The composition of the gut microbiota is associated with various disease states, most notably inflammatory bowel disease, obesity and malnutrition. This underlines that analysis of intestinal microbiota is potentially an interesting target for clinical diagnostics. Currently, the most commonly used sample types are feces and mucosal biopsy specimens. Because sampling method, storage and processing of samples impact microbiota analysis, each sample type has its own limitations. An ideal sample type for use in routine diagnostics should be easy to obtain in a standardized fashion without perturbation of the microbiota. Rectal swabs may satisfy these criteria, but little is known about microbiota analysis on these sample types. In this study we investigated the characteristics and applicability of rectal swabs for gut microbiota profiling in a clinical routine setting in patients presenting with various gastro-intestinal disorders. We found that rectal swabs appeared to be a convenient means of sampling the human gut microbiota. Swabs can be performed on demand, whenever a patient presents; swab-derived microbiota profiles are reproducible, whether they are gathered at home by patients or by medical professionals in an outpatient setting and may be ideally suited for clinical diagnostics and large-scale studies.

The human intestinal microbiota is known to play an important role in human health and disease, and with the advent of novel molecular techniques, disease-specific variations in its composition have been found. However, analysis of the intestinal microbiota has not yet been applicable in large-scale clinical research or routine diagnostics because of the complex and expensive nature of the techniques needed. Here, we describe a new PCR-based profiling technique for high-throughput analysis of the human intestinal microbiota, which we have termed IS-pro. This technique combines bacterial species differentiation by the length of the 16S-23S rDNA interspace region with instant taxonomic classification by phylum-specific fluorescent labeling of PCR primers. We validated IS-pro in silico, in vitro, and in vivo, on human colonic biopsies and feces, and introduced a standardized protocol for data analysis. IS-pro is easy to implement in general clinical microbiological laboratories with access to capillary gel electrophoresis, and the high-throughput nature of the test makes analysis of large numbers of samples feasible. This combination renders IS-pro ideally suited for use in clinical research and routine diagnostics.

Mucosa-associated duodenal microbiome composition and diversity did not differ between children with untreated CD and control children. Duodenal mucosa-associated bacteria do not seem to play an important role in the pathogenesis of CD.

Background and study aims  Since the introduction of open-access esophago-gastroduodenoscopy (OAE) there is an increase in the total number of performed OAEs whilst the frequency of clinical relevant findings has decreased. The aim of this study was to assess the appropriate use and the diagnostic yield of OAE in the Netherlands and to determine which patient variables are able to predict a malignant finding. Patients and methods  A retrospective chart review of all referrals for diagnostic OAE between October 2012 and October 2016 at the Northwest Clinics was performed. The indications were recorded from the referral letter and were classified as “appropriate” or “inappropriate” according to the NHG guideline. Logistic regression was used to detect significant predictive variables for a malignancy. Results  A total of 2006 patients were included, of whom 59.6 % had an ‘appropriate’ referral indication. The diagnostic yield of finding a clinical relevant finding was significantly higher for OAEs with an “appropriate” referral indication. Independent risk factors for malignancy were alarm symptoms, age and male gender with a combined AUC of 0.868. Conclusions  Only 3.8 % of the malignancies would be missed by strict adherence to the guideline. This indicates that the open-access system in the Netherlands works well. Further improvement of the system can be achieved by only accepting appropriate indications for OAE and by treating patients under the age of 40 without OAE. We showed that a risk-prediction model based on the variables age, alarm symptoms and male gender is a good predictor of malignant finding.

dMucosal biopsy samples from individuals not suspected of having Whipple's disease were tested for the presence of Tropheryma whipplei. A sensitive and specific real-time PCR assay targeting a sequence present seven times in the T. whipplei genome was used. T. whipplei DNA was detected in 2.0 and 3.8% of the patients undergoing gastroduodenoscopy and colonoscopy, respectively, who were tested.