Inflammatory bowel disease (IBD) is a growing disorder with unknown etiology. However, increasing evidence strongly highlights the role of gut microbiota with possible involvement of microbial plasmidome in the inflammatory process. Although the composition of the gut microbiota has been extensively studied, important functional groups such as butyrate producers remain poorly characterized, particularly in pediatric IBD. Furthermore, evaluation of the gut plasmidome in healthy and IBD children is missing. In this study, we used molecular techniques involving quantitative PCR (qPCR) and next-generation sequencing of functional and 16S rRNA genes to analyze the level and composition of butyrate-producing microbes in mucosal washes collected from the right colon of healthy children and Crohn's disease (CD) patients during diagnostic colonoscopy. Also, we isolated and characterized the gut plasmidome from the right colon mucosal washes collected from pediatric non-IBD control, ulcerative colitis (UC), and CD subjects. Although no difference was observed in the total amount of butyrate producers that utilize the butyrate kinase (BUK) pathway for butyrate synthesis, butyrate producers that use the butyryl CoA:acetate CoA-transferase (BCoAT) pathway were decreased in CD patients with inflamed colon as compared to controls. This functional gene approach shows that pediatric CD is characterized by generalized decreased abundance of Eubacterium rectale and increased abundance of Faecalibacterium prausnitzii in patients with inflamed colon. Also, phylogenetic analysis highlighted 15 Operational Taxonomic Units (OTUs) as potential novel butyrate producers, five of which were decreased in CD patients. Using 16S rRNA sequencing approach validated the functional gene results and showed decreased abundance of Coprococcus in CD patients with inflamed colon. Furthermore, non-IBD plasmidome has higher level of genes involved in butyrate synthesis and regulation of different cellular processes and stress response. On the other hand, IBD plasmidome is enriched with antibiotic resistance genes and phage elements, and pediatric CD plasmidome in particular has higher abundance of the adenosine-5'-phosphosulfate reductase gene. Altogether, our study represents the first comprehensive description of gut butyrate producers and plasmidome of pediatric subjects that emphasize a characteristic dysbiosis of butyrate producers in pediatric CD and a potential link between the gut plasmidome and IBD pathogenesis.

In recent years, the association between inflammatory bowel diseases (IBDs) and gut microbiota has been extensively studied in adults using post-treatment cohorts of patients. However, microbial composition and functional interplay between host genetics and microorganisms in newly diagnosed early IBD onset remain poorly defined. Using colonoscopic mucosal washes to collect mucosal-luminal microbiota from different intestinal locations, we studied the gut microbiome in a large number of children with either Crohn’s disease (CD) or ulcerative colitis (UC). Although no significant difference in the diversity was evident between the gut microbiota of IBD-affected and control children, the microbiome of IBD subjects is characterized by an increased abundance of potent hydrogen sulfide (H2S) producers and decreased abundance of beneficial butyrate producers. Microbiota and proteomic profiling revealed that the abundance of Atopobium parvulum, a potent H2S producer, was associated with increased CD severity and a concurrent reduction in the expression of the host H2S detoxification pathway. Gnotobiotic and conventionalized colitis-susceptible interleukin-10-deficient (Il-10-/-) mice showed that A. parvulum induces severe colitis, a phenotype requiring the presence of the gut microbiota. In addition, administration of bismuth, an H2S scavenger, prevented A. parvulum-induced colitis in Il-10-/- mice. Our findings have identified A. parvulum as a major mediator of inflammation severity. We also reveal an imbalance between the H2S production and detoxification in the gastrointestinal tract of pediatric IBD patients. Altogether, our findings provide new avenues for diagnostics as well as therapies to treat IBD.

BACKGROUND: Inflammatory Bowel Disease (IBD) is a collective term that refers to chronic inflammatory diseases involving the gastrointestinal (GI) tract. The most common forms of IBD include Crohn’s Disease (CD) and ulcerative colitis (UC). GOALS: The goal of this study is to compare baseline and one-year follow-up measures of anxiety, depression, and quality of life in children with newly diagnosed IBD. A secondary goal of this study is to determine if there are parallel changes in the psychologic parameters in the parents of these children over a similar one-year interval. METHODS: This prospective cohort study was conducted in the Center for Inflammatory Bowel Diseases at Boston Children’s Hospital (BCH). The parents and children with newly diagnosed IBD completed validated questionnaires about their disease at baseline (within six months of their diagnosis) and then again 12-18 months later. RESULTS: Baseline data were collected from 75 patients with IBD, and 15 of these patient/parent dyads have completed follow-up questionnaires. The incidence of anxiety and depression trended downwards after the first year, and overall quality of life trended upwards, indicating an improvement in a global state of adjustment. Measures of anxiety and depression, as well as the reported frequency and difficulty of adverse events, all decreased in parental responses after the first year. CONCLUSION: While a larger sample size is necessary to better assess changes in psychometrics over time, existing data suggests that parents manifest the most significant change in anxiety and depression over the course of the first year from diagnosis. Children appear to be less anxious and depressed at baseline. Further enrollment and data collection will permit a more definitive assessment of the relationship between patient and parent coping strategies. Ideally, the results of this ongoing study will determine if impaired parental coping lowers a patient’s quality of life, contributes to higher childhood anxiety and depression scores, and results in higher healthcare utilization.

BACKGROUND: Characterized as inflammation of the gastrointestinal tract, pediatric inflammatory bowel disease has become increasingly more prevalent throughout the world. Inflammatory bowel disease is chronic, and no definitive cure exists. Instead, patients aim to achieve remission from flair-ups. Adequate transition into adult gastrointestinal care has been shown to be critical for future patient outcomes. Hence, successful transition from pediatric to adult inflammatory bowel disease care plays an important role in maintaining patient wellbeing. Identifying factors that contribute to patient transition readiness may be able to improve the transition process. OBJECTIVE: To elucidate sociodemographic and disease related parameters that influence transition, synthesize models that can predict transition readiness, and make recommendations to improve the process. METHODS: As part of a larger quality improvement project conducted by Massachusetts General Hospital for Children, 274 patients with inflammatory bowel disease ranging from ages 12 to 27 were enrolled between June 2019 and October 2020. Sociodemographic information was gathered via chart review. The Abbreviated Pediatric Crohn’s Disease Activity Index, Disease Activity Index Score, and Physician Global Assessment were completed by patients and physicians to assess disease severity. Patients also completed PROMIS questionnaires to assess anxiety, depression, sleep disturbance and impairment. Patients completed the Transition Readiness Assessment Questionnaire to gauge transition readiness. Bivariate analyses were conducted to elucidate the relationships between sociodemographic information, disease related parameters, and transition readiness. Multivariate regressions were conducted to synthesize models aimed at predicting transition readiness. RESULTS: Females had significantly worse disease severity, mental health, and sleep quality compared to males. Poor sleep quality had a significant relationship with disease severity and mental health status. Females had significantly higher transition readiness scores compared to males. Older age had a significant relationship with greater transition readiness. More patient anxiety was significantly associated with weaker communication skills. Otherwise, no disease related parameters significantly correlated with transition readiness. Disease duration demonstrated a significant positive relationship with transition readiness, particularly for patients diagnosed between the ages of 10 – 17. Models synthesized to predict transition readiness demonstrated substantial variability in predictive value. CONCLUSION: Transitioning from pediatric to adult inflammatory bowel disease care is a complex process. Future research should be aimed at elucidating discrepancies in transition readiness between genders, and further understanding the role disease duration plays in the transition process. Providers should work towards incorporating structured transition programs and improving patients’ disease-related knowledge, as well as patient familiarity with logistical aspects of the current US healthcare system. / 2023-11-09T00:00:00Z

The intestinal microbiome contributes in immune system function. It contains a large number of microorganisms that interact with each other and thus affect the host. Currently, attention is being directed towards investigating the influence of the intestinal microbiome on hosts, but also on foreign substances. Foreign substances may influence its composition and subsequent microbial metabolism. Crohn's disease patients have been found to have lower bacterial representation of beneficial bacteria. Therefore it is appropriate to examine the intestinal microbiome of these patients and so understand in greater detail the influence of bacteria on the course of the disease progression and on the medication used. The RP-HPLC method were analysed the faecal samples collected (B, C, D), which were incubated at 0, 3 and 6 hours. The incubation took place the addition of myricetin in the McDougall buffer and BHI medium. The analysis was found that myricetin degradation takes place in faecal samples during incubation, regardless of the medium used. In the faecal sample B, degradation of myricetin occurs faster in the BHI medium than in the McDougall's buffer. In faecal samples C and D, degradation is similar in both media. From these results, it is impossible to judge which medium is more suitable for...

Background and aims: Chronic intestinal failure (CIF) has been long-recognized, however the underlying etiology and risk factors have not been historically well-studied. We aim to study the underlying etiologies of CIF and predictive factors for long-term parenteral support (PS). Methods: We retrospectively identified patients with newly diagnosed CIF who received PS to maintain nutrition at the Cleveland Clinic between 2000 and 2017. Long-term PS was defined as a duration of more than 3 months. Univariable and multivariable logistic regression analyses were performed to identify the predictors of the need for long-term PS. Results: We identified 350 patients with CIF, 150 (43%) and 200 (57%) were diagnosed before and after 2010, respectively. The most common etiology was Crohn's disease (CD) in both cohorts (34.7% versus 30.5%, p = 0.41). Graft-versus-host-disease (GVHD) was a less frequent cause of CIF after 2010 (12.7% versus 2.5%, p = 0.0002). The type of PS was mostly total parenteral nutrition before and after 2010, 95% and 96%, respectively (p = 0.55). On univariable analysis, absence of ileocecal valve (p < 0.0001), ischemic bowel disease (p = 0.009), and whole colon resection (p = 0.033) were associated with the need for long-term PS. On multivariable analysis, absence of ileocecal valve (OR 2.19, p = 0.011) and ischemic bowel disease (OR 3.04, p = 0.003) remained statistically significant predictors of long-term PS. Conclusion: In our cohort of patients with CIF, CD remains the leading etiology over the last 20 years, whereas GVHD is less common after 2010. The absence of ileocecal valve and ischemic bowel disease were reliable predictive factors for requiring long-term PS.

Background: Crohn's disease is a chronic inflammatory disease of the intestine in humans, with no known cause. Johne's disease is a chronic intestinal disease of ruminants caused by Mycobacterium avium suhspecies paratuberculosis (MAP), and has some features similar to Crohn's disease. Although MAP has been purported to play an etiologic role in Crohn's disease, this causal link is still under debate. Objective: The overall aim of this project is to analyze MAP strains from different hosts (cattle, sheep and humans) and regions in North Dakota by biochemical and epidemiological methods, in order to better understand the pathogenesis and epidemiology of MAP strains and the relationship between MAP and Crohn's disease. The specific aims of this research are the following: Aim 1. Investigate the epidemiological evidence for MAP as a cause of Crohn's disease. Aim 2. Conduct a comparative causality study to investigate whether MAP or other enteric pathogens cause Crohn's disease. Aim 3. Evaluate the occurrence of MAP infections in cattle in North Dakota, 1995-2005. Aim 4. Analyze MAP strains from symptomatic and asymptomatic cattle. Aim 5. Investigate the biochemical variations of rapid and slow growing MAP strains. Aim 6. Evaluate MAP strains from low shedders and high shedders. Methods: MAP isolates were analyzed by biochemical methods of gas chromatography, high performance liquid chromatography and mass spectrometry. In addition, extensive literature review was performed to (1) determine the epidemiologic causal link between MAP and Crohn' s disease and (2) determine whether MAP or other enteric pathogens cause Crohn's disease. Results: Results from our study indicated the availablity of epidemiologic evidence supporting the causal role of MAP in Crohn's disease. It was also demonstrated that MAP is the most implicated organism in the etiology of Crohn's disease when compared to other infectious agents. Investigation of the occurrence of MAP infection in North Dakota showed an increase in number of MAP cases reported, with seasonal trends. Biochemical typing of MAP strains from symptomatic and asymptomatic cattle indicated that the symptoms status of isolates was significantly associated with mass spectra patterns and shedder status (p < 0.05). However, the association between symptoms status and HPLC and GC patterns was not significant (p > 0.05). Investigation of biochemical variations of rapid and slow growing MAP strains showed associations between the biochemical variability of MAP strains and their growth rate and presence of symptoms in the source cattle. Evaluation of MAP strains of different shedding characteristics by univariate logistic regression revealed that the shedder status of isolates was significantly associated with growth rate of isolates, symptom status, and source regions, but not with mass spectra patterns of isolates. Conclusion: Overall, this study strengthens the theories of strain sharing, intraspecies and interspecies transmission, and supports an association between MAP and Crohn's disease. In addition, the understanding of the biochemical variation among MAP isolates will help in the future design of diagnostics, therapeutics and vaccines for Johne's and Crohn's diseases. / North Dakota State University. Department of Chemistry and Biochemistry

Hantavirus is a dangerous zoonotic viral pathogen that is found across Asia, Europe, and the Americas. This virus causes a range of symptoms from flu-like malaise to heart failure and death. It is normally transmitted to humans via the aerosolized feces or urine of infected rodents. Currently, there are no known treatments for the disease, and it continues to threaten human health in endemic areas. In order to identify possible future therapeutic targets, we ran a meta-analysis of existing transcriptomic data collected from infected human tissue. Several genes and cellular pathways were identified, in addition to several potential therapeutics that warrant additional testing as potential future therapeutics for hantavirus infection. Such genes include, but are not limited to SLC27A3, NOG, AMIGO1, NUSAP1, and CDC25C which have not been previously associated with hantavirus infection. In addition, we identified that RIG-I and MDA5-associated anti-viral response genes are downregulated, while downstream elements of these pathways are upregulated, indicative of immune activation via alternate pathways. Finally, among the potential therapeutics we identified are dinaciclib, alvodicib, and ruxolitinib, which limit cellular replication, as well as ruxolitinib, baricitinib, and tofacitinib, which target other human intracellular pathways that may aid in successful viral infection. Crohn's disease is an autoimmune disorder that affects the digestive system of more than six million people worldwide, with most cases found in North America and Europe. Although the disease can occur throughout the entire digestive tract, the classical sign of disease progression is inflammation of the intestine. There are a number of factors that have been associated with the onset and progression of the disease including diet, antibiotics, stress, and bacterial infections, but no putative cause has been found. As diet and the gut biome play a significant role in disease progression, we aimed to find commonalities in the gut microbiomes of Crohn's patients, even when located in different geographical areas.

For many years there has been a suggested association between multiple sclerosis (MS) and inflammatory bowel disease (IBD). Aside from their common epidemiological and immunological similarities, there appears to be an association between the incidence of both diseases coexisting. We report a case of a 41-year-old man with chronic diarrhea and weakness, who was found to have concomitant MS and Crohn's Disease. Our report underscores the importance clinicians of maintaining a high degree of suspicion about the potential association of these conditions among these patient populations.

Emerging rise in microbial drug resistance and the slow-growing characteristic of some intracellular pathogens such as MAP (Mycobacterium avium subspecies paratuberculosis) strongly urges the need for an effective approach for unconventional drug susceptibility testing. We designed a molecular-based PCR method for the evaluation of rifabutin (RFB) and rifampicin (RIF) resistance based on probable determinant regions within the rpoB gene of MAP, including the 81 bp variable site located between nucleotides 1363 and 1443. The minimum inhibitory concentration (MIC) for RIF was also determined against 10 MAP isolates in attempt to seek correlation with rpoB sequences. We determined that MAP strain 18 had an MIC ≥ 30 ug/ml and ≥ 5 ug/ml for RIF and RFB respectively, and a significant rpoB mutation C1367T, compared to an MIC of ≤ 1.0 ug/ml for both drugs in the wild type MAP. The 30-fold increase in the MIC was a direct result of the rpoB mutation C1367T, which caused an amino acid change Thr456 to Ile456 in the drug's binding site; the beta subunit of RNA polymerase. Our in vitro induced mutation in MAP strain UCF5 resulted in the generation of a new resistant strain (UCF5-RIF16r) that possessed T1442C rpoB mutation and an MIC ≥ 30 ug/ml and ≥ 10 ug/ml for RIF and RFB respectively. The T1442C mutation resulted in a Leu481 to Pro481 amino acid change, consequently altering the beta subunit sequence. Sequencing the entire 3.5 kb rpoB in strains 18 and UCF5-RIF16r revealed no additional expressed nucleotide mutation. Of the 10 MAP strains analyzed, an additional one strain (UCF4) exhibited a slight increase in the MIC against RIF and RFB compared to the wild-type. Nucleotide sequencing of the rpoB gene revealed an A2284C mutation in strain UCF4 that occurred further downstream of the expected probable rpoB region and resulted in an amino acid alteration Asn762 to His762. The location of this mutation outside the binding site and its correlation with the minor increase in MIC suggests a possible secondary interaction between the drug and the beta subunit. We have provided three dimensional images through the utilization of PyMol Molecular-based Graphics to display a clear comparison of the mutations observed in the beta subunit for MAP strains 18, UCF5-RIF16r, and UCF4. We propose that these alterations may have caused a less stable interaction between RIF and the beta subunit, resulting in the observed increased in MIC. Furthermore, the change in amino acid sequence did not affect the viability for our RIF resistant strains. The data clearly illustrates that clinical and in vitro-induced MAP mutants with rpoB mutations result in resistance to RIF and RFB. Consequently, unconventional drug susceptibility testing such as our molecular approach will be beneficial for evaluation of antibiotic effectiveness. This molecular approach may also serve as a model for other drugs used for treatment of MAP infections.