Gastrointestinal Infection Increases Odds of Inflammatory Bowel Disease in a Nationwide Case-Control Study

Enhancing enteric pathogen detection: implementation and impact of multiplex PCR for improved diagnosis and surveillance

BACKGROUND

Syndromic surveillance of acute gastroenteritis plays a significant role in the diagnosis and management of gastrointestinal infections that are responsible for a substantial number of deaths globally, especially in developing countries. In Lebanon, there is a lack of national surveillance for acute gastroenteritis, and limited data exists regarding the prevalence of pathogens causing diarrhea. The one-year study aims to investigate the epidemiology of common gastrointestinal pathogens and compare our findings with causative agents of diarrhea reported by our study collaborative centers.

METHODS

A multicenter, cross-sectional study was conducted over a one-year period. A total of 271 samples were obtained from outpatients and inpatients presenting with symptoms of acute gastroenteritis at various healthcare facilities. The samples were then analyzed using Allplex gastrointestinal assay that identifies a panel of enteric pathogens.

RESULTS

Overall, enteropathogens were detected in 71% of the enrolled cases, 46% of those were identified in patients as single and 54% as mixed infections. Bacteria were observed in 48%, parasites in 12% and viruses in 11%. Bacterial infections were the most prevalent in all age groups. Enteroaggregative E. coli (26.5%), Enterotoxigenic E. coli (23.2%) and Enteropathogenic E. coli (20.3%) were the most frequently identified followed by Blastocystis hominis (15.5%) and Rotavirus (7.7%). Highest hospitalization rate occurred with rotavirus (63%), Enterotoxigenic E. coli (50%), Blastocystis hominis (45%) and Enteropathogenic E. coli (43%). Enteric pathogens were prevalent during summer, fall and winter seasons.

CONCLUSIONS

The adoption of multiplex real-time PCR assays in the diagnosis of gastrointestinal infections has identified gaps and improved the rates of detection for multiple pathogens. Our findings highlight the importance of conducting comprehensive surveillance to monitor enteric infections. The implementation of a syndromic testing panel can therefore provide healthcare professionals with timely and accurate information for more effective treatment and public health interventions.

Eosinophilic esophagitis is associated with increased risk of later inflammatory bowel disease in a nationwide Swedish population cohort

BACKGROUND

Earlier studies on the possible association between eosinophilic esophagitis (EoE) and inflammatory bowel disease (IBD) have been contradictory.

METHODS

Patients with biopsy-verified EoE diagnosed between 1990 and 2017 in Sweden (n = 1587) were age- and sex-matched with up to five general population reference individuals (n = 7808). EoE was defined using pathology reports from all 28 pathology centers in Sweden (the ESPRESSO study). Multivariate Cox regression then estimated hazard ratios for future IBD. IBD was defined based on the international classification of disease codes and histopathology codes. In secondary analyses, sibling comparators were used to further reduce potential familial confounding. Additionally, we performed logistic regression examining earlier IBD in EoE.

RESULTS

During follow-up until 2020, 16 (0.01%) EoE patients and 21 (0.003%) general population reference individuals diagnosed with IBD, corresponding to a 3.5-fold increased risk of future IBD (aHR = 3.56; 95% CI 1.79-7.11). EoE was linked to Crohn's disease (aHR = 3.39 [95% CI 1.02-9.60]) but not to ulcerative colitis (aHR = 1.37; 95% CI 0.38-4.86). Compared to their siblings, patients with EoE were at a 2.48-fold increased risk of IBD (aHR = 2.48; 95% CI 0.92-6.70). Earlier IBD was 15 times more likely in EoE patients than in matched reference individuals (odds ratio, 15.39; 95% CI 7.68-33.59).

CONCLUSION

In this nationwide cohort study, EoE was associated with a 3.5-fold increased risk of later IBD diagnosis. This risk increase may be due to shared genetic or early environmental risk factors, but also surveillance bias could play a role.

Increasing ratio of opportunistic infections associated with sunshine exposure and economic level burdening Chinese inflammatory bowel disease hospitalized patients: the first nationwide survey from 2014 to 2019

BACKGROUND

The rising prevalence of opportunistic infections (OIs) in inflammatory bowel disease (IBD) in conjunction with the use of biologics/immunosuppressive agents has garnered attention. However, there is a dearth of research on OIs in Mainland China. This study seeks to evaluate the national ratio trend of OIs in IBD and elucidate the influence of economic and climate factors on IBD patients with OIs and their outcomes.

METHODS

The nationwide data was obtained from the Inpatient medical record home page via the Health Statistics and Information Reporting System (HSRS). Patients diagnosed with IBD were enlisted for participation, and their demographic and clinical information, encompassing infection type, surgical procedures, and expenses, were gathered. The National Bureau of Statistics provided data on monthly sunshine exposure hours and yearly Gross Domestic Product (GDP).

RESULTS

Findings indicate that between 2014 and 2019, a total of 381,752 patients with IBD were admitted to hospitals, with 364,249 patients lacking OIs and 17,503 patients presenting with OIs. The annual proportion of OIs exhibited an upward trend, rising from 3.54% in 2014 to 4.81% in 2019. There was a significant correlation observed between individuals who identified as male, those who visited hospitals in southern regions, or those originating from areas with lower GDP or shorter sunshine exposure hours, and a higher incidence of OIs. Among patients diagnosed with either Crohn's disease (CD) or ulcerative colitis (UC), Clostridium difficile was found to be the most prevalent infection, followed by Epstein-Barr virus and cytomegalovirus. Furthermore, the occurrence of OIs was found to be associated with an increased rate of surgical interventions in UC patients.

CONCLUSIONS

The rising prevalence of OIs among hospitalized patients with IBD necessitates heightened attention towards mitigating associated risk factors, particularly among IBD patients residing in less developed regions or experiencing limited exposure to sunlight. This approach aims to minimize hospital stays and associated costs.

Acetolactate Decarboxylase as an Important Regulator of Intracellular Acidification, Morphological Features, and Antagonism Properties in the Probiotic Lactobacillus reuteri

SCORE

This study identifies the coding gene (aldB) of acetolactate decarboxylase (ALDC) as an important regulatory gene of the intracellular pH in Lactobacillus reuteri (L. reuteri), uncovering the important role of ALDC in regulating intracellular pH, morphological features, and antagonism properties in the probiotic organism L. reuteri.

METHODS AND RESULTS

The aldB mutant (ΔaldB) of L. reuteri is established using the homologous recombination method. Compare to the wild-type (WT) strain, the ΔaldB strain shows a smaller body size, grows more slowly, and contains more acid in the cell cytoplasm. The survival rate of the ΔaldB strain is much lower in low pH and simulated gastric fluid (SGF) than that of the WT strain, but higher in simulated intestinal fluid (SIF). The antagonism test demonstrates the ΔaldB strain can inhibit Listeria monocytogenes (L. monocytogenes) and Salmonella more effectively than the WT strain. Additionally, there is a dramatic decrease in the adhesion rate of Salmonella to Caco-2 and HT-29 cells in the presence of the ΔaldB strain compared to the WT strain. Simultaneously analyze, the auto-aggregation, co-aggregation, cell surface hydrophobicity (CSH), hemolytic, temperature, NaCl, oxidative stress, and antibiotic susceptibility of the ΔaldB strain are consistent with the features of probiotics.

CONCLUSION

This study highlights that the aldB gene plays a significant role in the growth and antibacterial properties of L. reuteri.

Immunomodulation by Enteric Viruses

Enteric viruses display intricate adaptations to the host mucosal immune system to successfully reproduce in the gastrointestinal tract and cause maladies ranging from gastroenteritis to life-threatening disease upon extraintestinal dissemination. However, many viral infections are asymptomatic, and their presence in the gut is associated with an altered immune landscape that can be beneficial or adverse in certain contexts. Genetic variation in the host and environmental factors including the bacterial microbiota influence how the immune system responds to infections in a remarkably viral strain-specific manner. This immune response, in turn, determines whether a given virus establishes acute versus chronic infection, which may have long-lasting consequences such as susceptibility to inflammatory disease. In this review, we summarize our current understanding of the mechanisms involved in the interaction between enteric viruses and the immune system that underlie the impact of these ubiquitous infectious agents on our health.

Bidirectional association between infectious gastroenteritis and inflammatory bowel disease: a population-based study

BACKGROUND

Intertwined association between infectious gastroenteritis (IGE) and inflammatory bowel disease (IBD) has not been investigated clearly. We aimed to examine the bidirectional association between IGE and IBD.

METHODS

A bidirectional study using the Taiwan National Health Insurance Research Database was designed. Through a case-control design, we identified 2899 new IBD cases during 2006-2017 and matched to 28,990 non-IBD controls. We used conditional logistic regression model to estimate odds ratios (OR) of IBD for previous IGE in different exposure time-windows within 5-years before IBD diagnosis and Poisson regression model to estimate incidence rate ratio (IRR) of subsequent IGE for IBD group to non-IBD group.

RESULTS

The mean age at the initial IBD diagnosis was 41 years. More IBD patients (21.49%) than controls (12.60%) had been exposed to IGE during > 6 months to 5 years before IBD diagnosis, the OR of IBD for IGE was 1.89 [95% confidence interval: 1.69-2.11]. Excess OR decreased as IGE exposure time before the index date increased. More IGE episodes were associated with additional increase in IBD risk (OR: 1.64, 2.19, 2.57, 3.50, and 4.57 in patients with 1, 2, 3, 4, and ≥ 5 IGE episodes, respectively). The IRR of having IGE for IBD group to non-IBD group was 2.42 before IBD diagnosis and increased to 5.74 after IBD diagnosis.

CONCLUSIONS

These findings suggested an IGE-IBD bidirectional association. More attention is needed for physicians to develop preventive strategies and be aware of the higher risk of subsequent IGE in IBD patients.

Oncogenic potential of Campylobacter infection in the gastrointestinal tract: narrative review

BACKGROUND

Campylobacter jejuni is the leading cause of zoonotic gastroenteritis. The other emerging group of Campylobacters spp. are part of human oral commensal, represented by C. concisus (CC), which has been recently linked to non-oral conditions. Although long-term gastrointestinal (GI) complications from these two groups of Campylobacters have been previously reviewed individually, overall impact of Campylobacter infection on GI carcinogenesis and their inflammatory precursor lesions has not been assessed collectively.

AIMS

To evaluate the available evidence concerning the association between Campylobacter infection/colonization and inflammatory bowel disease (IBD), reflux esophagitis/metaplasia colorectal cancer (CRC) and esophageal cancer (EC).

METHODS

We performed a comprehensive literature search of PubMed for relevant original publications and systematic reviews/meta-analyses of epidemiological and clinical studies. In addition, we gathered additional information concerning microbiological data, animal models and mechanistic data from in vitro studies.

RESULTS

Both retrospective and prospective studies on IBD showed relatively consistent increased risk associated with Campylobacter infection. Despite lack of supporting prospective studies, retrospective studies based on tissue/fecal microbiome revealed consistent enrichment of Campylobacter in CRC samples. Studies on EC precursor lesions (esophagitis and metaplasia) were generally supportive for the association with Campylobacter, while inconsistent observations on EC. Studies on both IBD and EC precursors suggested the predominant role of CC, but studies on CRC were not informative of species.

CONCLUSIONS

There is sufficient evidence calling for concerted effort in unveiling direct and indirect connection of this organism to colorectal and esophageal cancer in humans.

Coronavirus disease 2019 and gastrointestinal disorders in children

During the past 3 years, the coronavirus disease 2019 (COVID-19) pandemic has had a great impact on people all over the world. However, it has become evident that disease manifestations and severity differ across age groups. Most children have a milder disease course than adults but possibly more pronounced gastrointestinal (GI) symptoms. Given the child's developing immune system, the impact of COVID-19 on disease development may differ compared to adults. This study reviews the potential bi-directional relationship between COVID-19 and GI diseases in children, focusing on common pediatric conditions such as functional GI disorders (FGID), celiac disease (CeD), and inflammatory bowel disease (IBD). Children with GI diseases, in general, and CeD and IBD, in particular, do not seem to have an increased risk of severe COVID-19, including risks of hospitalization, critical care need, and death. While infections are considered candidate environmental factors in both CeD and IBD pathogenesis, and specific infectious agents are known triggers for FGID, there is still not sufficient evidence to implicate COVID-19 in the development of either of these diseases. However, given the scarcity of data and the possible latency period between environmental triggers and disease development, future investigations in this field are warranted.

Is Autologous Fecal Microbiota Transfer after Exclusive Enteral Nutrition in Pediatric Crohn’s Disease Patients Rational and Feasible? Data from a Feasibility Test

Background: Exclusive enteral nutrition (EEN) is a highly effective therapy for remission induction in pediatric Crohn’s disease (CD), but relapse rates after return to a regular diet are high. Autologous fecal microbiota transfer (FMT) using stool collected during EEN-induced clinical remission might represent a novel approach to maintaining the benefits of EEN. Methods: Pediatric CD patients provided fecal material at home, which was shipped at 4 °C to an FMT laboratory for FMT capsule generation and extensive pathogen safety screening. The microbial community composition of samples taken before and after shipment and after encapsulation was characterized using 16S rRNA amplicon sequencing. Results: Seven pediatric patients provided fecal material for nine test runs after at least three weeks of nutritional therapy. FMT capsules were successfully generated in 6/8 deliveries, but stool weight and consistency varied widely. Transport and processing of fecal material into FMT capsules did not fundamentally change microbial composition, but microbial richness was <30 genera in 3/9 samples. Stool safety screening was positive for potential pathogens or drug resistance genes in 8/9 test runs. Conclusions: A high pathogen burden, low-diversity microbiota, and practical deficiencies of EEN-conditioned fecal material might render autologous capsule-FMT an unsuitable approach as maintenance therapy for pediatric CD patients.

Antibiotic use as a risk factor for inflammatory bowel disease across the ages: a population-based cohort study

BACKGROUND

There is an increasing incidence of inflammatory bowel disease (IBD) for which environmental factors are suspected. Antibiotics have been associated with development of IBD in earlier generations, but their influence on IBD risk in adults is uncertain.

OBJECTIVE

To assess the impact of antibiotic exposure, including dose-response, timing and antibiotic class, on the risk of IBD in all individuals aged ≥10 years.

DESIGN

Using Denmark nationwide registries, a population-based cohort of residents aged ≥10 years was established between 2000 and 2018. Incidence rate ratios (IRRs) for IBD following antibiotic exposure were calculated using Poisson regression.

RESULTS

There were a total of 6 104 245 individuals, resulting in 87 112 328 person-years of follow-up, and 52 898 new cases of IBD. Antibiotic exposure was associated with an increased risk of IBD as compared with no antibiotic exposure for all age groups, although was greatest among individuals aged 40-60 years and ≥60 years (age 10-40 years, IRR 1.28, 95% CI 1.25 to 1.32; age 40-60 years, IRR 1.48, 95% CI 1.43 to 1.54; age ≥60 years, IRR 1.47, 95% CI 1.42 to 1.53). For all age groups a positive dose-response was observed, with similar results seen for both ulcerative colitis and Crohn's disease. The highest risk of developing IBD was seen 1-2 years after antibiotic exposure, and after use of antibiotic classes often prescribed to treat gastrointestinal pathogens.

CONCLUSION

Antibiotic exposure is associated with an increased risk of IBD, and was highest among individuals aged 40 years and older. This risk increased with cumulative antibiotic exposure, with antibiotics targeting gastrointestinal pathogens and within 1-2 years after antibiotic exposure.

Yersinia enterocolitica in Crohn’s disease

Increasing attention is being paid to the unique roles gut microbes play in both physiological and pathological processes. Crohn’s disease (CD) is a chronic, relapsing, inflammatory disease of the gastrointestinal tract with unknown etiology. Currently, gastrointestinal infection has been proposed as one initiating factor of CD. Yersinia enterocolitica, a zoonotic pathogen that exists widely in nature, is one of the most common bacteria causing acute infectious gastroenteritis, which displays clinical manifestations similar to CD. However, the specific role of Y. enterocolitica in CD is controversial. In this Review, we discuss the current knowledge on how Y. enterocolitica and derived microbial compounds may link to the pathogenesis of CD. We highlight examples of Y. enterocolitica-targeted interventions in the diagnosis and treatment of CD, and provide perspectives for future basic and translational investigations on this topic.

Mouse mammary tumor virus is implicated in severity of colitis and dysbiosis in the IL-10-/- mouse model of inflammatory bowel disease

BACKGROUND

Following viral infection, genetically manipulated mice lacking immunoregulatory function may develop colitis and dysbiosis in a strain-specific fashion that serves as a model for inflammatory bowel disease (IBD). We found that one such model of spontaneous colitis, the interleukin (IL)-10 knockout (IL-10-/-) model derived from the SvEv mouse, had evidence of increased Mouse mammary tumor virus (MMTV) viral RNA expression compared to the SvEv wild type. MMTV is endemic in several mouse strains as an endogenously encoded Betaretrovirus that is passaged as an exogenous agent in breast milk. As MMTV requires a viral superantigen to replicate in the gut-associated lymphoid tissue prior to the development of systemic infection, we evaluated whether MMTV may contribute to the development of colitis in the IL-10-/- model.

RESULTS

Viral preparations extracted from IL-10-/- weanling stomachs revealed augmented MMTV load compared to the SvEv wild type. Illumina sequencing of the viral genome revealed that the two largest contigs shared 96.4-97.3% identity with the mtv-1 endogenous loci and the MMTV(HeJ) exogenous virus from the C3H mouse. The MMTV sag gene cloned from IL-10-/- spleen encoded the MTV-9 superantigen that preferentially activates T-cell receptor Vβ-12 subsets, which were expanded in the IL-10-/- versus the SvEv colon. Evidence of MMTV cellular immune responses to MMTV Gag peptides was observed in the IL-10-/- splenocytes with amplified interferon-γ production versus the SvEv wild type. To address the hypothesis that MMTV may contribute to colitis, we used HIV reverse transcriptase inhibitors, tenofovir and emtricitabine, and the HIV protease inhibitor, lopinavir boosted with ritonavir, for 12-week treatment versus placebo. The combination antiretroviral therapy with known activity against MMTV was associated with reduced colonic MMTV RNA and improved histological score in IL-10-/- mice, as well as diminished secretion of pro-inflammatory cytokines and modulation of the microbiome associated with colitis.

CONCLUSIONS

This study suggests that immunogenetically manipulated mice with deletion of IL-10 may have reduced capacity to contain MMTV infection in a mouse-strain-specific manner, and the antiviral inflammatory responses may contribute to the complexity of IBD with the development of colitis and dysbiosis. Video Abstract.

Risk Factors for Developing Inflammatory Bowel Disease Within and Across Families with a Family History of IBD

INTRODUCTION

A family history of inflammatory bowel disease [IBD] is the strongest risk factor for disease. However, some first-degree relatives (FDRs) will develop disease, while others will not.

METHODS

Using the nationwide Danish National Patient Register, we examined risk factors in families with two or more affected FDRs. First, we compared exposures between siblings with and without IBD within the same family [within-family analysis]. Second, we compared exposures between individuals with and without IBD across all families [across-family analysis]. Exposures included sex, birth order, mode of delivery, antibiotics, personal and family history of immune-mediated diseases, gastrointestinal infections, and surgical history preceding diagnosis. Uni- and multivariable conditional logistic regression analyses were conducted.

RESULTS

In the 'within-family analysis', 1669 families were included [1732 cases, 2447 controls]. Female sex (adjusted odds ratio [aOR]: 1.40, 95% confidence interval [CI] 1.23, 1.59), history of ankylosing spondylitis [aOR: 2.88, 95% CI 1.05, 7.91] and exposure to antibiotics [aOR: 1.28, 95% CI 1.02, 1.61] increased the risk for IBD. In the 'across-family analysis', 1254 cases and 37 584 controls were included, confirming an association with prior ankylosing spondylitis [aOR: 3.92, 95% CI 1.38, 11.12] and exposure to antibiotics [aOR: 1.29, 95% CI 1.04, 1.60]. Having two or more relatives [aOR: 6.26, 95% CI 1.34, 29.29] or a sibling with IBD [aOR: 1.36, 95% CI 1.18, 1.57] increased the risk of IBD. Appendectomy reduced the risk of ulcerative colitis [aOR: 0.32, 95% CI 0.14, 0.72].

CONCLUSION

In families with IBD, we identified risk factors for the unaffected FDR to develop disease. These findings provide an opportunity for counselling IBD relatives.

Salmonella Typhimurium Infection Reduces the Ascorbic Acid Uptake in the Intestine

Salmonella Typhimurium infection of the gastrointestinal tract leads to damage that compromises the integrity of the intestinal epithelium and results in enterocolitis and inflammation. Salmonella infection promotes the expression of inflammasome NLRP3, leading to activation and release of proinflammatory cytokines such as IL-1β, and the infected host often displays altered nutrient levels. To date, the effect of Salmonella infection and proinflammatory cytokine IL-1β on the intestinal uptake of ascorbic acid (AA) is unknown. Our results revealed a marked decrease in the rate of AA uptake in mouse jejunum infected with Salmonella wild type (WT). However, the nonpathogenic mutant (Δ invA Δ spiB) strain did not affect AA uptake. The decrease in AA uptake due to Salmonella WT infection is accompanied by significantly lower expression of mouse (m)SVCT1 protein, mRNA, and hnRNA levels. NLRP3 and IL-1β expression levels were markedly increased in Salmonella-infected mouse jejunum. IL-1β-exposed Caco-2 cells displayed marked inhibition in AA uptake and significantly decreased hSVCT1 expression at both protein and mRNA levels. Furthermore, the activity of the SLC23A1 promoter was significantly inhibited by IL-1β exposure. In addition, GRHPR (a known SVCT1 interactor) protein and mRNA expression levels were significantly reduced in Salmonella-infected mouse jejunum. These results indicate that Salmonella infection inhibits AA absorption in mouse jejunum and IL-1β-exposed Caco-2 cells. The observed inhibitory effect may partially be mediated through transcriptional mechanisms.

Genetic overlap between Parkinson's disease and inflammatory bowel disease

Parkinson's disease and inflammatory bowel disease have been increasingly associated, implying shared pathophysiology. To explore biological explanations for the reported connection, we leveraged summary statistics of updated genome-wide association studies and characterized the genetic overlap between the two diseases. Aggregated genetic association data were available for 37 688 cases versus 981 372 controls for Parkinson's disease and 25 042 cases versus 34 915 controls for inflammatory bowel disease. Genetic correlation was estimated with the high-definition likelihood method. Genetic variants with joint association to both diseases were identified by conditional false discovery rate framework and further annotated to reveal shared loci, genes, and enriched pathways. For both Crohn's disease and ulcerative colitis, the two main subtypes of inflammatory bowel disease, we detected weak but statistically significant genetic correlations with Parkinson's disease (Crohn's disease: r_g = 0.06, P = 0.01; ulcerative colitis: r_g = 0.06, P = 0.03). A total of 1290 variants in 27 independent genomic loci were detected to associate with Parkinson's disease and Crohn's disease at conjunctional false discovery rate under 0.01 and 1359 variants in 15 loci were pleiotropic to Parkinson's disease and ulcerative colitis. Among the identified pleiotropic loci, 23 are novel and have never been associated with both phenotypes. A mixture of loci conferring either same or opposing genetic effects on two phenotypes was also observed. Positional and expression quantitative trait loci mapping prioritized 296 and 253 genes for Parkinson's disease with Crohn's disease and ulcerative colitis, respectively, among which only <10% are differentially expressed in both colon and substantia nigra. These genes were identified to overrepresent in pathways regulating gene expression and post-translational modification beyond several immune-related pathways enriched by major histocompatibility complex genes. In conclusion, we found robust evidence for a genetic link between Parkinson's disease and inflammatory bowel disease. The identified genetic overlap is complex at the locus and gene levels, indicating the presence of both synergistic and antagonistic pleiotropy. At the functional level, our findings implied a role of immune-centered mechanisms in the reported gut-brain connection.

Mouse models for bacterial enteropathogen infections: insights into the role of colonization resistance

Globally, enteropathogenic bacteria are a major cause of morbidity and mortality.1-3 Campylobacter, Salmonella, Shiga-toxin-producing Escherichia coli, and Listeria are among the top five most commonly reported zoonotic pathogens in the European Union.4 However, not all individuals naturally exposed to enteropathogens go on to develop disease. This protection is attributable to colonization resistance (CR) conferred by the gut microbiota, as well as an array of physical, chemical, and immunological barriers that limit infection. Despite their importance for human health, a detailed understanding of gastrointestinal barriers to infection is lacking, and further research is required to investigate the mechanisms that underpin inter-individual differences in resistance to gastrointestinal infection. Here, we discuss the current mouse models available to study infections by non-typhoidal Salmonella strains, Citrobacter rodentium (as a model for enteropathogenic and enterohemorrhagic E. coli), Listeria monocytogenes, and Campylobacter jejuni. Clostridioides difficile is included as another important cause of enteric disease in which resistance is dependent upon CR. We outline which parameters of human infection are recapitulated in these mouse models, including the impact of CR, disease pathology, disease progression, and mucosal immune response. This will showcase common virulence strategies, highlight mechanistic differences, and help researchers from microbiology, infectiology, microbiome research, and mucosal immunology to select the optimal mouse model.

Increased incidence of late-onset inflammatory bowel disease and microscopic colitis after a Cryptosporidium hominis outbreak

OBJECTIVES

In 2010, 27,000 inhabitants (45% of the population) of Östersund, Sweden, contracted clinical cryptosporidiosis after drinking water contaminated with Cryptosporidium hominis. After the outbreak, local physicians perceived that the incidence of inflammatory bowel disease (IBD), including ulcerative colitis (UC), Crohn's disease (CD), and IBD-unclassified, and microscopic colitis (MC) increased. This study assessed whether this perception was correct.

MATERIALS AND METHODS

This observational study included adult patients (≥18 years old) from the local health care region who were diagnosed with pathology-confirmed IBD or MC during 2006-2019. We collected and validated the diagnosis, date of diagnosis, age at diagnosis, and sex from the Swedish quality register SWIBREG and electronic patient records. Population data were collected from Statistics Sweden. The incidences for 2006-2010 (pre-outbreak) and 2011-2019 (post-outbreak) were evaluated by negative binomial regression analysis and presented as incidence rate ratios (IRRs). Data were analyzed for IBD, for UC and CD separately, and MC.

RESULTS

During the study period, we identified 410 patients with new onset IBD and 155 new cases of MC. Overall, we found a trend toward an increased incidence of IBD post-outbreak (IRR 1.39, confidence interval (CI) 0.99-1.94). In individuals ≥40 years old, the post-outbreak incidence significantly increased for IBD (IRR 1.69, CI 1.13-2.51) and CD (IRR 2.23, CI 1.08-4.62). Post-outbreak incidence of MC increased 6-fold in all age groups (IRR 6.43, CI 2.78-14.87).

CONCLUSIONS

The incidence of late-onset IBD and MC increased after the Cryptosporidium outbreak. Cryptosporidiosis may be an environmental risk factor for IBD and MC.

Early-Life Mebendazole Exposure Increases the Risk of Adult-Onset Ulcerative Colitis: A Population-Based Cohort Study

INTRODUCTION

According to the hygiene hypothesis, exposure to parasites may protect against inflammatory bowel disease (IBD). Our aim was to examine the risk of IBD with childhood exposure to mebendazole, a broad-spectrum antihelminthic agent.

METHODS

We conducted a population-based cohort study using prospectively collected historical data of all individuals born in Denmark between 1995 and 2018. We identified mebendazole exposure at age younger than 18 years and during early life (younger than 5 years). We performed adjusted Cox proportional hazards regression analysis to determine the risk of IBD, ulcerative colitis (UC), and Crohn's disease with mebendazole exposure after adjusting for potential confounders.

RESULTS

Of 1,520,290 individuals in the cohort, 615,794 had childhood or adolescence mebendazole exposure. One thousand five hundred fifty-five and 1,499 individuals were subsequently diagnosed with pediatric-onset and adult-onset IBD, respectively. On multivariable analysis, mebendazole exposure at age younger than 18 years did not affect pediatric-onset or adult-onset IBD risk (adjusted hazard ratio [aHR] 0.97, 95% confidence interval [CI] 0.87, 1.07, and 1.08, 95% CI 0.97, 1.19, respectively). On limiting mebendazole exposure to age younger than 5 years while there was no association with pediatric-onset IBD (aHR 0.98, 95% CI 0.87, 1.11), adult-onset IBD risk was increased (aHR 1.17, 95% CI 1.04, 1.31). This increase in risk was driven by UC (aHR 1.32, 95% CI 1.12, 1.55), but not Crohn's disease (1.03, 95% CI 0.87, 1.22).

DISCUSSION

Early-life mebendazole exposure is associated with an increase in the risk of adult-onset UC. These findings suggest the importance of early-life exposures in shaping the risk of IBD later in life.

Prior hospital-based infection and risk of eosinophilic esophagitis in a Swedish nationwide case-control study

BACKGROUND AND AIMS

Eosinophilic esophagitis (EoE) is an increasingly common, largely food allergen-driven disease characterized by dysphagia. Prior infections are known to associate with other loss of tolerance diseases such as autoimmunity. We aimed to determine if antecedent infection was associated with later EoE development.

METHODS

We performed a case-control study of all patients with biopsy-verified EoE diagnosed between 2000 and 2017 in Sweden (n = 1587) and matched to 5 general population controls (n = 7660). Cases were identified using histopathology codes from the Epidemiology Strengthened by histopathology Reports in Sweden study, a validated cohort of gastrointestinal pathology reports from all 28 pathology centers in Sweden. We used logistic regression to estimate odds ratios (ORs) and 95% confidence intervals for antecedent infections from patients seen at hospital-based outpatient clinics or inpatients. In secondary analyses, we compared EoE patients with their full siblings to further reduce residual confounding.

RESULTS

564 (35.7%) EoE patients and 1793 (23.4%) matched controls had an earlier record of infection. This corresponded to a 2-fold increased risk of infections in EoE patients (OR 2.01; 95%CI: 1.78-2.27). ORs for earlier gastrointestinal or respiratory infection were 2.73 (n = 128 EoE, 268 control; 95%CI: 2.17-3.41) and 1.89 (n = 305 EoE, 960 control; 95%CI: 1.63-2.20), respectively. Having an EoE diagnosis was linked to a 3.39-fold increased odds of sepsis (n = 14 EoE, 21 control; 95%CI: 1.68-6.65). Individuals with EoE were also more likely to have had an infection compared to their non-EoE siblings (n = 427 EoE, 593 control; OR = 1.57; 95%CI = 1.30-1.89).

CONCLUSION

In this nationwide cohort study, prior infection, was associated with subsequent EoE. Risks were particularly high after sepsis, and gastrointestinal or respiratory infections.

Development and validation of a CRISPR interference system for gene regulation in Campylobacter jejuni

BACKGROUND

Campylobacter spp. are the leading cause of bacterial food-borne illness in humans worldwide, with Campylobacter jejuni responsible for 80% of these infections. There is an urgent need to understand fundamental C. jejuni biology for the development of new strategies to prevent and treat infections. The range of molecular tools available to regulate gene expression in C. jejuni is limited, which in turn constrains our ability to interrogate the function of essential and conditionally essential genes. We have addressed this by developing and utilising a CRISPR-based interference system known as CRISPRi in C. jejuni to control gene expression. To achieve this, a catalytically inactive ("dead") cas9 and sgRNA backbone from the Streptococcus pyogenes CRISPRi system was combined with C. jejuni-derived promoters of predetermined expression activities to develop a CRISPRi-based repression tool in C. jejuni strains M1Cam and 81-176.

RESULTS

The CRISPRi tool was validated through successful repression of the arylsulphatase-encoding gene astA using a range of sgRNA target sequences spanning the astA gene. The tool was also applied to target astA in an M1Cam CRISPR-Cas9 deletion strain, which showed that the presence of an endogenous CRISPR-Cas9 system did not affect the activity of the CRISPRi-based repression tool. The tool was further validated against the hippicurase-encoding gene hipO. Following this, the flagella genes flgR, flaA, flaB and both flaA and flaB were targeted for CRISPRi-based repression, which resulted in varying levels of motility reduction and flagella phenotypes as determined by phenotypical assays and transmission electron microscopy (TEM).

CONCLUSIONS

This is the first report of a CRISPRi-based tool in C. jejuni, which will provide a valuable resource to the Campylobacter community.

Bacterial diarrhoea

PURPOSE OF REVIEW

This review describes recent findings about the burden of bacterial diarrhoea and its potential complications, newer diagnostics, the emerging threat of multidrug resistance, and the promise of vaccines in development.

RECENT FINDINGS

Introduction of rotavirus vaccines in over 110 countries has changed the landscape of diarrheal pathogens. In upper middle and high-income countries, the incidence of rotavirus-specific and all-cause gastroenteritis has declined substantially, and norovirus has become the major pathogen in many settings. Bacterial pathogens cause approximately 10-15% of episodes, most often Shigella, nontyphoidal Salmonella (NTS) Campylobacter and Shiga toxin-producing Escherichia coli (STEC). In lower income countries, bacterial pathogens remain a major cause of medically attended diarrhoea with Shigella, Campylobacter and enterotoxigenic Escherichia coli (ETEC) predominating. Multidrug-resistant strains of Shigella, NTS and, Campylobacter have emerged globally requiring judicious use of antibiotics according to current guidance.

SUMMARY

Management of bacterial diarrhoea includes standard fluid and electrolyte therapy, vigilance for potential complications, and use of antibiotics for children who have moderate-severe illness due to pathogens for which efficacy has been demonstrated, or for those at high risk for severe disease. The threat of multiply resistant strains provides impetus for preventive strategies such as development of vaccines.

The Distribution of Gastrointestinal Pathogens on Stool PCR Prior to the Development of IBD

GOALS

We investigated the distribution of pathogens on stool gastrointestinal (GI) polymerase chain reaction (PCR) testing in those who subsequently developed inflammatory bowel disease (IBD).

BACKGROUND

Infectious gastroenteritis has been associated with later development of IBD.

STUDY

This retrospective study includes patients of all ages hospitalized for diarrhea with positive GIPCR panel and subsequently a new diagnosis of IBD [confirmed by chart review and International Classification of Disease, Clinical Modification code for Crohn's disease (CD) or ulcerative colitis (UC)], between March 2015 to September 2019 at our quaternary care institution. Patients with IBD diagnosis before GIPCR were excluded. Descriptive statistics characterized the distribution of microbial pathogens in relation to later IBD diagnosis.

RESULTS

Fifty-four participants were eligible (UC 44%; CD 56%). Median age at time of IBD diagnosis was 35 years [interquartile range (IQR) 18 to 65]. Median time between GIPCR and IBD diagnosis was 3 months (IQR 2 to 9) for all patients. When stratified by organism class, median time to diagnosis was 6 months (IQR 2 to 10) for patients with bacteria, 3 months (IQR 1 to 8) for patients with viruses, and 1 month (IQR 0.75 to 1) for patients with parasites (log-rank P=0.001). Sixty-nine unique pathogens (83% bacteria) were identified on all tests. Escherichia coli was the most common species (71%), of which enteropathogenic E. coli was predominant (38%).

CONCLUSIONS

The E. coli species, specifically enteropathogenic E. coli, may be implicated in the development of IBD. This is one of the first studies to evaluate the results of stool GIPCR in the link between the microbiome and IBD pathogenesis.

New Insights and Advances in Pathogenesis and Treatment of Very Early Onset Inflammatory Bowel Disease

Very early onset inflammatory bowel disease (VEO-IBD) is characterized by multifactorial chronic recurrent intestinal inflammation. Compared with elderly patients, those with VEO-IBD have a more serious condition, not responsive to conventional treatments, with a poor prognosis. Recent studies found that genetic and immunologic abnormalities are closely related to VEO-IBD. Intestinal immune homeostasis monogenic defects (IIHMDs) are changed through various mechanisms. Recent studies have also revealed that abnormalities in genes and immune molecular mechanisms are closely related to VEO-IBD. IIHMDs change through various mechanisms. Epigenetic factors can mediate the interaction between the environment and genome, and genetic factors and immune molecules may be involved in the pathogenesis of the environment and gut microbiota. These discoveries will provide new directions and ideas for the treatment of VEO-IBD.

Retrospective analysis of Clostridioides difficile and other intestinal infections in patients with Crohn's disease and ulcerative colitis in the tertiary hospital in Poland. POLIBD survey results

Background

There are several studies which evaluated the number of infections caused by enteric pathogens, including Clostridioides difficile in patients with inflammatory bowel disease (IBD). Our aim was to assess the prevalence of intestinal infections among patients suffering from IBD, when admitted to the hospital due to exacerbation of the disease.

Results

The performed, retrospective analysis covered test results for C. difficile toxins A and B along with rectal swab cultures sampled from patients, treated in a tertiary IBD center in Poland, between 2017 and 2019. Main objective was to estimate the presence of any infection, which could imitate or co-exist along with the exacerbation of the IBD. All in all 1471 patients had microbiological tests performed, including 1112 tested for C. difficile toxins A and B; and 359 patients who had rectal swab culture. Positive test results for C. difficile toxins A and B were reported in 358 cases, positive results from rectal swab culture were confirmed altogether in case of 25 samples. As far as patients with IBD are concerned, positive results for C. difficile toxins A and B were detected in 82 cases, positive results in rectal swab culture from patients with IBD were reported in 20 cases.

Conclusion

Intestinal infections were reported in 14.9% of patients (102/685) with IBD symptoms. Positive test results for C. difficile toxins A and B and rectal swab cultures among patients without IBD symptoms were reported in 35.7% of cases (281/786). Intestinal superinfections may complicate the clinical picture of IBD patients, increasing the diagnostic and therapeutic burden. Appropriate early procedures are thus needed in these patients.

Serious Infections in Pediatric Inflammatory Bowel Disease 2002-2017-A Nationwide Cohort Study

OBJECTIVE

To assess absolute and relative risks of serious infections (resulting in inpatient care) in children with inflammatory bowel disease (IBD) compared with the general population.

STUDY DESIGN

We identified children (<18 years of age) with a first diagnosis of IBD in the Swedish nationwide health registry (2002-2017; n = 5767) and individuals from the general population matched for sex, age, calendar year, and place of residence (reference group; n = 58 418). Hazard ratios (HRs) for serious infections were estimated using Cox regression separately in children with ulcerative colitis (n = 2287), Crohn's disease (n = 2365), and IBD unclassified (n = 1115).

RESULTS

During 17 408 person-years of follow-up, 672 serious infections (38.6/1000 person-years) occurred among the children with IBD compared with 778 serious infections in the reference group (4.0/1000 person-years; adjusted HR (95% CI), 9.46 [8.53-10.5]). HRs were increased for children with ulcerative colitis 8.48 (7.21-9.98), Crohn's disease 9.30 (7.86-11.0), and IBD unclassified 12.1 (9.66-16.1). HRs were highest in the first year of follow-up (HR = 12.6 [10.7-14.9]), then decreasing to a 4.8-fold increased risk beyond 10 years of follow-up. Particularly high HRs were also seen in children with IBD undergoing surgery. Apart from a high relative risk of gastrointestinal infections resulting in hospitalization, children with IBD were also at an increased risk of opportunistic infections (HR = 11.8 [6.17-22.5]).

CONCLUSIONS

Children with IBD have an increased risk of serious infection requiring hospitalization compared with the general population.

Acute Gastroenteritis in the Etiology of Inflammatory Bowel Disease: Systematic Review and Meta-analysis

Background

Inflammatory bowel disease (IBD) consists of a spectrum of disorders including ulcerative colitis and Crohn's disease, with a rising incidence worldwide. However, despite this prevalence the etiology of IBD remains uncertain. It has been suggested that an episode of gastroenteritis may precipitate IBD.

Methods

Studies were identified using a literature search of Pubmed/Medline and Embase/Ovid. This review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. The primary outcome was incidence of new-onset IBD after gastroenteritis. Secondary outcomes included incidence of IBD after bacterial, viral, and parasitic gastrointestinal infections.

Results

Eleven studies (n = 923 608 patients) were included. Four studies assessed patients with gastroenteritis, subsequently developing IBD as the primary outcome. Patients with gastroenteritis had a higher incidence of subsequent IBD but this did not reach statistical significance (odds ratio [OR] 3.81, 95% CI 0.52-27.85, P = .19). Seven studies examined the incidence of antecedent gastroenteritis (primary outcome) in patients with a confirmed diagnosis of IBD, compared to the controlled population. There was no difference between incidence of antecedent gastroenteritis across the 2 population groups (OR 1.07, 95% CI 0.55-2.08, P = .85). There was no association between IBD and bacterial, viral, or parasitic infections.

Conclusions

In summary, our meta-analysis has shown that there is considerable heterogeneity in the literature regarding the role of gastroenteritis in the development of IBD. Further higher quality studies need to be performed to ascertain the true nature of this.

Adult-onset inflammatory bowel disease and rate of serious infections compared to the general population: a nationwide register-based cohort study 2002-2017

OBJECTIVES

To investigate absolute and relative risk of serious infections in adult/elderly inflammatory bowel disease (IBD) diagnosed 2002-2017.

METHODS

Nationwide, register-based cohort study of Swedish patients with IBD compared with general population matched reference individuals with regard to time to first serious infection, equal to hospital admission. Multivariable Cox regression estimated hazard ratios (HRs) for any serious infection. Secondary outcomes included site-specific infections, opportunistic infections and sepsis.

RESULTS

We identified 47 798 individuals with IBD. During a follow-up of 329 000 person-years, they had 8752 first serious infections (26.6 per 1000 person-years). This compared with an incidence rate of 10.7 per 1000 person-years in matched reference individuals, corresponding to a 2.53-fold increased hazard of serious infections (95%CI = 2.47-2.59). The HR for serious infection in elderly-onset IBD was 2.01 (95%CI = 1.95-2.08). The relative hazard of serious infection was somewhat higher in Crohn's disease (2.94; 95%CI = 2.81-3.06) than in ulcerative colitis (2.24; 95%CI = 2.17-2.31). The HR for serious infections was high in the first year of follow-up (5.17; 95%CI = 4.93-5.42). Individuals with IBD were at a particularly high relative hazard of gastrointestinal and opportunistic infections. The HR for sepsis was 2.47 (95%CI = 2.32-2.63). The relative rates for serious infections in IBD increased in recent years.

CONCLUSIONS

Patients with adult-onset IBD are at increased risk of serious infections, particularly gastrointestinal and opportunistic infections. Relative rates were highest just after IBD diagnosis, and seem to have increased in recent years.

Campylobacter jejuni persistently colonizes gnotobiotic altered Schaedler flora C3H/HeN mice and induces mild colitis

Campylobacter jejuni is a major cause of food-borne human bacterial gastroenteritis but animal models for C. jejuni mediated disease remain limited because C. jejuni poorly colonizes immunocompetent, conventionally-reared (Conv-R) mice. Thus, a reliable rodent model (i.e. persistent colonization) is desirable in order to evaluate C. jejuni-mediated gastrointestinal disease and mechanisms of pathogenicity. As the nature and complexity of the microbiota likely impacts colonization resistance for C. jejuni, Conv-R and gnotobiotic C3H/HeN mice were used to evaluate the persistence of C. jejuni colonization and development of disease. A total of four C. jejuni isolates readily and persistently colonized ASF mice and induced mild mucosal inflammation in the proximal colon, but C. jejuni did not stably colonize nor induce lesions in Conv-R mice. This suggests that the pathogenesis of C. jejuni is influenced by the microbiota, and that ASF mice offer a reproducible model to study the influence of the microbiota on the ability of C. jejuni to colonize the gut and to mediate gastroenteritis.

Enteric viruses evoke broad host immune responses resembling those elicited by the bacterial microbiome

The contributions of the viral component of the microbiome-the virome-to the development of innate and adaptive immunity are largely unknown. Here, we systematically defined the host response in mice to a panel of eukaryotic enteric viruses representing six different families. Infections with most of these viruses were asymptomatic in the mice, the magnitude and duration of which was dependent on the microbiota. Flow cytometric and transcriptional profiling of mice mono-associated with these viruses unveiled general adaptations by the host, such as lymphocyte differentiation and IL-22 signatures in the intestine, as well as numerous viral-strain-specific responses that persisted. Comparison with a dataset derived from analogous bacterial mono-association in mice identified bacterial species that evoke an immune response comparable with the viruses we examined. These results expand an understanding of the immune space occupied by the enteric virome and underscore the importance of viral exposure events.

Early life exposures and the risk of inflammatory bowel disease: Systematic review and meta-analyses

BACKGROUND

Early life exposures impact immune system development and therefore the risk of immune-mediated diseases, including inflammatory bowel disease (IBD). We systematically reviewed the impact of pre-, peri‑, and postnatal exposures up to the age of five years on subsequent IBD diagnosis.

METHODS

We identified case-control and cohort studies reporting on the association between early life environmental factors and Crohn's disease (CD), ulcerative colitis (UC), or IBD overall. Databases were search from their inception until May 24th, 2019 until July 14th, 2020. We conducted meta-analyses for quantitative review of relevant risk factors that were comparable across studies and qualitative synthesis of the literature for a wide range of early life exposures, including maternal health and exposures during pregnancy, perinatal factors, birth month and related-factors, breastfeeding, hygiene-related factors and social factors, immigration, antibiotics, offspring health, including infections, and passive smoking. PROSPERO registration: CRD42019134980.

FINDINGS

Prenatal exposure to antibiotics (OR 1.8; 95% CI 1.2-2.5) and tobacco smoke (OR 1.5; 95% CI 1.2-1.9), and early life otitis media (OR 2.1; 95% CI 1.2-3.6) were associated with IBD. There was a trend towards an association between exposure to antibiotics in infancy and IBD (OR: 1.7, 95% CI 0.97, 2.9), supported by positive data on population-based data. Breastfeeding was protective against IBD. Other early life risk factors had no association with IBD, but data were limited and heterogenous.

INTERPRETATION

Early life is an important period of susceptibility for IBD development later in life. Tobacco smoke, infections and antibiotics were associated positively, and breastfeeding was associated negatively with IBD. Our findings offer an opportunity to develop primary prevention strategies.

FUNDING

This study did not receive any funding.

A systematic review of quantitative bias analysis applied to epidemiological research

BACKGROUND

Quantitative bias analysis (QBA) measures study errors in terms of direction, magnitude and uncertainty. This systematic review aimed to describe how QBA has been applied in epidemiological research in 2006-19.

METHODS

We searched PubMed for English peer-reviewed studies applying QBA to real-data applications. We also included studies citing selected sources or which were identified in a previous QBA review in pharmacoepidemiology. For each study, we extracted the rationale, methodology, bias-adjusted results and interpretation and assessed factors associated with reproducibility.

RESULTS

Of the 238 studies, the majority were embedded within papers whose main inferences were drawn from conventional approaches as secondary (sensitivity) analyses to quantity-specific biases (52%) or to assess the extent of bias required to shift the point estimate to the null (25%); 10% were standalone papers. The most common approach was probabilistic (57%). Misclassification was modelled in 57%, uncontrolled confounder(s) in 40% and selection bias in 17%. Most did not consider multiple biases or correlations between errors. When specified, bias parameters came from the literature (48%) more often than internal validation studies (29%). The majority (60%) of analyses resulted in >10% change from the conventional point estimate; however, most investigators (63%) did not alter their original interpretation. Degree of reproducibility related to inclusion of code, formulas, sensitivity analyses and supplementary materials, as well as the QBA rationale.

CONCLUSIONS

QBA applications were rare though increased over time. Future investigators should reference good practices and include details to promote transparency and to serve as a reference for other researchers.

Gastrointestinal Infection and Risk of Microscopic Colitis: A Nationwide Case-Control Study in Sweden

BACKGROUND AND AIMS

Gastrointestinal infections have been linked to changes in the composition and function of gut microbiome and development of inflammatory bowel diseases. We therefore sought to examine the relationship between gastroenteritis and risk of microscopic colitis (MC).

METHODS

We conducted a case-control study of all adult patients with MC diagnosed between 1990 and 2016 in Sweden matched to up to 5 general population controls according to age, sex, calendar year, and county. Cases of MC were identified using Systematized Nomenclature of Medicine codes from the ESPRESSO (Epidemiology Strengthened by histoPathology Reports in Sweden) study, a cohort of gastrointestinal pathology reports from all 28 pathology centers in Sweden. We used logistic regression modeling to estimate adjusted odds ratios (aORs) and 95% confidence intervals (CIs).

RESULTS

Through December of 2016, we matched 13,468 MC cases to 64,479 controls. The prevalence of previous diagnosed gastrointestinal infection was 7.5% among patients with MC, which was significantly higher than in controls (3.0%, P_comparison < .001). After adjustment, gastroenteritis was associated with an increased risk of MC (aOR 2.63; 95% CI 2.42-2.85). Among specific pathogens, Clostridioides difficile (aOR 4.39; 95% CI 3.42-5.63), Norovirus (aOR 2.87; 95% CI 1.66-4.87), and Escherichia species (aOR 3.82; 95% CI 1.22-11.58), but not Salmonella species, were associated with an increased risk of MC. The association between gastrointestinal infections and risk of MC was stronger for collagenous subtype (aOR 3.23; 95% CI 2.81-3.70) as compared with lymphocytic colitis (aOR 2.51; 95% CI 2.28-2.76; P_{heterogeneity} = .005). The associations remained significant after adjustment for immune-mediated conditions and polypharmacy and when compared with unaffected siblings.

CONCLUSION

In a nationwide study, we found that gastrointestinal infection, particularly Clostridioides difficile, is associated with an increased risk of subsequent MC. This study was approved by the Regional Ethics Committee, Stockholm, Sweden (Protocol no. 2014/1287-31/4).

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.

Confounding and bias in observational studies in inflammatory bowel disease: a meta-epidemiological study

BACKGROUND

Observational research concerning inflammatory bowel disease (IBD) is highly susceptible to spurious findings because of confounding and bias.

AIM

To investigate how these issues were reported in this research field.

METHODS

We identified and appraised a random sample of 160 observational studies concerning IBD published in high-impact gastroenterology journals and the most respected specialty journals of the condition. We applied a standardised methodology to assess how confounding and bias were reported and discussed, and investigated the association between yearly citations and study characteristics using mixed-effect multivariable regression analysis.

RESULTS

The authors of 67 out of 160 articles (41.9%) mentioned confounding, and in 89 cases (55.6%) reported any bias. Although most authors applied strategies to minimise confounding or bias (n = 139; 86.9%) and acknowledged at least one unadjusted confounder (n = 116; 72.5%), a minority commented about whether the main findings could have been affected (n = 60; 37.5%). Very few authors (n = 7; 4.4%) called for caution in interpreting the results in the discussion. Reporting of confounding and bias was particularly lacking for case-control studies, those not using routinely collected data, those employing laboratory analyses as the primary method of assessment and studies investigating non-modifiable exposures. In adjusted analyses, mentioning or alluding to confounding was positively associated with yearly citations (P = 0.010), whereas calling for a cautious interpretation of the findings was not.

CONCLUSIONS

Reporting of confounding is inadequate and its acknowledgement is often neglected in interpreting high-impact observational research in IBD. These results encourage a more careful evaluation of the consequences of confounding and bias.

Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases

The intestinal microbiota comprises diverse fungal and viral components, in addition to bacteria. These microbes interact with the immune system and affect human physiology. Advances in metagenomics have associated inflammatory and autoimmune diseases with alterations in fungal and viral species in the gut. Studies of animal models have found that commensal fungi and viruses can activate host-protective immune pathways related to epithelial barrier integrity, but can also induce reactions that contribute to events associated with inflammatory bowel disease. Changes in our environment associated with modernization and the COVID-19 pandemic have exposed humans to new fungi and viruses, with unknown consequences. We review the lessons learned from studies of animal viruses and fungi commonly detected in the human gut and how these might affect health and intestinal disease.

The Gut Microbiome and the Triple Environmental Hit Concept of Inflammatory Bowel Disease Pathogenesis

The incidence of chronic inflammatory bowel diseases (IBDs), such as Crohn's disease (CD) and ulcerative colitis (UC) have significantly increased in recent decades implicating environmental effects. The developmental origin of disease concept provides a theoretical framework by which the complex interplay between environmental factors and host cells, particularly during vulnerable time periods, ultimately cause disease, such as IBD. Epigenetics has been proposed as the underlying mechanism within this concept, turning environmental triggers into stable changes of cellular function. Adding further to the complexity of IBD is the gut microbiome, which is equally responsive to the environment, and can impact host cell function, where recent findings underscore the stochastic and individualized nature of such effects. We review the microbiome literature through a novel triple environmental hit concept (priming, modulation, and trigger) of IBD pathogenesis. We propose that there are at least 3 distinct stages during an individual's lifespan where random/stochastic events driven by environmental influences are necessary for ultimately developing IBD. By this means, we speculate that microbiome-directed therapeutics carry potential for individualized prevention and dynamic treatment of IBD.

Nonclostridium difficile enteric infection and the risk of developing inflammatory bowel disease: A systematic review and meta-analysis

BACKGROUND

Inflammatory bowel disease (IBD) is a chronic inflammatory intestinal disorder. Some studies have investigated the association between non-Clostridium difficile infection (CDI) enteric infection and the risk of developing IBD with conflicting conclusions. The objective of our study was to perform a meta-analysis of available studies evaluating the possible association between non-CDI enteric infection and the risk of developing IBD.

METHODS

We performed a systematic literature search of multiple online electronic databases. Inclusion criteria entailed studies about non-CDI enteric infection and IBD; A meta-analysis was conducted to evaluate relative risk (RR) and 95% confidence intervals (CIs) of combined studies for the association between non-CDI enteric infection and the risk of developing IBD. Publication bias was assessed by funnel plot analysis.

RESULTS

Eight studies comprising 345,490 enteric infected patients, 3223 ulcerative colitis (UC) patients, and 2133 CD patients were included in the meta-analysis. Meta-analysis showed a significantly higher risk of UC in patients with enteric infection compared with noninfected patients (RR, 2.28; 95% CI, 1.85-2.8) (I2 = 91.3%, P < 0.001). It also showed a significantly higher risk of CD in patients with enteric infection compared with noninfected patients (RR, 1.88; 95% CI, 1.66-2.14) (I2 = 49%, P = 0.024).

CONCLUSION

Our meta-analysis has found that patients with non-CDI enteric infection were associated with an increased risk of IBD. Future studies are needed to determine the association between non-CDI enteric infection and the risk of developing IBD and elucidate the potential underlying mechanisms.

Epithelial inflammasomes in the defense against Salmonella gut infection

The gut epithelium prevents bacterial access to the host's tissues and coordinates a number of mucosal defenses. Here, we review the function of epithelial inflammasomes in the infected host and focus on their role in defense against Salmonella Typhimurium. This pathogen employs flagella to swim towards the epithelium and a type III secretion system (TTSS) to dock and invade intestinal epithelial cells. Flagella and TTSS components are recognized by the canonical NAIP/NLRC4 inflammasome, while LPS activates the non-canonical Caspase-4/11 inflammasome. The relative contributions of these inflammasomes, the activated cell death pathways and the elicited mucosal defenses are subject to environmental control and appear to change along the infection trajectory. It will be an important future task to explain how this may enable defense against the challenges imposed by diverse bacterial enteropathogens.

How Food Affects Colonization Resistance Against Enteropathogenic Bacteria

Food has a major impact on all aspects of health. Recent data suggest that food composition can also affect susceptibility to infections by enteropathogenic bacteria. Here, we discuss how food may alter the microbiota as well as mucosal defenses and how this can affect infection. Salmonella Typhimurium diarrhea serves as a paradigm, and complementary evidence comes from other pathogens. We discuss the effects of food composition on colonization resistance, host defenses, and the infection process as well as the merits and limitations of mouse models and experimental foods, which are available to decipher the underlying mechanisms.

Systematic review: gastrointestinal infection and incident inflammatory bowel disease

BACKGROUND

The initiating events of chronic gastrointestinal (GI) inflammation in Crohn's disease (CD) and ulcerative colitis (UC) are not well-defined, but GI infections are implicated.

AIMS

To define the role of GI infections in risk of incident inflammatory bowel disease (IBD) and synthesise the current body of relevant translational data to provide biological context for associations between GI infections and IBD risk.

METHODS

We systematically reviewed electronic databases through February 2020. Clinical studies that provided risk estimates of the association between GI infections and incident IBD were included. Inclusion criteria were broader for translational studies aiming to define mechanisms of GI infections and predisposition to or protection from IBD.

RESULTS

Of the studies identified, 63 met full inclusion criteria. Among studies of clinical gastroenteritis, bacteria-specifically, Salmonella species, Campylobacter species and Clostridioides difficile-demonstrated consistent positive associations with risk of incident IBD. Of viruses, norovirus was associated with increased risk of incident CD. Regarding inverse associations with incident IBD, Helicobacter pylori and helminth infections were associated with a generally consistent reduced risk of IBD. Based on a qualitative analysis of the translational data, putative mechanisms involve multiple microbial and immunologic pathways.

CONCLUSIONS

Based on this systematic review, certain enteric pathogens are associated with an increased risk of incident IBD, while others are potentially protective. Prospective studies are required to clarify the clinical implications of these enteric pathogens on the risk and course of IBD, and possible therapeutic or preventative benefit.

Incidence, risk factors, and health service burden of sequelae of campylobacter and non-typhoidal salmonella infections in England, 2000-2015: A retrospective cohort study using linked electronic health records

BACKGROUND

Reactive arthritis, irritable bowel syndrome (IBS), Guillain-Barré syndrome, ulcerative colitis, and Crohn's disease may be sequelae of Campylobacter or non-typhoidal Salmonella (NTS) infections. Proton pump inhibitors (PPI) and antibiotics may increase the risk of gastrointestinal infections (GII); however, their impact on sequelae onset is unclear. We investigated the incidence of sequelae, their association with antibiotics and PPI prescription, and assessed the economic impact on the NHS.

METHODS

Data from the Clinical Practice Research Datalink for patients consulting their GP for Campylobacter or NTS infection, during 2000-2015, were linked to hospital, mortality, and Index of Multiple Deprivation data. We estimated the incidence of sequelae and deaths in the 12 months following GII. We conducted logistic regression modelling for the adjusted association with prescriptions. We compared differences in resource use and costs pre- and post-infection amongst patients with and without sequelae.

FINDINGS

Of 20,471 patients with GII (Campylobacter 17,838), less than 2% (347) developed sequelae, with IBS (268) most common. Amongst Campylobacter patients, those with prescriptions for PPI within 12 months before and cephalosporins within 7-days before/after infection had elevated risk of IBS (adjusted odds ratio [aOR] 2.1, 1.5-2.9) and (aOR 3.6, 1.1-11.7) respectively. Campylobacter sequelae led to ∼ £1.3 million, (£750,000, £1.7 million) in additional annual NHS expenditure.

INTERPRETATION

Sequelae of Campylobacter and NTS infections are rare but associated with increased NHS costs. Prior prescription of PPI may be a modifiable risk factor. Incidence of sequelae, healthcare resource use and costs are essential parameters for future burden of disease studies.

Rapid expansion of Treg cells protects from collateral colitis following a viral trigger

Foxp3⁺ regulatory T (Treg) cells are essential for maintaining peripheral tolerance and preventing autoimmunity. While genetic factors may predispose for autoimmunity, additional environmental triggers, such as viral infections, are usually required to initiate the onset of disease. Here, we show that viral infection with LCMV results in type I IFN-dependent Treg cell loss that is rapidly compensated by the conversion and expansion of Vβ5⁺ conventional T cells into iTreg cells. Using Vβ5-deficient mice, we show that these Vβ5⁺ iTreg cells are dispensable for limiting anti-viral immunity. Rather, the delayed replenishment of Treg cells in Vβ5-deficient mice compromises suppression of microbiota-dependent activation of CD8⁺ T cells, resulting in colitis. Importantly, recovery from clinical symptoms in IBD patients is marked by expansion of the corresponding Vβ2⁺ Treg population in humans. Collectively, we provide a link between a viral trigger and an impaired Treg cell compartment resulting in the initiation of immune pathology.

Are infectious diseases risk factors for sarcoidosis or a result of reverse causation? Findings from a population-based nested case-control study

Findings from molecular studies suggesting that several infectious agents cause sarcoidosis are intriguing yet conflicting and likely biased due to their cross-sectional design. As done in other inflammatory diseases to overcome this issue, prospectively-collected register data could be used, but reverse causation is a threat when the onset of disease is difficult to establish. We investigated the association between infectious diseases and sarcoidosis to understand if they are etiologically related. We conducted a nested case-control study (2009-2013) using incident sarcoidosis cases from the Swedish National Patient Register (n = 4075) and matched general population controls (n = 40,688). Infectious disease was defined using inpatient/outpatient visits and/or antimicrobial dispensations starting 3 years before diagnosis/matching. Adjusted odds ratios (aOR) of sarcoidosis were estimated using conditional logistic regression and tested for robustness assuming the presence of reverse causation bias. The aOR of sarcoidosis associated with history of infectious disease was 1.19 (95% confidence interval [CI] 1.09, 1.29; 21% vs. 16% exposed cases and controls, respectively). Upper respiratory and ocular infections conferred the highest OR. Findings were similar when we altered the infection definition or varied the infection-sarcoidosis latency period (1-7 years). In bias analyses assuming one in 10 infections occurred because of preclinical sarcoidosis, the observed association was completely attenuated (aOR 1.02; 95% CI 0.90, 1.15). Our findings, likely induced by reverse causation due to preclinical sarcoidosis, do not support the hypothesis that common symptomatic infectious diseases are etiologically linked to sarcoidosis. Caution for reverse causation bias is required when the real disease onset is unknown.

Prevalence of coexisting autoimmune thyroidal diseases in coeliac disease is decreasing

BACKGROUND

Coeliac disease (CD) is associated with an increased risk of other immune-mediated conditions. Aim: To investigate the prevalence of coexistent immune-mediated diseases in CD patients, and changes in the prevalence of autoimmune thyroidal diseases over the last 50 years.

METHODS

Medical record data were collected retrospectively from 749 CD patients in Ireland. Prevalence of autoimmune diseases was compared with previously published results from general populations. Patients were divided into four groups based on the year of diagnosis to analyse changes in the prevalence of autoimmune thyroidal disease over time.

RESULTS

Median age at the time of CD diagnosis was 56 years (range 18-91 years). A total of 233 (31.1%) patients had a coexistent immune-mediated condition (IMC). Autoimmune thyroidal diseases were seen in 149 (19.9%) patients, hypothyroidism in 110 (14.7%), type 1 diabetes in 27 (3.6%), psoriasis in 20 (2.7%), inflammatory bowel disease in 14 (1.9%) and rheumatoid arthritis in 12 (1.6%). All conditions were more common in CD patients than in the general population. Type 1 diabetes was diagnosed mainly before CD, whereas there was no such trend in other conditions. Autoimmune thyroidal diseases became less common in female CD patients over time.

CONCLUSIONS

Prevalence of autoimmune diseases is increased in adult CD patients compared with the general population. However, concomitant autoimmune thyroidal diseases became less common over time in women.

Fecal microbiota transplantation for ulcerative colitis: a prospective clinical study

Background

Fecal microbiota transplantation may contribute to disease remission in ulcerative colitis; however, the factors that determine the effects of treatment remain unknown. The aim of the present study was to prospectively investigate the clinical efficacy of fecal microbiota transplantation in patients with ulcerative colitis and identify the bacterial signatures associated with clinical remission.

Methods

A total of 20 patients with ulcerative colitis were included in this prospective and uncontrolled study. All patients underwent gastroscopy five times, once every 3 weeks. Clinical indices were used to assess the efficacy of fecal microbiota transplantation, as well as the Mayo score, a score used to evaluate the extent of intestinal mucosal lesions in patients with ulcerative colitis. The changes in intestinal flora were detected by 16S ribosomal RNA-sequencing, and the relationship between ulcerative colitis and intestinal flora was analyzed.

Results

After treatment, clinical index scores for diarrhea, abdominal pain, and blood stool decreased significantly (p < 0.05). Erythrocyte sedimentation rate and C-reactive protein levels had not changed significantly; however, the clinical index score for intestinal mucosal lesions and the Mayo score decreased significantly. In addition, 16S ribosomal RNA-sequencing revealed that the intestinal flora in patients diagnosed with ulcerative colitis was different from that of donors.

Conclusion

Fecal microbiota transplantation has a potential therapeutic value for the treatment of ulcerative colitis as it changes the abundance of bacterial flora and improves the scores for diarrhea, abdominal pain, and mucous membrane lesions in patients with this disease.

Trial registration

The clinical trial was retrospectively registered with ClinicalTrials.gov (NCT03016780) on January 11th, 2017.

Evidence of Disturbed Gut Microbial Metabolic Activity in Pediatric Crohn’s Disease

Background

Dysbiosis, that is, disturbed gut microbial balance, is well documented in Crohn’s disease (CD). We aimed at studying CD-linked dysbiosis in children by analyzing fecal microbe-associated characteristics, previously not reported in children.

Methods

This observational study included 28 children with active CD and healthy controls. We assessed the following three indicators of gut microbiota metabolism in the feces: the presence of tryptic activity, the conversion of cholesterol to coprostanol, and the conversion of bilirubin to urobilinogen.

Results

The fecal tryptic activity was significantly higher in children with active CD compared to the control group (P &lt; 0.01). The fecal coprostanol of the CD children was close to zero and differed significantly from the controls (P &lt; 0.001). Furthermore, the children with CD had very low fecal urobilinogen, differing significantly from the control group (P &lt; 0.001).

Conclusions

The significant differences in levels of fecal bacterial metabolites in patients with active CD compared to healthy controls reflect major perturbation of gut microbial functions and have not previously been reported in children. This fits well with the prevailing concept of a dysbiotic gut microbiota in CD and may have important clinical implications by bringing the dysbiosis back into balance.

Salmonella Infection in Chronic Inflammation and Gastrointestinal Cancer

Salmonella not only causes acute infections, but can also cause patients to become chronic "asymptomatic" carriers. Salmonella has been verified as a pathogenic factor that contributes to chronic inflammation and carcinogenesis. This review summarizes the acute and chronic Salmonella infection and describes the current research progress of Salmonella infection contributing to inflammatory bowel disease and cancer. Furthermore, this review explores the underlying biological mechanism of the host signaling pathways manipulated by Salmonella effector molecules. Using experimental animal models, researchers have shown that Salmonella infection is related to host biological processes, such as host cell transformation, stem cell maintenance, and changes of the gut microbiota (dysbiosis). Finally, this review discusses the current challenges and future directions in studying Salmonella infection and its association with human diseases.