Detection of Listeria monocytogenes by polymerase chain reaction in intestinal mucosal biopsies from patients with inflammatory bowel disease and controls

The emerging microbiome-based approaches to IBD therapy: From SCFAs to urolithin A

Inflammatory bowel disease (IBD) is a group of chronic gastrointestinal inflammatory conditions which can be life-threatening, affecting both children and adults. Crohn's disease and ulcerative colitis are the two main forms of IBD. The pathogenesis of IBD is complex and involves genetic background, environmental factors, alteration in gut microbiota, aberrant immune responses (innate and adaptive), and their interactions, all of which provide clues to the identification of innovative diagnostic or prognostic biomarkers and the development of novel treatments. Gut microbiota provide significant benefits to its host, most notably via maintaining immunological homeostasis. Furthermore, changes in gut microbial populations may promote immunological dysregulation, resulting in autoimmune diseases, including IBD. Investigating the interaction between gut microbiota and immune system of the host may lead to a better understanding of the pathophysiology of IBD as well as the development of innovative immune- or microbe-based therapeutics. In this review we summarized the most recent findings on innovative therapeutics for IBD, including microbiome-based therapies such as fecal microbiota transplantation, probiotics, live biotherapeutic products, short-chain fatty acids, bile acids, and urolithin A.

Differential prevalence of pathobionts and host gene polymorphisms in chronic inflammatory intestinal diseases: Crohn's disease and intestinal tuberculosis

BACKGROUND AND OBJECTIVES

Crohn's disease (CD) and Intestinal tuberculosis (ITB) are chronic inflammatory ulcero-constrictive intestinal diseases with similar phenotype. Although both are disease models of chronic inflammation and their clinical presentations, imaging, histological and endoscopic findings are very similar, yet their etiologies are diverse. Hence, we aimed to look at differences in the prevalence of pathobionts like adherent-invasive Escherichia coli (AIEC), Listeria monocytogenes, Campylobacter jejuni and Yersinia enterocolitica in CD and ITB as well as their associations with host-associated genetic polymorphisms in genes majorly involved in pathways of microbial handling and immune responses.

METHODS

The study cohort included 142 subjects (69 patients with CD, 32 with ITB and 41 controls). RT- PCR amplification was used to detect the presence of AIEC, L. monocytogenes, C. jejuni, and Y. enterocolitica DNA in colonic mucosal biopsies. Additionally, we tested three SNPs in IRGM (rs13361189, rs10065172, and rs4958847), one SNP in ATG16L1 (rs2241880) and one SNP in TNFRSF1A (rs4149570) by real-time PCR with SYBR green from peripheral blood samples in this cohort.

RESULTS

In patients with CD, AIEC was most frequently present (16/ 69, 23.19%) followed by L. monocytogenes (14/69, 20.29%), C. jejuni (9/69, 13.04%), and Y. enterocolitica (7/69, 10.14%). Among them, L. monocytogenes and Y. enterocolitica were significantly associated with CD (p = 0.02). In addition, we identified all the three SNPs in IRGM (rs13361189, rs10065172, and rs4958847), one SNP in ATG16L1 (rs2241880) and TNFRSF1A (rs4149570) with a significant difference in frequency in patients with CD compared with ITB and controls (p<0.05).

CONCLUSION

Higher prevalence of host gene polymorphisms, as well as the presence of pathobionts, was seen in the colonic mucosa of patients with CD as compared to ITB, although both are disease models of chronic inflammation.

The role of gastrointestinal pathogens in inflammatory bowel disease: a systematic review

The inflammatory bowel diseases (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), are chronic, progressive, inflammatory conditions of the gastrointestinal tract. Imbalance in the gut microbial community, or dysbiosis, and the subsequent immune response, represent the critical relationship between genetic susceptibility, microbes, and environment factors, that result in IBD. Gastrointestinal pathogens - a common cause of dysbiosis - have been implicated as an environmental trigger in new onset IBD, as well as flare of existing IBD. In this article, we systematically review clinical data regarding the association between specific gastrointestinal pathogens and IBD. Numerous bacteria, viruses, fungi, and parasites have been implicated in the pathogenesis of IBD, and exacerbations of existing disease. In this article, we will also specifically discuss the less recognized microbes that have an inverse association with IBD, including certain bacterial pathogens, such as Helicobacter pylori, and parasites, such as Trichuris species. Future prospective and experimental studies are required to establish causality and clarify potential mechanisms of enteric pathogens in modifying the risk and course of IBD.

Bacteriotherapy for inflammatory bowel disease

The number of patients with inflammatory bowel disease is rapidly increasing in developed countries. The main cause of this increase is thought not to be genetic, but secondary to rapidly modernized environmental change. Changes in the environment have been detrimental to enteric probiotics useful for fermentation, inducing an increase in pathobionts that survive by means other than fermentation. This dysregulated microbiota composition, the so-called dysbiosis, is believed to have increased the incidence of inflammatory bowel disease. Bacteriotherapy, a treatment that prophylactically and therapeutically corrects the composition of disturbed intestinal microbiota, is a promising recent development. In fact, fecal microbiome transplantation for recurrent Clostridioides difficile infection in 2013 was a significant contribution for bacteriotherapy. In this paper, we comprehensively review bacteriotherapy in an easy-to-understand format.

Influence of Microbiota on Intestinal Immune System in Ulcerative Colitis and Its Intervention

Ulcerative colitis (UC) is an inflammatory bowel disease (IBD) with chronic and recurrent characteristics caused by multiple reasons. Although the pathogenic factors have not been clarified yet, recent studies have demonstrated that intestinal microbiota plays a major role in UC, especially in the immune system. This review focuses on the description of several major microbiota communities that affect UC and their interactions with the host. In this review, eight kinds of microbiota that are highly related to IBD, including Faecalibacterium prausnitzii, Clostridium clusters IV and XIVa, Bacteroides, Roseburia species, Eubacterium rectale, Escherichia coli, Fusobacterium, and Candida albicans are demonstrated on the changes in amount and roles in the onset and progression of IBD. In addition, potential therapeutic targets for UC involved in the regulation of microbiota, including NLRPs, vitamin D receptor as well as secreted proteins, are discussed in this review.

The human gastrointestinal tract and oral microbiota in inflammatory bowel disease: a state of the science review

Inflammatory bowel disease (IBD) includes a spectrum of diseases from ulcerative colitis (UC) to Crohn's disease (CD). Many studies have addressed the changes in the microbiota of individuals affected by UC and CD. A decrease in biodiversity and depletion of the phyla Bacteroidetes and Firmicutes has been reported, among others. Changes in microbial composition also result in changes in the metabolites generated in the gut from microbial activity that may involve the amount of butyrate and other metabolites such as H₂ S being produced. Other factors such as diet, age, or medication need to be taken into consideration when studying dysbiosis associated with IBD. Diverse bacterial species have been associated specifically or non-specifically to IBD, but none of them have been demonstrated to be its ethiological agent. Recent studies also suggest that micro-eukaryotic populations may also be altered in IBD patients. Last, but not least, viruses, and specially bacteriophages, can play a role in controlling microbial populations in the gastrointestinal tract. This may affect both bacterial diversity and metabolism, but possible implications for IBD still remain to be solved. Dysbiosis in the oral microbiome associated with IBD remains an emerging field for future research.

Bacterial Intestinal Superinfections in Inflammatory Bowel Diseases Beyond Clostridum difficile

Besides genetics and environmental factors, intestinal microbiota seem to play a major role in the pathogenesis of inflammatory bowel diseases. For many decades, it has been said that some enteropathogens may even trigger both inflammatory bowel disease development and disease flares. For this reason, stool testing had been performed in inflammatory bowel disease flares but current guidelines only recommend to rule out Clostridium difficile infection and there is no clear advice for other enteropathogens given that the scarce available evidence points at a low prevalence of this sort of intestinal superinfections with no clear impact on disease course. The present article reviews the current knowledge about the role of bacterial enteropathogens on disease pathogenesis and flares beyond C. difficile.

A breakthrough in probiotics: Clostridium butyricum regulates gut homeostasis and anti-inflammatory response in inflammatory bowel disease

Intestinal immune homeostasis is regulated by gut microbiota, including beneficial and pathogenic microorganisms. Imbalance in gut bacterial constituents provokes host proinflammatory responses causing diseases such as inflammatory bowel disease (IBD). The development of next-generation sequencing technology allows the identification of microbiota alterations in IBD. Several studies have shown reduced diversity in the gut microbiota of patients with IBD. Advances in gnotobiotic technology have made possible analysis of the role of specific bacterial strains in immune cells in the intestine. Using these techniques, we have shown that Clostridium butyricum as a probiotic induces interleukin-10-producing macrophages in inflamed mucosa via the Toll-like receptor 2/myeloid differentiation primary response gene 88 pathway to prevent acute experimental colitis. In this review, we focus on the new approaches for the role of specific bacterial strains in immunological responses, as well as the potential of bacterial therapy for IBD treatments.

Listeria monocytogenes infection in inflammatory bowel disease patients: case series and review of the literature

BACKGROUND

Listeria monocytogenes (LM) is a gram-positive intracellular bacillus that in immunodeficient patients, children, geriatric patients, pregnant women, and even in healthy individuals can cause central nervous system infection, bacteremia, and other clinical manifestations, becoming a relevant pathogen.

MATERIALS AND METHODS

From the Microbiology Service data of 'Gregorio Marañón' Hospital, we selected all positive biological sample cultures for LM from inflammatory bowel disease (IBD) patients, from January 1986 until January 2011. These cases were included in an SPSS database, analyzing several basal clinical characteristics and factors related to the infection.

RESULTS

Three patients diagnosed with IBD had positive cultures for LM during this period. All of them were male, and also all of them had a diagnosis of Crohn's disease. Every patient had a corticosteroid cumulated dose of more than 400 mg (equivalency in methylprednisolone doses), adding anti-tumor necrosis factor-α treatment (certolizumab) in one patient. Prior colonoscopy with biopsy was performed in two patients. Clinical presentation of the infection was bacteremia in two patients, accompanied by central nervous system infection in one patient. One patient had isolated meningoencephalitis. Despite correct empiric treatment, one patient died from a cause related to the infection, that is, rombencephalitis. Increased incidence of LM bacteremia was found in IBD patients, compared with the general population (12.2 bacteremias/100 000 IBD patient-years, compared with 1.6 bacteremias/100 000 person-years), with an odds ratio of 7.4.

CONCLUSION

IBD patients may be at risk for more frequent and serious LM infection compared with the general population.

Mycobacterium avium subspecies paratuberculosis in the etiology of Crohn’s disease, cause or epiphenomenon?

The origin of inflammatory bowel disease is unknown. Attempts have been made to isolate a microorganism that could explain the onset of inflammation, but no pathological agent has ever been identified. Johne’s disease is a granulomatous chronic enteritis of cattle and sheep caused by Mycobacterium avium subspecies paratuberculosis (MAP) and shows some analogies with Crohn’s disease (CD). Several studies have tried to clarify if MAP has a role in the etiology of CD. The present article provides an overview of the evidence in favor and against the “MAP-hypothesis”, analyzing the methods commonly adopted to detect MAP and the role of antimycobacterial therapy in patients with inflammatory bowel disease. Studies were identified through the electronic database, MEDLINE, and were selected based on their relevance to the objective of the review. The presence of MAP was investigated using multiple diagnostic methods for MAP detection and in different tissue samples from patients affected by CD or ulcerative colitis and in healthy controls. On the basis of their studies, several authors support a close relationship between MAP and CD. Although increasing evidence of MAP detection in CD patients is unquestionable, a clear etiological link still needs to be proven.

Infectious etiopathogenesis of Crohn’s disease

Important advances during the last decade have been made in understanding the complex etiopathogenesis of Crohn’s disease (CD). While many gaps in our knowledge still exist, it has been suggested that the etiology of CD is multifactorial including genetic, environmental and infectious factors. The most widely accepted theory states that CD is caused by an aggressive immune response to infectious agents in genetically predisposed individuals. The rise of genome-wide association studies allowed the identification of loci and genetic variants in several components of host innate and adaptive immune responses to microorganisms in the gut, highlighting an implication of intestinal microbiota in CD etiology. Moreover, numerous independent studies reported a dysbiosis, i.e., a modification of intestinal microbiota composition, with an imbalance between the abundance of beneficial and harmful bacteria. Although microorganisms including viruses, yeasts, fungi and bacteria have been postulated as potential CD pathogens, based on epidemiological, clinicopathological, genetic and experimental evidence, their precise role in this disease is not clearly defined. This review summarizes the current knowledge of the infectious agents associated with an increased risk of developing CD. Therapeutic approaches to modulate the intestinal dysbiosis and to target the putative CD-associated pathogens, as well as their potential mechanisms of action are also discussed.

Influence of Sterilized Human Fecal Extract on the Sensitivity of Salmonella enterica ATCC 13076 and Listeria monocytogenes ATCC 15313 to Enrofloxacin

There is much debate on whether continuous exposure of commensal bacteria and potential pathogens residing in the human intestinal tract to low levels of antimicrobial agents from treated food animals pose a public health concern. To investigate antimicrobial effects on bacteria under colonic conditions, we studied resistance development in Salmonella enterica and Listeria monocytogenes exposed to enrofloxacin in the presence of fecal extract. The bacteria were incubated at 37 °C in Mueller-Hinton broth, with and without 0.01~0.5 μg/mL enrofloxacin, in the presence and absence of sucrose, and with 1% or 2.5% filter-sterilized fecal extract, for three passages. In the second and third passages, only the bacteria incubated in the media containing sterilized fecal extract grew in 0.5 μg/mL of enrofloxacin. Fecal extract (1% and 2.5%) decreased the sensitivity of S. enterica to enrofloxacin in the medium containing the efflux pump inhibitors reserpine and carbonyl cyanide-m-chlorophenylhydrazone (CCCP) and affected the accumulation of ethidium bromide (EtBr) in this bacterium. Enrofloxacin (0.06 µg/mL) and fecal extract altered the composition of fatty acids in S. enterica and L. monocytogenes. We conclude that fecal extract decreased the susceptibilities of S. enterica and L. monocytogenes to concentrations of enrofloxacin higher than the MIC and resulted in rapid resistance selection.

Immunohistochemical search for viral and bacterial antigens in Crohn's disease

BACKGROUND

Recent studies show that diseased intestinal tissues of patients with Crohn's disease (CD) contain obstructed lymphatics, granulomas, and tertiary lymphoid organs, representing responses to persistent antigen.

METHODS

Forty-seven tissue sections from 28 CD patients and 20 tissue sections from 17 control patients were studied. Tissues were immunostained with antibody directed against adenovirus, Epstein-Barr virus, herpes simplex virus I, parvovirus B19, Listeria monocytogenes, Escherichia coli, Clostridium perfringens, and Mycobacterium avium subspecies paratuberculosis.

RESULTS

There was no evidence of adenovirus, Epstein-Barr virus, parvovirus B19, or M. avium subsp. paratuberculosis in the tissues. Clostridia were positively stained in the mucus of 18.5% of CD patients versus 35.3% of controls and in the tissue of 11.1% of CD patients but in no controls. Immunoreactivity to listeria antibody occurred in the mucus of 3.7% of CD patients and in 5.9% of controls while it occurred in the tissue of 37.0% of CD patients and 29.4% of controls. E. coli occurred in the mucus of 48.1% CD and 64.7% controls and in the tissue of 18.5% and 5.9% respectively.

CONCLUSIONS

Of the agents demonstrated in this search, none was located in granulomas or inflamed lymphatics. Finding the common gut microbes, E. coli and clostridia, in the mucus of patients and controls was not unexpected. The minor focal staining of E. coli and clostridia does not suggest a primary role for these pathogens in CD. Positive staining for listeria in patients and controls may very well represent cross reactivity rather than specific identification.

Crohn's disease and the mycobacterioses: a quarter century later. Causation or simple association?

It has been more than 25 years since Mycobacterium paratuberculosis was first proposed as an etiologic agent in Crohn's disease based on the isolation of this organism from several patients. Since that time, a great deal of information has been accumulated that clearly establishes an association between M. paratuberculosis and Crohn's disease. However, data are conflicting and difficult to interpret and the field has become divided into committed advocates and confirmed skeptics. This review is an attempt to provide a thorough and objective summary of current knowledge from both basic and clinical research from the views and interpretations of both the antagonists and proponents. The reader is left to draw his or her own conclusions related to the validity of the issues and claims made by the opposing views and data interpretations. Whether M. paratuberculosis is a causative agent in some cases or simply represents an incidental association remains a controversial topic, but current evidence suggests that the notion should not be so readily dismissed. Remaining questions that need to be addressed in defining the role of M. paratuberculosis in Crohn's disease and future implications are discussed.

Characterization of the gastrointestinal microbiota in health and inflammatory bowel disease

The enteric bacterial flora play a key role in maintaining health. Inflammatory bowel disease is associated with quantitative and qualitative alterations in the microbiota. Early characterization of the microbiota involved culture-dependent techniques. The advent of metagenomic techniques, however, allows for structural and functional characterization using culture-independent methods. Changes in diversity, together with quantitative alterations in specific bacterial species, have been identified. The functional significance of these changes, and their pathogenic role, remain to be elucidated.

Gut microbiota, immunity, and disease: a complex relationship

Our immune system has evolved to recognize and eradicate pathogenic microbes. However, we have a symbiotic relationship with multiple species of bacteria that occupy the gut and comprise the natural commensal flora or microbiota. The microbiota is critically important for the breakdown of nutrients, and also assists in preventing colonization by potentially pathogenic bacteria. In addition, the gut commensal bacteria appear to be critical for the development of an optimally functioning immune system. Various studies have shown that individual species of the microbiota can induce very different types of immune cells (e.g., Th17 cells, Foxp3(+) regulatory T cells) and responses, suggesting that the composition of the microbiota can have an important influence on the immune response. Although the microbiota resides in the gut, it appears to have a significant impact on the systemic immune response. Indeed, specific gut commensal bacteria have been shown to affect disease development in organs other than the gut, and depending on the species, have been found to have a wide range of effects on diseases from induction and exacerbation to inhibition and protection. In this review, we will focus on the role that the gut microbiota plays in the development and progression of inflammatory/autoimmune disease, and we will also touch upon its role in allergy and cancer.

The role of bacteria and pattern-recognition receptors in Crohn's disease

Crohn's disease is widely regarded as a multifactorial disease, and evidence from human and animal studies suggests that bacteria have an instrumental role in its pathogenesis. Comparison of the intestinal microbiota of patients with Crohn's disease to that of healthy controls has revealed compositional changes. In most studies these changes are characterized by an increase in the abundance of Bacteroidetes and Proteobacteria and a decrease in that of Firmicutes. In addition, a number of specific mucosa-associated bacteria have been postulated to have a role in Crohn's disease, including Mycobacterium avium subspecies paratuberculosis, adherent and invasive Escherichia coli, Campylobacter and Helicobacter species. The association between mutations in pattern-recognition receptors (Toll-like receptors and Nod-like receptors) and autophagy proteins and Crohn's disease provides further evidence to suggest that defective sensing and killing of bacteria may drive the onset of disease. In this Review, we present recent advances in understanding the role of bacteria and the contribution of pattern-recognition receptors and autophagy in the pathogenesis of Crohn's disease.

[Neurological complications of inflammatory bowel disease]

Although ulcerative colitis and Crohn's disease have traditionally been considered to be inflammatory diseases limited to the gastrointestinal tract, it has been shown that both pathologies are frequently accompanied by various extraintestinal disorders. There is an increasing evidence that they may also manifest in the nervous system, including the peripheral and the central parts. Although some of these neurological complications have been known for a long time, such as cerebrovascular disease, vasculitis and autoinmune processes including neuropathies and cerebral demyelination, others have been recently described. With the exception of some of this complications such as the thromboembolism, evidence for a casual relationship relies merely on single case reports or case series. In this article, we try to review the existing evidence on neurological manifestations of both variants of inflammatory bowel disease.

Geographic distribution and ecological studies of inflammatory bowel disease in southeastern Norway in 1990-1993

BACKGROUND

The purpose was to study the spatial distribution of cases of inflammatory bowel disease (IBD) and characterize municipalities with high incidences in a search for environmental risk factors.

METHODS

Spatial clustering of patients diagnosed with IBD during 1990-1993 were studied in 4 counties in southeastern Norway, and an ecological analysis was conducted to study the relationship between risk of IBD in the municipalities and their characteristics such as population, health care, urban/rural change, and socioeconomic change.

RESULTS

One cluster consisting of 4 municipalities was identified for IBD in Østfold county (P = 0.011). The ecological analysis showed that the incidence rate of IBD was 33% (95% confidence interval [CI]: 2%-75%) higher in municipalities with the highest level of education compared to the lowest level of education and 35% (2%-78%) higher in urban than rural municipalities. The incidence rate was 11% (1%-20%) lower in municipalities with a high urban/rural change compared to municipalities with low urban/rural change. Individuals living in high-risk municipalities were 3 times (1.57-5.45) more likely to have a first-degree family member with IBD than individuals living in normal-risk municipalities.

CONCLUSIONS

The geographic distribution of cases with IBD is not uniformly distributed and is related to urbanization, level of education, and moving pattern. Geographic distribution may be explained by either changes in environment-host relationships or neurobiological mechanisms due to stress and economic frustration. These factors and genetic predisposition might also explain increased familial clustering. Spatial clustering was significant neither for Crohn's disease CD nor ulcerative colitis (UC) but showed a stronger tendency within the CD group.

Pathogenic agents in inflammatory bowel diseases

PURPOSE OF REVIEW

Infectious agents are still thought to be involved in the origin of inflammatory bowel disease. The focus in recent years has been more on Mycobacterium avium subsp paratuberculosis, adherent-invasive Escherichia coli or yeasts.

RECENT FINDINGS

A metaanalysis has shown a significant association of M. avium subsp paratuberculosis and Crohn's disease and a large randomized placebo-controlled trial reported an absence of sustained beneficial effects of combined antibiotic therapy on remission of active Crohn's disease. Adherent-invasive E. coli adhere via type 1 pili to carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6), abnormally expressed by intestinal epithelial cells in Crohn's disease patients. Both colonization of the ileal mucosa and stimulation of ileal epithelial cells by tumour necrosis factor-alpha induce overexpression of CEACAM6, leading to an amplification loop of colonization and inflammation. Anti-Saccharomyces cerevisiae mannan antibodies are the most prevalent serologic marker in Crohn's disease. Major oligomannose epitopes supporting antibody formation are expressed by Candida albicans in human tissues, suggesting that a loss of tolerance to C. albicans could lead to antibody formation in a subset of Crohn's disease patients who are genetically predisposed.

SUMMARY

M. avium subsp paratuberculosis, adherent-invasive E. coli and Candida are good candidates for an infectious aetiology of Crohn's disease on the basis of genetic susceptibility, which relates to impaired function in the defence against intracellular bacteria.

Analysis of bacterial bowel communities of IBD patients: what has it revealed?

The bacterial community, in whole or in part, resident in the bowel of humans is considered to fuel the chronic immune inflammatory conditions characteristic of Crohn's disease and ulcerative colitis. Chronic or recurrent pouchitis in ulcerative colitis patients is responsive to antibiotic therapy, indicating that bacteria are the etiological agents. Microbiological investigations of the bacterial communities in stool or of biopsy-associated bacteria have so far failed to reveal conclusively the existence of pathogens or bacterial communities of consistently altered composition in IBD patients relative to control subjects. Confounding factors need to be eliminated from future studies by using better-defined patient populations of newly diagnosed and untreated individuals and by improved sampling procedures.

Bacteria in the pathogenesis of inflammatory bowel disease

PURPOSE OF REVIEW

Inflammatory bowel disease is thought to result from an abnormal response to the gut microbiota. This review discusses advances in knowledge of the changes in gut microbiota and host response in inflammatory bowel disease.

RECENT FINDINGS

Approximately 15% of Crohn's disease cases in western populations result from mutations in NOD2/CARD15. This disease leads to defective intestinal defensin production and defective monocyte interleukin-8 response to bacterial peptidoglycan. A similar defective interleukin-8 response and consequent delayed neutrophil recruitment have also been shown in patients with Crohn's disease who do not have the NOD2 mutation. A consequence seems to be the accumulation in tissue of macrophages containing various bacteria, perhaps particularly Escherichia coli. In keeping with this patients with Crohn's disease have circulating antibodies against bacterial flagellar proteins of enterobacteria and clostridia. In ulcerative colitis, there is less evidence for invasion by or immune response to bacteria but changes in gut microbiota include a relative deficiency of bifidobacteria. There is considerable interest in probiotic or prebiotic therapies although so far little evidence for their efficacy.

SUMMARY

Molecular techniques are giving us better insight into the gut microbiota in inflammatory bowel disease that should translate into improved therapies.

Validation of 16S rDNA sequencing in microdissected bowel biopsies from Crohn's disease patients to assess bacterial flora diversity

The bowel flora is implicated in Crohn's disease (CD) pathogenesis but its precise role is still unclear. Several non-mutually exclusive hypotheses have been proposed: an unidentified persistent pathogen; excessive bacterial translocation; an immune system abnormality in response to normal bacteria; or a breakdown in the balance between protective and harmful bacteria. These hypotheses can be tested by identifying bacteria in specific microscopic bowel structures or lesions. The present paper describes a novel technique to assess bacterial flora diversity in bowel biopsies, by combining laser capture microdissection with broad-range 16S rDNA sequencing. Fifty-four samples comprising histologically normal and pathological mucosa, MALT, ulcers, submucosal lymphangiectasias, epithelioid granulomas, and lymph nodes were microdissected out of 30 bowel biopsies from five CD patients. Bacterial 16S rDNA was successfully amplified by PCR in all samples, and PCR products from 15 samples were selected for cloning and sequence analysis. A total of 729 bacterial DNA sequences were analysed, which could be attributed to six different phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, and Planctomycetes). DNA from typical bowel bacteria (Enterobacteriaceae, Clostridiales, Bacteroidetes, Fusobacteria) was detected in all microdissected areas. It was thus convincingly demonstrated that 16S rDNA sequencing can be combined with microdissection to study the bowel flora. However, no specific persistent pathogen causal for CD was identified. The results suggest that Enterobacteriaceae may initiate or colonize ulcers in CD. Translocation of bacteria through established mucosal lesions or as a result of increased permeability may be involved in the evolution towards chronic inflammation and in the establishment of persistent lesions. Further study is needed to confirm these preliminary findings.

[Environmental risk factors in Crohn's disease and ulcerative colitis (excluding tobacco and appendicectomy)]

A rapid increase in the incidence of Crohn's disease and ulcerative colitis in developed countries, the occurrence of Crohn's disease in spouses, and a lack of complete concordance in monozygotic twins are strong arguments for the role of environmental factors in inflammatory bowel disease (IBD). Research in the field of environmental factors in IBD is based upon epidemiological (geographical and case-control), clinical and experimental studies. The role of two environmental factors has clearly been established in IBD. Smoking is a risk factor for Crohn's disease and a protective factor for ulcerative colitis; appendectomy is a protective factor for ulcerative colitis. Many other environmental factors for IBD have been investigated, including infectious agents, diet, drugs, stress and social status. They are detailed in the present review. Among them, atypical Mycobacteria, oral contraceptives and antibiotics could play a role in Crohn's disease. To date, three hypotheses associate environmental factors with the pathophysiology of IBD (loss of tolerance of intestinal immune system towards commensal bacterial flora): the hygiene, infection and cold chain hypotheses. Much work remains to be done to identify risk factors for IBD. Research identifying environmental factors that might cause a predisposition to IBD is useful. It may lead to disease prevention in subjects who are genetically predisposed and disease improvement in patients.

Risk factors for intussusception in infants in Vietnam and Australia: adenovirus implicated, but not rotavirus

OBJECTIVE

This study aimed to investigate risk factors for the development of intussusception in infants in a developing country with a suspected high incidence and in a developed country with a low incidence.

STUDY DESIGN

A prospective case-control study of infants <2 years of age with idiopathic intussusception confirmed by air enema or surgery was conducted at the National Hospital of Paediatrics (NHP), Vietnam (n = 533) and the Royal Children's Hospital (RCH), Australia (n = 51). Diagnosis was validated in a subset (84% NHP; 67% RCH) by an independent blinded radiologist. Risk factor assessment was performed using a standardized questionnaire. Stool specimens were assayed for bacterial, viral, and parasitic agents.

RESULTS

The incidence of intussusception in Vietnam was 302/100,000 in infants <1 year of age (95% CI: 258-352), substantially higher than in Australia (71/100,000). A strong association with adenovirus infection was observed at both sites (cases positive at NHP: 34%, OR 8.2; cases positive at RCH: 40%, OR 44). No association was identified between intussusception and rotavirus, other enteric pathogens, oral polio vaccine, feeding practices, or living conditions.

CONCLUSIONS

The incidence of intussusception in infants was markedly higher in Vietnam than in Australia. A strong association between adenovirus infection and intussusception was identified at both sites suggesting that adenovirus may play a role in the etiology of intussusception.

Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease

We review the evidence that strongly suggests a role of the intestinal microbiota in the onset and perpetuation of inflammatory bowel disease (IBD). Experimental studies consisted of suppressing micro-organisms from the microbiota (using germ-free or gnotoxenic animals or antibiotics), introducing new micro-organisms or microbial components (e.g. probiotics, CpG-DNA) or selectively increasing some endogenous bacteria (e.g. using prebiotics). Intervention studies were performed in patients or animal models of spontaneous or chemically-induced colitis. Information was also obtained from observational studies that described the composition of the faecal and mucosal microbiota at various stages of the disease process and in controls. Many have used culture-independent techniques that identify bacteria based on the nucleic acid sequence of ribosomal RNA molecules. Microbiota in patients with IBD seem to be characterized by high concentrations of bacteria in contact with the mucosa, instability, the presence of high numbers of unusual bacteria and sometimes a reduction in the biodiversity. Studies searching for a generalized or localized dysbiosis in IBD are discussed, as well as those trying to identify bacterial molecules and receptors, which may be implicated in triggering the inflammatory process.

Specificities of the fecal microbiota in inflammatory bowel disease

BACKGROUND

Abnormalities have been described in the fecal microbiota of patients with IBD, but it is not known whether they are specific for inflammatory bowel disease (IBD) or to some extent common to other forms of colitis. The aim of this study was to compare the bacterial composition of the dominant fecal microbiota in patients with Crohn's disease (CD), ulcerative colitis (UC), infectious colitis (IC), and in healthy subjects (HS).

METHODS

Fluorescent in situ hybridization adapted to flow cytometry was used to analyze the bacterial composition of fecal samples from 13 patients with active CD, 13 patients with active UC, 5 patients with IC, and 13 HS. We used 6 group-specific probes targeting 16S rRNA and spanning the main phylogenetic groups of the fecal microbiota.

RESULTS

A significantly higher proportion of the total fecal bacteria were recognized by the 6 probes in HS (86.6%+/-12.7) and in IC (84.0%+/-11.7) than in patients with IBD (70.9%+/-15 in CD and 60.1%+/-25.7 in UC). The Clostridium coccoides group was reduced in UC (20.0%+/-13.3 versus 42.0%+/-12.0 in HS; P<.001), whereas the C leptum group was reduced in CD (13.1%+/-11.9 versus 25.2%+/-14.2 in HS; P=.002). The Bacteroides group was more abundant in IC (36.4%+/-22.9) than in the other 3 groups (13.8%+/-11.8 in CD, 11.7%+/-11.7 in UC, 12.1%+/-7.0 in HS; P<.001 for all 3 comparisons).

CONCLUSIONS

In IBD the dominant fecal microbiota comprises unusual bacterial species. Moreover, CD and UC fecal microbiota harbor specific discrepancies and differ from that of IC and healthy subjects.

Does sporadic Listeria gastroenteritis exist? A 2-year population-based survey in Nova Scotia, Canada

BACKGROUND

Febrile gastroenteritis due to Listeria monocytogenes (LM) has been primarily described in foodborne outbreaks. We decided to determine the incidence of sporadic, febrile gastroenteritis due to LM in a large, well-defined North American population over a 2-year period and to compare these cases to sporadic cases of Campylobacter and Salmonella infections occurring concurrently in the community.

METHODS

From 1 September 2002 through 31 August 2004, all stool specimens submitted for evaluation of diarrheal illness to a public health laboratory and to a children's hospital serving a population of approximately 350,000 were examined for the presence of Listeria species. Patients identified as having LM in their stool samples were matched with 2 temporally-matched patients with cultures positive for Campylobacter and Salmonella species. Patients with LM and control patients were contacted by telephone, and they answered a questionnaire that examined clinical features and risk factors for diarrheal illness.

RESULTS

A total of 7775 stool specimens were submitted during the period 1 September 2002-31 August 2004. Thirty-nine Listeria species were recovered. Seventeen of the species were LM, 13 were Listeria innocua, 3 were Listeria welshimeri, 1 was Listeria grayi, and 4 were other species. Pulsed-field gel electrophoresis results demonstrated no temporal or other clusters, and no seasonality was noted for isolates of LM. Preexisting gastrointestinal problems were much more common in patients with LM (P=.001) than in patients with Campylobacter or Salmonella infections.

CONCLUSIONS

Sporadic gastroenteritis due to LM appears to be an uncommon illness, and routine screening of stool samples for LM remains unwarranted. Preexisting gastrointestinal disease may be a risk factor for infection of the gastrointestinal tract with LM.

Methods for the isolation and identification of Listeria spp. and Listeria monocytogenes: a review

Listeria monocytogenes is an important food-borne pathogen and is widely tested for in food, environmental and clinical samples. Identification traditionally involved culture methods based on selective enrichment and plating followed by the characterization of Listeria spp. based on colony morphology, sugar fermentation and haemolytic properties. These methods are the gold standard; but they are lengthy and may not be suitable for testing of foods with short shelf lives. As a result more rapid tests were developed based on antibodies (ELISA) or molecular techniques (PCR or DNA hybridization). While these tests possess equal sensitivity, they are rapid and allow testing to be completed within 48 h. More recently, molecular methods were developed that target RNA rather than DNA, such as RT-PCR, real time PCR or nucleic acid based sequence amplification (NASBA). These tests not only provide a measure of cell viability but they can also be used for quantitative analysis. In addition, a variety of tests are available for sub-species characterization, which are particularly useful in epidemiological investigations. Early typing methods differentiated isolates based on phenotypic markers, such as multilocus enzyme electrophoresis, phage typing and serotyping. These phenotypic typing methods are being replaced by molecular tests, which reflect genetic relationships between isolates and are more accurate. These new methods are currently mainly used in research but their considerable potential for routine testing in the future cannot be overlooked.

Review article: gut flora and inflammatory bowel disease

The pathogenesis of inflammatory bowel disease involves interactions between the host susceptibility, mucosal immunity and intestinal microflora. There is therefore great interest in the changes in the endogenous flora in inflammatory bowel disease patients and in the establishment of potential genetic variations in host responses to endogenous bacteria. In this review, we summarize the modifications in the various regional ecosystems in the gastrointestinal tract during inflammatory bowel disease (luminal bacteria in faeces or inside the gastrointestinal tract, bacteria in mucus and bacteria directly attached to the mucosa). Results were obtained following a 'candidate microorganism strategy' and, as is occurring increasingly frequently, following a 'full description strategy', which has progressed largely due to the development of culture-independent techniques. The possibility of modifying the ecosystem using prebiotics or probiotics offers hope for new treatment developments, particularly in the prevention of relapse.

Crohn's disease: the cold chain hypothesis

Crohn's disease is the result of an abnormal immune response of the gut mucosa triggered by one or more environmental risk factors in people with predisposing gene variations, including CARD15 mutations. Epidemiological data allow assessment of familial environmental risk factors related to western lifestyle, diet, bacteria, and domestic hygiene. All findings point to refrigeration as a potential risk factor for Crohn's disease. Furthermore, cold-chain development paralleled the outbreak of Crohn's disease during the 20th century. The cold chain hypothesis suggests that psychrotrophic bacteria such as Yersinia spp and Listeria spp contribute to the disease. These bacteria have been identified in Crohn's disease lesions and we discuss their pathogenic properties with respect to our knowledge of the disease. From a molecular perspective, we postulate that the disease is a result of a defect in host recognition by pathogenic bacterial components that usually escape the immune response (eg, Yop molecules), which results in an excessive host response to these bacteria.

Detection of Chlamydia pneumoniae by polymerase chain reaction-enzyme immunoassay in intestinal mucosal biopsies from patients with inflammatory bowel disease and controls

BACKGROUND AND AIM

It has been suggested that Chlamydia is an organism that may have the potential to cause inflammatory bowel disease (IBD) in susceptible individuals. Chlamydia pneumoniae has emerged as an important human pathogen in the last decade. The objective of the present study was to investigate the frequency of the presence of C. pneumoniae DNA in intestinal biopsies from patients with IBD and from non-IBD controls.

METHODS

The DNA was extracted from 222 colonoscopic biopsies, which were obtained from 11 patients with Crohn's disease (CD), 18 patients with ulcerative colitis (UC) and from 37 non-IBD control patients. The presence of the C. pneumoniae omp1 gene and C. trachomatis 16S rRNA gene was determined using a rapid and sensitive polymerase chain reaction-enzyme immunoassay (PCR-EIA).

RESULTS

The C. pneumoniae-specific DNA was detected in 32 (14.4%) of 222 endoscopic biopsies. Among them, C. pneumoniae DNA were found in nine of 42 (21.4%) biopsies from patients with CD, nine of 59 (15.3%) biopsies from patients with UC, and 14 out of 122 (11.4%) biopsies from non-IBD control patients, respectively. Moreover, the percentage of patients with at least one biopsy positive for C. pneumoniae was higher, although not statistically significant, in CD (36.4%) and UC patients (38.9%) compared to non-IBD controls (16.2%). In contrast, C. trachomatis DNA was detected in only two of 222 (0.9%) biopsy samples.

CONCLUSION

The C. pneumoniae DNA was detected in the intestine of both patients with IBD and in non-IBD control patients, probably reflecting the high prevalence of this organism in the environment. The moderate yield of positive biopsies in our IBD patients and the fact that the detection rate of C. pneumoniae DNA was similar in endoscopic biopsies from IBD patients and non-IBD controls does not support a direct role for this organism in the pathogenesis of IBD.