Michelle J. Alfa

Background and Study Aims Flexible endoscope-related infection outbreaks with respect to the biofilm in endoscope channels continue to be reported. This article reviews how endoscope fixed-biofilm accumulation (EFBA) develops in flexible endoscope channels over repeated clinical use. The aim of this review is to highlight how EFBA differs from dry surface biofilm (DSB) and hydrated biofilm (HB). Patients/Materials and Methods The process of (EFBA) formation in patient-used endoscope channels is compared to that of DSB and HB. The inadequate (or lack) of cleaning in narrow endoscope channels and the impact of high level disinfection (HLD) fixing of the EBFA within the endoscope channels result in a very different matrix compared to DSB or HB. The impact of fixed EFBA on microorganism survival within the matrix provides a more stringent and realistic challenge compared to DSB or HB. The choice of an appropriate multispecies biofilm model is also crucial to ensuring that it closely mirrors the clinical aspects related to EFBA. Results This comprehensive review confirms that EFBA is a driver of persistent endoscope channel contamination and exogenous transfer of pathogens to patients that can lead to infection. The literature review demonstrates that mono-microbic HB is the most common biofilm model used over the past 20 years, whereas models that integrate rounds of fixation such as the endoscope cyclic buildup biofilm (ECBB) and endoscope buildup biofilm (EBBF) better reflect the clinical aspects of EFBA in patient-used endoscope channels. Conclusions The published data support the need for the use of an appropriate fixed-biofilm model when validating cleaning and disinfection processes for flexible endoscope channels, thereby ensuring an optimal margin of safety during clinical use.

Reprocessing of flexible endoscopes is a multi-stage system with many sequential stages. Errors in any one of the stages can result in microbial contamination that persists in patient ready endoscopes despite full reprocessing. One stage that is especially prone to errors is the manual cleaning of channels and exterior surfaces of flexible endoscopes. This editorial discusses the current factors in manual cleaning that lead to errors in cleaning adequacy. It also reviews novel technologies that provide improvements in cleaning of flexible endoscope channels.

The effects of resistant starch at high doses have been well-characterized, but the potential prebiotic effects of resistant starch at doses comparable to oligosaccharide prebiotics have not been evaluated. A three-arm randomized, double-blind, placebo-controlled clinical trial was conducted to evaluate the effect of 3.5 g and 7 g daily doses of Solnul^™ resistant potato starch (RPS) on beneficial populations of gut bacteria and stool consistency after a 4-week period. The relative abundance of Bifidobacterium and Akkermansia was determined by employing 16Sv4 sequencing of stool samples. To assess the effect of RPS on laxation and bowel movements, stools were recorded and scored using the Bristol Stool Form Scale. Participants consuming 3.5 g/day of RPS experienced significantly greater changes in Bifidobacterium and Akkermansia compared to the placebo after 4 weeks. The number of diarrhea- and constipation-associated bowel movements were both significantly lower in the 3.5 g RPS arm compared to the placebo group. Participants consuming 7 g of RPS responded similarly to those in the 3.5 g arm. Our analyses demonstrate that Solnul^™ RPS has a prebiotic effect when consumed for 4 weeks at the 3.5 g per day dose, stimulating increases in beneficial health-associated bacteria and reducing diarrhea- and constipation-associated bowel movements when compared to the placebo group.

Objective: Assess the accumulation of protein and biofilm on the inner surfaces of new flexible gastroscope (FG) channels after 30 and 60 days of patient use and full reprocessing.Design: Clinical use study of biofilm accumulation in FG channels.Setting: Endoscopy service of a public hospital.Methods: First, we tested an FG in clinical use before the implementation of a revised reprocessing protocol (phase 1 baseline; n = 1). After replacement of the channels by new ones and the implementation of the protocol, 3 FGs were tested after 30 days of clinical use (phase 2; n = 3) and 3 FGs were tested after 60 days of clinical use (phase 3; n = 3), and the same FGs were tested in phase 2 and 3. Their biopsy, air, water, and air/water junction channels were removed and subjected to protein testing (n = 21), bacteriological culture (n = 21), and scanning electron microscopy (SEM) (n = 28). Air–water junction channels fragments were subjected to SEM only.Results: For the FGs, the average number of uses and reprocessing cycles was 60 times. Extensive biofilm was detected in air, water, and air–water junction channels (n = 18 of 28). All channels (28 of 28) showed residual matter, and structural damage was identified in most of them (20 of 28). Residual protein was detected in the air and water channels of all FG evaluated (phases 1–3), except for 1 air channel from phase 2. Bacteria were recovered from 8 of 21 channels, most air or water channels.Conclusions: The short time before damage and biofilm accumulation in the channels was evident and suggests that improving the endoscope design is necessary. Better reprocessing methods and channel maintenance are needed.

Recently, infection transmission risk associated with contaminated, patient-ready flexible endoscopes has attracted attention. Outbreaks of multidrug-resistant organisms resulting in infection and/or colonization have been particularly concerning. Recent CDC and FDA recommendations focus on reducing “exogenous” infection transmission and specifically recommend that endoscopy sites have quality systems in place for endoscope reprocessing. Another key recommendation is the culture of patient-ready endoscopes to detect contamination with organisms of concern. Remaining gaps in the guidelines include ensuring that optimal endoscope-channel sample methods are used and ensuring effective root-cause analysis and remediation when contamination is detected. In this review, we summarize the critical aspects of endoscope sample collection and present a practical approach to root-cause analysis and remedial action plans.

Background and study aims Prevention of infection transmission from contaminated endoscopes would benefit from a rapid test that could detect low levels of viable bacteria after high level disinfection. The aim of this study was to evaluate the rapid NOW! (RN) test’s ability to detect endoscope contamination. Materials and methods The RN test kit and the accompanying fluorometer were evaluated. The manufacturer states that a fluorometer signal > 300 units is indicative of viable Gram-negative bacteria. Suspension testing of varying concentrations of Escherichia coli, Pseudomonas aeruginosa and Enterococcus faecalis were used to determine the RN test limit of detection. Simulated-use testing was done using a duodenoscope inoculated with 10 % blood containing approximately 35 CFU E. coli per channel. Samples were extracted from the duodenoscope instrument channel and tested using the manufacturer’s instructions. Results The RN test could consistently detect 10 CFU of E. coli and P. aeruginosa (fluorescent signal of 9,000 to 11,000 units) but not E. faecalis. Sensitivity and specificity for Gram-negative bacteria were 93 % and 90 %, respectively, using all of the suspensions in the study. Extraction of E. coli from an inoculated duodenoscope instrument channel repeatedly provided a positive signal (i. e. > 2,000 units). Conclusions The RN test can reliably detect low levels of Gram-negative bacteria in suspension as well as from samples extracted from endoscope channels. These preliminary findings are encouraging but further assessment of extraction efficacy, impact of organic residuals and clinical workflow are still needed.

Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. While an ambiguous etiology is common to all IMIDs, in recent years, considerable knowledge has emerged regarding the plausible role of the gut microbiome in IMIDs. This study used 16S rRNA gene amplicon sequencing to compare the gut microbiota of patients with Crohn’s disease (CD; N = 20), ulcerative colitis (UC; N = 19), multiple sclerosis (MS; N = 19), and rheumatoid arthritis (RA; N = 21) versus healthy controls (HC; N = 23). Biological replicates were collected from participants within a 2-month interval. This study aimed to identify common (or unique) taxonomic biomarkers of IMIDs using both differential abundance testing and a machine learning approach. Significant microbial community differences between cohorts were observed (pseudo F = 4.56; p = 0.01). Richness and diversity were significantly different between cohorts (pFDR < 0.001) and were lowest in CD while highest in HC. Abundances of Actinomyces, Eggerthella, Clostridium III, Faecalicoccus, and Streptococcus (pFDR < 0.001) were significantly higher in all disease cohorts relative to HC, whereas significantly lower abundances were observed for Gemmiger, Lachnospira, and Sporobacter (pFDR < 0.001). Several taxa were found to be differentially abundant in IMIDs versus HC including significantly higher abundances of Intestinibacter in CD, Bifidobacterium in UC, and unclassified Erysipelotrichaceae in MS and significantly lower abundances of Coprococcus in CD, Dialister in MS, and Roseburia in RA. A machine learning approach to classify disease versus HC was highest for CD (AUC = 0.93 and AUC = 0.95 for OTU and genus features, respectively) followed by MS, RA, and UC. Gemmiger and Faecalicoccus were identified as important features for classification of subjects to CD and HC. In general, features identified by differential abundance testing were consistent with machine learning feature importance. This study identified several gut microbial taxa with differential abundance patterns common to IMIDs. We also found differentially abundant taxa between IMIDs. These taxa may serve as biomarkers for the detection and diagnosis of IMIDs and suggest there may be a common component to IMID etiology.