Lessons learnt on the impact of an unprecedented soil decontamination program in Fukushima on contaminant fluxes.

In the context of elevated concerns related to nuclear accidents and warfare, the lessons learnt from the Fukushima Daiichi Nuclear Power Plant accident in 2011 are important. In particular, Japanese authorities implemented an ambitious decontamination program to reduce the air dose rate in order to facilitate the return of the local inhabitants to previously evacuated areas. This approach contrasts the strategy adopted in Chernobyl, where the most contaminated areas remain off limits. Nonetheless, the effectiveness of the Japanese decontamination strategy on the dispersion of radioactive contaminant fluxes across mountainous landscapes exposed to typhoons has not been quantified. Based on the unique combination of river monitoring and modeling in a catchment representative of the most impacted area in Japan, we demonstrate that decontamination of 16% of the catchment area resulted in a decrease of 17% of sediment-bound radioactive fluxes in rivers. Decontamination operations were therefore relatively effective, although they could only be conducted in a small part of the area due to the dominance of steep forested slopes. In fact, 67% of the initial radiocesium contamination was calculated to remain stored in forested landscapes, which may contribute to future downstream radiocesium dispersion during erosive events. Given that only a limited proportion of the initial population had returned in 2019 (~30%), it raises the question as to whether decontaminating a small percentage of the contaminated area was worth the effort, the price, and the amount of waste generated?

Short-duration selective decontamination of the digestive tract infection control does not contribute to increased antimicrobial resistance burden in a pilot cluster randomised trial (the ARCTIC Study).

OBJECTIVE: Selective decontamination of the digestive tract (SDD) is a well-studied but hotly contested medical intervention of enhanced infection control. Here, we aim to characterise the changes to the microbiome and antimicrobial resistance (AMR) gene profiles in critically ill children treated with SDD-enhanced infection control compared with conventional infection control. DESIGN: We conducted shotgun metagenomic microbiome and resistome analysis on serial oropharyngeal and faecal samples collected from critically ill, mechanically ventilated patients in a pilot multicentre cluster randomised trial of SDD. The microbiome and AMR profiles were compared for longitudinal and intergroup changes. Of consented patients, faecal microbiome baseline samples were obtained in 89 critically ill children. Additionally, samples collected during and after critical illness were collected in 17 children treated with SDD-enhanced infection control and 19 children who received standard care. RESULTS: SDD affected the alpha and beta diversity of critically ill children to a greater degree than standard care. At cessation of treatment, the microbiome of SDD patients was dominated by Actinomycetota, specifically Bifidobacterium, at the end of mechanical ventilation. Altered gut microbiota was evident in a subset of SDD-treated children who returned late longitudinal samples compared with children receiving standard care. Clinically relevant AMR gene burden was unaffected by the administration of SDD-enhanced infection control compared with standard care. SDD did not affect the composition of the oral microbiome compared with standard treatment. CONCLUSION: Short interventions of SDD caused a shift in the microbiome but not of the AMR gene pool in critically ill children at the end mechanical ventilation, compared with standard antimicrobial therapy.

Application of cold argon plasma on germination, root length, and decontamination of soybean cultivars.

Applying cold discharge plasma can potentially alter plants' germination characteristics by triggering their physiological activities. As a main crop in many countries, soybean was examined in the present study using cultivars such as Arian, Katoul, Saba, Sari, and Williams in a cold argon plasma. This study has been motivated by the importance of plant production worldwide, considering climate change and the increasing needs of human populations for food. This study was performed to inspect the effect of cold plasma treatment on seed germination and the impact of argon plasma on microbial decontamination was investigated on soybeans. Also, the employed cultivars have not been studied until now the radicals generated from argon were detected by optical emission spectrometry (OES), and a collisional radiative model was used to describe electron density. The germination properties, including final germination percentage (FGP), mean germination time (MGT), root length, and electrical conductivity of biomolecules released from the seeds, were investigated after the plasma treatments for 30, 60, 180, 300, and 420 s. The decontamination effect of the plasma on Aspergillus flavus (A.flavus) and Fusarium solani (F.solani) was also examined. The plasma for 60 s induced a maximum FGP change of 23.12 ± 0.34% and a lowest MGT value of 1.40 ± 0.007 days. Moreover, the ultimate root length was 56.12 ± 2.89%, in the seeds treated for 60 s. The plasma exposure, however, failed to yield a significant enhancement in electrical conductivity, even when the discharge duration was extended to 180 s or longer. Therefore, the plasma duration of 180 s was selected for the blotter technique. Both fungi showed successful sterilization; their infectivity inhibition was 67 ± 4 and 65 ± 3.1%, respectively. In general, the cold plasma used for soybeans in the present study preserved their healthy qualities and reduced the degree of fungal contamination.

Hostile: accurate decontamination of microbial host sequences.

MOTIVATION: Microbial sequences generated from clinical samples are often contaminated with human host sequences that must be removed for ethical and legal reasons. Care must be taken to excise host sequences without inadvertently removing target microbial sequences to the detriment of downstream analyses such as variant calling and de novo assembly. RESULTS: To facilitate accurate host decontamination of both short and long sequencing reads, we developed Hostile, a tool capable of accurate host read removal using a laptop. We demonstrate that our approach removes at least 99.6% of real human reads and retains at least 99.989% of simulated bacterial reads. Using Hostile with a masked reference genome further increases bacterial read retention (≥99.997%) with negligible (≤0.001%) reduction in human read removal performance. Compared with an existing tool, Hostile removes 21%-23% more human short reads and 21-43 times fewer bacterial reads, typically in less time. AVAILABILITY AND IMPLEMENTATION: Hostile is implemented as an MIT-licensed Python package available from https://github.com/bede/hostile together with supplementary material.

Enhanced antimicrobial efficacy and energy efficiency of low irradiance 405-nm light for bacterial decontamination.

Due to its increased safety over ultraviolet light, there is interest in the development of antimicrobial violet-blue light technologies for infection control applications. To ensure compatibility with exposed materials and tissue, the light irradiances and dose regimes used must be suitable for the target application. This study investigates the antimicrobial dose responses and germicidal efficiency of 405 nm violet-blue light when applied at a range of irradiance levels, for inactivation of surface-seeded and suspended bacteria. Bacteria were seeded onto agar surfaces (101-108 CFUplate-1) or suspended in PBS (103-109 CFUmL-1) and exposed to increasing doses of 405-nm light (≤ 288 Jcm-2) using various irradiances (0.5-150 mWcm-2), with susceptibility at equivalent light doses compared. Bacterial reductions ≥ 96% were demonstrated in all cases for lower irradiance (≤ 5 mWcm-2) exposures. Comparisons indicated, on a per unit dose basis, that significantly lower doses were required for significant reductions of all species when exposed at lower irradiances: 3-30 Jcm-2/0.5 mWcm-2 compared to 9-75 Jcm-2/50 mWcm-2 for low cell density (102 CFUplate-1) surface exposures and 22.5 Jcm-2/5 mWcm-2 compared to 67.5 Jcm-2/150 mWcm-2 for low density (103 CFUmL-1) liquid exposures (P ≤ 0.05). Similar patterns were observed at higher densities, excluding S. aureus exposed at 109 CFUmL-1, suggesting bacterial density at predictable levels has minimal influence on decontamination efficacy. This study provides fundamental evidence of the greater energy efficacy of 405-nm light for inactivation of clinically-significant pathogens when lower irradiances are employed, further supporting its relevance for practical decontamination applications.

Ultraviolet C intensity dependence of decontamination efficiency for pathogens as function of repacked metamaterials with screw channels.

A new method for repackaging optical metamaterials formed from quartz spheres (fibers) of various diameters is proposed for ultraviolet C disinfection of infected liquids by pathogens (viruses and bacteria). The main idea of the new equipment is connected with the rotation of a contaminated fluid by screw channels within a metamaterial matrix prepared from UVC fibers/spherical optics, to improve the decontamination efficiency. In demonstration of the viability of this approach, dynamic and static inactivation of Baker's yeast via Ultraviolet C radiation regimes are used in this paper to show the efficacy of decontamination within the screw channels.

Does selective digestive decontamination (SDD) increase antibiotic resistance? Long-term comparison of two intensive care units (with and without SDD) of the same tertiary hospital.

PURPOSE: The aim of this study was to to compare the antimicrobial resistance rate and its relationship with the antibiotic consumption in two separate Intensive Care Units (ICUs) of the same hospital, one with and other without selective decontamination of the digestive tract (SDD). METHODS: We performed a retrospective study in the two ICUs of the Araba University Hospital. Trauma and neurosurgical patients are admitted to the SDD-ICU, and general digestive surgery patients go to the no SDD-ICU. From 2014 to 2018 we analyzed the number of isolates, and the bacterial resistance trends of 47 antimicrobial-microorganism combinations. Additionally, antimicrobial consumption was estimated in both ICUs. Resistance rates were also compared with those reported in ENVIN-HELICS Spanish national registry. RESULTS: In the ICU with SDD protocol, there was a significant decrease in the resistance of E. coli to amoxicillin/clavulanic acid and in the resistance of E. faecalis to high concentration of gentamycin and high concentration of streptomycin. A significant increase of resistance of Staphylococcus coagulasa negative (CoNS) to linezolid in the no SDD-ICU was also detected. Overall, the level of resistance in the SDD-ICU was lower or of the same order than in the ICU without SDD and that reported in the Spanish national registry. CONCLUSIONS: SDD had neither a clinically relevant impact on emergence and spread of resistance, nor in the overall systemic antimicrobial use. The patient type rather than the SDD protocol showed to condition the ecology and therefore, the resistance rate in the ICUs.

aPDI meets PPE: photochemical decontamination in healthcare using methylene blue-where are we now, where will we go?

Personal protective equipment (PPE) reuse, first recommended in the context of the SARS-CoV-2 pandemic, can mitigate shortages in crisis situations and can greatly reduce the environmental impact of typically single-use PPE. Prior to safe reuse, PPE must be sanitized and contaminating pathogens-in current circumstances viruses in particular-must be inactivated. However, many established decontamination procedures are not equitable and remain unavailable in low-resource settings. In mid-2020, an interdisciplinary consortium of researchers first studied the potential of implementing cheap and easy-to-use antimicrobial photodynamic inactivation (aPDI) using methylene blue as photosensitizer to decontaminate face masks and filtering facepiece respirators. In this perspective piece, we describe the development of this novel method, discuss recent advances, and offer insights into how equitable PPE decontamination via methylene blue-based aPDI may be integrated into circular economy policies in the healthcare sector.

Development of a New Permanganate/Chlorite Process for Water Decontamination.

Development of new technologies with strong selectivity for target pollutants and low sensitivity toward a water matrix remains challenging. Herein, we introduced a novel strategy that used chlorite as an activator for Mn(VII) at pH 4.8, turning the inert reactivity of the pollutants toward Mn(VII) into a strong reactivity. This paved a new way for triggering reactions in water decontamination. By utilizing sulfamethoxazole (SMX) as a typical pollutant, we proposed coupled pathways involving electron transfer across hydrogen bonds (TEHB) and oxidation by reactive manganese species. The results indicated that a hydrogen bonding complex, SMX-ClO2-*, formed through chlorite binding the amino group of SMX initially in the TEHB route; such a complex exhibited a stronger reduction capability toward Mn(VII). Chlorite, in the hydrogen bonding complex SMX-ClO2-*, can then complex with Mn(VII). Consequently, a new reactive center (SMX-ClO2--Mn(VII)*) was formed, initiating the transfer of electrons across hydrogen bonds and the preliminary degradation of SMX. This is followed by the involvement of the generated Mn(V)-ClO2-/Mn(III) in the reduction process of Mn(VII). Such a process showed pH-dependent degradation, with a removal ratio ranging from 80% to near-stagnation as pH increased from 4.8 to 7. Combining with pKa analysis showed that the predominant forms of contaminants were crucial for the removal efficiency of pollutants by the Mn(VII)/chlorite process. The impact of the water matrix was demonstrated to have few adverse or even beneficial effects. With satisfactory performance against numerous contaminants, this study introduced a novel Mn(VII) synergistic strategy, and a new reactivity pattern focused on reducing the reduction potential of the contaminant, as opposed to increasing the oxidation potential of oxidants.

Statistical computational optimization approach for photocatalytic-ozonation decontamination of metronidazole in aqueous media using CuFe2O4/SiO2/ZnO nanocomposite.

The increasing use of pharmaceuticals and the ongoing release of drug residues into the environment have resulted in significant threats to environmental sustainability and water safety. In this sense, developing a robust and easy-recovered magnetic nanocomposite with eminent photocatalytic activity is very imperative for detoxifying pharmaceutical compounds. Herein, a systematic study was conducted to investigate the photocatalytic ozonation for eliminating metronidazole (MET) from aqueous media utilizing the CuFe2O4/SiO2/ZnO heterojunction under simulated sunlight irradiation. The composite material was fabricated by a facile hydrothermal method and diagnosed by multiple advanced analytical techniques. Modelling and optimization of MET decontamination by adopting the central composite design (CCD) revealed that 90 % of MET decontamination can be achieved within 120 min of operating time at the optimized circumstance (photocatalyst dose: 1.17 g/L, MET dose: 33.20 mg/L, ozone concentration: 3.99 mg/min and pH: 8.99). In an attempt to scrutinize the practical application of the CuFe2O4/SiO2/ZnO/xenon/O3 system, roughly 56.18% TOC and 73% COD were removed under the optimized operational circumstances during 120 min of degradation time. According to the radical quenching experiments, hydroxyl radicals (HO•) were the major oxidative species responsible for the elimination of MET. The MET degradation rate maintained at 83% after seven consecutive runs, manifesting the efficiency of CuFe2O4/SiO2/ZnO material in the MET removal. Ultimately, the photocatalytic ozonation mechanism over the CuFe2O4/SiO2/ZnO heterojunction of the fabricated nanocomposites was rationally proposed for MET elimination. In extension, the results drawn in this work indicate that integrating photocatalyst and ozonation processes by the CuFe2O4/SiO2/ZnO material can be applied as an efficient and promising method to eliminate tenacious and non-biodegradable contaminants from aqueous environments.

Dispersant-enhanced migration of radiocesium among soil size fractions: A novel strategy for volume reduction of radioactively contaminated soil.

In the aftermath of the Fukushima Daiichi Nuclear Power Plant accident, a pioneering large-scale decontamination project was initiated, aiming to enable the return of evacuees. This project, the first of its kind in human history, involved the transportation of soils collected during decontamination to interim storage facilities. Before recycling or disposal, these soils undergo processes like volume reduction. However, there's a need for innovative methods to reduce volume effectively and treat secondary wastes more efficiently. The current study explores the impact of a dispersant, sodium hexametaphosphate (SHMP), on the behavior of radiocesium (r-Cs: 137Cs) dynamics in different size fractions of radioactively contaminated soils from Fukushima. The solid-phase speciation analysis of Fukushima soils validated that at least 50% of the 137Cs or other minerals are associated with difficult-to-extract soil phases. Nonetheless, the low 137Cs/133Cs ratio in corresponding soil phases implies a slower r-Cs fixation mechanism. The wet-sieving of r-Cs contaminated soil fraction, < 2 mm, with SHMP, resulted in different soil subfractions (2000-212, 212-53, and < 53 µm). Following SHMP treatment, dispersion of > 92% of 137Cs associated with < 212 µm soil size fractions was observed. The migration of 137Cs towards smaller soil size fractions can be attributed to either SHMP-induced cation exchange or the formation of polyvalent complexes involving SHMP and soil minerals. The condensation of 137Cs in < 212 µm, as induced by SHMP, enabled the subsequent reuse of the larger soil fraction (> 212 µm), which was less contaminated. This study provides a new perspective on the effects of dispersants and contributes to a better understanding of the complex interactions among organic carbon, 137Cs, monovalent and polyvalent cations, and soil functional groups concerning the volume reduction of soils contaminated with r-Cs.

Carbon and graphene quantum dots based architectonics for efficient aqueous decontamination by adsorption chromatography technique - Current state and prospects.

Aquatic ecosystems and potable water are being exploited and depleted due to urbanization and the encouragement of extensive industrialization, which induces the scarcity of pure water. However, current decontamination methods are limited and inefficient. Various innovative remediation strategies with novel nanomaterials have recently been demonstrated for wastewater treatment. Carbon dots (C-dots) and graphene quantum dots (GQ-dots) are the most recent frontiers in carbon nanomaterial-based adsorption studies. C-dots are extremely small (1-10 nm) quasi-spherical carbon nanoparticles (mostly sp3 hybridized carbon), whereas GQ-dots are fragments of graphene (1-20 nm) composed of primarily sp2 hybridized carbon. This article highlights the function of C-dots and GQ-dots with their specifications and characteristics for the efficient removal of organic and inorganic contaminants in water via adsorption chromatography. The alteration of adsorption attributes with the hybrid blending of these dots has been critically analyzed. Moreover, various top-down and bottom-up approaches for synthesizing C-dots and GQ-dots, which ultimately affect their morphology and structure, are described in detail. Finally, we review the research deficit in the adsorption of diverse pollutants, fabrication challenges, low molecular weight, self-agglomeration, and the future of the dots by providing research prospects and selectivity and sensitivity perspectives, the importance of post-adsorption optimization strategies and the path toward scalability at the tail of the article.

Insights into the biogeochemical transformation, environmental impacts and biochar-based soil decontamination of antimony.

Every year, a significant amount of antimony (Sb) enters the environment from natural and anthropogenic sources like mining, smelting, industrial operations, ore processing, vehicle emissions, shooting activities, and coal power plants. Humans, plants, animals, and aquatic life are heavily exposed to hazardous Sb or antimonide by either direct consumption or indirect exposure to Sb in the environment. This review summarizes the current knowledge about Sb global occurrence, its fate, distribution, speciation, associated health hazards, and advanced biochar composites studies used for the remediation of soil contaminated with Sb to lessen Sb bioavailability and toxicity in soil. Anionic metal(loid) like Sb in the soil is significantly immobilized by pristine biochar and its composites, reducing their bioavailability. However, a comprehensive review of the impacts of biochar-based composites on soil Sb remediation is needed. Therefore, the current review focuses on (1) the fundamental aspects of Sb global occurrence, global soil Sb contamination, its transformation in soil, and associated health hazards, (2) the role of different biochar-based composites in the immobilization of Sb from soil to increase biochar applicability toward Sb decontamination. The review aids in developing advanced, efficient, and effective engineered biochar composites for Sb remediation by evaluating novel materials and techniques and through sustainable management of Sb-contaminated soil, ultimately reducing its environmental and health risks.

Treatment of peri-implantitis with a flapless surgical access combined with implant surface decontamination and adjunctive systemic antibiotics: A retrospective case series study.

AIM: To evaluate the effectiveness of a flapless surgical approach in the treatment of peri-implantitis and to explore the factors influencing its outcome. MATERIALS AND METHODS: The present retrospective study evaluated patients with at least one implant diagnosed with peri-implantitis and treated with a flapless surgical access, with or without systemic antimicrobials, curettage and, when needed, prostheses modification. Clinical and radiographic parameters were assessed at baseline and at 3 months and at least 12 months. The primary outcome was disease resolution (≤1 bleeding sites, probing depth [PD] ≤5 mm, no bone loss >0.5 mm). Multilevel regression analyses were used to identify predictors influencing the probability of attaining disease resolution. RESULTS: One hundred and seventeen patients with 338 implants were included. Disease resolution was attained in 54.4% of the 338 implants receiving flapless surgical access. At the end of the follow-up period, 111 patients (94.9%) with 295 implants (87.3%) did not require any further treatment, with 81.4% of these implants presenting PD ≤ 5 mm. History of periodontitis and PD at baseline were identified as negative predictors, while compliance with supportive peri-implant care, a machined surface and the adjunctive use of systemic azithromycin or metronidazole were identified as positive predictive factors for disease resolution. CONCLUSIONS: A flapless surgical approach led to disease resolution in 54.4% of the implants with peri-implantitis. Several risk/protective predictors for disease resolution were identified.

Efficacy of a novel three-step decontamination protocol for titanium-based dental implants: An in vitro and in vivo study.

AIM: The aim of the study was to evaluate several mechanical and chemical decontamination methods associated with a newly introduced biofilm matrix disruption strategy for biofilm cleaning and preservation of implant surface features. MATERIALS AND METHODS: Titanium (Ti) discs were obtained by additive manufacturing. Polymicrobial biofilm-covered Ti disc surfaces were decontaminated with mechanical [Ti curette, Teflon curette, Ti brush, water-air jet device, and Er:YAG laser] or chemical [iodopovidone (PVPI) 0.2% to disrupt the extracellular matrix, along with amoxicillin; minocycline; tetracycline; H2 O2 3%; chlorhexidine 0.2%; NaOCl 0.95%; hydrocarbon-oxo-borate-based antiseptic] protocols. The optimal in vitro mechanical/chemical protocol was then tested in combination using an in vivo biofilm model with intra-oral devices. RESULTS: Er:YAG laser treatment displayed optimum surface cleaning by biofilm removal with minimal deleterious damage to the surface, smaller Ti release, good corrosion stability, and improved fibroblast readhesion. NaOCl 0.95% was the most promising agent to reduce in vitro and in vivo biofilms and was even more effective when associated with PVPI 0.2% as a pre-treatment to disrupt the biofilm matrix. The combination of Er:YAG laser followed by PVPI 0.2% plus NaOCl 0.95% promoted efficient decontamination of rough Ti surfaces by disrupting the biofilm matrix and killing remnants of in vivo biofilms formed in the mouth (the only protocol to lead to ~99% biofilm eradication). CONCLUSION: Er:YAG laser + PVPI 0.2% + NaOCl 0.95% can be a reliable decontamination protocol for Ti surfaces, eliminating microbial biofilms without damaging the implant surface.

Immediate dry decontamination using efficient absorbent materials is beneficial following skin exposure to low-volatile toxic chemicals.

In a chemical mass casualty incident requiring skin decontamination, dry removal using absorbent materials may be beneficial to enable immediate decontamination. The efficacy of absorbent materials has therefore been evaluated, alone or procedures including both dry and wet decontamination, following skin exposure to two low volatile toxic chemicals using an in vitro human skin penetration model. Additionally, removal using active carbon wipes was evaluated with or without the Dahlgren Decon solution. All dry decontamination procedures resulted in a significantly decreased skin penetration rate of the industrial chemical 2-butoxyethanol compared to the control without decontamination. Wet decontamination following dry absorption significantly improved the efficacy compared to dry removal alone. Dry decontamination post-exposure to the chemical warfare nerve agent VX showed no decontamination efficacy. However, dry and wet decontamination resulted in a decreased agent skin penetration rate during the last hour of the experiment. At -15°C, significantly reduced VX skin penetration rates were demonstrated for both dry decontamination alone and the dry and wet decontamination procedure. The Dahlgren Decon solution significantly reduced the amount of VX penetrating the skin, but the active carbon wipe alone did not impact the skin penetration rate. In conclusion, absorbent materials are beneficial for the removal of low-volatile chemicals from the skin, but the degree of efficacy varies between chemicals. Despite the variability, immediate dry decontamination using available absorbent materials prior to wet decontamination is recommended as a general procedure for skin decontamination. The procedure should also be prioritized in cold-weather conditions to prevent patient hypothermia.

Glove decontamination procedures to prevent pathogen and DNA cross-contamination among frogs.

Working with aquatic organisms often requires handling multiple individuals in a single session, potentially resulting in cross-contamination by live pathogens or DNA. Most researchers address this problem by disposing of gloves between animals. However, this generates excessive waste and may be impractical for processing very slippery animals that might be easier to handle with cotton gloves. We tested methods to decontaminate cotton or nitrile gloves after contamination with cultured Batrachochytrium dendrobatidis (Bd) or after handling heavily Bd-infected Xenopus laevis with layered cotton and nitrile gloves. Bleach eliminated detectable Bd DNA from culture-contaminated nitrile gloves, but gloves retained detectable Bd DNA following ethanol disinfection. After handling a Bd-infected frog, Bd DNA contamination was greatly reduced by removal of the outer cotton glove, after which either bleach decontamination or ethanol decontamination followed by drying hands with a paper towel lowered Bd DNA below the detection threshold of our assay. These results provide new options to prevent pathogen or DNA cross-contamination, especially when handling slippery aquatic organisms. However, tradeoffs should be considered when selecting an animal handling procedure, such as the potential for cotton gloves to abrade amphibian skin or disrupt skin mucus. Disposing of gloves between animals should remain the gold standard for maintaining biosecurity in sensitive situations.

In adults receiving mechanical ventilation, selective decontamination of the digestive tract reduces hospital mortality.

SOURCE CITATION: Hammond NE, Myburgh J, Seppelt I, et al. Association between selective decontamination of the digestive tract and in-hospital mortality in intensive care unit patients receiving mechanical ventilation: a systematic review and meta-analysis. JAMA. 2022;328:1922-34. 36286098.

Benchmarking MicrobIEM - a user-friendly tool for decontamination of microbiome sequencing data.

BACKGROUND: Microbiome analysis is becoming a standard component in many scientific studies, but also requires extensive quality control of the 16S rRNA gene sequencing data prior to analysis. In particular, when investigating low-biomass microbial environments such as human skin, contaminants distort the true microbiome sample composition and need to be removed bioinformatically. We introduce MicrobIEM, a novel tool to bioinformatically remove contaminants using negative controls. RESULTS: We benchmarked MicrobIEM against five established decontamination approaches in four 16S rRNA amplicon sequencing datasets: three serially diluted mock communities (108-103 cells, 0.4-80% contamination) with even or staggered taxon compositions and a skin microbiome dataset. Results depended strongly on user-selected algorithm parameters. Overall, sample-based algorithms separated mock and contaminant sequences best in the even mock, whereas control-based algorithms performed better in the two staggered mocks, particularly in low-biomass samples (≤ 106 cells). We show that a correct decontamination benchmarking requires realistic staggered mock communities and unbiased evaluation measures such as Youden's index. In the skin dataset, the Decontam prevalence filter and MicrobIEM's ratio filter effectively reduced common contaminants while keeping skin-associated genera. CONCLUSIONS: MicrobIEM's ratio filter for decontamination performs better or as good as established bioinformatic decontamination tools. In contrast to established tools, MicrobIEM additionally provides interactive plots and supports selecting appropriate filtering parameters via a user-friendly graphical user interface. Therefore, MicrobIEM is the first quality control tool for microbiome experts without coding experience.

Training in the use of the water jet and cold atmospheric plasma jet for the decontamination of dental implants.

OBJECTIVES: Clinical trials testing new devices require prior training on dummies to minimize the "learning curve" for patients. Dentists were trained using a novel water jet device for mechanical cleaning of dental implants and with a novel cold plasma device for surface functionalisation during a simulated open flap peri-implantitis therapy. The hypothesis was that there would be a learning curve for both devices. MATERIALS AND METHODS: 11 dentists instrumented 44 implants in a dummy-fixed jaw model. The effect of the water jet treatment was assessed as stain removal and the effect of cold plasma treatment as surface wettability. Both results were analysed using photographs. To improve treatment skills, each dentist treated four implants and checked the results immediately after the treatment as feedback. RESULTS: Water jet treatment significantly improved from the first to the second implant from 62.7% to 75.3% stain removal, with no further improvement up to the fourth implant. The wettability with cold plasma application reached immediately a high level at the first implant and was unchanged to the 4th implant (mean scores 2.7 out of 3). CONCLUSION: A moderate learning curve was found for handling of the water jet but none for handling of the cold plasma. CLINICAL RELEVANCE: Scientific rational for study: Two new devices were developed for peri-implantitis treatment (Dental water jet, cold plasma). Dentists were trained in the use of these devices prior to the trial to minimize learning effects. PRINCIPAL FINDINGS: Experienced dentists learn the handling of the water jet very rapidly and for cold plasma they do not need much training. PRACTICAL IMPLICATIONS: A clinical study is in process. When the planned clinical study will be finished, we will find out, if this dummy head exercise really minimised the learning curve for these devices.