A metagenomic prospective cohort study on gut microbiome composition and clinical infection in small bowel transplantation.

Two-thirds of small-bowel transplantation (SBT) recipients develop bacteremia, with the majority of infections occurring within 3 months post-transplant. Sepsis-related mortality occurs in 31% of patients and is commonly caused by bacteria of gut origin, which are thought to translocate across the implanted organ. Serial post-transplant surveillance endoscopies provide an opportunity to study whether the composition of the ileal and colonic microbiota can predict the emergence as well as the pathogen of subsequent clinical infections in the SBT patient population. Five participants serially underwent aspiration of ileal and colonic bowel effluents at transplantation and during follow-up endoscopy either until death or for up to 3 months post-SBT. We performed whole-metagenome sequencing (WMS) of 40 bowel effluent samples and compared the results with clinical infection episodes. Microbiome composition was concordant between participants and timepoint-matched ileal and colonic samples. Four out of five (4/5) participants had clinically significant infections thought to be of gut origin. Bacterial translocation from the gut was observed in 3/5 patients with bacterial infectious etiologies. In all three cases, the pathogens had demonstrably colonized the gut between 1-10 days prior to invasive clinical infection. Recipients with better outcomes received donor grafts with higher alpha diversity. There was an increase in the number of antimicrobial resistance genes associated with longer hospital stay for all participants. This metagenomic study provides preliminary evidence to support the pathogen translocation hypothesis of gut-origin sepsis in the SBT cohort. Ileal and colonic microbiome compositions were concordant; therefore, fecal metagenomic analysis could be a useful surveillance tool for impeding infection with specific gut-residing pathogens.

Spontaneous haemopericardium due to vitamin K deficiency in an adult patient with cardiofaciocutaneous syndrome.

We present the case of an adult man with cardiofaciocutaneous syndrome, who initially presented to the emergency department with severe abdominal pain and distension, but was diagnosed with cardiac tamponade on CT after distended neck veins and tachycardia were identified on examination. He had emergency pericardial drainage to relieve the haemopericardium and was treated with colchicine. He was further found to be deficient in factors II, VII and X despite not being on warfarin, and was therefore supplemented with vitamin K. This confirms a diagnosis of vitamin K deficiency, likely multifactorial from malabsorption due to chronic intestinal pseudo-obstruction, small bowel obstruction and possibly exacerbated by subsequent ciprofloxacin use for small intestine bacterial overgrowth. This is the first report of spontaneous haemopericardium secondary to vitamin K deficiency in an adult patient not on anticoagulation, and is an important learning point due to the life-threatening progression of the haemopericardium and cardiac tamponade.

Transplant-associated thrombotic microangiopathy and immune haematological complications following intestine-containing organ transplantation: experience from over 100 consecutive cases.

Descriptions of passenger lymphocyte syndrome (PLS), immune cytopenias and transplant-associated thrombotic microangiopathy (TA-TMA) after intestine-containing transplants remain scarce. We describe our centre's experience of these complications from 2007 to 2019. Ninety-six patients received 103 transplants. PLS occurred in 9 (9%) patients (median 12 days post-transplant); all due to ABO antibodies. There were 31 minor ABO mismatch transplants. No patient required change in immunosuppression. Immune cytopenias (excluding PLS) occurred in six patients at an incidence of 1·7/100 patient years; three immune haemolysis, one immune thrombocytopenia, one acquired Glanzmann's and one immune neutropenia; 50% occurred with other cytopenias. All cases eventually responded to treatment, with a median of four treatments (range 1-8) and 5/6 were treated with rituximab. One patient with immune haemolysis required bortezomib. Complications were common in patients with immune cytopenias; 4/6 with infection needing intravenous antibiotics and 3/6 with venous thromboembolism. In 3/6 cases, a secondary cause for the immune cytopenia was evident. Switching from tacrolimus to ciclosporin was not necessary. There were five cases of transplant-associated thrombotic microangiopathy (TA-TMA; 1·5/100 patient years) requiring calcineurin inhibitor withdrawal; two cases associated with acute rejection. Two cases were managed with plasma exchange, one with plasma infusions and one with eculizumab. Further research in this patient group is required.

The Long and Short of IT: intestinal failure-associated liver disease (IFALD) in adults-recommendations for early diagnosis and intestinal transplantation.

Intestinal failure-associated liver disease (IFALD) often presents in adults unexpectedly with advanced disease. Non-invasive tests can be falsely reassuring. Patients with 'ultrashort' intestine (<20 cm) ending in a stoma are at particular risk of developing IFALD, which may occur rapidly. Recent experience and studies suggest that IFALD can be reversed by isolated intestine transplant occurring before the development of high grade fibrosis or cirrhosis. Post-transplant survival is superior for isolated intestinal grafts compared with liver containing intestinal grafts; waiting time and waiting list mortality is higher for a combined graft, and donor liver supply is limited. Therefore, the aim of clinicians treating patients with intestinal failure should be to identify IFALD early and refer to an intestinal transplant centre while isolated intestine transplantation can be contemplated and before the liver disease has progressed to a stage requiring consideration of combined liver and intestinal transplantation.

Fatal breakthrough mucormycosis in a multivisceral transplant patient receiving micafungin: Case report and literature review.

Introduction: Antifungal agents are routinely used in the post-transplant setting for both prophylaxis and treatment of presumed and proven fungal infections. Micafungin is an echinocandin-class antifungal with broad antifungal cover and favorable side effect profile but, notably, it has no activity against molds of the order Mucorales. Presentation of case: A 47-year-old woman underwent multivisceral transplantation for intestinal failure-associated liver disease. She had a prolonged post-operative recovery complicated by invasive candidiasis and developed an intolerance to liposomal amphotericin B. In view of her immunosuppression, she was commenced on micafungin as prophylaxis to prevent invasive fungal infection. However, she developed acute graft versus host disease with bone marrow failure complicated by disseminated mucormycosis which was only diagnosed post mortem. Discussion: Non-Aspergillus breakthrough mold infections with micafungin therapy are rare with only eight other cases having been described in the literature. Breakthrough infections have occurred within one week of starting micafungin. Diagnosis is problematic and requires a high degree of clinical suspicion and microscopic/histological examination of an involved site. The management of these aggressive infections involves extensive debridement and appropriate antifungal cover. Conclusion: A high level of suspicion of invasive fungal infection is required at all times in immunosuppressed patients, even those receiving antifungal prophylaxis. Early biopsy is required. Even with early recognition and aggressive treatment of these infections, prognosis is poor.

Nasal unsedated seated percutaneous endoscopic gastrostomy (nuPEG): a safe and effective technique for percutaneous endoscopic gastrostomy placement in high-risk candidates.

OBJECTIVE: Percutaneous endoscopic gastrostomy (PEG) tube placement is associated with a high risk of cardiorespiratory complications in patients with significant respiratory compromise. This study reports a case series of high-risk patients undergoing PEG placement using a modified technique-nasal unsedated seated PEG (nuPEG) placement. DESIGN: Retrospective review of 67 patients at high risk of complications undergoing PEG placement between September 2012 and December 2016. SETTING: UK specialist tertiary centre for clinical nutrition support. INTERVENTIONS: Patients underwent 'push' PEG placement using nasal endoscopy without sedation in a seated position. MAIN OUTCOME MEASURES: Procedural success and tolerability, short term (within 24 hours), medium term (24 hours to 30 days) complications and survival were recorded. RESULTS: 67 patients underwent 68 nuPEG placements. The majority had motor neuron disease (46/67). One patient developed a lower respiratory tract infection the following day. Two patients experienced accidental displacement of their PEG within 2 weeks. One patient died within 30 days of nuPEG insertion due to reasons unrelated to the procedure. Endoscopic comfort scores of 1 or 2 (98.0%) indicated good tolerance. A failure rate of 10.5% was attributed to intrathoracic displacement of the stomach, almost certainly due to the advanced stage of the neurological disease and associated diaphragmatic weakness. CONCLUSIONS: Our experience with the nuPEG technique suggests that it is safe and well tolerated in high-risk patients. As a result, it has now entirely supplanted radiologically inserted gastrostomy insertion in our institution and we recommend it as the method of choice for gastrostomy tube insertion in such patients.

Splenic rupture due to metastatic disease: a rare complication.

We report a case of splenic rupture in an 83-year-old woman presenting with symptoms concerning for upper gastrointestinal malignancy. CT imaging revealed marked gastric thickening and a 33×33 mm splenic metastasis, with subsequent gastroscopy demonstrating a large lesion at the gastro-oesophageal junction. While awaiting further investigation, the patient developed acute onset left upper quadrant pain, peritonism and hypovolaemic shock. Urgent CT imaging demonstrated a ruptured spleen with extensive haemoperitoneum, necessitating emergency splenectomy.

Using saccades to diagnose covert hepatic encephalopathy.

Covert Hepatic Encephalopathy (CHE), previously known as Minimal Hepatic Encephalopathy, is a subtle cognitive defect found in 30-70 % of cirrhosis patients. It has been linked to poor quality of life, impaired fitness to drive, and increased mortality: treatment is possible. Despite its clinical significance, diagnosis relies on psychometric tests that have proved unsuitable for use in a clinical setting. We investigated whether measurement of saccadic latency distributions might be a viable alternative. We collected data on 35 cirrhosis patients at Addenbrooke's Hospital, Cambridge, with no evidence of clinically overt encephalopathy, and 36 age-matched healthy controls. Performance on standard psychometric tests was evaluated to determine those patients with CHE as defined by the World Congress of Gastroenterology. We then compared visually-evoked saccades between those with CHE and those without, as well as reviewing blood test results and correlating saccadic latencies with biochemical parameters and prognostic scores. Cirrhosis patients have significantly longer median saccadic latencies than healthy controls. Those with CHE had significantly prolonged saccadic latencies when compared with those without CHE. Analysis of a cirrhosis patient's saccades can diagnose CHE with a sensitivity of 75 % and a specificity of 75 %. We concluded that analysis of a cirrhosis patient's saccadic latency distributions is a fast and objective measure that can be used as a diagnostic tool for CHE. This improved early diagnosis could direct avoidance of high-risk activities such as driving, and better inform treatment strategies.

Mucosal genome-wide methylation changes in inflammatory bowel disease.

BACKGROUND: DNA methylation constitutes a key epigenetic mechanism by which cells regulate gene transcription. Among its roles are the dynamic regulation of gene expression, for example, as part of an evolving immune response, and cell differentiation in specialized tissues. Here our aim was to study the impact of differences in methylation patterns in the intestine with regard to inflammatory bowel disease (IBD) susceptibility and activity. METHODS: Having extracted DNA from rectal biopsies, we conducted genome-wide methylation profiling using the HumanMethylation27 BeadChip microarray to identify genes showing evidence of differential methylation between cases of ulcerative colitis and Crohn's disease and healthy controls. Selected methylation signals were validated in an independent replication panel by pyrosequencing. Correlation with gene expression was sought by quantitative real-time polymerase chain reaction (RT-PCR). RESULTS: Multiple genes showed significant evidence of differential methylation, several appearing in both ulcerative colitis and Crohn's disease comparisons including THRAP2, FANCC, GBGT1, DOK2, TNFSF4, TNFSF12, and FUT7. Many more than expected by chance overlapped with genes previously implicated as playing a role in IBD susceptibility in genome-wide association scans, including CARD9, ICAM3, and IL8RB (P < 0.001). Correlation between methylation and gene expression was identified for selected transcripts. CONCLUSIONS: Consistent differences in DNA methylation between IBD cases and controls at regulatory sites within these genes suggest that their altered transcription contributes to IBD pathogenesis.

Genetic association between NLRP3 variants and Crohn's disease does not replicate in a large UK panel.

BACKGROUND: NLRP3 (formerly known as CIAS1 or NALP3) encodes a key component of the inflammasome and is a strong candidate gene for Crohn's disease (CD) susceptibility. A recent study reported significant and internally replicated association between CD and six single nucleotide polymorphisms (SNPs) in a regulatory region 5.3 kb downstream of NLRP3. Independent replication is required to verify these findings. METHODS: In all, 1298 CD cases and 1244 healthy controls were genotyped for the six SNPs using Taqman. Single locus, haplotype, and subphenotype analyses were conducted using logistic regression-based methods and PLINK, respectively. RESULTS: No significant associations were found, either on single locus, subphenotype, or haplotype analysis. CONCLUSIONS: Given our high (>90%) power to replicate findings from the index study, our data suggest either a much smaller effect size for the association between NLRP3 and CD susceptibility than previously reported or the possibility of a false-positive result in the index study. Further studies in other populations are required to determine what role, if any, NLRP3 variants play in CD susceptibility.

Regulation of mammalian autophagy in physiology and pathophysiology.

(Macro)autophagy is a bulk degradation process that mediates the clearance of long-lived proteins and organelles. Autophagy is initiated by double-membraned structures, which engulf portions of cytoplasm. The resulting autophagosomes ultimately fuse with lysosomes, where their contents are degraded. Although the term autophagy was first used in 1963, the field has witnessed dramatic growth in the last 5 years, partly as a consequence of the discovery of key components of its cellular machinery. In this review we focus on mammalian autophagy, and we give an overview of the understanding of its machinery and the signaling cascades that regulate it. As recent studies have also shown that autophagy is critical in a range of normal human physiological processes, and defective autophagy is associated with diverse diseases, including neurodegeneration, lysosomal storage diseases, cancers, and Crohn's disease, we discuss the roles of autophagy in health and disease, while trying to critically evaluate if the coincidence between autophagy and these conditions is causal or an epiphenomenon. Finally, we consider the possibility of autophagy upregulation as a therapeutic approach for various conditions.

Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.

Ulcerative colitis is a common form of inflammatory bowel disease with a complex etiology. As part of the Wellcome Trust Case Control Consortium 2, we performed a genome-wide association scan for ulcerative colitis in 2,361 cases and 5,417 controls. Loci showing evidence of association at P < 1 x 10(-5) were followed up by genotyping in an independent set of 2,321 cases and 4,818 controls. We find genome-wide significant evidence of association at three new loci, each containing at least one biologically relevant candidate gene, on chromosomes 20q13 (HNF4A; P = 3.2 x 10(-17)), 16q22 (CDH1 and CDH3; P = 2.8 x 10(-8)) and 7q31 (LAMB1; P = 3.0 x 10(-8)). Of note, CDH1 has recently been associated with susceptibility to colorectal cancer, an established complication of longstanding ulcerative colitis. The new associations suggest that changes in the integrity of the intestinal epithelial barrier may contribute to the pathogenesis of ulcerative colitis.

Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship.

BACKGROUND & AIMS: Identifying shared and disease-specific susceptibility loci for Crohn's disease (CD) and ulcerative colitis (UC) would help define the biologic relationship between the inflammatory bowel diseases. More than 30 CD susceptibility loci have been identified. These represent important candidate susceptibility loci for UC. Loci discovered by the index genome scans in CD have previously been tested for association with UC, but those identified in the recent meta-analysis await such investigation. Furthermore, the recently identified UC locus at ECM1 requires formal testing for association with CD. METHODS: We analyzed 45 single nucleotide polymorphisms, tagging 29 of the loci recently associated with CD in 2527 UC cases and 4070 population controls. We also genotyped the UC-associated ECM1 variant rs11205387 in 1560 CD patients and 3028 controls. RESULTS: Nine regions showed association with UC at a threshold corrected for the 29 loci tested (P < .0017). The strongest association (P = 4.13 x 10(-8); odds ratio = 1.27) was identified with a 170-kilobase region on chromosome 1q32 that contains 3 genes. We also found association with JAK2 and replicated a recently reported association with STAT3, further implicating the role of this signaling pathway in inflammatory bowel disease. Additional novel UC susceptibility genes were LYRM4 and CDKAL1. Twenty of the loci were not associated with UC, and several appear to be specific to CD. ECM1 variation was not associated with CD. CONCLUSIONS: Collectively, these data help define the genetic relationship between CD and UC and characterize common, as well as disease-specific mechanisms of pathogenesis.

Genetics of inflammatory bowel disease: clues to pathogenesis.

INTRODUCTION OR BACKGROUND: It has long been recognized from epidemiological data that inflammatory bowel diseases (IBD), Crohn's disease (CD) and ulcerative colitis (UC), have a strong genetic predisposition, interacting with unknown environmental drivers to render susceptible individuals at risk for relapsing intestinal inflammation. Substantial progress has been made in the last 2 years in characterizing the susceptibility genes involved. SOURCES OF DATA: The recent acceleration in understanding has resulted from the use of new technologies of genome-wide association scanning in large panels of cases and controls. AREAS OF AGREEMENT: Genome scans have robustly identified 11 susceptibility genes and loci and highlighted a number of new, previously unsuspected pathways as playing an important role in IBD pathogenesis-including the IL23 pathway in IBD overall and specific aspects of innate immunity (particularly NOD2 and the autophagy genes ATG16L1 and IRGM) in CD. AREAS OF CONTROVERSY: The next challenge is to identify specific causal variants at each of the confirmed susceptibility loci and then characterize their biological impact on gene expression and function of the protein product. GROWING POINTS: To date, most attention has focused on CD. A recent meta-analysis has increased the number of confirmed susceptibility loci to 32-more than for any other common disease to date. Attention is now turning to the use of the same techniques in UC to identify new, disease-specific genes and understand areas of overlap. AREAS TIMELY FOR DEVELOPING RESEARCH: This review explores genetic clues to the pathogenesis of IBD derived from the growing list of confirmed IBD susceptibility genes, and briefly elaborates some of the important themes and overlaps that are becoming evident both within IBD and also with other complex diseases.

Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease.

We report results of a nonsynonymous SNP scan for ulcerative colitis and identify a previously unknown susceptibility locus at ECM1. We also show that several risk loci are common to ulcerative colitis and Crohn's disease (IL23R, IL12B, HLA, NKX2-3 and MST1), whereas autophagy genes ATG16L1 and IRGM, along with NOD2 (also known as CARD15), are specific for Crohn's disease. These data provide the first detailed illustration of the genetic relationship between these common inflammatory bowel diseases.

Contribution of TNFSF15 gene variants to Crohn's disease susceptibility confirmed in UK population.

BACKGROUND: Identification of Crohn's disease (CD)-associated genetic variants is key to understanding pathogenic pathways underlying disease susceptibility. Recent reports of an association between TNFSF15 variants and CD have been modestly replicated in European populations, suggesting heterogeneity at this locus with stronger CD association in Japanese than European populations. METHODS: We investigated the association between variants in TNFSF15 and CD in 756 CD patients and 636 controls. Disease subphenotype associations were also investigated. RESULTS: TNFSF15 single nucleotide polymorphism (SNP) variants were associated with CD in our panel with peak odds ratio (OR) 1.2 (95% confidence interval [CI] 1.01-1.41) P = 0.033. The presence of a risk haplotype was replicated for the first time in a European population (frequency 67% in cases and 61% in controls) OR = 1.44 (95% CI 1.23-1.68) P = 0.00012. This result mirrors the UK panel in the index study (Yamazaki et al [2005] Hum Mol Genet 14:3499-3506) but is less significant than that reported in Japanese populations. There was no evidence of association with any individual CD subphenotype. CONCLUSIONS: Variants in TNFSF15 contribute to overall CD susceptibility in European populations, although to a lesser extent than that seen in the Japanese. Further studies to define the precise disease-causing variants as well as targeted functional studies are now required in human CD as TNFSF15 is a potential target for biological therapies.

Genome-wide association scanning highlights two autophagy genes, ATG16L1 and IRGM, as being significantly associated with Crohn's disease.

The era of genome-wide association (GWA) scanning has shed new light on the genetic basis of common disease and nowhere is this better illustrated than Crohn's disease (CD). CD is a chronic debilitating inflammatory bowel disease characterized by stricturing and fistula formation. Mainstays of current therapy are immune suppression and surgery. The pathogenesis of CD is poorly understood, but it has long been recognized that both genetic susceptibility and bacterial antigens play important roles. A variety of intracellular bacteria have been postulated to trigger CD, but the evidence for any one organism is equivocal. The current consensus is that commensal gut bacteria provide the drive for CD-related inflammation. Three GWA scans undertaken in the last 6 months have identified 10 new loci demonstrating highly significant and replicated association with CD. Two of the strongest hits implicate genes IRGM and ATG16L1, which encode proteins thought to be critical to the autophagy pathway. The critical next step is functional characterization of the CD-associated genetic variants in IRGM and ATG16L. It seems highly plausible that variation in these genes holds the key to understanding exactly which bacteria drive the intestinal inflammation of CD and the mechanism by which they do this.

Common pathways in Crohn's disease and other inflammatory diseases revealed by genomics.

Genetics may not provide all the answers but it will, in highlighting the pathways relevant to the pathogenesis of Crohn's disease and other inflammatory conditions, at least indicate which questions need answering.