ENDOSCOPE SAMPLING AND CULTURING METHODS.

Contamination rates reported in the literature for patient-ready flexible endoscopes vary from 0.4% to 49%. Unfortunately, the comparison and interpretation of these results is almost impossible since several factors including sampling and culturing methods, target levels for contamination or definition of indicator microorganisms vary widely from one study to the other. The objective of this study was to compare the efficacy of six duodenoscope sampling and culturing methods by means of extraction efficacy comparison, while at the same time identifying key parameters that provide optimal microbial recovery. The duodenoscope sample extraction efficacy of each method was assessed using the repetitive recovery method described in ISO 11737-1: 2018. The results obtained indicated that the mean overall bioburden extraction efficacy varied from 1% for the Australian method to 39% for the French one. The lowest endoscope sample extraction efficacy was associated with the absence of any neutralizer, friction, or tensioactive agent and when only a small portion of the sampling solution collected was inoculated onto culture media. The efficacy of the sampling and culturing methods also varied according to the nature of microorganisms present in the endoscope, and the time between sampling and culturing. This study supports the need for a harmonized and standardized sampling and culturing method for flexible endoscopes.

Consumption of Solnul™ Resistant Potato Starch Produces a Prebiotic Effect in a Randomized, Placebo-Controlled Clinical Trial.

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.

Minimizing the Risks of Simethicone in Endoscope Reprocessing.

This statement was written under the auspices of the World Gastroenterology Organization's Guidelines Committee. The authors are members of the Review Team of the WGO Endoscope Disinfection Guideline and have experience in endoscopy, endoscope reprocessing, and microbiology, including biofilms. During the preparation of the WGO Update on Endoscope Disinfection Guidelines, concerns about simethicone on endoscope channel surfaces compromising cleaning and disinfection were raised. Publications on simethicone, including modes of delivery, effectiveness, and risks, have been reviewed. The paper was written as a companion to the new guidelines with a focus on minimizing the risks of simethicone in endoscope reprocessing.

A prospective, multicenter, clinical study of duodenoscope contamination after reprocessing.

OBJECTIVE: Several clinical procedures utilize duodenoscopes, which are processed for reuse after the procedures are completed. However, infection outbreaks due to improper duodenoscope processing occur frequently. To address this, we aimed to assess the contamination rates of duodenoscopes after reprocessing in nonoutbreak settings. DESIGN AND SETTING: Prospective study in 16 clinical sites in the United States. METHODS: We sampled and cultured reprocessed duodenoscopes following the FDA/CDC/ASM guideline; "Duodenoscope Surveillance Sampling and Culturing - Reducing the Risks of Infection." High-concern (HC) organisms were those highly associated with disease, including gram-negative rods, Staphylococcus aureus, Staphylococcus lugdunensis, ß-hemolytic Streptococcus, Enterococcus spp, and yeasts. We evaluated duodenoscopes with ≥1 CFU of organisms after reprocessing. The reprocessing environments were also sampled and cultured. RESULTS: We assessed 859 newer-model (NM) duodenoscopes (TJF-Q180V) and 850 older-model (OM) duodenoscopes (TJF-160F/VF); of these, 35 NM samples (4.1%) and 56 OM samples (6.6%) were contaminated with HC organisms. We detected and classified the HC organisms as gastrointestinal (45.4%), human origin (16.7%), environmental (24.1%), waterborne (13.0%), and unidentified (0.9%). CONCLUSIONS: We detected an overall HC contamination rate of 5.3% in nonoutbreak settings. Although the relationship between endoscopic contamination and the occurrence of infections remains unclear, attempts should continue to be made to further reduce contamination rates. Additional improvements to the manufacturer's instructions for use, human factors during the reprocessing procedure, ongoing training programs, cleanliness of reprocessing environments, and the design of the distal end of the duodenoscope should be considered.

Biofilm accumulation in new flexible gastroscope channels in clinical use.

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.

Contaminated flexible endoscopes: Review of impact of channel sampling methods on culture results and recommendations for root-cause analysis.

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.

Increasing levels of Parasutterella in the gut microbiome correlate with improving low-density lipoprotein levels in healthy adults consuming resistant potato starch during a randomised trial.

BACKGROUND: Prebiotics, defined as a substrate that is selectively utilized by host microorganisms conferring a health benefit, present a potential option to optimize gut microbiome health. Elucidating the relationship between specific intestinal bacteria, prebiotic intake, and the health of the host remains a primary microbiome research goal. OBJECTIVE: To assess the correlations between gut microbiota, serum health parameters, and prebiotic consumption in healthy adults. METHODS: We performed ad hoc exploratory analysis of changes in abundance of genera in the gut microbiome of 75 participants from a randomized, placebo-controlled clinical trial that evaluated the effects of resistant potato starch (RPS; MSPrebiotic®, N = 38) intervention versus a fully digestible placebo (N = 37) for which primary and secondary outcomes have previously been published. Pearson correlation analysis was used to identify relationships between health parameters (ie. blood glucose and lipids) and populations of gut bacteria. RESULTS: Abundance of Parasutterella (phylum Proteobacteria) tended to increase in the gut microbiome of individuals consuming RPS and those increases in Parasutterella were correlated with reductions in low-density lipoprotein (LDL) levels in participants consuming RPS but not placebo. Segregating RPS-consuming individuals whose LDL levels decreased (ie "Responders") from those who did not (ie. "Non-Responders") revealed that LDL Responders had significantly higher levels of Parasutterella both at baseline and after 12 weeks of consuming RPS. CONCLUSION: Our analyses suggest that RPS may help improve LDL levels depending upon the levels of Parasutterella in an individual's gut microbiome. TRIAL REGISTRATION: This study protocol was reviewed and approved by Health Canada (Submission #188517; "Notice of Authorization" dated 06/05/13) and registered as NCT01977183 (10/11/13) listed on NIH website: ClinicalTrials.gov. Data generated in this study have been submitted to NCBI ( http://www.ncbi.nlm.nih.gov/bioproject/381931 ). FUNDING: MSP Starch Products Inc.

Quality Systems Approach for Endoscope Reprocessing: You Don't Know What You Don't Know!

Several factors affect the efficacy of endoscope reprocessing, including human factors, inadequate cleaning, simethicone residuals, moisture in channels during storage, and biofilm or buildup biofilm formation. These factors all contribute to contamination of patient-ready endoscopes that may contribute to transmission of microorganisms resulting in infection and/or colonization. This article reviews monitoring as part of a quality management system that includes manual cleaning, dry storage, and culture to detect endoscope contamination. The published data for rapid tests that detect organic residuals and adenosine triphosphate to monitor manual cleaning are reviewed.

Impact of wet storage and other factors on biofilm formation and contamination of patient-ready endoscopes: a narrative review.

The 2019 U.S. Food and Drug Administration report indicates that the clinical studies undertaken by the 3 main GI endoscope manufacturers demonstrate 5.4% of patient-ready duodenoscopes remain culture positive for high-concern organisms. The root causes of this persistent contamination are poorly understood. The objectives of this review include summarizing (1) the impact of inadequate manual cleaning and inadequate drying during storage on the formation of build-up biofilm in endoscope channels, (2) the impact of defoaming agents used during patient procedures on drying efficacy, (3) the data showing the importance of build-up biofilm on persistent microbial survival, and (4) the potential impact of implementation of a quality systems approach in GI endoscopy reprocessing.

Turbulent fluid flow is a novel closed-system sample extraction method for flexible endoscope channels of various inner diameters.

OVERVIEW: Effective sample extraction from endoscope channels is crucial for monitoring manual cleaning adequacy as well as for ensuring optimal sensitivity for culture after disinfection. The objective of this study was to compare the efficacy of Turbulent Fluid Flow (TFF) to Flush (F) or Flush-Brush-Flush (FBF) methods. MATERIALS & METHODS: Pseudomonas aeruginosa and Enterococcus faecalis in artificial test soil-2015 (ATS2015) were used as bacterial markers while protein and carbohydrate were the organic markers for biofilm formed inside 3.2-mm and 1.37-mm polytetrafluoroethylene (PTFE) channels. TFF was generated using compressed air and sterile water to provide friction for sample extraction. Extraction for biofilm coated PTFE channels as well as for colonoscope channels perfused with ATS2015 containing 108 CFU/mL P. aeruginosa, E. faecalis and Candida albicans was determined using TFF compared to FBF and F. RESULTS: The extraction ratio for P. aeruginosa and E. faecalis from biofilm extracted by TFF compared to the positive control was significantly better than F for 1.37-mm channels (≥0.94 for both bacteria by TFF versus 0.69 to 0.72 by F for P. aeruginosa and E. faecalis, respectively) but not significantly different between TFF and FBF for 3.2-mm channels. F was also ineffective for extraction of protein and carbohydrate from 1.37-mm channels. Extraction efficacy by TFF from inoculated colonoscope channels was >98% for all test markers. CONCLUSIONS: The novel TFF method for extraction of samples from colonoscope channels is a more effective method than the existing FBF and F methods.

The polytetrafluoroethylene (PTFE) channel model of cyclic-buildup biofilm and traditional biofilm: The impact of friction, and detergent on cleaning and subsequent high-level disinfection.

OBJECTIVE: To evaluate the efficacy of detergent and friction on removal of traditional biofilm and cyclic-buildup biofilm (CBB) from polytetrafluoroethylene (PTFE) channels and to evaluate the efficacy of glutaraldehyde to kill residual bacteria after cleaning. METHODS: PTFE channels were exposed to artificial test soil containing 108 CFU/mL of Pseudomonas aeruginosa and Enterococcus faecalis, followed by full cleaning and high-level disinfection (HLD) for five repeated rounds to establish CBB. For traditional biofilm, the HLD step was omitted. Cleaning with enzymatic and alkaline detergents, bristle brush, and Pull Thru channel cleaner were compared to a water flush only. Carbohydrate, protein, viable count, adenosine triphosphate (ATP) levels were analyzed and atomic force microscopy (AFM) was performed. RESULTS: In the absence of friction, cleaning of traditional biofilm and CBB was not effective compared to the positive control (Dunn-Bonferroni tests; P > .05) regardless of the detergent used. ATP, protein, and carbohydrate analyses were unable to detect traditional biofilm or CBB. The AFM analysis showed that fixation resulted in CBB being smoother and more compact than traditional biofilm. CONCLUSION: Friction during the cleaning process was a critical parameter regardless of the detergent used for removal of either traditional biofilm or CBB. Glutaraldehyde effectively killed the remaining microorganisms regardless of the cleaning method used.

Medical instrument reprocessing: current issues with cleaning and cleaning monitoring.

The complexity of medical devices has increased over the past 10 years, and outbreaks of infections due to contaminated devices have focused attention on the need to adequately clean medical devices in order to ensure the adequacy of disinfection and sterilization. There has been a paradigm shift in reprocessing of medical devices, with increased emphasis on a quality management systems approach that requires validated cleaning instructions from manufacturers and ongoing monitoring by reprocessing personnel to ensure adequacy of cleaning. This article reviews the current issues related to medical device reprocessing and summarizes the approaches used for monitoring cleaning efficacy for surgical instruments and flexible endoscopes.

Biofilms on instruments and environmental surfaces: Do they interfere with instrument reprocessing and surface disinfection? Review of the literature.

There is a growing appreciation for the role of biofilm-embedded microbes in many different aspects of infection transmission. The format of biofilm includes traditional hydrated biofilm, build-up biofilm, and dry surface biofilm. The objectives of this article are to discuss how traditional biofilm differs from build-up biofilm and dry surface biofilm, and to review the evidence supporting infection transmission from biofilm that accumulates in reprocessed instruments and from dry biofilm that forms environmental reservoirs.

Evaluation of an overnight non-culture test for detection of viable Gram-negative bacteria in endoscope channels.

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.

A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

Clostridium neonatale sp. nov. linked to necrotizing enterocolitis in neonates and a clarification of species assignable to the genus Clostridium (Prazmowski 1880) emend. Lawson and Rainey 2016.

A description of an outbreak of necrotizing enterocolitis among neonates, linked to the putative novel species Clostridium neonatale and assignable to the genus Clostridium, was previously reported in brief but that name had never been validly published (Alfa et al. Clin Inf Dis 2002;35:S101-S105). Features of this taxon group and its phylogenetic position with respect to contemporary species in the genus Clostridium were recently reviewed and still found to be unique. Therefore, we provide here a description based on biochemical, chemotaxonomic and antimicrobial susceptibility testing (AST), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, 16S rRNA gene sequencing as well as information obtained by whole genome sequencing (WGS) for strains 99A005T and 99A006. Those two C. neonatale strains were essentially identical to each other, with genome sizes of 4 658 596-4 705 520 bp and G+C content of 28.4-28.5 mol% (WGS). AST inferred susceptibility to 14 antibiotics. MALDI-TOF spectra were unique and could potentially be used for identification. The type strain is (NML) LCDC 99A005T [=ATCC BAA-265T=CCUG 46077T=St. Boniface Hospital 30686T]. While performing this review, we found that the names of 24 validly published species assignable to the genus Clostridium had been omitted from the emended description of the genus (Lawson and Rainey Int J Syst Evol Microbiol 2016;66 :1009-1016). Those species are listed in brief here. Lastly, based on this review, we also propose that Eubacterium budayi, Eubacterium nitritogenes and Eubacterium combesii be transferred to the emended genus Clostridium, as Clostridium budayi comb. nov., Clostridium nitritogenes comb. nov. and Clostridium combesii comb. nov., respectively.

Evaluation of adenosine triphosphate test for cleaning assessment of gastroscopes and the effect on workload in a busy endoscopy center.

OBJECTIVE: Using adenosine triphosphate (ATP) tests to assess manual cleaning of gastroscopes and to determine the associated workload in a busy endoscopy unit. METHODS: Patient-used gastroscopes were sampled before and after cleaning to assess ATP levels, bioburden, and protein. Samples were collected by flushing 20 mL of sterile water through the biopsy port to the distal end. Time spent for reprocessing and performing the ATP test was recorded. RESULTS: Twenty-four samples were collected from 10 gastroscopes. After manual cleaning, 14/24 (58.3%) samples had no microbial growth (mean, 21 colony-forming units/cm2), and in 22/24 (91.7%) samples the protein was undetectable (mean, 0.04 µg/cm2). ATP test was above the cutoff (200 relative light units [RLU]) in 17/24 (70.8%) samples (mean, 498 RLU). After the second cleaning, 11/17 (64.7%) gastroscopes still failed the ATP test (mean, 321.2 RLU). The mean time spent to perform manual cleaning and ATP tests was 16 and 8 minutes, respectively. Hence, each test increased the length of time for cleaning plus testing cleanliness by 50%. CONCLUSION: Further studies regarding the optimal cutoff for ATP tests are needed. ATP tests for cleaning monitoring are easy to perform and provide immediate feedback to the team. However, the increased workload needs to be considered.

Multisite evaluation of environmental cleanliness of high-touch surfaces in intensive care unit patient rooms.

The efficacy of discharge cleaning and disinfection of high-touch surfaces of intensive care unit patient rooms in Brazil, Canada, the Netherlands, and the United States was evaluated and the effect of an educational intervention was determined. Significant site-to-site differences in cleaning regimens and baseline cleanliness levels were observed using ATP levels, colony-forming units, and reflective surface marker removal percent pass rates. An educational intervention that includes rapid feedback of the ATP measurements could significantly improve the quality of the cleaning and disinfection regimens.

Impact of cleaning monitoring combined with channel purge storage on elimination of Escherichia coli and environmental bacteria from duodenoscopes.

BACKGROUND AND AIMS: We aimed to determine whether monitoring of duodenoscope cleaning by rapid adenosine triphosphate (ATP) combined with channel-purge storage could eliminate high-concern microorganisms. METHODS: In a simulated-use study, suction channels, as well as lever recesses, from 2 duodenoscopes models and the unsealed elevator guidewire (EGW) channel from 1 of these 2 duodenoscopes (the other model has a sealed EGW) were perfused with ATS2015 containing approximately 8 Log10 colony-forming units (CFU)/mL of both Enterococcus faecalis and Escherichia coli. Pump-assisted cleaning was monitored by rapid ATP testing. Duodenoscopes exceeding 200 relative light units (RLUs) were recleaned. Clean duodenoscopes were processed through an automated endoscope reprocessor and then stored in a channel-purge storage cabinet for 1 to 3 days. Cultures of EGW channel and instrument channel combined with the lever recess (IC-LR) were taken after storage. The impacts of extended cleaning and alcohol flush were evaluated. RESULTS: E coli was reliably eliminated in IC-LR and EGW channels of 119 duodenoscope tests (59 with sealed EGW and 60 with nonsealed EGW). However, actionable levels of E faecalis and environmental bacteria persisted. Neither alcohol flush nor extended cleaning resulted in a reduction of actionable levels for these organisms. Identification of isolates indicated that residual organisms in duodenoscope channels were hardy Gram-positive bacteria (often spore formers) that likely originated from environmental sources. CONCLUSIONS: These data indicate that high-concern Gram-negative bacteria but not E faecalis or environmental bacteria can be reliably eliminated by use of the manufacturer's instructions for reprocessing with ATP monitoring of cleaning and channel-purge storage conditions.