Nanopore adaptive sampling of a metagenomic sample derived from a human monkeypox case.

In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside the known endemic areas. Setup of proper genomic surveillance is of utmost importance to control such outbreaks. To this end, we performed Nanopore (PromethION P24) and Illumina (NextSeq. 2000) Whole Genome Sequencing (WGS) of a monkeypox sample. Adaptive sampling was applied for in silico depletion of the human host genome, allowing for the enrichment of low abundance viral DNA without a priori knowledge of sample composition. Nanopore sequencing allowed for high viral genome coverage, tracking of sample composition during sequencing, strain determination, and preliminary assessment of mutational pattern. In addition to that, only Nanopore data allowed us to resolve the entire monkeypox virus genome, with respect to two structural variants belonging to the genes OPG015 and OPG208. These SVs in important host range genes seem stable throughout the outbreak and are frequently misassembled and/or misannotated due to the prevalence of short read sequencing or short read first assembly. Ideally, standalone standard Illumina sequencing should not be used for Monkeypox WGS and de novo assembly, since it will obfuscate the structure of the genome, which has an impact on the quality and completeness of the genomes deposited in public databases and thus possibly on the ability to evaluate the complete genetic reason for the host range change of monkeypox in the current pandemic.

Containment of a Large SARS-CoV-2 Outbreak Among Healthcare Workers in a Pediatric Intensive Care Unit.

OBJECTIVE: Healthcare workers (HCWs) are particularly exposed SARS-CoV-2 because they are critical in preventing viral transmission and treating COVID-19 patients. Within HCWs, personnel of intensive care units (ICUs) are at the forefront of treating patients with a severe course of COVID-19 infection and therefore represent an extremely vulnerable group. Thus, our objective is to contribute to establish means of infection control protecting HCWs in the frontline of the current pandemic. DESIGN: An outbreak of SARS-CoV-2 was detected and contained in a pediatric ICU (PICU). The first positive case was identified with a point-of-care diagnostic system on site. Real-time PCR-based testing systems from self-collected nasopharyngeal samples swabs were used to test for viral RNA of SARS-CoV-2 in the follow-up. SETTING: PICU within a tertiary university hospital in Germany. PARTICIPANTS: Healthcare workers of the PICU. INTERVENTIONS: Positive HCWs were sent into quarantine. Containment measures were implemented including wearing of surgical-masks, physical distancing and systematic testing. RESULTS: Among 432 HCWs, 91 (25%) were tested. Forty-five percent reported symptoms corresponding to characteristics of COVID-19. Of those, only 19,5% (8 HCWs) were tested positive for SARS-CoV-2. No infection occurred outside the PICU. After the implementation of containment measures, viral transmission was stopped. CONCLUSIONS: In the present study, a large outbreak within a team of healthcare workers of a PICU, affecting almost one fifth of the entire personnel is documented, along with detailed insights about how the outbreak was contained and how operability of the unit was maintained.

Air quality in the operating room: Surgical site infections, HVAC systems and discipline - position paper of the German Society of Hospital Hygiene (DGKH).

In recent years, there has been an ongoing discussion about the value of laminar airflow (LAF=low turbulence displacement ventilation) in the operating room for prevention of surgical site infections (SSI). Some publications, e.g., from the WHO, issued the demand to no longer build LAF ceilings in operating rooms. The present statement deals critically with this position and justifies the use of LAF ceilings in different ways: Many of the papers cited by the WHO and others for the case against LAF do not provide reliable data.The remaining studies which might be used for answering the question give quite different results, also in favor of LAF.The size of the LAF ceiling in many studies is not given or mostly too small in comparison to actual technical requirements.LAF in different countries can mean quite different techniques (e.g., the US in comparison to Germany) so that the results of studies that do not take this into account may not be comparable.LAF has positive effects in terms of reducing particulate and bacterial load, associated with increased airflow in the surgical working area. A reduction of carcinogenic substances in the air may also be assumed, which would increase workers' safety. Thus, this paper recommends building LAF ceilings in the future as well, depending on the operations intended. Further, this paper gives an overview of possible reasons for surgical site infections and highlights the importance of discipline in the operating theatre.

Patients with Rheumatic Diseases do not have an Increased Risk of MRSA Carrier Status.

INTRODUCTION: The aim of this study was to determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) both in rheumatologic and non-rheumatologic rehabilitation centers. In addition, we sought to evaluate the practice value of existing screening recommendations of the German Commission for Hospital Hygiene and Infection Prevention (KRINKO). METHODS: The analysis was performed in four rehabilitation clinics (rheumatology, psychosomatic medicine, oncology, and cardiology) with at least 200 patients per clinic tested for MRSA. RESULTS: Nine (1.1%) of the 842 patients were colonized with MRSA. Only five of them should have been tested according to the commission's recommendations. The prevalence was 0.5% (n = 207) in rheumatologic, 0.9% (n = 224) in psychosomatic, 1.4% (n = 209) in oncologic and 1.5% (n = 202) in cardiologic patients. We found a greater exposure to risk factors in cardiologic and oncologic patients. Among patients with carrier status, a higher percentage was exposed to three potential risk factors not applied by the commission. CONCLUSIONS: The prevalence of MRSA in our cohort correlates with data from previous studies. The low percentage among rheumatologic patients suggests that they are not more likely to reveal MRSA carrier status than other patient groups and that long-term immunosuppression does not necessarily represent a risk factor for MRSA colonization. Since only five out of nine patients with carrier status would have been detected following the recommendations of the KRINKO, further studies on potential risk factors are warranted.

Microbial contamination of anesthetic syringes in relation to different handling habits.

This single-center study prospectively assessed the microbial contamination of anesthetic syringes handled perioperatively under different conditions. We documented high rates of bacterial contamination, with strong but statistically nonsignificant differences between handling groups. Our results identify skin contact as the main source of contamination, and thus we emphasize the impact of proper hand hygiene.

Principles of infection prevention and reprocessing in ENT endoscopy.

This article gives an overview on the principles of reprocessing of rigid and flexible endoscopes used in ENT units including structural and spatial requirements based on general and ENT-specific risks of infection associated with diagnostic and therapeutic endoscopy. The underlying legal principles as well as recommendations from scientific societies will be exemplified in order to give a practical guidance to the otorhinolaryngologist. Preliminary results of a small nation-wide survey on infection control standards based on data of 29 ENT practices in Germany reveal current deficits of varying degree concerning infection control management including reprocessing of endoscopes. The presented review aims to give support to the establishment of a structured infection control management program including the evaluation of results by means of a prospective surveillance.

Real-time PCR detection of Pseudomonas aeruginosa in clinical and municipal wastewater and genotyping of the ciprofloxacin-resistant isolates.

Real-time quantification of Pseudomonas aeruginosa was performed in various wastewater systems including clinical, municipal wastewaters and inflow from a wastewater treatment plant. The highest concentrations of P. aeruginosa-specific targets were detected in clinical wastewaters. Limitations of the detection system resulting from inhibition or cross-reaction were identified. Ciprofloxacin-resistant P. aeruginosa strains were isolated after specific enrichment from clinical and municipal wastewaters. In some cases they were also cultivated from effluent of a wastewater treatment plant, and from its downstream river water. A total of 119 isolates were phenotypically characterized as ciprofloxacin-resistant via antibiogram testing. Subsequently, the fluoroquinolone-resistance-mediating mutations in the genes gyrA codon positions 83 and 87, gyrB codon position 466 and parC codon positions 87 and 91 were determined by mini-sequencing. Ciprofloxacin resistance was mainly associated with mutations in gyrA codon position 83 and parC mutation in codon positions 87 or 91 of the bacterial gyrase and topoisomerase II genes. All ciprofloxacin-resistant P. aeruginosa strains were compared with genotypes from clinical data of fluoroquinolone-resistant P. aeruginosa infections. The results were in agreement with data from clinical analyses, with the exception that no gyrA 87 and no gyrB mutations were found in ciprofloxacin-resistant P. aeruginosa wastewater isolates.

Microbiological quality of carbonated drinking water produced with in-home carbonation systems.

The microbiological quality of carbonated water produced with tap water in commercial in-home carbonation systems was determined, the results being discussed in the context of the microbiological quality of the tap water used, the properties of the drink makers, and the procedures of preparation and washing of various parts of the appliance. The last-mentioned data were received from each participant of the study by questionnaire. Escherichia coli, coliforms, fecal streptococci and spore-forming sulphite-reducing anaerobes were used as indicators for the hygienic quality of the water. Tap-water samples were collected according to the usual procedure when filling the carbonating bottle, i.e., without previous flushing and disinfection of the faucet. In 12% of tap-water samples, coliforms could be detected. On the other hand, in 20 of 52 carbonated waters (39%), coliforms as indicators of water pollution were found. By means of fecal streptococci and Pseudomonas aeruginosa, it was possible to establish additional contamination not involving E. coli or coliforms alone. Analysis revealed that, in addition to contaminated tap water, a bacterial biofilm on the inner surface of the re-usable bottles had a predominant influence on the microbiological quality of the carbonated water.

In vitro evaluation of the biocompatibility of contaminated implant surfaces treated with an Er : YAG laser and an air powder system.

Titanium platelets with a sand-blasted and acid-etched surface were coated with bovine serum albumin and incubated with a suspension of Porphyromonas gingivalis (ATCC 33277). Four groups with a total of 48 specimens were formed. Laser irradiation of the specimens (n = 12) was performed on a computer-controlled XY translation stage at pulse energy 60 mJ and frequency 10 pps. Twelve specimens were treated with an air powder system. After the respective treatment, human gingival fibroblasts were incubated on the specimens. The proliferation rate was determined by means of fluorescence activity of a redox indicator (Alamar Blue Assay) which is reduced by metabolic activity related to cellular growth. Proliferation was determined up to 72 h. Contaminated and non-treated as well as sterile specimens served as positive and negative controls. Proliferation activity was significantly (Mann-Whitney U-test, P < 0.05) reduced on contaminated and non-treated platelets when compared to sterile specimens. Both on laser as well as air powder-treated specimens, cell growth was not significantly different from that on sterile specimens. Air powder treatment led to microscopically visible alterations of the implant surface whereas laser-treated surfaces remained unchanged. Both air powder and Er : YAG laser irradiation have a good potential to remove cytotoxic bacterial components from implant surfaces. At the irradiation parameters investigated, the Er : YAG laser ensures a reliable decontamination of implants in vitro without altering surface morphology.

Infections associated with medical devices: pathogenesis, management and prophylaxis.

The insertion or implantation of foreign bodies has become an indispensable part in almost all fields of medicine. However, medical devices are associated with a definitive risk of bacterial and fungal infections. Foreign body-related infections (FBRIs), particularly catheter-related infections, significantly contribute to the increasing problem of nosocomial infections. While a variety of micro-organisms may be involved as pathogens, staphylococci account for the majority of FBRIs. Their ability to adhere to materials and to promote formation of a biofilm is the most important feature of their pathogenicity. This biofilm on the surface of colonised foreign bodies is regarded as the biological correlative for the clinical experience with FBRI, that is, that the host defence mechanisms often seem to be unable to handle the infection and, in particular, to eliminate the micro-organisms from the infected device. Since antibacterial chemotherapy is also frequently not able to cure these infections despite the use of antibacterials with proven in vitro activity, removal of implanted devices is often inevitable and has been standard clinical practice. However, in specific circumstances, such as infections of implanted medical devices with coagulase-negative staphylococci, a trial of salvage of the device may be justified. All FBRIs should be treated with antibacterials to which the pathogens have been shown to be susceptible. In addition to systemic antibacterial therapy, an intraluminal application of antibacterial agents, referred to as the 'antibiotic-lock' technique, should be considered to circumvent the need for removal, especially in patients with implanted long-term catheters. To reduce the incidence of intravascular catheter-related bloodstream infections, specific guidelines comprising both technological and nontechnological strategies for prevention have been established. Quality assurance, continuing education, choice of the catheter insertion site, hand hygiene and aseptic techniques are aspects of particular interest. Furthermore, all steps in the pathogenesis of biofilm formation may represent targets against which prevention strategies may be directed. Alteration of the foreign body material surface may lead to a change in specific and nonspecific interactions with micro-organisms and, thus, to a reduced microbial adherence. Medical devices made out of a material that would be antiadhesive or at least colonisation resistant would be the most suitable candidates to avoid colonisation and subsequent infection. Another concept for the prevention of FBRIs involves the impregnation of devices with various substances such as antibacterials, antiseptics and/or metals. Finally, further studies are needed to translate the knowledge on the mechanisms of biofilm formation into applicable therapeutic and preventive strategies.

Antimicrobial efficacy of semiconductor laser irradiation on implant surfaces.

PURPOSE: This study was conducted to investigate the antimicrobial effect of an 809-nm semiconductor laser on common dental implant surfaces. MATERIALS AND METHODS: Sandblasted and acid-etched (SA), plasma-sprayed (TPS), and hydroxyapatite-coated (HA) titanium disks were incubated with a suspension of S. sanguinis (ATCC 10556) and subsequently irradiated with a gallium-aluminum-arsenide (GaAlAs) laser using a 600-microm optical fiber with a power output of 0.5 to 2.5 W, corresponding to power densities of 176.9 to 884.6 W/cm2. Bacterial reduction was calculated by counting colony-forming units on blood agar plates. Cell numbers were compared to untreated control samples and to samples treated with chlorhexidine digluconate (CHX). Heat development during irradiation of the implants placed in bone blocks was visualized by means of shortwave thermography. RESULTS: In TPS and SA specimens, laser irradiation led to a significant bacterial reduction at all power settings. In an energy-dependent manner, the number of viable bacteria was reduced by 45.0% to 99.4% in TPS specimens and 57.6% to 99.9% in SA specimens. On HA-coated disks, a significant bacterial kill was achieved at 2.0 W (98.2%) and 2.5 W (99.3%) only (t test, P < .05). For specimens treated with CHX, the bacterial counts were reduced by 99.99% in TPS and HA-coated samples and by 99.89% in SA samples. DISCUSSION: The results of the study indicate that the 809-nm semiconductor laser is capable of decontaminating implant surfaces. Surface characteristics determine the necessary power density to achieve a sufficient bactericidal effect. The bactericidal effect, however, was lower than that achieved by a 1-minute treatment with 0.2% CHX. The rapid heat generation during laser irradiation requires special consideration of thermal damage to adjacent tissues. CONCLUSION: No obvious advantage of semiconductor laser treatment over conventional methods of disinfection could be detected in vitro.

Development of a long-lasting ventricular catheter impregnated with a combination of antibiotics.

A ventricular silicone catheter impregnated with a combination of rifampin and a quinolone was developed in order to prevent ventricular shunt related infections. As model substance for the quinolones we used sparfloxacin, because of its specific physicochemical properties resulting in a quantitative detection also in the presence of a second antibiotic. In our study we focused especially on an optimization of the antibiotic release out of the impregnated catheters in order to develop long lasting devices with a broad antimicrobial spectrum. A release-optimized catheter was tested with an in vitro colonization test and additionally with a method developed to examine the spread of bacteria on a catheter surface. In vitro experiments showed that the impregnated catheters reduce the colonization with Staphylococcus epidermidis for at least 1 year and prevent the spread of bacteria along the catheter surface.

Detection of antibiotic-resistant bacteria and their resistance genes in wastewater, surface water, and drinking water biofilms.

Abstract In view of the increasing interest in the possible role played by hospital and municipal wastewater systems in the selection of antibiotic-resistant bacteria, biofilms were investigated using enterococci, staphylococci, Enterobacteriaceae, and heterotrophic bacteria as indicator organisms. In addition to wastewater, biofilms were also investigated in drinking water from river bank filtrate to estimate the occurrence of resistant bacteria and their resistance genes, thus indicating possible transfer from wastewater and surface water to the drinking water distribution network. Vancomycin-resistant enterococci were characterized by antibiograms, and the vanA resistance gene was detected by molecular biology methods, including PCR. The vanA gene was found not only in wastewater biofilms but also in drinking water biofilms in the absence of enterococci, indicating possible gene transfer to autochthonous drinking water bacteria. The mecA gene encoding methicillin resistance in staphylococci was detected in hospital wastewater biofilms but not in any other compartment. Enterobacterial ampC resistance genes encoding beta-lactamase activities were amplified by PCR from wastewater, surface water and drinking water biofilms.

Bactericidal effect of the Er:YAG laser on dental implant surfaces: an in vitro study.

BACKGROUND: The aim of the in vitro study was to examine the bactericidal effect of an Er:YAG laser on common dental implant surfaces. METHODS: Seventy-two titanium platelets with 3 different surfaces--sandblasted and acid-etched (SA), titanium plasma-sprayed (TPS), and hydroxyapatite-coated (HA)--were incubated with a suspension of Streptococcus sanguinis (ATCC 10556). Irradiation at pulse energies of 60 and 120 mJ and a frequency of 10 pps was performed on a computer-controlled XY translation stage. After laser treatment the specimens were sonicated and the bacterial growth examined by counting colony forming units on blood agar plates. Temperature elevations during irradiation were investigated using K-type thermocouples. Laser treated implant surfaces were analyzed by means of electron microscopy. RESULTS: Compared to non-irradiated specimens, mean bacterial reductions of 99.51% (SA), 98.39% (HA), and 99.6% (TPS) at a pulse energy of 60 mJ and 99.92% (SA), 99.85% (HA), and 99.94% (TPS) at 120 mJ were calculated. At these laser parameters, no excessive temperature elevations or morphological implant surface alterations were detected. CONCLUSIONS: Even at low energy densities, the Er:YAG laser has a high bactericidal potential on common implant surfaces. Clinical studies are justified to evaluate the applicability and efficacy of the Er:YAG laser in the treatment of peri-implantitis.