Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome.

Unlabelled: The rapid spread of antimicrobial resistance (AMR) is a threat to global health, and the nature of co-occurring antimicrobial resistance genes (ARGs) may cause collateral AMR effects once antimicrobial agents are used. Therefore, it is essential to identify which pairs of ARGs co-occur. Given the wealth of next-generation sequencing data available in public repositories, we have investigated the correlation between ARG abundances in a collection of 214,095 metagenomic data sets.

ARGprofiler-a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets.

Motivation: Analyzing metagenomic data can be highly valuable for understanding the function and distribution of antimicrobial resistance genes (ARGs). However, there is a need for standardized and reproducible workflows to ensure the comparability of studies, as the current options involve various tools and reference databases, each designed with a specific purpose in mind.

Results: In this work, we have created the workflow ARGprofiler to process large amounts of raw sequencing reads for studying the composition, distribution, and function of ARGs.

A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome.

The growing threat of antimicrobial resistance (AMR) calls for new epidemiological surveillance methods, as well as a deeper understanding of how antimicrobial resistance genes (ARGs) have been transmitted around the world. The large pool of sequencing data available in public repositories provides an excellent resource for monitoring the temporal and spatial dissemination of AMR in different ecological settings. However, only a limited number of research groups globally have the computational resources to analyze such data.

Global Distribution of Gene Variants in 214K Metagenomic Samples.

Since the initial discovery of a mobilized colistin resistance gene (), several other variants have been reported, some of which might have circulated a while beforehand. Publicly available metagenomic data provide an opportunity to reanalyze samples to understand the evolutionary history of recently discovered antimicrobial resistance genes (ARGs). Here, we present a large-scale metagenomic study of 442 Tbp of sequencing reads from 214,095 samples to describe the dissemination and emergence of nine gene variants ( to ).

NetSolP: predicting protein solubility in Escherichia coli using language models.

Motivation: Solubility and expression levels of proteins can be a limiting factor for large-scale studies and industrial production. By determining the solubility and expression directly from the protein sequence, the success rate of wet-lab experiments can be increased.

Results: In this study, we focus on predicting the solubility and usability for purification of proteins expressed in Escherichia coli directly from the sequence.

Efficacy of five 'sporicidal' surface disinfectants against Clostridioides difficile spores in suspension tests and 4-field tests.

Background: A sporicidal surface disinfection is recommended both for the outbreak and the endemic setting but a comparative evaluation on the efficacy of 'sporicidal' surface disinfectants using suspension tests and 4-field tests has not been performed.

Aim: To determine the efficacy of five 'sporicidal' surface disinfectants (three ready-to-use wipes (A, B, E), two concentrates (C, D) based on peroxides or aldehydes against C. difficile spores.

Deep protein representations enable recombinant protein expression prediction.

A crucial process in the production of industrial enzymes is recombinant gene expression, which aims to induce enzyme overexpression of the genes in a host microbe. Current approaches for securing overexpression rely on molecular tools such as adjusting the recombinant expression vector, adjusting cultivation conditions, or performing codon optimizations. However, such strategies are time-consuming, and an alternative strategy would be to select genes for better compatibility with the recombinant host.

Interlaboratory reproducibility of a test method following 4-field test methodology to evaluate the susceptibility of Clostridium difficile spores.

Background: Sporicidal surface disinfection is recommended to control transmission of Clostridium difficile in healthcare facilities. EN 17126 provides a method to determine the sporicidal activity in suspension and has been approved as a European standard. In addition, a sporicidal surface test has been proposed.

Standards of hygiene for ultrasound-guided core cut biopsies of the breast.

Purpose:  The aim was to obtain an overview of the hygiene measures undertaken during ultrasound guided core cut biopsies of the breast by experts certified by the German Society for Ultrasound in Medicine in order to derive recommendations for clinical routine, taking into account the available literature and the lack of evidence based guidelines.

Materials And Methods:  A survey was conducted with all members of the levels I to III of the breast ultrasound working group of the German Society for Ultrasound in Medicine. The estimation of the risk of infection after a core cut biopsy of the breast was asked for as well as the hygiene measures undertaken in practice to avoid infection.

DEGUM Recommendations on Infection Prevention in Ultrasound and Endoscopic Ultrasound.

Microbial contamination of ultrasound probes for percutaneous or endoscopic use is common. However, infectious diseases caused by transmission of microorganisms by US procedures have rarely been reported. In Germany, legal regulations address hygiene in ultrasound procedures.

Efficacy of cleaning tablets for removable orthodontic appliances: an in vivo pilot study.

Objectives: The purpose of this study was to test the cleaning effect of three commercially available effervescent tablet products on acrylic resin surfaces compared to water as control medium.

Methods: A total of 20 volunteers were instructed to wear a vacuum-formed maxillary splint continuously for 96 h. Each splint incorporated four resin discs in the palate area.

Is peracetic acid suitable for the cleaning step of reprocessing flexible endoscopes?

The bioburden (blood, protein, pathogens and biofilm) on flexible endoscopes after use is often high and its removal is essential to allow effective disinfection, especially in the case of peracetic acid-based disinfectants, which are easily inactivated by organic material. Cleaning processes using conventional cleaners remove a variable but often sufficient amount of the bioburden. Some formulations based on peracetic acid are recommended by manufacturers for the cleaning step.

Recommendations and requirements for soap and hand rub dispensers in healthcare facilities.

Hand hygiene is one of the most important measures to prevent transmission of infectious agents and plays a major role in prevention of infection in any type of healthcare setting. While requirements for the efficacy of hand disinfectants are defined in European testing norms such as the EN 1500 for hygienic hand disinfection or EN 12791 for surgical hand preparation, no specific recommendations for hand rub dispensers and liquid soap dispensers have been given yet. Therefore, the intention of the present recommendation on soap and hand rub dispensers in healthcare facilities is to close this gap and to enhance future improvement of dispenser functionality and design.

Natural-orifice transluminal endoscopic surgery (NOTES) in Europe: summary of the working group reports of the Euro-NOTES meeting 2010.

The fourth Euro-NOTES workshop took place in September 2010 and focused on enabling intensive scientific dialogue and interaction between participants to discuss the state of the practice and development of natural-orifice transluminal endoscopic surgery (NOTES) in Europe. Five working groups were formed, consisting of participants with varying scientific and medical backgrounds. Each group was assigned to an important topic: the correct strategy for dealing with bacterial contamination and related complications, the question of the ideal entry point and secure closure, interdisciplinary collaboration and indications, robotics and platforms, and matters related to training and education.

Comparison of the cleaning and disinfecting efficacy of four washer-disinfectors for flexible endoscopes.

Four washer-disinfectors (AdaptaScope, ETD-2Plus, Innova-E3, LS-2000) were compared. The cleaning and process efficacies of the washer-disinfectors were determined by visible examination and by microbial reduction factor (RF) using the German test method (EN ISO/TS 15883-5). Test pieces were contaminated with blood and Enterococcus faecium.

Suitability of the German test method for cleaning efficacy in washer-disinfectors for flexible endoscopes according to prEN ISO 15883.

In Europe, the evaluation of processing flexible endoscopes in washer-disinfectors (WDs) is performed in compliance with prEN ISO 15883-1 which includes determination of the efficacy of the cleaning process. Recent data suggest that cleaning processes show large differences when the prEN ISO 15883-1 German test model is applied. Hence, we analysed a total of 72 experiments in order to evaluate the test method.

Intralaboratory reproducibility of the German test method of prEN ISO 15883-1 for determination of the cleaning efficacy of washer-disinfectors for flexible endoscopes.

In Europe, the evaluation of processing flexible endoscopes in washer-disinfectors (WDs) is performed in accordance with prEN ISO 15883-1, which includes determination of cleaning efficacy. Recent data suggest that large differences are found between cleaning processes when the prEN ISO 15883-1 German test model is applied. Therefore, we analysed 12 separate cleaning processes, and each was assessed by determining the means of three experiments.

Surface fixation of dried blood by glutaraldehyde and peracetic acid.

The difficulties of successful prion inactivation by chemical agents has led to changes in recommendations regarding the reprocessing of instruments including flexible endoscopes. One of the changes is the preference for peracetic acid instead of glutaraldehyde in order to avoid fixation of organic material, but the surface fixation by various active agents has not been fully investigated. We used a standardized amount of dried blood soil on metal carriers (on average 22 mg).

The importance of cleaning for the overall results of processing endoscopes.

Reprocessing comprises three steps: cleaning, disinfection and-if required-sterilisation. While the extents of disinfection and of sterilisation are quantitatively defined, there are only imprecise (qualitative) definitions of cleaning. There are two main reasons for accurate cleaning.

Efficacy of 10 different cleaning processes in a washer-disinfector for flexible endoscopes.

Successful cleaning of medical devices, such as flexible endocopes, has been recognized to be of major importance for effective processing. Washer-disinfectors (WD) are considered to be an important step in this direction. The cleaning process in WD, however, has only been partially assessed regarding its effectiveness, and therefore to study this in more detail, tests were carried out, according prEN ISO 15883, using transparent teflon tubes as test pieces (length 2 m).

Gastroscope processing in washer-disinfectors at three different temperatures.

Endoscopes are processed chemo-thermally at approximately 56 degrees C in washer-disinfectors in Germany. In this study we investigated the processing of gastroscopes by an endoscope washer-disinfector at different temperatures. A total of 87 gastroscopes were tested hygienically and microbiologically before manual cleaning (after patient use), as well as after manual cleaning and after endoscope washer-disinfector processing at running temperatures of 43, 51 and 56 degrees C.

Automated method for determination of glutardialdehyde residues in flexible endoscopes after disinfection.

Glutardialdehyde (GDA) is the most commonly used disinfectant for flexible endoscopes. After inappropriate rinsing of endoscopes residual GDA in the narrow endoscope channels may lead to toxic effects in patients. Common methods for determination of aldehydes in water involve derivatization with 2,4-dinitrophenylhydrazine (DNPH), liquid-liquid or solid-phase extraction and HPLC determination.

Cleaning efficacy of nine different cleaners in a washer-disinfector designed for flexible endoscopes.

Studies on processing endoscopes usually involve the combined cleaning and disinfecting activity. We compared nine cleaning agents designed for automatic processing for cleaning efficacy alone using soft and hard water as controls in 12 different processes in a washer-disinfector. Experiments were performed according to the German Endoscopy Working Group recommendations using transparent Teflon tubes (internal diameter 2mm, length 2m) as test pieces.

Residuals on medical devices following reprocessing.

Micro-organisms may be transmitted by medical devices. A large variety of infectious agents may be involved in infections transmitted by endoscopic procedures. We review a series of examples that demonstrate to what extent micro-organisms can be detected on medical devices and how transmission on to subsequently examined persons due to inadequate reprocessing can occur.