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AIM: To evaluate the incidence of late biliary complications in non-resectable alveolar echinococcosis (AE) under long-term chemotherapy with benzimidazoles. METHODS: Retrospective analysis of AE patients with biliary complications occurring more than three years after the diagnosis of AE. We compared characteristics of patients with and without biliary complications, analyzed potential risk factor for biliary complications and performed survival analyses. RESULTS: Ninety four of 148 patients with AE in Zurich had non-resectable AE requiring long-term benzimidazole chemotherapy, of which 26 (28%) patients developed late biliary complications. These patients had a median age of 55.5 (35.5-65) years at diagnosis of AE and developed biliary complications after 15 (8.25-19) years of chemotherapy. The most common biliary complications during long-term chemotherapy were late-onset cholangitis (n = 14), sclerosing cholangitis-like lesions (n = 8), hepatolithiasis (n = 5), affection of the common bile duct (n = 7) and secondary biliary cirrhosis (n = 7). Thirteen of the 26 patients had undergone surgery (including 12 resections) before chemotherapy. Previous surgery was a risk factor for late biliary complications in linear regression analysis (P = 0.012). CONCLUSION: Late biliary complications can be observed in nearly one third of patients with non-resectable AE, with previous surgery being a potential risk factor. After the occurrence of late biliary complications, the median survival is only 3 years, suggesting that late biliary complications indicate a poor prognostic outcome.

BACKGROUND: While the numbers of hepatitis-C-virus (HCV) infections among men who have sex with men (MSM) who are co-infected with the human immunodeficiency virus (HIV) are on the rise, with vast evidence for sexual transmission of HCV in this population, concerns have also been raised regarding sexual HCV-transmission among MSM without HIV infection. Therefore, the aim of this study was to estimate the prevalence of hepatitis C among MSM without HIV diagnosis in Zurich (Switzerland). METHODS: Participants were recruited from a gay health centre and various locations such as dark rooms, saunas and cruising areas in Zurich. Participants self-completed a questionnaire assessing known and suspected risk factors for HCV-infection, and provided a blood sample for detection of past (antibodies) and present (core antigen, RNA) infections with HCV. RESULTS: In total, 840 MSM aged 17-79 (median: 33 years) underwent HCV-testing and completed the questionnaire, among whom 19 reported living with HIV. Overall, seven tested positive for HCV-antibodies, and two were also positive for HCV core antigen and HCV-RNA-these two were immigrants, one from a country where HCV is endemic. None of the seven were aware of their infection. The seroprevalence of hepatitis C among the 821 non-HIV-diagnosed MSM was 0.37% (95%-CI: 0.12-1.69%), and one man harboured replicating virus (0.12%; 0.02-0.69%), resulting in a number needed to test of 821 to detect one active infection. Significant univariable associations of lifetime HCV-infection were found with known HIV-diagnosis (OR=72.7), being tattooed (OR=10.4), non-injection use of cocaine/amphetamines (OR=8.8), and non-Swiss origin (OR=8.5). For MSM without HIV-diagnosis, the only variable marginally associated with positive HCV-serostatus was being tattooed (OR=8.3). No significant associations were observed with reported injection drug use, unprotected anal intercourse, sexual practices that may lead to mucosal trauma, or proxy measures for group sex and lesion-prone STIs. CONCLUSIONS: Our findings suggest that in Switzerland, hepatitis C among MSM without diagnosed HIV is not more prevalent than in the general population. We found no evidence of elevated rates of sexual transmission of HCV among MSM without HIV-infection. Therefore, we currently see no reason for promoting HCV-testing among all MSM in Switzerland.

BACKGROUND The CCR5 receptor, expressed on Th1 cells, may influence clinical outcomes of HCV infection. We explored a possible link between a CCR5 32-base deletion (CCR5delta32), resulting in the expression of a non-functioning receptor, and clinical outcomes of HCV infection. METHODS CCR5 and HCV-related phenotypes were analysed in 1,290 chronically infected patients and 160 patients with spontaneous clearance. RESULTS Carriage of the CCR5delta32 allele was observed in 11% of spontaneous clearers compared to 17% of chronically infected patients (OR = 0.59, 95% CI interval 0.35-0.99, P = 0.047). Carriage of this allele also tended to be observed more frequently among patients with liver inflammation (19%) compared to those without inflammation (15%, OR = 1.38, 95% CI interval 0.99-1.95, P = 0.06). The CCR5delta32 was not associated with sustained virological response (P = 0.6), fibrosis stage (P = 0.8), or fibrosis progression rate (P = 0.4). CONCLUSIONS The CCR5delta32 allele appears to be associated with a decreased rate of spontaneous HCV eradication, but not with hepatitis progression or response to antiviral therapy.

The use of thiopurines as immunosuppression for the treatment of refractory or chronic active inflammatory bowel disease is established for both Crohn's disease and ulcerative colitis. Nevertheless, many questions remain concerning the optimal treatment regimens of azathioprine, 6-mercaptopurine and thioguanine. We will briefly summarize dose recommendations, indications for thiopurine therapy and side effects which are relevant in clinical practice. We discuss some currently debated topics, including the combination of azathioprine and allopurinol, switching of thiopurine therapy in case of side effects, the use of azathioprine in pregnancy, the infection risk using thiopurines and the evidence when to stop thiopurines. Excellent reviews have been published on the thiopurine metabolic pathway which will not be discussed here in detail.

Background Tumor necrosis factor (TNF) is an important cytokine in the pathogenesis of inflammatory bowel disease (IBD). Anti-TNF antibodies have been successfully implemented in IBD therapy, however their efficacies differ among IBD patients. Here we investigate the influence of CD64 Fc receptor on the inhibitory activity of anti-TNFs in cells of intestinal wall. Methods Intestinal cell lines, monocytes/macrophages and peripheral blood mononuclear cells (PBMCs) were used as models. The efficacies of adalimumab, infliximab and certolizumab-pegol were assessed by RT-PCR for target genes. Protein levels and localizations were examined by Western blotting and immunofluorescence. Antibody fragments were obtained by proteolytic digestion, immunoprecipitation and protein chip analysis. Knock-down of specific gene expression was performed using siRNAs. Results Infliximab had limited efficacy towards soluble TNF in cell types expressing Fc gamma receptor CD64. Both adalimumab and infliximab had lower efficacies in PBMCs of IBD patients, which express elevated levels of CD64. Infliximab-TNF complexes were more potent in activating CD64 in THP-1 cells than adalimumab, which was accompanied by distinct phospho-tyrosine signals. Blocking Fc parts and isolation of Fab fragments of infliximab improved its efficacy. IFN-γ-induced expression of CD64 correlated with a loss of efficacy of infliximab, whereas reduction of CD64 expression by either siRNA or PMA treatment improved inhibitory activity of this drug. Colonic mRNA expression levels of CD64 and other Fc gamma receptors were significantly increased in the inflamed tissues of infliximab non-responders. Conclusions CD64 modulates the efficacy of infliximab both in vitro and ex vivo, whereas the presence of this receptor has no impact on the inhibitory activity of certolizumab-pegol, which lacks Fc fragment. These data could be helpful in both predicting and evaluating the outcome of anti-TNF therapy in IBD patients with elevated systemic and local levels of Fc receptors.

AIM: To determine free and conjugated serum bile acid (BA) levels in inflammatory bowel disease (IBD) subgroups with defined clinical manifestations. METHODS: Comprehensive serum BA profiling was performed in 358 IBD patients and 310 healthy controls by liquid chromatography coupled to electrospray ionization tandem mass spectrometry. RESULTS: Serum levels of hyodeoxycholic acid, the CYP3A4-mediated detoxification product of the secondary BA lithocholic acid (LCA), was increased significantly in Crohn’s disease (CD) and ulcerative colitis (UC), while most other serum BA species were decreased significantly. Total BA, total BA conjugate, and total BA glycoconjugate levels were decreased only in CD, whereas total unconjugated BA levels were decreased only in UC. In UC patients with hepatobiliary manifestations, the conjugated primary BAs glycocholic acid, taurocholic acid, and glycochenodeoxycholic acid were as significantly increased as the secondary BAs LCA, ursodeoxycholic acid, and tauroursodeoxycholic acid compared to UC patients without hepatobiliary manifestations. Finally, we found that in ileocecal resected CD patients, the unconjugated primary BAs, cholic acid and chenodeoxycholic acid, were increased significantly compared to controls and patients without surgical interventions. CONCLUSION: Serum BA profiling in IBD patients that indicates impaired intestinal barrier function and increased detoxification is suitable for advanced diagnostic characterization and differentiation of IBD subgroups with defined clinical manifestations.

Background and Aim: Contamination of endoscopy suites with bacteria during procedures is of concern particularly through droplets during handling of biopsy specimens. It has been advocated that suctioning while removing the biopsy forceps could help to reduce potentially hazardous bioaerosols. The aim of the present study was to evaluate the efficacy of air suctioning during removal of the biopsy forceps. Materials and Methods: Airborne bacteria were collected by an impactor air-sampler (MAS-100). Fifty liters of air were collected continuously for 30 seconds at a 30 cm distance from the colonoscope suction channel. Room air samples were taken in the endoscopy suite in the morning prior to the beginning of the endoscopy program, during colonoscopy with a sham biopsy in the descending colon with and without suctioning and at the end of the procedure day. Standard 90 mm Petri dishes containing a selective medium for gram-positive cocci (CNA blood agar) were used with the impaction sampler and colony forming units/m3 (cfu) were determined. Results: Measurements were performed at fifty consecutive colonoscopies. Prior to the beginning of the endoscopy program, the bioaerosol burden in the colonoscopy suite reached a mean of 4.2 cfu/m3. During colonoscopies performed without suctioning at biopsy the bioaerosol burden increased to 29.4 cfu/m3 whereas this burden increased only to 15.1 cfu/m3 when the suctioning was applied during removal of the biopsy forceps. The difference in bioaerosol burden between suctioning and no suctioning was highly significant (p < 0.0005). At the end of the procedure day the airborne bacteria count dropped to 15.6 cfu/m3. The analysis of the colonies on the CNA blood agar identified predominantly enterococci. Staphylococci spp. and other gram-positive bacteria were rarely isolated. Conclusion: The present study indicates that the bioaerosol burden during handling of biopsy specimens is not neglectable but can be reduced by the simple habit of applying suctioning during acquisition of biopsies. This practice might be an important infection-control measure during gastrointestinal endoscopies.

The fourth scientific workshop of the European Crohn's and Colitis Organization (ECCO) focused on the relevance of intestinal fibrosis in the disease course of inflammatory bowel disease (IBD). The objective was to better understand the pathophysiological mechanisms of intestinal fibrosis, to identify useful markers and imaging modalities of fibrosis in order to assess its presence and progression, and, finally, to point out possible approaches for the prevention and the treatment of fibrosis.The results of this workshop are presented in three separate manuscripts. This first section describes the most important mechanisms that contribute to the initiation and progression of intestinal fibrosis in IBD including the cellular and molecular mediators, the extracellular matrix molecules and matrix metalloproteinases/tissue inhibitors of metalloproteinases-system, the microbiota products, the role of fat, genetic and epigenetic factors, as well as the currently available experimental models. Furthermore, it identifies unanswered questions in the field of intestinal fibrosis and provides a framework for future research.

Background Genome-wide CRISPR-Cas9 dropout screens can identify genes whose knockout affects cell viability. Recent CRISPR screens detected thousands of essential genes required for cellular survival and key cellular processes; however discovering novel lineage-specific genetic dependencies from the many hits still remains a challenge. Results To assess whether CRISPR-Cas9 dropout screens can help identify cancer dependencies, we screened two human cancer cell lines carrying known and distinct oncogenic mutations using a genome-wide sgRNA library. We found that the gRNA targeting the driver mutation EGFR was one of the highest-ranking candidates in the EGFR-mutant HCC-827 lung adenocarcinoma cell line. Likewise, sgRNAs for NRAS and MAP2K1 (MEK1), a downstream kinase of mutant NRAS, were identified among the top hits in the NRAS-mutant neuroblastoma cell line CHP-212. Depletion of these genes targeted by the sgRNAs strongly correlated with the sensitivity to specific kinase inhibitors of the EGFR or RAS pathway in cell viability assays. In addition, we describe other dependencies such as TBK1 in HCC-827 cells and TRIB2 in CHP-212 cells which merit further investigation. Conclusions We show that genome-wide CRISPR dropout screens are suitable for the identification of oncogenic drivers and other essential genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3042-2) contains supplementary material, which is available to authorized users.

BackgroundIntestinal fibrosis and subsequent stricture formation represent frequent complications of Crohn's disease (CD). In many organs, fibrosis develops as a result of epithelial to mesenchymal transition (EMT). Recent studies suggested that EMT could be involved in intestinal fibrosis as a result of chronic inflammation. Here, we investigated whether EMT might be involved in stricture formation in CD patients. MethodsHuman colonic tissue specimens from fibrotic areas of 18 CD and 10 non‐IBD control patients were studied. Immunohistochemical staining of CD68 (marker for monocytes/macrophages), transforming growth factor‐β1 (TGFβ1), β‐catenin, SLUG, E‐.cadherin, α‐smooth muscle actin and fibroblast activation protein (FAP) were performed using standard techniques. ResultsIn fibrotic areas in the intestine of CD patients, a large number of CD68‐positive mononuclear cells was detectable suggesting an inflammatory character of the fibrosis. We found stronger expression of TGFβ1, the most powerful driving force for EMT, in and around the fibrotic lesions of CD patients than in non‐IBD control patients. In CD patients membrane staining of β‐catenin was generally weaker than in control patients and more cells featured nuclear staining indicating transcriptionally active β‐catenin, in fibrotic areas. In these regions we also detected nuclear localisation of the transcription factor, SLUG, which has also been implicated in EMT pathogenesis. Adjacent to the fibrotic tissue regions, we observed high levels of FAP, a marker of reactive fibroblasts. ConclusionsWe demonstrate the presence of EMT‐associated molecules in fibrotic lesions of CD patients. These findings support the hypothesis that EMT might play a role for the development of CD‐associated intestinal fibrosis.

BACKGROUND: The single nucleotide polymorphism (SNP) rs2542151 within the gene locus region encoding protein tyrosine phosphatase non receptor type 2 (PTPN2) has been associated with Crohn's disease (CD) ulcerative colitis (UC) type I diabetes and rheumatoid arthritis. We have previously shown that PTPN2 regulates mitogen activated protein kinase (MAPK) signaling and cytokine secretion in human THP 1 monocytes and intestinal epithelial cells (IEC). Here we studied whether intronic PTPN2 SNP rs1893217 regulates immune responses to the nucleotide oligomerization domain 2 (NOD2) ligand muramyl dipeptide (MDP). MATERIALS AND METHODS: Genomic DNA samples from 343 CD and 663 non IBD control patients (male and female) from a combined German Swiss and Polish cohort were genotyped for the presence of the PTPN2 SNPs rs2542151 and rs1893217. PTPN2 variant rs1893217 was introduced into T(84) IEC or THP 1 cells using a lentiviral vector. RESULTS: We identified a novel association between the genetic variant rs1893217 located in intron 7 of the PTPN2 gene and CD. Human THP 1 monocytes carrying this variant revealed increased MAPK activation as well as elevated mRNA expression of T bet transcription factor and secretion of interferon ? in response to the bacterial wall component MDP. In contrast secretion of interleukin 8 and tumor necrosis factor were reduced. In both T(84) IEC and THP 1 monocytes autophagosome formation was impaired. CONCLUSIONS: We identified a novel CD associated PTPN2 variant that modulates innate immune responses to bacterial antigens. These findings not only provide key insights into the effects of a functional mutation on a clinically relevant gene but also reveal how such a mutation could contribute to the onset of disease. (Inflamm Bowel Dis 2011;).