Looking into Enteric Virome in Patients with IBD: Defining Guilty or Innocence?

Causal relationship between primary biliary cholangitis and inflammatory bowel disease: a Mendelian randomization study

Background

Several studies indicated that inflammatory bowel disease (IBD) may contribute to increased susceptibility to primary biliary cholangitis (PBC). However, the causal relationship between IBD and PBC remains unclear.

Methods

The genetic variant data of patients with IBD and PBC were obtained from published genome-wide association studies (GWASs). The IBD data were further divided into a discovery dataset and a validation dataset depending on the data source. We conducted a two-sample Mendelian randomization (MR) analysis using the inverse variance weighting (IVW), MR-Egger, weighted median (WM), MR robust adjusted profile score (MR-RAPS), and maximum likelihood (ML) methods, with IVW being the main focus, to verify the causal relationship between IBD and PBC. Additionally, a series of sensitivity analyses were performed to ensure the reliability of the results.

Results

In the discovery cohort, the IVW analysis results (OR = 1.114, P = 0.011) indicated a significant association between IBD and PBC. The MR-RAPS (OR = 1.130, P = 0.007) and ML (OR = 1.115, P = 0.011) analyses yielded results consistent with those of IVW in confirming IBD as a risk factor for PBC. In the validation cohort, consistent findings were observed regarding the causal relationship between IBD and PBC using IVW, MR-RAPS, and ML analyses; all three methods identified IBD as a risk factor for developing PBC. By the IVW analysis, Crohn's disease (CD) emerged as the most prominent subtype of IBD associated with an increased risk of developing PBC in both the discovery cohort (OR = 1.068, P = 0.049) and the validation cohort (OR = 1.082, P = 0.019).

Conclusion

The results of the MR analysis suggest a causal relationship between IBD and PBC, highlighting the necessity for proactive PBC prevention in patients with IBD, particularly those with CD.

From ASCA breakthrough in Crohn's disease and Candida albicans research to thirty years of investigations about their meaning in human health

Anti-Saccharomyces cerevisiae antibodies (ASCA) are human antibodies that can be detected using an enzyme-linked immunosorbent assay involving a mannose polymer (mannan) extracted from the cell wall of the yeast S. cerevisiae. The ASCA test was developed in 1993 with the aim of differentiating the serological response in two forms of inflammatory bowel disease (IBD), Crohn's disease and ulcerative colitis. The test, which is based on the detection of anti-oligomannosidic antibodies, has been extensively performed worldwide and there have been hundreds of publications on ASCA. The earlier studies concerned the initial diagnostic indications of ASCA and investigations then extended to many human diseases, generally in association with studies on intestinal microorganisms and the interaction of the micro-mycobiome with the immune system. The more information accumulates, the more the mystery of the meaning of ASCA deepens. Many fundamental questions remain unanswered. These questions concern the heterogeneity of ASCA, the mechanisms of their generation and persistence, the existence of self-antigens, and the relationship between ASCA and inflammation and autoimmunity. This review aims to discuss the gray areas concerning the origin of ASCA from an analysis of the literature. Structured around glycobiology and the mannosylated antigens of S. cerevisiae and Candida albicans, this review will address these questions and will try to clarify some lines of thought. The importance of the questions relating to the pathophysiological significance of ASCA goes far beyond IBD, even though these diseases remain the preferred models for their understanding.

Causal associations between inflammatory bowel disease and primary biliary cholangitis: a two-sample bidirectional Mendelian randomization study

Inflammatory bowel disease (IBD) has been reported to be associated with hepatobiliary diseases. Previous observational and Mendelian randomization (MR) studies have suggested a causal association between IBD and primary sclerosing cholangitis (PSC). However, it is unclear whether IBD has a causal association with primary biliary cholangitis (PBC): another autoimmune liver disease. We obtained genome-wide association study (GWAS) statistics from published GWASs for PBC, UC, and CD. We screened qualified instrumental variables (IVs) based on the three major assumptions of MR. To determine the causal relationships between UC or CD and PBC, two-sample MR analyses were performed using inverse variance-weighted (IVW), MR-Egger, and weighted median (WM) methods, and sensitivity analyses were conducted to validate the robustness of the results. We also conducted reverse MR analysis to reveal the causal association between PBC and UC or CD. UC was associated with a higher risk of PBC (OR 1.35, 95% CI 1.05-1.73, P = 0.02) in the IVW method, and CD was associated with an increased risk of PBC (OR 1.18, 95% CI 1.03-1.36, P = 0.02) in IVW. The weighted median and MR-Egger regression of both diseases showed a consistent direction but were not statistically significant. Results of the reverse MR analysis did not suggest genetic susceptibility that PBC was associated with an increased risk of UC (OR 1.05, 95% CI 0.95-1.17, P = 0.34) or CD (OR 1.1, 95% CI 0.99-1.20, P = 0.06). The present study revealed that IBD subtypes could increase the incidence of PBC, but in turn, PBC did not increase the incidence of IBD subtypes. Understanding that IBD and PBC constitute mutual risk factors can help with the clinical management of both diseases.

Epstein–Barr virus seroprevalence and viral load at disease onset in children with inflammatory bowel disease

Background and Aim

Patients with inflammatory bowel disease (IBD) are at increased risk for life‐threatening complications of Epstein–Barr virus (EBV), including lymphoproliferative diseases. These complications are likely related to inherent immune dysfunction and immunomodulating therapies often used. We aimed to determine the seroprevalence of EBV at diagnosis in our population, its impact on disease at onset, and the risk of active EBV infection.

Methods

We included patients newly diagnosed with IBD for whom an EBV serology was performed over a 2‐year period. Demographic information and data on disease characteristics were collected retrospectively. Stored serum from the time of diagnosis was retrieved when available for the patients with positive EBV serology, and quantitative polymerase chain reaction testing was performed to assess the pre‐treatment viral load of EBV.

Results

One hundred twenty patients were included in the study. Fifty‐three patients (44.2%) had positive EBV serology at diagnosis. Stratified by age group, the prevalence of seropositive patients was for 0 to <10 years 35%, 10 to <17 years 46%, and ≥17 years 50%. Overall, therapies started within 6 months of diagnosis were similar in both the seropositive and seronegative groups. Within the seropositive group, 66% received systemic corticosteroids, 32.1% infliximab, 5.7% adalimumab, and 5.7% azathioprine.

Conclusion

EBV seroprevalence is high in pediatric patients with IBD. EBV seropositivity did not seem to influence the severity of disease at onset or initial choice of therapy.

[Cytomegalovirus Infection in Patients with Inflammatory Bowel Disease]

A diagnostic evaluation for cytomegalovirus (CMV) infection is required in patients with inflammatory bowel disease (IBD) who do not respond to steroid or immunomodulatory treatment. However, there is no consensus on an accurate diagnostic method for CMV infection in patients with IBD, and it is difficult to clearly distinguish the exacerbation of ulcerative colitis from CMV colitis. According to several recent studies, the most accurate test method for CMV colitis is quantitative tissue DNA-quantitative PCR, which is recommended as the first-line diagnostic technique along with an immunohistochemistry stain. The benefit of antiviral therapy for CMV infection in patients with IBD is also controversial. Although the definition of viral load is unclear, antiviral therapy can lower the rate of colectomy in CMV infections with a high viral load in patients with IBD. This review presents the latest findings about CMV infections in IBD, based on recently reported studies.

Epstein-Barr Virus and Human Cytomegalovirus Infection in Intestinal Mucosa of Chinese Patients With Inflammatory Bowel Disease

Objective

This study aimed to determine the frequency of Epstein–Barr virus (EBV), cytomegalovirus (CMV) in mucosa and blood of inflammatory bowel disease (IBD) patients in China and evaluate their correlation with the clinical disease activities.

Methods

Peripheral blood and endoscopic fresh colonic mucosal samples were collected from a cohort of 287 IBD patients and 50 controls. Viral DNA load was analyzed through quantitative real-time PCR. The clinical disease activity of ulcerative colitis (UC) and Crohn’s disease (CD) was assessed by the Mayo Clinic Score and Crohn’s disease activity index, respectively.

Results

Among 287 IBD patients, 228 (79.4%) were positive for EBV and 99 (34.5%) were positive for CMV. EBV and CMV infection rates are significantly higher than those in the control group (28.0%, p < 0.05; 4.0%, p < 0.05). In addition, EBV/CMV prevalence increases as clinical activities progress [For EBV infection, the prevalence was 53.93% (48/89) in the mild group, 87.00% (87/100) in the moderate group, and 94.90% (93/98) in the severe group; and for CMV infection, the prevalence was 3.37% (3/89) in the mild group, 27.00% (27/100) in the moderate group, and 70.41% (69/98) in the severe group]. EBV and CMV loads are related to clinical disease activities (p < 0.05). In addition, viral load in the intestinal mucosa of patients with acute exacerbation of IBD is higher than that of patients in remission.

Conclusion

High prevalence of EBV and CMV is found in patients with IBD, and their prevalence is related to clinical disease activities. In addition, the viral load in the intestinal mucosa is associated with the status of mucosa in the same patients (active phase versus remission phase). Detection of viral load on mucosal specimens with quantitative real-time PCR is a feasible method to monitor EBV and CMV infection in IBD patients.

Chronic active Epstein-Barr virus enteritis: A literature review

Chronic active Epstein-Barr virus (CAEBV) enteritis is a rare disease that has not been well described. Owing to the similarities between CAEBV enteritis and inflammatory bowel diseases such as ulcerative colitis and Crohn's disease, it is easy to be misdiagnosed and mistreated in clinical practice, resulted in complications and even death in severe cases. Through a literature review, this study aimed to summarize the clinical characteristics, pathological features, examinations, and treatment strategies of CAEBV enteritis and its similarities and differences with inflammatory bowel diseases.

The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications

The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases, viral metagenomic approaches have been used to explore known components of the virome and discover new viruses from various types of samples. The virome has attracted substantial interest since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Increasing numbers of studies and review articles have documented the diverse virome in various sites in the human body, as well as interactions between the human host and the virome with regard to health and disease. However, there have been few studies of direct causal relationships. Viral metagenomic analyses often lack standard references and are potentially subject to bias. Moreover, most virome-related review articles have focused on the gut virome and did not investigate the roles of the virome in other sites of the body in human disease. This review presents an overview of viral metagenomics, with updates regarding the relations between alterations in the human virome and the pathogenesis of human diseases, recent findings related to COVID-19, and therapeutic applications related to the human virome.

Epstein-Barr Virus Positive B-Cell Lymphoproliferative Disorder of the Gastrointestinal Tract

Epstein-Barr virus positive B-cell lymphoproliferative disorder (EBV+ B-LPD) encompasses a broad clinicopathological spectrum and distinct clinical behavior that relatively favors the gastrointestinal (GI) tract. In this review, we provide an update on the clinicopathological features and biological behavior of EBV-positive mucocutaneous ulcer (EBVMCU) and primary EBV+ diffuse large B-cell lymphoma (DLBCL) of the GI tract. EBVMCU is a newly recognized entity but well known as an indolent and self-limited EBV+ B-LPD occurring in various immunodeficiencies. In contrast, EBV+ DLBCL constitutes the largest group of EBV+ B-LPDs and is regarded as an aggressive neoplasm. These two distinct diseases have historically been distinguished in the reappraisal of age-related EBV-associated B-LPDs but are challenging in routine practice regarding their differential diagnostic and therapeutic approaches. An increasing number of reports indicate that they are epidemiologically prevalent beyond western and eastern countries, but their comprehensive analysis is still limited. We also describe the PD-L1 positivity of tumorous large cells and non-malignant immune cells, which is relevant for the prognostic delineation among patients with primary DLBCL of the GI tract with and without EBV on tumor cells.

Impact of Epstein-Barr virus infection on inflammatory bowel disease (IBD) clinical outcomes

OBJECTIVE

To evaluate the role of Epstein-Barr virus (EBV) on the intestinal mucosa in the evolution of inflammatory bowel disease (IBD), to investigate the risk factors for EBV infection and the frequency of EBV-associated lymphoproliferative disorders in IBD patients.

METHODS

Intestinal biopsies of IBD patients with available EBV status determined by Epstein-Barr-encoding RNA (EBER) in situ hybridization were searched in the Pathology Database of our center. Clinical information, including phenotypic characteristics of IBD, previous treatments, diagnosis of lymphoma, and patient outcome, were reviewed for all cases.

RESULTS

56 patients with IBD (28 Crohn´s disease, 27 ulcerative colitis and one unclassified colitis) were included. EBV in intestinal mucosa was positive in 26 patients (46%), in one case associated to a lymphoproliferative syndrome. EBV positivity was associated with severe histological activity (52% vs. 17.2%; p 0.007), presence of a lymphoplasmacytic infiltrate (50% vs. 33.3%; p 0.03) and active steroid treatment (61.5% vs. 33.3%; p 0.03). Multivariate analyses only found association between EBV and lymphoplasmacytosis (p 0.001). Escalation in previous treatment was significantly more frequent in the EBER+ group (53.8% vs. 26.7%; p 0.038). No cases developed lymphoma in the follow-up.

CONCLUSIONS

EBV on the intestinal mucosa is associated with a poor outcome of IBD and the need for escalation in therapy. Lymphoplasmacytic infiltrate is associated with EBV infection. EBER+ patients used steroids more frequently compared with EBER- patients. No EBER+ patients developed a lymphoma during follow-up.

Viral infections in inflammatory bowel disease: Tips and tricks for correct management

Over the past decades, the treatment of inflammatory bowel diseases (IBD) has become more targeted, anticipating the use of immune-modifying therapies at an earlier stage. This top-down approach has been correlated with favorable short and long-term outcomes, but it has also brought with it concerns regarding potential infectious complications. This large IBD population treated with immune-modifying therapies, especially if combined, has an increased risk of severe infections, including opportunistic infections that are sustained by viral, bacterial, parasitic, and fungal agents. Viral infections have emerged as a focal safety concern in patients with IBD, representing a challenge for the clinician: they are often difficult to diagnose and are associated with significant morbidity and mortality. The first step is to improve effective preventive strategies, such as applying vaccination protocols, adopt adequate prophylaxis and educate patients about potential risk factors. Since viral infections in immunosuppressed patients may present atypical signs and symptoms, the challenges for the gastroenterologist are to suspect, recognize and diagnose such complications. Appropriate treatment of common viral infections allows us to minimize their impact on disease outcomes and patients’ lives. This practical review supports this standard of care to improve knowledge in this subject area.

Enterocytes, fibroblasts and myeloid cells synergize in anti-bacterial and anti-viral pathways with IL22 as the central cytokine

IL22 is an important cytokine involved in the intestinal defense mechanisms against microbiome. By using ileum-derived organoids, we show that the expression of anti-microbial peptides (AMPs) and anti-viral peptides (AVPs) can be induced by IL22. In addition, we identified a bacterial and a viral route, both leading to IL22 production by T cells, but via different pathways. Bacterial products, such as LPS, induce enterocyte-secreted SAA1, which triggers the secretion of IL6 in fibroblasts, and subsequently IL22 in T cells. This IL22 induction can then be enhanced by macrophage-derived TNFα in two ways: by enhancing the responsiveness of T cells to IL6 and by increasing the expression of IL6 by fibroblasts. Viral infections of intestinal cells induce IFNβ1 and subsequently IL7. IFNβ1 can induce the expression of IL6 in fibroblasts and the combined activity of IL6 and IL7 can then induce IL22 expression in T cells. We also show that IL22 reduces the expression of viral entry receptors (e.g. ACE2, TMPRSS2, DPP4, CD46 and TNFRSF14), increases the expression of anti-viral proteins (e.g. RSAD2, AOS, ISG20 and Mx1) and, consequently, reduces the viral infection of neighboring cells. Overall, our data indicates that IL22 contributes to the innate responses against both bacteria and viruses.

The association between enteric viruses and necrotizing enterocolitis

Studies on necrotizing enterocolitis (NEC) have not largely focused on enteric viruses. In order to demonstrate the association between enteric viruses and NEC, stool specimens of 51 neonates with NEC and 39 "normal" neonates were collected to detect rotavirus (RV), astrovirus (ASV), sapovirus, enterovirus (EV), adenovirus (ADV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), and human bocavirus (HBoV). Rotavirus A (RVA), ASV, EBV, and ADV were detected in both the NEC and control groups; however, EV and HBoV were detected only in the NEC group and CMV was not detected in either group. ASV was the most common enteric virus, but no significant differences were found between NEC and control groups, as was similarly the case for EBV and EV. The prevalence of ADV and HBoV was higher in the NEC group than in the control group (P = 0.011, P = 0.005, respectively) but RVA showed the opposite trend (P = 0.014). Virus positivity or negativity had no influence on the clinical manifestation of NEC.Conclusion: The roles of different viruses in NEC are not congruent. Some, such as ASV, may be regarded as commensal in neonates, while in NEC patients, the presence of ADV and EBV may be related to severity of disease. What is known: • The etiology of NEC remains unknown. Studies on necrotizing enterocolitis (NEC) have not largely focused on enteric viruses and the conclusions were inconsistent. What is new: • Enteric viruses are common in the gut of neonates, but not all of them are pathogenic. • The existence of ADV and EBV may be related to the severity of NEC.

Virome Sequencing of the Human Intestinal Mucosal-Luminal Interface

While the human gut virome has been increasingly explored in recent years, nearly all studies have been limited to fecal sampling. The mucosal-luminal interface has been established as a viable sample type for profiling the microbial biogeography of the gastrointestinal tract. We have developed a protocol to extract nucleic acids from viruses at the mucosal-luminal interface of the proximal and distal colon. Colonic viromes from pediatric patients with Crohn's disease demonstrated high interpatient diversity and low but significant intrapatient variation between sites. Whole metagenomics was also performed to explore virome-bacteriome interactions and to compare the viral communities observed in virome and whole metagenomic sequencing. A site-specific study of the human gut virome is a necessary step to advance our understanding of virome-bacteriome-host interactions in human diseases.

Clinical features of Epstein-Barr virus in the intestinal mucosa and blood of patients with inflammatory bowel disease

BACKGROUND

The role of Epstein-Barr virus (EBV) in inflammatory bowel disease (IBD) remains to be elucidated. The aim of this study was to investigate the presence of EBV in the blood and intestinal mucosa of patients with IBD and evaluate the association between EBV positivity and IBD.

METHODS

Patients with IBD, hospitalized between January 2015 and April 2018, were enrolled. The EBV-DNA load in blood samples from each subject was analyzed by quantitative real-time polymerase chain reaction. EBV-encoded small-RNA 1 (EBER-1) was detected by in-situ hybridization in intestinal mucosa tissue sections of patients with IBD.

RESULT

EBV-DNA was detected in 48 out of 568 patients with IBD (8.4%), and EBER-1 positivity was detected in 27 of these patients (56.3%). Refractory IBD and severe mucosal inflammation were more common in patients with detectable levels of EBER-1 than in those without; the number of EBER-1-positive cells positively correlated with mucosal inflammation (P value < 0.05). Age (≥60 years old) and use of azathioprine were risk factors for EBV infection. There was no significant difference in clinical remission rate and surgical rate between the EBER-1 positive group and EBER-1 negative group, antiviral group and the non-antiviral group, among IBD patients who tested positive for EBV-DNA.

CONCLUSION

Elderly patients with IBD, treated with azathioprine, are more susceptible to EBV positivity. Further, EBV mucosal detection correlated with the severity of mucosal damage and refractoriness, but not prognosis.

Ulcerative Colitis and Cytomegalovirus Infection: From A to Z

Despite multiple studies, the role of cytomegalovirus [CMV] infection in exacerbating the severity of inflammation in ulcerative colitis [UC], and its response to treatment, remain debatable. Additionally, the optimal diagnostic tests for CMV infection in the setting of UC relapse, and timing of antiviral treatment initiation, remain unclear. The challenge faced by gastroenterologists is to differentiate between an acute UC flare and true CMV colitis. It seems that the presence of CMV colitis, as defined by the presence of intranuclear or intracellular inclusion bodies on haematoxylin and eosin [H&E] staining and/or positive immunohistochemistry [IHC] assay on histology, is associated with more severe colitis. Patients with CMV infection and acute severe colitis are more resistant to treatment with corticosteroids than non-infected patients. This refractoriness to steroids is related to colonic tissue CMV viral load and number of inclusion bodies [high-grade CMV infection] which may have a pronounced effect on clinical outcomes and colectomy rates. Whereas many studies showed no effect for antiviral treatment on colectomy rates in CMV-infected UC patients, there was a significant difference in colectomy rates of patients with high-grade infection who received anti-viral therapy compared with those who did not receive treatment. It was therefore proposed that high-grade CMV disease indicates that the virus is acting as a pathogen, whereas in those with low-grade CMV disease, the severity of IBD itself is more likely to influence outcome. The different algorithms that have been put forward for the management of patients with UC and concomitant CMV infection are discussed.

Prospective study of blood viral load of Epstein-Barr virus, herpes virus type 6 and human parvovirus B19 in Crohn's disease: Does therapy matter?

BACKGROUND

The interplay between inflammatory bowel disease (IBD) and DNA viruses, such as Epstein-Barr (EBV), human parvovirus B19 (HPVB19) and human herpes type 6 (HHV6) is scarcely studied. The main aim of this prospective study is to screen for EBV, HSV6, and HPVB19 DNA viremia in adult patients with stable Crohn's disease (CD), correlating the results with IBD treatment.

METHODS

From July 2015 - March 2017, 100 patients were enrolled and divided in four groups of 25 participants each, according to in course treatment. Blood collections were performed every 5 months in all patients. Antibodies for EBV and HPVB19 were screened and repeated if negative. Blood EBV DNA, HPVB19 DNA, and HHV6 DNA were quantified by quantitative real-time Polymerase Chain Reaction.

RESULTS

Patients had evidence of EBV (100 %) and HPVB19 (70 %) past infection. Across the study timeline, EBV-DNA, HPVB19-DNA, and HHV6-DNA were detected in the blood of 25, 11, and 7 patients, respectively. Viremia was detected only once in 72 %, 73 %, and 86 % of the patients in the studied period, for EBV, HPVB19, and HHV6, respectively. We did not find significant differences between treatment groups, independently of the viral cut-off for the three viruses.

CONCLUSIONS

The detection of EBV, HPVB19, and HHV6 viremia, in stable CD patients, was not impacted by biological/immunosuppressant therapy. Although attractive as a non-invasive technique, this approach did not prove to be useful in stable patients. More and larger studies are needed to address the relevance of these viruses on IBD course, in stable patients and during exacerbations.

Infection of Epstein-Barr Virus is Associated with the Decrease of Helios+FoxP3+Regulatory T Cells in Active Ulcerative Colitis Patients

Background: Loss of immune homeostasis to enteric pathogens is considered to be involved in the pathogenesis of ulcerative colitis (UC), and regulatory T cells (Tregs) are key for this immune homeostasis. Helios exhibits an important effect on regulating the suppressive function of Tregs. Epstein-Barr virus (EBV) is more commonly detected in UC. However, whether there is an association between EBV infection and Helios⁺Tregs and its impact on disease activity of UC remain unclear. We aimed to explore the clinical significance of Helios⁺Tregs and their potential association with EBV infection in UC. Methods: Seventy-six UC patients and 38 controls were consecutively enrolled. Helios⁺FoxP3⁺Tregs were analyzed using flow cytometry and compared among groups. Eight active UC patients treated with 5-aminosalicylic acid were followed up. Correlation analyses were conducted between Helios⁺FoxP3⁺Tregs and disease activity indicators. In addition, EBV viral loads in the mucosal lesion were quantified in active UC by quantitative polymerase chain reaction and were comprehensively analyzed in subgroups of different disease severity, and their associations with Helios⁺FoxP3⁺Tregs were also analyzed. Results: Helios⁺FoxP3⁺Tregs were significantly decreased in active UC and were inversely correlated with serum C-reactive protein and Mayo score. Moreover, we observed the recovery of Helios⁺FoxP3⁺Tregs in followed-up active UC achieving remission after treatment. EBV loads were higher in active UC, and levels of Helios⁺FoxP3⁺Tregs in the EBV-positive subgroup were lower than the EBV-negative subgroup in moderate and severe active patients. Most importantly, we found that Helios⁺FoxP3⁺Tregs were significantly negatively correlated with EBV viral loads. Conclusion: Helios⁺FoxP3⁺Tregs are likely to play a pivotal role in disease activity of UC and may be influenced by EBV infection.

Primary biliary cholangitis in patients with inflammatory bowel disease

BACKGROUND & AIMS

Inflammatory bowel diseases (IBD) are associated with various hepatobiliary disorders. There is a strong association for primary sclerosing cholangitis (PSC). Primary biliary cholangitis (PBC), another autoimmune cholestatic liver disease, is not usually associated with IBD. The aim of this study is to report cases of PBC-associated IBD, their clinical features, response to therapy, and long-term outcome.

METHODS

Retrospective analysis of a prospectively collated database identified patients presenting with PBC-associated IBD from 2006 to 2016. PBC has been diagnosed according to accepted criteria, and staged according to Ludwig classification. A magnetic resonance cholangiopancreatography (MRCP) was performed to rule out PSC. Response to ursodeoxycholic acid (UDCA) therapy has been assessed by using the Paris II criteria.

RESULTS

A total of six patients (five females) with PBC-associated IBD were identified. Median age at IBD diagnosis was 44.7 years (range 22.5-48.8). Three had Crohn's disease and three ulcerative colitis. PBC was diagnosed in all after IBD had been diagnosed. All patients presented with cholestasis, all were positive for anti-mitochondrial antibodies. MRCP was normal in all. Liver biopsy was consistent with PBC (stage I in one, stage II in five). One year after initiation of UDCA, all patients responded to therapy.

CONCLUSION

Herein we describe the largest series reported to date of PBC-associated IBD. Although the coexistence of the two conditions is rare, PBC should be considered during the work-up of abnormal liver function tests in patients with IBD.

Characterization of Stool Virome in Children Newly Diagnosed With Moderate to Severe Ulcerative Colitis

BACKGROUND

Viral infections have been suggested as possible triggers for the onset of ulcerative colitis (UC).

METHODS

We employed VirCapSeq-Vert, a high-throughput sequencing virus capture platform, to examine the stool virome of children with newly diagnosed moderate to severe UC. We surveyed fecal samples collected at presentation, after symptom remission, and from a control group diagnosed with irritable bowel syndrome.

RESULTS

Seventy subjects with UC (mean age 13 years, 45 had moderate symptoms, 25 had severe, 69 of 70 had a Mayo endoscopy subscore 2/3) were studied. We detected a wide range of animal viruses that were taxonomically classified into 12 viral families. A virus was present in 50% of fecal samples collected at presentation, 41% of samples collected after remission, and 40% of samples in our control group. The most frequently identified viruses were diet-based gyroviruses. The UC cohort had a significantly higher prevalence of anelloviruses compared with the control cohort. However, we did not identify a single virus that can be implicated in the onset of UC and did not find an association between UC disease severity and viral presence.

CONCLUSION

Presence of virus in stool was not associated with the onset of pediatric UC.

A review on co-existent Epstein-Barr virus-induced complications in inflammatory bowel disease

There have been growing reports regarding the presence of Epstein-Barr virus (EBV) in the intestine portions of patients suffering from ulcerative colitis and Crohn's disease, collectively termed as inflammatory bowel disease (IBD). Indeed, the prevalence of EBV infection increases in IBD patients due to prolonged employment of immunosuppressive drugs including azathioprine and infliximab. In turn, coinfection with EBV increases the propensity of development of lymphoproliferative disorders in the gastrointestinal tract including Hodgkin lymphoma, non-Hodgkin lymphomas, and lymphoepithelioma-like cholangiocarcinoma. Therefore, it is recommended that IBD patients on prolonged immunomodulator therapy should be monitored for the presence of primary intestinal lymphoproliferative diseases. Moreover, coinfection of EBV complicates the clinical course of IBD by increasing the severity, chronicity, inducing refractoriness and increasing relapse incidences. Therefore, it is recommended that antiviral drugs should be added in the conventional IBD therapy in the suspected cases of EBV infection. Research has also revealed that EBV-induced colitis is very similar to IBD and there are chances of misdiagnosis of IBD in the presence of EBV colitis. The proper diagnosis of EBV infection along with its timely treatment is necessary to avoid the severe complications in patients of IBD. The present review discusses the role of EBV coinfection in increasing the clinical complications of IBD patients.

Phantom of the inflammasome in the gut: Cytomegalovirus

Cytomegalovirus (CMV) is frequently detected in inflammatory bowel tissue, especially in corticosteroid-refractory patients, and it has been blamed for adverse outcomes. However, the first acquisition of CMV does not involve the colon. In particular in the colonic mucosa, which evolved due to the gut microbial relationship, CMV promotes inflammation via recruited monocytes and not through replication in resident macrophages. Whether CMV is the last straw in the process of mucosal inflammation, a doomed agent, or an innocent bystander is a difficult question that remains elusive. With this work, we will try to review the relationship between intestinal mucosa and CMV in the framework of basic virological principles.

Clinical and endoscopic complications of Epstein-Barr virus in inflammatory bowel disease: an illustrative case series

BACKGROUND AND AIM

Epstein-Barr virus (EBV) is a proposed trigger in the etiopathogenesis of inflammatory bowel disease (IBD) and is associated with lymphoproliferative diseases. Nevertheless, testing for EBV DNA in the intestinal mucosa and screening for EBV infection before initiation of a drug therapy are not routinely performed. The aim of this article is to increase awareness of the relevance of EBV infection in specific clinical situations.

METHODS

In this short communication, we describe the disease course of three IBD patients with EBV infection, varying from EBV reactivation during disease flare up to a trigger of EBV-related mucocutaneous ulcer (EBV-MCU) and haemophagocytic lymphohistiocytosis (HLH).

RESULTS

Our first patient was diagnosed with EBV reactivation-associated severe colitis and showed a rapid clinical improvement after induction therapy with infliximab and azathioprine. Without antiviral treatment, the patient remained in complete remission and no complications of EBV were seen. After diagnosing EBV-MCU in the second patient, immunosuppressive medication was discontinued and four infusions of rituximab resulted in a rapid clinical recovery and eventually complete response. After discontinuation of the immunosuppression in our last patient with haemophagocytic lymphohistiocytosis, treatment with a combination of corticosteroid and antiviral therapy resulted in a complete recovery over a time span of several weeks.

CONCLUSION

EBV infection has a wide variety of potentially life-threatening clinical manifestations in IBD patients. Testing for EBV in case of a flare up and screening for EBV before the start of immunosuppressive therapy will create awareness for EBV-related symptoms or complications during follow-up.

Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease

Intestinal dysbiosis is one of the causes underlying the pathogenesis of inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn's disease (CD). Besides bacteria, microbiota comprises both prokaryotic and eukaryotic viruses, that together compose the gut virome. Few works have defined the viral composition of stools, while the virome populating intestinal mucosae from early-diagnosed IBD patients has never been studied. Here we show that, by in-depth metagenomic analysis of RNA-Seq data obtained from gut mucosae of young treatment-naïve patients, early-diagnosed for CD and UC, and from healthy subjects (Ctrl), UC patients display significantly higher levels of eukaryotic Hepadnaviridae transcripts by comparison with both Ctrl and CD patients, whereas CD patients show increased abundance of Hepeviridae versus Ctrl. Moreover, we found that UC gut mucosa is characterized by lower levels of Polydnaviridae and Tymoviridae, whereas the mucosa of patients with CD showed a reduced abundance of Virgaviridae. Our findings support the idea that certain eukaryotic viruses might trigger intestinal inflammation and contribute to IBD pathogenesis and pave the way not only for the discovery of novel diagnostic biomarkers but also for the development of anti-viral drugs for the treatment of IBD.

The gut microbiota: cause and cure of gut diseases

The gastrointestinal microbiota is emerging as a central factor in the pathogenesis of a range of gastrointestinal and hepatic disorders. Epidemiological studies, and experimental studies in animals and humans, have highlighted a likely causative role of this microbial community in the modern global epidemics of inflammatory bowel disease, non-alcoholic fatty liver disease, non-alcoholic steato-hepatitis, obesity and metabolic syndrome. New techniques for microbial culture and gene sequencing are enabling the identification of specific pathogens and protective organisms in these conditions. Factors that change the microbiota are being defined: dietary pattern, specific foods, food additives in processed food and drinks, such as emulsifiers and non-sugar sweeteners, and antibiotics. Microbiota changes in early life appear critical to the later development of a range of inflammatory disorders. For many of these conditions, the treatment paradigm will change, at least in part, from immune suppression and drug therapy to treatments that reshape the microbiota or restore its integrity. These treatments include dietary changes, specific microbial manipulation and faecal microbiota transplantation. A dialogue is needed regarding population strategies that target disease prevention. This will include how food is produced, what additives it contains, and how it is processed. Widespread use of antibiotics, from agricultural and veterinary to medicinal settings, needs more attention. At the individual level, microbial profiles may be able to predict who is at risk of disease when subjected to particular environmental influences, and what microbial restoration is needed to minimise risk.

Specific changes of enteric mycobiota and virome in inflammatory bowel disease

One of the important features of inflammatory bowel disease (IBD) is dysbiosis of the gut microbiota. It has been well documented that changes in the commensal bacterial population are involved in IBD development. However, the function of the fungal and viral communities in IBD remains unclear. Moreover, the optimal treatment for IBD patients with opportunistic infections is still undecided. This review focused on how the enteric mycobiota and virome changes during the pathogenesis of IBD and discussed potential treatment strategies that open new insights into the managements of IBD.