Benchmarking microbial DNA enrichment protocols from human intestinal biopsies.

Shotgun metagenomic sequencing is a powerful tool for studying bacterial communities in their natural habitats or sites of infection, without the need for cultivation. However, low microbial signals in metagenomic sequencing can be overwhelmed by host DNA contamination, resulting in decreased sensitivity for microbial read detection. Several commercial kits and other methods have been developed to enrich bacterial sequences; however, these assays have not been tested extensively for human intestinal tissues yet. Therefore, the objective of this study was to assess the effectiveness of various wet-lab and software-based approaches for depleting host DNA from microbiome samples. Four different microbiome DNA enrichment methods, namely the NEBNext Microbiome DNA Enrichment kit, Molzym Ultra-Deep Microbiome Prep, QIAamp DNA Microbiome kit, and Zymo HostZERO microbial DNA kit, were evaluated, along with a software-controlled adaptive sampling (AS) approach by Oxford Nanopore Technologies (ONT) providing microbial signal enrichment by aborting unwanted host DNA sequencing. The NEBNext and QIAamp kits proved to be effective in shotgun metagenomic sequencing studies, as they efficiently reduced host DNA contamination, resulting in 24% and 28% bacterial DNA sequences, respectively, compared to <1% in the AllPrep controls. Additional optimization steps using further detergents and bead-beating steps improved the efficacy of less efficient protocols but not of the QIAamp kit. In contrast, ONT AS increased the overall number of bacterial reads resulting in a better bacterial metagenomic assembly with more bacterial contigs with greater completeness compared to non-AS approaches. Additionally, AS also allowed for the recovery of antimicrobial resistance markers and the identification of plasmids, demonstrating the potential utility of AS for targeted sequencing of microbial signals in complex samples with high amounts of host DNA. However, ONT AS resulted in relevant shifts in the observed bacterial abundance, including 2 to 5 times more Escherichia coli reads. Furthermore, a modest enrichment of Bacteroides fragilis and Bacteroides thetaiotaomicron was also observed with AS. Overall, this study provides insight into the efficacy and limitations of various methods for reducing host DNA contamination in human intestinal samples to improve the utility of metagenomic sequencing

The effect of non-medical factors on variations in the performance of colonoscopy among different health care settings

Background: Previous studies in the literature have shown significant variations in colonoscopy performance, even when medical factors are taken into account. This study aimed to examine the role of non-medical factors (i.e. embodied in health care system design) as possible contributors to variations in colonoscopy performance. Methods: We used patient data from a multicenter observational study conducted between 2000 and 2002 in 21 centers across 11 western countries. Variability was captured through two performance outcomes (diagnostic yield and colonoscopy withdrawal time), jointly studied as dependent variables using a multilevel two-equation system. Results: Results showed that open-access systems and high-volume colonoscopy centers were independently associated with a higher likelihood of detecting significant lesions and higher withdrawal durations. Fee for service (FFS) payment was associated with shorter withdrawal durations, and had an indirect negative impact on the diagnostic yield. Teaching centers exhibited lower detection rates and higher withdrawal times. Conclusions: Our results suggest that gate-keeping colonoscopy is likely to miss patients with significant lesions and that developing specialized colonoscopy units is important to improve performance. Results also suggest that FFS may result in a lower quality of care in colonoscopy practice and highlight that longer withdrawal times do not necessarily mean higher quality in teaching-centers.Medical Practice Variation (MPV), performance, non-medical factors, panel two-equation linear-probit model, colonoscopy

Vacuum-Sponge Therapy Placed through a Percutaneous Gastrostomy to Treat Spontaneous Duodenal Perforation.

Duodenal perforation is rare and associated with a high mortality. Therapeutic strategies to address duodenal perforation include conservative, surgical, and endoscopic measures. Surgery remains the gold standard. However, endoscopic management is gaining ground mostly with the use of over-the-scope clips and vacuum-sponge therapy. A 67-year-old male patient was admitted to the emergency room for persistent epigastric pain, melena, and signs of sepsis. The physical assessment revealed reduced bowel sounds, involuntary guarding, and rebound tenderness in the upper abdominal quadrant. A contrast-enhanced computed tomography (CT) scan confirmed the suspicion of ulcer perforation. The initial laparoscopic surgical approach required conversion to laparotomy with overstitching of the perforation. In the postoperative course, the patient developed signs of increased inflammation and dyspnea. A CT scan and an endoscopy revealed a postoperative leakage and pneumonia. We placed an endoscopic duodenal intraluminal vacuum-sponge therapy with endoscopic negative pressure for 21 days. The leakage healed and the patient was discharged. Most experience in endoscopic vacuum-sponge therapy for gastrointestinal perforations has been gained in the area of esophageal and rectal transmural defects, whereas only few reports have described its use in duodenal perforations. In our case, the need for further surgical management could be avoided in a patient with multiple comorbidities and a reduced clinical status. Moreover, the pull-through technique via PEG for sponge placement reduces the intraluminal distance of the Eso-Sponge tube by shortcutting the length of the esophagus, thus decreasing the risk of dislocation and increasing the chance of successful treatment

Positioning biologics in the treatment of IBD: A practical guide - Which mechanism of action for whom?

The number of available biological therapies have doubled over the last 10 years and the arrival of novel molecules (interleukin 23p19 inhibitors) is ongoing alongside the development of small molecules. As a result of this vast landscape of treatment, positioning advanced therapies (according to clinical situation, efficacy and safety) is of paramount importance to providing personalized, appropriate IBD treatment. In this publication the recent available literature is summarized for practical integration into clinical practice including comparative efficacy data, patient and disease demographics. We refer to recent publications and expert opinion in order to facilitate the decision making process of positioning biologicals IBD treatment

Swiss expert opinion: current approaches in faecal microbiota transplantation in daily practice

INTRODUCTION Faecal microbiota transplantation (FMT) is an established therapy for recurrent C. difficile infection, and recent studies have reported encouraging results of FMT in patients with ulcerative colitis. Few international consensus guidelines exist for this therapy, and thus FMT policies and practices differ among European countries. As of 2019, stool transplants are considered a non-standardised medicinal product in Switzerland, and a standardised production process requires authorisation by the Swiss Agency for Therapeutic Products. This authorisation leads to prolonged administrative procedures and increasing costs, which reduces treatment accessibility. In particular, patients with ulcerative colitis in Switzerland can only benefit from FMT off-label, even though it is a valid therapeutic option. Therefore, this study summarised the available data on FMT and established a framework for the standardised use of FMT. METHODS A panel of Swiss gastroenterologists with a special interest in inflammatory bowel disease was established to identify the current key issues of FMT. After a comprehensive review of the literature, statements were formulated about FMT indications, donor screening, stool transplant preparation and administration, and safety aspects. The panel then voted on the statements following the Delphi process; the statements were reformulated and revoted until a consensus was reached. The manuscript was then reviewed by an infectiologist (the head of Lausanne's FMT centre). RESULTS The established statements are summarised in the supplementary tables in the appendix to this paper. The working group hopes these will help standardise FMT practice in Switzerland and contribute to making faecal microbiota transplantation a safe and accessible treatment for patients with recurrent C. difficile infections and selected patients with ulcerative colitis, as well as other indications in the future

Bone health in patients with inflammatory bowel disease.

Patients with inflammatory bowel disease (IBD) are prone to reduced bone mineral density and elevated overall fracture risk. Osteopenia affects up to 40% of patients with IBD (high regional variability). Besides disease activity, IBD specialists must consider possible side effects of medication and the presence of associated diseases and extraintestinal manifestations. Osteopenia and osteoporosis remain frequent problems in patients with IBD and are often underestimated because of widely differing screening and treatment practices. Malnutrition, chronic intestinal inflammation and corticosteroid intake are the major pathophysiological factors contributing to osteoporosis. Patients with IBD are screened for osteoporosis using dual-energy X-ray absorptiometry (DXA), which is recommended for all patients with a prolonged disease course of more than three months, with repeated corticosteroid administration, aged >40 years with a high FRAX risk score or aged <40 years with multiple risk factors. From a therapeutic perspective, besides good disease control, vitamin D supplementation and glucocorticoid sparing, several specific osteological options are available: bisphosphonates, receptor activator of nuclear factor kappa-B ligand (RANKL) inhibitors (denosumab), parathyroid hormone (PTH) analogues and selective estrogen receptor modulators. This review provides an overview of the pathophysiology, diagnosis, prevention and treatment of IBD-associated bone loss