeneous lesions and variable demographic characteristics (including age, sex and ethnicity), which are known to affect the gut microbiome and have been overlooked in most studies. Finally, multiple gut microbiome sequencing tools and NAFLD diagnostic methods have been used across studies that could account for discrepant microbiome signatures. This Review provides a broad insight into microbiome signatures for human NAFLD and explores issues with disentangling these signatures from underlying metabolic disorders. More advanced metagenomics and multi-omics studies using system biology approaches are needed to improve microbiome biomarkers.

An epidemic of an acute respiratory syndrome caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, now known as coronavirus disease 2019 (COVID-19), beginning in December 2019, has attracted an intense amount of attention worldwide. As the natural history and variety of clinical presentations of this disease unfolds, extrapulmonary symptoms of COVID-19 have emerged, especially in the digestive system. While the respiratory mode of transmission is well known and is probably the principal mode of transmission of this disease, a possibility of the fecal-oral route of transmission has also emerged in various case series and clinical scenarios. In this review article, we summarize four different aspects in published studies to date: (a) gastrointestinal manifestations of COVID-19; (b) microbiological and virological investigations; (c) the role of fecal-oral transmission; and (d) prevention and control of SARS-CoV-2 infection in the digestive endoscopy room. A timely understanding of the relationship between the disease and the digestive system and implementing effective preventive measures are of great importance for a favorable outcome of the disease and can help climnicians to mitigate further transmission by taking appropriate measures., (© 2020 Chinese Medical Association Shanghai Branch, Chinese Society of Gastroenterology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine and John Wiley & Sons Australia, Ltd.)

Background: The role of adjunctive steroids in abdominal tuberculosis is unclear., Objective: To evaluate effect of adjunctive use of steroids for abdominal tuberculosis in reducing/preventing complications., Methods: We searched electronic databases (Medline, Embase, CENTRAL, Scopus, Web of Science, CINAHL) from inception to 25th June 2018 using the terms "abdominal tuberculosis" OR "intestinal tuberculosis" OR "peritoneal tuberculosis" OR "tuberculous peritonitis" AND steroids OR methylprednisolone OR prednisolone. Bibliography of potential articles was also searched. We included studies comparing adjunctive steroids to antitubercular therapy (ATT) alone. We excluded non-English articles, case reports, reviews and unrelated papers. The primary outcome was a comprehensive clinical outcome including need for surgery or the presence of symptomatic stricture (abdominal pain or intestinal obstruction). Quality assessment of included studies was done using ROBINS-I tool. Random-effects model was used to calculate the summary effect for all the outcomes., Results: Of total 633 records, three studies on peritoneal tuberculosis were included in meta-analysis. These papers were of poor quality (one quasi-randomised study and two retrospective cohort studies). Meta-analyses showed adjunctive steroids, with ATT is more effective than ATT alone in tuberculous peritonitis patients for the prevention of composite end point (RR 0.15 [0.04, 0.62], p = 0.008), symptomatic stricture(RR 0.15 [0.04-0.62] p = 0.008) and intestinal obstruction (RR 0.18 [0.03-0.99] p = 0.05)., Conclusion: The data on use of steroids for abdominal tuberculosis are limited to peritoneal tuberculosis. Although steroids seem to have some benefit in patients of tubercular peritonitis, the poor quality of studies limits the generalisability of the findings., Systematic Review Registration Number: CRD42016047347.

In the last decade, a barge body of scientific literature has suggested that specific alterations of the gut microbiota may be associated with ther development and clinical course of several gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel disease, celiac disease, gastrointestinal cancer and Clostridium difficile infection. These alterations are often referred to as "dysbiosis", a generic term designing reduction of gut microbiota biodiversity and alterations in its composition. Here, we provide a synthetic overview of the key concepts on the relationship between intestinal microbiota and gastrointestinal diseases, focusing on the translation of these concepts into clinical practice.

Competing Interests: Competing interests: None declared.

HIV infection causes a disruption of gut-associated lymphoid tissue, driving a shift in the composition of gut microbiota. A deeper understanding of the metabolic changes and how they affect the interplay with the host is needed. Here, we assessed functional modifications of HIV-associated microbiota by combining metagenomic and metatranscriptomic analyses. The transcriptionally active microbiota was well-adapted to the inflamed environment, overexpressing pathways related to resistance to oxidative stress. Furthermore, gut inflammation was maintained by the Gram-negative nature of the HIV-associated microbiota and underexpression of anti-inflammatory processes, such as short chain fatty acid biosynthesis or indole production. We performed co-occurrence and metabolic network analyses that showed relevance in the microbiota structure of both taxonomic and metabolic HIV-associated biomarkers. The Bayesian network revealed the most determinant pathways for maintaining the structure stability of the bacterial community. In addition, we identified the taxa's contribution to metabolic activities and their interactions with host health.

The human microbiome project promoted further understanding on human oral microbes. Besides oral diseases such as dental caries, periodontal disease, and oral cancer, oral microbes are closely associated with systematic diseases. They have a close connection with digestive system diseases and even contribute to the origination and progression of colorectal cancer. By reviewing recent studies involving oral microbe-related digestive systemic diseases, we aim to propose the considerable role of oral microbes in relation to digestive systemic diseases and the way of oral microbes to multiple organs of digestive system.

Objective: The objective of this systematic review is to assess the effect of selective digestive decontamination (SDD) or non-absorbable enteral antibiotics (EA) on mortality, the incidence of infection and its adverse effects in burn patients., Material and Methods: Systematic review of randomized clinical trials (RCT) or observational studies enrolling burn patients, and comparing SDD or EA prophylaxis with placebo or no treatment. The search includes Pubmed/Medline, EMBASE, WOS, Cochrane Library (1970-2015). Bibliographic references were also reviewed, as well as communications presented at conferences (2012-2015), without language restrictions. Two reviewers inspected each reference identified by the search independently; the risk of bias was assessed with the Cochrane Collaboration method for RCT and the Newcastle Ottawa Scale for observational studies., Results: Five RCT and 5 observational studies were identified enrolling a total of 1680 patients. The overall methodological quality of the studies was poor. The pooled effect of RCT using EA was OR: 0.62 (95% CI: 0.20-1.94). The only RCT using SDD reported OR 0.20 (95% CI: 0.09-0.81). The incidence of Enterobacteriaceae bloodstream was lower in cases treated with SDD or EA. The incidence of pneumonia was only reduced in the studies using SDD. None of the studies reported an increase in antibiotic resistance but in one RCT SDD was associated to an increase in methicillin-resistant Staphylococcus aureus infections, that was controlled with enteral vancomycin., Conclusions: SDD and EA have shown a beneficial effect in burn patients. Both practices are safe. Higher quality RCTs should be conducted to properly assess the efficacy and safety of SDD in this population., (Copyright © 2017 Elsevier Ltd and ISBI. All rights reserved.)

Objective: The presence of resistant microorganisms is a major cause of failure in initial empirical antimicrobial therapy. The objectives of this study are to determine the resistance profile of microorganisms that cause bacteraemia of abdominal origin and to identify whether the previous use of antibiotics and the place of acquisition of bacteraemia are risk factors associated with the presence of resistant organisms., Material and Methods: A clinical, observational, epidemiological, retrospective cohort study was conducted with all the adult patients admitted to a university hospital from 2011-2013. Antimicrobial resistance profiles were described and a 95% confidence interval chi-square test was used to determine whether the variables studied were risk factors in the isolation of resistant microorganisms., Results: Of the 1245 patients with bacteraemia, 212 (17%) presented bacteraemia of abdominal origin. The resistance profile highlights the incidence of methicillin resistant Staphylococcus aureus (50%), coagulase-negative staphylococci resistant to linezolid (20.58%), enterococci resistant to vancomycin (3.12%), Escherichia coli resistant to third-generation cephalosporins (9.9%) and fluoroquinolones (35.64%), Klebsiella pneumoniae resistant to third-generation cephalosporins (8.33%), Pseudomonas aeruginosa resistant to fluoroquinolones and carbapenem (25% and 25% respectively) and Acinetobacter baumanii resistant to fluoroquinolones and carbapenem (100% and 100% respectively), Candida albicans resistant to fluconazole (11.11%), single Candida krusei isolate resistant to fluconazole and Candida parapsilosis resistant to echinocandins (12.5%). In our study, previous use of antibiotics had a statistically significant association with the isolation of resistant microorganisms (P=.013) but not the place of acquisition of bacteraemia (P=.239)., Conclusion: Establishing the incidence of resistant organisms can improve empirical antimicrobial therapy in patients with bacteraemia of abdominal origin. Previous use of antibiotics was statistically significantly related to the isolation of resistant microorganisms., (Copyright © 2017 Sociedad Española de Anestesiología, Reanimación y Terapéutica del Dolor. Publicado por Elsevier España, S.L.U. All rights reserved.)

The concept of prebiotics, probiotics, and symbiotics and their use in different situations of daily clinical practice related to clinical nutrition is reviewed, as well as their role in the treatment/prevention of diarrhea (acute, induced by antibiotics, secondary to radiotherapy), inflammatory bowel disease (ulcerative colitis and pouchitis), in colonic health (constipation, irritable bowel), in liver disease (steatosis and minimum encephalopathy), and in intensive care, surgical, and liver transplantation. While their effectiveness for preventing antibiotic-induced diarrhea and pouchitis in ulcerative colitis appears to be shown, additional studies are needed to establish recommendations in most clinical settings. The risk of infection associated to use of probiotics is relatively low; however, there are selected groups of patients in whom they should be used with caution (as jejunum infusion)., (Copyright © 2016 SEEN. Publicado por Elsevier España, S.L.U. All rights reserved.)

Human microbiota are distinct communities of microorganisms that resides at different body niches. Exploration of the human microbiome has become a reality due to the availability of powerful metagenomics and metatranscriptomic analysis technologies. Recent advances in sequencing and bioinformatics over the past decade help provide a deep insight into the nature of the host-microbial interactions and identification of potential deriver genes and pathways associated with human health, well-being, and predisposition to different diseases. In the present review, we outline recent studies devoted to elucidate the possible link between the microbiota and various type of diseases. The present review also highlights the potential utilization of microbiota as a potential therapeutic option to treat a wide array of human diseases. J. Cell. Physiol. 231: 1688-1694, 2016. © 2015 Wiley Periodicals, Inc., (© 2015 Wiley Periodicals, Inc.)

Performance and mortality of hares were evaluated for 2 consecutive years in a large farm in Veneto Region (Northern Italy). On average, fertile reproductive pairs (n=318) gave birth 4.8 times and produced 11.4 live leverets, weaned 8.4 leverets and produced 7.0 growing hares (60 days) every year. Mean mortality was 3.6%, 22.9%, 9.7% and 2.5% in newborn (0 to 2 days of age), suckling (3 to 25 days), growing (26 to 60 days) and sub-adult (61 days until sale) hares, respectively. The main causes of mortality were enteric diseases (75.5%, 75.9% and 12.1% in suckling, growing and sub-adult hares, respectively), followed by respiratory diseases (3.4%, 8.0% and 36.2% in suckling, growing and sub-adult hares, respectively), starvation (11.3% and 8.8% in suckling and growing hares, respectively) and trauma (7.1%, 2.3% and 30.2% in suckling, growing and sub-adult hares, respectively). In reproducing hares, mortality was 24.7% and 15.4% in 2010 and 2011, respectively. Respiratory diseases (34.8%) and ulcerative pododermatitis (18.9%) were the most common pathological changes detected in reproducing hares. Farmed hares seem to be affected by diseases resembling those of rabbits reared under intensive conditions. It seems necessary to improve the husbandry of hares to reach satisfactory technical standards and to preserve their health.

Contemporary diagnostic microbiology is increasingly adopting molecular methods as front line tests for a variety of samples. This trend holds true for detection of enteric pathogens (EP), where nucleic acid amplification tests (NAAT) for viruses are well established as the gold standard, and an increasing number of commercial multi-target assays are now available for bacteria and parasites. NAAT have significant sensitivity and turnaround time advantages over traditional methods, potentially returning same-day results. Multiplex panels offer an attractive 'one-stop shop' that may provide workflow and cost advantages to laboratories processing large sample volumes. However, there are a number of issues which need consideration. Reflex culture is required for antibiotic susceptibility testing and strain typing when needed for food safety and other epidemiological investigations. Surveillance systems will need to allow for differences in disease incidence due to the enhanced sensitivity of NAAT. Laboratories should be mindful of local epidemiology when selecting which pathogens to include in multiplex panels, and be thoughtful regarding which pathogens will not be detected. Multiplex panels may not be appropriate in certain situations, such as hospital-onset diarrhoea, where Clostridium difficile testing might be all that is required, and laboratories may wish to retain the flexibility to run single tests in such situations. The clinical impact of rapid results is also likely to be relatively minor, as infective diarrhoea is a self-limiting illness in the majority of cases. Laboratories will require strategies to assist users in the interpretation of the results produced by NAAT, particularly where pathogens are detected at low levels with uncertain clinical significance. These caveats aside, faecal NAAT are increasingly being used and introduce a new era of diagnosis of gastrointestinal infection.

Here, recent developments in the detection and identification of parasites causing enteric infection are reviewed including the utility and challenges of multi-target molecular assays. Difficulties in clinical interpretation arising from increased detection of parasites, of co-infection with other enteropathogens and of asymptomatic carriage are discussed. Published approaches for detection across a broad range of organisms are described, including commercial assays available to Australian laboratories. Using local data, the impact of introduction of modern molecular assays is assessed. In addition, recent advances in high density multi-target molecular platforms are discussed as potential platforms for increasing the scope of enteric pathogens to be detected whilst maintaining appropriate costs.

It is now well known that intestinal microbiota exerts not only several physiological functions, but has also been implied in the mechanisms of many conditions, both intestinal and extraintestinal. These advances, to the best of our knowledge, have been made possible by the development of new ways of studying gut flora. Metagenomics, the study of genetic material taken directly from environmental samples, avoiding individual culture, has become an excellent tool to study the human microbiota. Therefore, it has demonstrated an association between an altered intestinal microbiota and inflammatory bowel disease or irritable bowel syndrome, perhaps the most extensively studied conditions associated with this particular subject. However, microbiota has a potential role in the development of other diseases; their manifestations are not confined to the intestine only. In this article, an extensive updated review is conducted on the role intestinal microbiota has in health and in different diseases. Focus is made on the following conditions: inflammatory bowel disease, irritable bowel syndrome, celiac disease, hepatic encephalopathy, and obesity.

Introduction: The general reported recurrence rate of H. pylori infection in Peru is high, implying that the long term effectiveness of anti H. pylori therapy is lower than expected. This would lead to an increase in the prevalence of gastric cancer and other associated pathologies., Materials and Methods: This is a prospective cohort study including Peruvian patients with postprandial distress and H. pylori infection confirmed by gastric biopsy who recieved treatment and achieved bacterial eradication. Two years after the initial diagnosis, patients were contacted to determine the recurrence rate of H. pylori infection through the Urea breath test., Results: 101 /129 of the patients that were infected with H. pylori had a successful eradication of the infection and 28/129 failed to eradicate the bacteria. The effectiveness rate of treatment was 77.2%. Two years after successful eradication we were able to contact 65/101 participants, 5 of them presented positive urea breath tests (recurrence rate of infection of 7.7%) (IC 1.5%-13.5%, α = 0.05). The annual recurrence rate was 3.85% per year/ patient. 94% of the patients in the cohort came from poor city areas, 95.4% had drinking water at home and 90.8% drank boiled drinking water on a daily basis., Conclusions: The recurrence rate of H. pylori in some populations of Peru is lower than expected and comparable with developed countries.

Human beings and gut microbiota are in a symbiotic relationship, and the hypothesis of a "super organism" composed of the human organism and microbes has been recently proposed. The gut microbiota fulfills important metabolic and immunological tasks, and the impairment of its composition might alter homeostasis and lead to the development of microbiota-related diseases. The most common illnesses associated with alterations of the gut microbiota include inflammatory bowel disease, gastroenteric infections, irritable bowel syndrome and other gastrointestinal functional diseases, colorectal cancer, metabolic syndrome and obesity, liver diseases, allergic diseases, and neurological diseases such as autism. In theory, every disease associated with the impairment of intestinal microflora might benefit from the therapeutic modulation of the gut microbiota. A number of attempts to manipulate the microbiota have not produced identical results for every disease. Although antibiotics and probiotics have been available for a long time, the so-called fecal microbiota transplantation, which is a very old remedy, was only recently re-evaluated as a promising therapeutic approach for microbiota impairment. A comprehensive understanding of the gut microbiota composition, in states of both health and various diseases, is needed for the development of future approaches for microbiota modulation and for developing targeted therapies. In this review, we describe the role of the microbiota in several diseases and the related treatment options that are currently available.

Cystic fibrosis (CF) causes chronic infections in the respiratory tract and alters the digestive tract. This paper reviews the most important aspects of drug treatment and changes in the digestive tract of patients with CF. This is a review of the literature, emphasizing the discoveries made within the last 15 years by analyzing scientific papers published in journals indexed in the Scientific Electronic Library Online, Sciences Information, United States National Library of Medicine and Medical Literature Analysis and Retrieval System Online databases, both in English and Portuguese, using the key words: cystic fibrosis, medication, therapeutic, absorption, digestion. Randomized, observational, experimental, and epidemiological clinical studies were selected, among others, with statistical significance of 5%. This review evaluates the changes found in the digestive tract of CF patients including pancreatic insufficiency, constipation and liver diseases. Changes in nutritional status are also described. Clinical treatment, nutritional supplementation and drug management were classified in this review as essential to the quality of life of CF patients, and became available through public policies for monitoring and treating CF. The information gathered on CF and a multi professional approach to the disease is essential in the treatment of these patients.

A perspective direction of the treatment of dysbacteriosis is the use of so-called metabolic prebiotics--products of metabolism of positive flora (for example, water substrate of the products of metabolism of E. coli, S. faecalis, L. acidophilus, L. helveticus (strains of DSM), out of which, as known, drug Hylak Forte is made. Our earlier systematic analysis of metabolomics, representatives of positive microflora, pointed to the fact that the latter contain specific biochemical mechanisms for biosynthesis and processing of a number of vitamins. In the present paper the results of a systematic analysis of the effects of vitamins B2, B6 and K on the survival of the representatives of the positive microflora on the basis of the substrate of metabolic products of positive flora have been presented. The results of the analysis allow us clarify the molecular mechanisms of the therapeutic effects of this drug with a very complex structure and confirm the available clinical data and are an important foundation for subsequent microbiological research. Metabolites in the preparation composition contribute to the normalization of metabolism of pyridoxalphosphate (vitamin B6), flavin adenin dinucleotide (FAD, a derivative of vitamin B2) and nicotinamide dinucleotide (NAD, a derivative of vitamin B3)--cofactors of enzymes that have a significant impact on the survival of microbiota. The proposed molecular mechanisms also indicate on a possible synergies between certain vitamins and micro elements, on the one hand, and molecular components of the preparations on the basis of waste products of microbiota on the other.

The purpose of this study was to demonstrate that shellfish can be used to detect enteric viruses in marine waters where they are present at very low concentrations. Aqua-cultured mussels were placed in the sea just off the mouth of a drainage channel affected by human and animal faecal contamination. Samples were taken from the channel, the sea and the mussels at intervals over two 4-week periods. The samples were tested to verify the presence of both rotaviruses and E. coli. Rotaviruses were detected by Real Time-PCR, typed by multiplex PCR and subsequently sequenced. E. coli was enumerated in water matrices by a filtering method and in mussels by the MPN method. The presence of E. coli in the examined matrices demonstrates contamination of faecal origin throughout the studied environments. Rotaviruses were recorded in channel waters, but not in sea water. In both experiments, rotaviruses were detected in mussels 21 and 28 days after being placed in the sea water off the channel mouth. The use of mussels thus enabled the detection of rotaviruses in waters where the high dilution rendered direct investigation impossible. This study indicates that mussels can be used in marine virological surveillance programs.

Background: Selective digestive decontamination (SDD) and selective oropharyngeal decontamination (SOD) are effective in improving survival in patients under intensive care. In this study possible differential effects in surgical and non-surgical patients were investigated., Methods: This was a post hoc subgroup analysis of data from a cluster-randomized multicentre trial comparing three groups (SDD, SOD or standard care) to quantify effects among surgical and non-surgical patients. The primary study outcome was 28-day mortality rate. Duration of mechanical ventilation, duration of intensive care unit (ICU) and hospital length of stay, and bacteraemia rates were secondary outcomes., Results: The subgroup analyses included a total of 2762 surgical and 3165 non-surgical patients. Compared with standard care, adjusted odds ratios (ORs) for mortality were comparable in SDD-treated surgical and non-surgical patients: 0·86 (95 per cent confidence interval 0·69 to 1·09; P = 0·220) and 0·85 (0·70 to 1·03; P = 0·095) respectively. However, duration of mechanical ventilation, ICU stay and hospital stay were significantly reduced in surgical patients who had SDD. SOD did not reduce mortality compared with standard treatment in surgical patients (adjusted OR 0·97, 0·77 to 1·22; P = 0·801); in non-surgical patients it reduced mortality (adjusted OR 0·77, 0·63 to 0·94; P = 0·009) by 16·6 per cent, representing an absolute mortality reduction of 5·5 per cent with number needed to treat of 18., Conclusion: Subgroup analysis found similar effects of SDD in reducing mortality in surgical and non-surgical ICU patients, whereas SOD reduced mortality only in non-surgical patients. The hypothesis-generating findings mandate investigation into mechanisms between different ICU populations., (Copyright © 2011 British Journal of Surgery Society Ltd. Published by John Wiley & Sons, Ltd.)

The lumen of the gastrointestinal (GI) tract is home to an enormous quantity of different bacterial species, our microbiota, that thrive in an often symbiotic relationship with the host. Given that the healthy host must regulate contact between the microbiota and its immune system to avoid overwhelming systemic immune activation, humans have evolved several mechanisms to attenuate systemic microbial translocation (MT) and its consequences. However, several diseases are associated with the failure of one or more of these mechanisms, with consequent immune activation and deleterious effects on health. Here, we discuss the mechanisms underlying MT, diseases associated with MT, and therapeutic interventions that aim to decrease it.

Purpose of Review: In this era of increasing antimicrobial resistance, use of probiotics in infection prevention has brought new perspective. However, in 2008 the, until then considered, safe use of probiotics became an important topic after publication of a trial showing excess mortality in patients on probiotic prophylaxis. In this article, we review the concept of infection prevention by probiotics and the present knowledge of the efficacy of probiotics in prevention of infections among patients with abdominal diseases and in intensive care. Safety issues of probiotics will be discussed extensively., Recent Findings: Over 30 clinical trials with probiotics to prevent infections have been published, some of which were prematurely stopped recently. Studies with critically ill patients and patients with abdominal diseases showed conflicting results regarding the effects of probiotics on infection rates, as did meta-analyses. These studies are difficult to compare because different probiotics were used which all have different efficacy and safety profiles., Summary: The efficacy of probiotics in infection prevention among critically ill patients is still not unequivocally determined. The safety profile differs per probiotic strain and should not be generalized towards other strains and patient populations. A well designed and well powered clinical trial with clear endpoints to demonstrate efficacy is warranted.

Systemic and local inflammation in relation to the resident microbiota of the human gastro-intestinal (GI) tract and administration of probiotics are the main themes of the present review. The dominating taxa of the human GI tract and their potential for aggravating or suppressing inflammation are described. The review focuses on human trials with probiotics and does not include in vitro studies and animal experimental models. The applications of probiotics considered are systemic immune-modulation, the metabolic syndrome, liver injury, inflammatory bowel disease, colorectal cancer and radiation-induced enteritis. When the major genomic differences between different types of probiotics are taken into account, it is to be expected that the human body can respond differently to the different species and strains of probiotics. This fact is often neglected in discussions of the outcome of clinical trials with probiotics.

The gut flora carries out important functions for human health, although most of them are still unknown, and an alteration of any of them, due to a condition of dysbiosis, can lead to relevant pathological implications. Commensal bacteria in the gut are essential for the preservation of the integrity of the mucosal barrier function and an alteration in the anatomic functional integrity of this barrier has been implicated in the pathophysiologic process of different diseases. The gut microflora plays a role in modulating the intestinal immune system; in fact, it is essential for the maturation of gut-associated lymphatic tissue, the secretion of IgA and the production of antimicrobial peptides. The enteric flora represents a potent bioreactor which controls several metabolic functions, even if most of them are still unknown. The main metabolic functions are represented by the fermentation of indigestible food substances into simple sugars, absorbable nutrients, and short-chain fatty acids. Furthermore, the gut microbiota exerts important trophic and developmental functions on the intestinal mucosa. This overview focuses briefly on the physiological role of the gut microbiota in maintaining a healthy state and the potential role played by disturbances of both the function and composition of the gut microbiota in determining important pathological conditions, such as irritable bowel syndrome, inflammatory bowel disease, metabolic syndrome, obesity, and cancer., (Copyright © 2011 S. Karger AG, Basel.)

Purpose of Review: Dramatic advances in molecular characterization of the largely noncultivable enteric microbiota have facilitated better understanding of the composition of this complex ecosystem at broad phylogenetic levels. This review outlines current understanding of mechanisms by which commensal bacteria are controlled and shaped into functional communities by innate and adaptive immune responses, antimicrobial peptides produced by epithelial cells and host genetic factors., Recent Findings: Secretory IgA, which targets enteric bacteria, regulates the number, composition, and function of luminal bacteria. Likewise, epithelial production of antimicrobial peptides helps control enteric microbiota growth, translocation, and perhaps composition. The developing role of innate signaling pathways, such as Toll-like receptors and NOD2, is beginning to be studied, with dysbiosis following their genetic deletion. Inflammation and effector immune responses lead to decreased diversity and selective alterations of functionally active bacterial species such as Escherichia coli and Faecalibacterium prausnitzii that have proinflammatory and protective activities, respectively. Studies of humans, mice, and comparative species indicate that both genetic and early environmental factors influence the development of a stable intestinal microbiota., Summary: Genetic and mucosal immunity strongly influence the composition and function of enteric commensal bacteria. This understanding should help develop strategies to correct dysfunctional altered microbiota in genetically susceptible individuals, better diagnose and correct potential dysbiosis in high-risk individuals at a preclinical stage, and therapeutically target pathogenic bacterial species that help drive chronic inflammatory conditions.

The human body is actually a super-organism that is composed of 10 times more microbial cells than our body cells. Metagenomic study of the human microbiome has demonstrated that there are 3.3 million unique genes in human gut, 150 times more genes than our own genome, and the bacterial diversity analysis showed that about 1000 bacterial species are living in our gut and a majority of them belongs to the divisions of Firmicutes and Bacteriodetes. In addition, most people share a core microbiota that comprises 50-100 bacterial species when the frequency of abundance at phylotype level is not considered, and a core microbiome harboring more than 6000 functional gene groups is present in the majority of human gut surveyed till now. Gut bacteria are not only critical for regulating gut metabolism, but also important for host immune system as revealed by animal studies.

Autistic behavior is often accompanied by numerous disturbing symptoms on the part of gastrointestinal system, such as abdominal pain, constipation or diarrhea. These problems are often connected with deregulation of physiological microflora in intestine. The aim of this study was to determine differences in intestinal microflora of autistic and healthy children. Strains of Clostridium spp. and enterococci were isolated more frequently from stool samples of autistic children and rarely lactobacilli. Quantitative differences were observed maliny among staphylococci, Candida spp. and Clostridium perfringens. Monitoring and stabilization of intestinal microflora and knowledge about role of particular strains in etiology of autistic disorders can increase the chances for appropriate therapy.

Objective: to determine the simultaneous presence of H. pylori in both the oral cavity and gastric mucosal in patients suffering digestive pathologies and to establish the possible association between the presence of H. pylori in the oral cavity and the gingivoperiodontal pathology., Study Design: Patients with gastric symptoms (case group) and asymptomatic patients (control group) seen at the Gastroenterology Department of Dr. Julio C. Perrando Hospital (Resistencia, Argentina) were selected. Dental plaque and saliva samples from both groups were obtained. In the case group, gastric biopsy samples were also taken. H. pylori was detected in gastric biopsies by histological stains, and Polymerase Chain Reaction (PCR) was carried out on the oral samples., Results: Among the 98 patients (43 cases and 55 controls), 196 oral samples (saliva 98, dental plaque 98) and 43 gastric biopsias were obtained. H. pylori was detected in oral samples in 18/98 patients, in gastric biopsies in 38/43 patients, and in both samples in 15/43 patients., Conclusions: The presence of H. pylori in the oral cavity of patients suffering digestive pathologies is more frequent in those patients harbouring a gingivoperiodontal disease, and this fact could represent an obstacle for the eradication of the bacterium. At the same time, it could constitute a risk factor for gastrointestinal reinfection after treatment.

Background/aims: Helicobacter pylori infection is accepted to be associated with two mutually exclusive diseases duodenal ulcer and gastric cancer. The aim of this study was to explore the relationship and prevalence of Helicobacter pylori infection in different surgical diseases., Methodology: With use of simple serologic assays for detecting IgA and IgG antibodies to HP antigen, we studied the association of infection with HP and 15 surgical diseases., Results: The prevalence of HP was 68.60% (results of assays were positive for 142 patients out of 207). This study confirmed statistically significant correlation between HP seropositivity and pancreatic cancer (p = 0.02), hepatocellular cancer (p = 0.000), gastric cancer (p = 0.01), colon cancer (p = 0.002), rectal cancer (p = 0.001), intestinal cancer (p = 0.026), stenosis pylori (p = 0.01), ulcer diseases (p = 0.004), jaundice (p = 0.002); statistically significant inverse association between HP seropositivity and the acute appendicitis (p = 0.013) and no correlation with HP infection and cholecystitis (p = 0.716), cholelithiasis (p = 0.06), and ulcer hemorrhage (p = 0.064)., Conclusion: The use of simple serological tests to identify patients with HP infection could help to calculate the risk of development of severe gastrointestinal diseases.

Biofilm formation by 102 Bacillus cereus and B. thuringiensis strains was determined. Strains isolated from soil or involved in digestive tract infections were efficient biofilm formers, whereas strains isolated from other diseases were poor biofilm formers. Cell surface hydrophobicity, the presence of an S layer, and adhesion to epithelial cells were also examined.

Intra-abdominal infections (IAIs) are a frequent cause of morbidity and mortality. These infections can be caused by a wide variety of microorganisms, including both aerobes and anaerobes, and are often polymicrobial. Several studies have reported that mortality depends on initiating early appropriate antimicrobial therapy. The inappropriate choice of initial antibiotic therapy results in a longer hospital stay and higher costs of hospitalization compared with appropriate initial antibiotic therapy. The aim of this review is to summarize the recommendations of several guidelines on the management of IAIs.

Complicated intra-abdominal infections (cIAIs) represent a heavy burden for the italian National Health System (NHS) and the italian society, with estimated annual costs of 1.5 and 3 billion euros, respectively. Both monotherapy and antibiotic combinations induce significantly different acquisition and administration costs but substantially equivalent therapeutic results, with average clinical effectiveness rates of 70-80%. this apparent equivalence presumably depends on the widespread trend to individualize the therapeutic strategy according to the clinical severity and the community or nosocomial origin of cIAIs, as well as to the degree of non-appropriateness when empirically choosing a first-line antibiotic.The average cost of nosocomial management of cIAI patients depends on several factors: posology, antibiotic drug acquisition, administration costs, duration of therapy, mix of antibiotic schedules, rates of the therapeutic failures, prolonged hospitalization. The introduction of a new antibiotic like tigecycline to the therapeutic arsenal leads to a small increase in average antibiotic acquisition and treatment costs per patient: this increase is proportional to the percentage of patients treated with the new antibiotic. According to a decisional model, implemented on international outcome data and italian costs, the mean cost for first-line antibiotic acquisition and the mean cost for first- and second-line antibiotic treatment represent respectively only 2% and 8% of the mean overall hospitalization cost. the mean hospitalization cost estimated by the model is noticeably higher than the mean value of Diagnosis Related Group (DRG) tariffs presumably reimbursed by the italian NHS to hospitals for ciAi-related hospitalizations. Greater overall efficiency levels in the nosocomial management of cIAI patients are achievable mainly through the reduction of non-appropriateness rates in first-line antibiotic choices and better treatment individualization, possible if the physician is offered the choice of as many valid therapeutic options as possible, in order to guarantee the best possibility of cure for each patient.

Abdominal sepsis results in high morbidity and mortality. Intra-abdominal infectious complications are one of the most common infectious pathologies seen in critically ill patients. Approximately 30% of patients admitted to an ICU with intra-abdominal infection succumb to their illness, and when peritonitis arises as a complication of a previous surgical procedure, or recurs during ICU admission, mortality rates exceed 50%. Thus early detection and treatment are essential to minimize patient complications.Critically ill patients are often clinically unevaluable due to distracting injuries, respiratory failure, obtundation, or other pathology. even when patients can be examined, the clinical exam is frequently unreliable and/or misleading. the diagnostic approach to identifying abdominal problems will differ, depending upon the hemodynamic stability of the patient. Patients who have low systolic blood pressures, who are pressor-dependent, may be too unstable to undergo analyses that require trips away from the ICU or emergency department. intra-abdominal pathology may be detected by ultrasound or diagnostic peritoneal lavage. When critically ill patients are stable enough to undergo some diagnostic evaluation of their abdomen, the approach is somewhat simpler. Overall, computerized tomography (CT) is the imaging modality of choice for most intra-abdominal processes. for diagnosis of intra-abdominal conditions using CT scanning it is optimal if patients receive both oral and intravenous contrast. An exception to the use of CT scanning is evaluation of suspected biliary pathology, which is best imaged by ultrasound. it will identify calculous and acalculous cholecystitis and may show changes in the gallbladder or common bile duct associated with biliary obstruction.

Antimicrobial therapy of intra-abdominal infection must be based on its etiology, which is generally polymicrobial, and its location, with the aim of selecting the most suitable antimicrobial agents not only according to their spectrum but also their pharmacokinetic profile. Currently, both monotherapy and combination therapy can be used, thanks to the availability of newer drugs characterized by a wide range of antimicrobial activity against both aerobes and anaerobes. Antibiotic choice and duration of therapy also vary according to the severity of the infection.

Tigecycline is the first of a new class of antibiotics, the glycylcyclines, with properties which can overcome many common resistance mechanisms, making it appropriate for treatment of many serious and life-threatening infections for which other antibiotics are no longer appropriate. its wide antibacterial spectrum includes most methicillin-resistant staphylococci, vancomycin-resistant enterococci, ESBL-producing and other multi-resistant Gram-negative bacteria such as Acinetobacter and Stenotrophomonas spp. it is also active against anaerobes and atypical pathogens. Tigecycline is available only as parenteral formulation. it has a high volume of distribution (>10 L/kg) and long half-life (36 h). It is approved in the USA and europe for treatment of complicated skin and soft tissue infections and complicated communityacquired intra-abdominal infections. Phase II studies for treatment of community- and nosocomial-acquired pneumonia and sepsis due to multidrug resistant pathogens are ongoing.