Dynamics of nanocluster aerosol in the indoor atmosphere during gas cooking.

Nanocluster aerosol (NCA: particles in the size range of 1-3 nm) are a critically important, yet understudied, class of atmospheric aerosol particles. NCA efficiently deposit in the human respiratory system and can translocate to vital organs. Due to their high surface area-to-mass ratios, NCA are associated with a heightened propensity for bioactivity and toxicity. Despite the human health relevance of NCA, little is known regarding the prevalence of NCA in indoor environments where people spend the majority of their time. In this study, we quantify the formation and transformation of indoor atmospheric NCA down to 1 nm via high-resolution online nanoparticle measurements during propane gas cooking in a residential building. We observed a substantial pool of sub-1.5 nm NCA in the indoor atmosphere during cooking periods, with aerosol number concentrations often dominated by the newly formed NCA. Indoor atmospheric NCA emission factors can reach up to ∼1016 NCA/kg-fuel during propane gas cooking and can exceed those for vehicles with gasoline and diesel engines. Such high emissions of combustion-derived indoor NCA can result in substantial NCA respiratory exposures and dose rates for children and adults, significantly exceeding that for outdoor traffic-associated NCA. Combustion-derived indoor NCA undergo unique size-dependent physical transformations, strongly influenced by particle coagulation and condensation of low-volatility cooking vapors. We show that indoor atmospheric NCA need to be measured directly and cannot be predicted using conventional indoor air pollution markers such as PM2.5 mass concentrations and NO x (NO + NO2) mixing ratios.

Siloxane Emissions and Exposures during the Use of Hair Care Products in Buildings.

Cyclic volatile methyl siloxanes (cVMS) are ubiquitous in hair care products (HCPs). cVMS emissions from HCPs are of concern, given the potential adverse impact of siloxanes on the environment and human health. To characterize cVMS emissions and exposures during the use of HCPs, realistic hair care experiments were conducted in a residential building. Siloxane-based HCPs were tested using common hair styling techniques, including straightening, curling, waving, and oiling. VOC concentrations were measured via proton-transfer-reaction time-of-flight mass spectrometry. HCP use drove rapid changes in the chemical composition of the indoor atmosphere. cVMS dominated VOC emissions from HCP use, and decamethylcyclopentasiloxane (D5) contributed the most to cVMS emissions. cVMS emission factors (EFs) during hair care routines ranged from 110-1500 mg/person and were influenced by HCP type, styling tools, operation temperatures, and hair length. The high temperature of styling tools and the high surface area of hair enhanced VOC emissions. Increasing the hair straightener temperature from room temperature to 210 °C increased cVMS EFs by 50-310%. Elevated indoor cVMS concentrations can result in substantial indoor-to-outdoor transport of cVMS via ventilation (0.4-6 tons D5/year in the U.S.); thus, hair care routines may augment the abundance of cVMS in the outdoor atmosphere.

25 year experience of patterns of plasma vitamin C levels in patients requiring home parenteral support.

OBJECTIVE: Vitamin C deficiency is common in patients with chronic intestinal failure. Risk factors are poorly understood and guidelines for monitoring largely based on expert opinion. The aim of this study was to describe patterns of vitamin C deficiency in patients on long-term home parenteral support (HPS). DESIGN: A retrospective review of a prospectively collated database for 236 HPS patients cared for in Glasgow, from 1998 to 2023, was interrogated for subjects with paired CRP and vitamin C measurements. Following analysis of the impact of CRP on vitamin C levels, further review of associated clinical, micronutrient and dietetic details in those with a paired CRP <5 mg L-1 were used to identify risk factors for hypoascorbataemia. RESULTS: 1527 recorded episodes with paired CRP and vitamin C measurements were analysed. Period prevalence of hypoascorbataemia was between 29.3 and 52.5%, depending on choice of the lower reference range for vitamin C as either 15 µmol L-1 or 26.1 µmol L-1. The influence of CRP appeared most significant early during HPS with other factors, including extensive mucosal disease, precedent surgery or presence of a colostomy identified as more significant on multivariate analysis for those on long-term HPS (OR 1.3261-1.5609, 1.0752-1.1008, and 0.6260-0.6663 for threshold vitamin C of 26.1 or 15 µmol L-1 respectively). CONCLUSION: Vitamin C may present differently in long term HPS patients in comparison to those in the acute phase of illness. An evidence based approach to guideline development should be promoted to reduce morbidity.

Investigating the Relationship between Home Parenteral Support and Needs-Based Quality of Life in Patients with Chronic Intestinal Failure: A National Multi-Centre Longitudinal Cohort Study.

Home parenteral support (HPS) is an essential but potentially burdensome treatment that can affect quality of life (QoL). The aims of this longitudinal study were to understand whether any changes in HPS over time were associated with QoL. The Parenteral Nutrition Impact Questionnaire (PNIQ) was used, and data were collected on HPS prescribed at three time points. Data were analysed using multi-level mixed regression models presented as effect size and were adjusted for confounders. Study recruited 572 participants from 15 sites. Of these, 201 and 145 completed surveys at second and third time-points, respectively. PNIQ score was out of 20 with a higher score indicating poorer QoL. Any reduction in HPS infusions per week was associated with an improved PNIQ score of -1.10 (95% CI -2.17, -0.02) unadjusted and -1.34 (95% CI -2.45, -0.24) adjusted. Per day change to the number of infusions per week was associated with a change in the PNIQ score of 0.32 (95% CI -0.15, 0.80) unadjusted and 0.34 (95% CI -0.17, 0.85) adjusted. This is the largest national study to demonstrate improvements in QoL associated with HPS reduction over time using an HPS-specific and patient-centric tool, adding unique data for use of therapies in intestinal failure.

Measurements of Hydroxyl Radical Concentrations during Indoor Cooking Events: Evidence of an Unmeasured Photolytic Source of Radicals.

The hydroxyl radical (OH) is the dominant oxidant in the outdoor environment, controlling the lifetimes of volatile organic compounds (VOCs) and contributing to the growth of secondary organic aerosols. Despite its importance outdoors, there have been relatively few measurements of the OH radical in indoor environments. During the House Observations of Microbial and Environmental Chemistry (HOMEChem) campaign, elevated concentrations of OH were observed near a window during cooking events, in addition to elevated mixing ratios of nitrous acid (HONO), VOCs, and nitrogen oxides (NOX). Particularly high concentrations were measured during the preparation of a traditional American Thanksgiving dinner, which required the use of a gas stove and oven almost continually for 6 h. A zero-dimensional chemical model underpredicted the measured OH concentrations even during periods when direct sunlight illuminated the area near the window, which increases the rate of OH production by photolysis of HONO. Interferences with measurements of nitrogen dioxide (NO2) and ozone (O3) suggest that unmeasured photolytic VOCs were emitted during cooking events. The addition of a VOC that photolyzes to produce peroxy radicals (RO2), similar to pyruvic acid, into the model results in better agreement with the OH measurements. These results highlight our incomplete understanding of the nature of oxidation in indoor environments.

Primed and cued: long-term acoustic telemetry links interannual and seasonal variations in freshwater flows to the spawning migrations of Common Snook in the Florida Everglades.

BACKGROUND: Spawning migrations are a widespread phenomenon among fishes, often occurring in response to environmental conditions prompting movement into reproductive habitats (migratory cues). However, for many species, individual fish may choose not to migrate, and research suggests that conditions preceding the spawning season (migratory primers) may influence this decision. Few studies have provided empirical descriptions of these prior conditions, partly due to a lack of long-term data allowing for robust multi-year comparisons. To investigate how primers and cues interact to shape the spawning migrations of coastal fishes, we use acoustic telemetry data from Common Snook (Centropomus undecimalis) in Everglades National Park, Florida, USA. A contingent of Snook migrate between rivers and coastal spawning sites, varying annually in both the proportion of the population that migrates and the timing of migration within the spawning season. However, the specific environmental factors that serve as migratory primers and cues remain unknown. METHODS: We used eight years of acoustic telemetry data (2012-2019) from 173 tagged Common Snook to investigate how primers and cues influence migratory patterns at different temporal scales. We hypothesize that (1) interannual differences in hydrologic conditions preceding the spawning season contribute to the number of individuals migrating each year, and (2) specific environmental cues trigger the timing of migrations during the spawning season. We used GLMMs to model both the annual and seasonal migratory response in relation to flow characteristics (water level, rate of change in water level), other hydrologic/abiotic conditions (temperature, salinity), fish size, and phenological cues independent of riverine conditions (photoperiod, lunar cycle). RESULTS: We found that the extent of minimum marsh water level prior to migration and fish size influence the proportion of Snook migrating each year, and that high river water level and daily rates of change serve as primary cues triggering migration timing. CONCLUSION: Our findings illustrate how spawning migrations are shaped by environmental factors acting at different temporal scales and emphasize the importance of long-term movement data in understanding these patterns. Research providing mechanistic descriptions of conditions that promote migration and reproduction can help inform management decisions aimed at conserving ecologically and economically important species.

Comparison of Simultaneous Measurements of Indoor Nitrous Acid: Implications for the Spatial Distribution of Indoor HONO Emissions.

Despite its importance as a radical precursor and a hazardous pollutant, the chemistry of nitrous acid (HONO) in the indoor environment is not fully understood. We present results from a comparison of HONO measurements from a time-of-flight chemical ionization mass spectrometer (ToF-CIMS) and a laser photofragmentation/laser-induced fluorescence (LP/LIF) instrument during the House Observations of Microbial and Environmental Chemistry (HOMEChem) campaign. Experiments during HOMEChem simulated typical household activities and provided a dynamic range of HONO mixing ratios. The instruments measured HONO at different locations in a house featuring a typical air change rate (ACR) (0.5 h-1) and an enhanced mixing rate (∼8 h-1). Despite the distance between the instruments, measurements from the two instruments agreed to within their respective uncertainties (slope = 0.85, R2 = 0.92), indicating that the lifetime of HONO is long enough for it to be quickly distributed indoors, although spatial gradients occurred during ventilation periods. This suggests that emissions of HONO from any source can mix throughout the house and can contribute to OH radical production in sunlit regions, enhancing the oxidative capacity indoors. Measurement discrepancies were likely due to interferences with the LP/LIF instrument as well as calibration uncertainties associated with both instruments.

Chemistry and human exposure implications of secondary organic aerosol production from indoor terpene ozonolysis.

Surface cleaning using commercial disinfectants, which has recently increased during the coronavirus disease 2019 pandemic, can generate secondary indoor pollutants both in gas and aerosol phases. It can also affect indoor air quality and health, especially for workers repeatedly exposed to disinfectants. Here, we cleaned the floor of a mechanically ventilated office room using a commercial cleaner while concurrently measuring gas-phase precursors, oxidants, radicals, secondary oxidation products, and aerosols in real-time; these were detected within minutes after cleaner application. During cleaning, indoor monoterpene concentrations exceeded outdoor concentrations by two orders of magnitude, increasing the rate of ozonolysis under low (<10 ppb) ozone levels. High number concentrations of freshly nucleated sub-10-nm particles (≥105 cm-3) resulted in respiratory tract deposited dose rates comparable to or exceeding that of inhalation of vehicle-associated aerosols.

The impacts of mangrove range expansion on wetland ecosystem services in the southeastern United States: Current understanding, knowledge gaps, and emerging research needs.

Climate change is transforming ecosystems and affecting ecosystem goods and services. Along the Gulf of Mexico and Atlantic coasts of the southeastern United States, the frequency and intensity of extreme freeze events greatly influence whether coastal wetlands are dominated by freeze-sensitive woody plants (mangrove forests) or freeze-tolerant grass-like plants (salt marshes). In response to warming winters, mangroves have been expanding and displacing salt marshes at varying degrees of severity in parts of north Florida, Louisiana, and Texas. As winter warming accelerates, mangrove range expansion is expected to increasingly modify wetland ecosystem structure and function. Because there are differences in the ecological and societal benefits that salt marshes and mangroves provide, coastal environmental managers are challenged to anticipate the effects of mangrove expansion on critical wetland ecosystem services, including those related to carbon sequestration, wildlife habitat, storm protection, erosion reduction, water purification, fisheries support, and recreation. Mangrove range expansion may also affect wetland stability in the face of extreme climatic events and rising sea levels. Here, we review the current understanding of the effects of mangrove range expansion and displacement of salt marshes on wetland ecosystem services in the southeastern United States. We also identify critical knowledge gaps and emerging research needs regarding the ecological and societal implications of salt marsh displacement by expanding mangrove forests. One consistent theme throughout our review is that there are ecological trade-offs for consideration by coastal managers. Mangrove expansion and marsh displacement can produce beneficial changes in some ecosystem services, while simultaneously producing detrimental changes in other services. Thus, there can be local-scale differences in perceptions of the impacts of mangrove expansion into salt marshes. For very specific local reasons, some individuals may see mangrove expansion as a positive change to be embraced, while others may see mangrove expansion as a negative change to be constrained.

Influence of Mechanical Ventilation Systems and Human Occupancy on Time-Resolved Source Rates of Volatile Skin Oil Ozonolysis Products in a LEED-Certified Office Building.

Building mechanical ventilation systems are a major driver of indoor air chemistry as their design and operation influences indoor ozone (O3) concentrations, the dilution and transport of indoor-generated volatile organic compounds (VOCs), and indoor environmental conditions. Real-time VOC and O3 measurements were integrated with a building sensing platform to evaluate the influence of mechanical ventilation modes and human occupancy on the dynamics of skin oil ozonolysis products (SOOPs) in an office in a LEED-certified building during the winter. The ventilation system operated under variable recirculation ratios (RRs) from RR = 0 (100% outdoor air) to RR = 1 (100% recirculation air). Time-resolved source rates for 6-methyl-5-hepten-2-one (6-MHO), 4-oxopentanal (4-OPA), and decanal were highly dynamic and changed throughout the day with RR and occupancy. Total SOOP source rates during high-occupancy periods (10:00-18:00) varied from 2500-3000 µg h-1 when RR = 0.1 to 6300-6700 µg h-1 when RR = 1. Source rates for gas-phase reactions, outdoor air, and occupant-associated emissions generally decreased with increasing RR. The recirculation air source rate increased with RR and typically became the dominant source for RR > 0.5. SOOP emissions from surface reservoirs were also a prominent source, contributing 10-50% to total source rates. Elevated per person SOOP emission factors were observed, potentially due to multiple layers of soiled clothing worn during winter.

Optimization of sepsis therapy based on patient-specific digital precision diagnostics using next generation sequencing (DigiSep-Trial)-study protocol for a randomized, controlled, interventional, open-label, multicenter trial.

BACKGROUND: Sepsis is triggered by an infection and represents one of the greatest challenges of modern intensive care medicine. With regard to a targeted antimicrobial treatment strategy, the earliest possible pathogen detection is of crucial importance. Until now, culture-based detection methods represent the diagnostic gold standard, although they are characterized by numerous limitations. Culture-independent molecular diagnostic procedures represent a promising alternative. In particular, the plasmatic detection of circulating, cell-free DNA by next-generation sequencing (NGS) has shown to be suitable for identifying disease-causing pathogens in patients with bloodstream infections. METHODS: The DigiSep-Trial is a randomized, controlled, interventional, open-label, multicenter trial characterizing the effect of the combination of NGS-based digital precision diagnostics with standard-of-care microbiological analyses compared to solely standard-of-care microbiological analyses in the clinical picture of sepsis/septic shock. Additional anti-infective expert consultations are provided for both study groups. In 410 patients (n = 205 per arm) with sepsis/septic shock, the study examines whether the so-called DOOR-RADAR (Desirability of Outcome Ranking/Response Adjusted for Duration of Antibiotic Risk) score (representing a combined endpoint including the criteria (1) intensive/intermediate care unit length of stay, (2) consumption of antibiotics, (3) mortality, and (4) acute kidney injury (AKI)) can be improved by an additional NGS-based diagnostic concept. We also aim to investigate the cost-effectiveness of this new diagnostic procedure. It is postulated that intensive/intermediate care unit length of stay, mortality rate, incidence of AKI, the duration of antimicrobial therapy as well as the costs caused by complications and outpatient aftercare can be reduced. Moreover, a significant improvement in patient's quality of life is expected. DISCUSSION: The authors´ previous work suggests that NGS-based diagnostics have a higher specificity and sensitivity compared to standard-of-care microbiological analyses for detecting bloodstream infections. In combination with the here presented DigiSep-Trial, this work provides the optimal basis to establish a new NGS-driven concept as part of the national standard based on the best possible evidence. TRIAL REGISTRATIONS: DRKS-ID DRKS00022782 . Registered on August 25, 2020 ClinicalTrials.gov NCT04571801 . Registered October 1, 2020.

Next-Generation Sequencing-Based Decision Support for Intensivists in Difficult-to-Diagnose Disease States: A Case Report of Invasive Cerebral Aspergillosis.

Aspergillus spp. are widespread environmental pathogens that can induce invasive aspergillosis, especially in immunocompromised patients. An 86-year-old female patient presented with a rare case of invasive cerebral aspergillosis. The aspergilloma invaded the intracranial region originating from the ethmoidal sinus and the orbital apex. In contrast to routine diagnostic procedures, next-generation sequencing (NGS) was able to identify the fungal pathogen in the cerebrospinal fluid as well as in plasma samples, supporting the biopsy-based diagnosis of invasive cerebral aspergillosis. Therefore, NGS-based diagnostics may be of particular importance for difficult-to-diagnose disease states, when conventional diagnostic procedures fail.

Tropicalization of temperate ecosystems in North America: The northward range expansion of tropical organisms in response to warming winter temperatures.

Tropicalization is a term used to describe the transformation of temperate ecosystems by poleward-moving tropical organisms in response to warming temperatures. In North America, decreases in the frequency and intensity of extreme winter cold events are expected to allow the poleward range expansion of many cold-sensitive tropical organisms, sometimes at the expense of temperate organisms. Although ecologists have long noted the critical ecological role of winter cold temperature extremes in tropical-temperate transition zones, the ecological effects of extreme cold events have been understudied, and the influence of warming winter temperatures has too often been left out of climate change vulnerability assessments. Here, we examine the influence of extreme cold events on the northward range limits of a diverse group of tropical organisms, including terrestrial plants, coastal wetland plants, coastal fishes, sea turtles, terrestrial reptiles, amphibians, manatees, and insects. For these organisms, extreme cold events can lead to major physiological damage or landscape-scale mass mortality. Conversely, the absence of extreme cold events can foster population growth, range expansion, and ecological regime shifts. We discuss the effects of warming winters on species and ecosystems in tropical-temperate transition zones. In the 21st century, climate change-induced decreases in the frequency and intensity of extreme cold events are expected to facilitate the poleward range expansion of many tropical species. Our review highlights critical knowledge gaps for advancing understanding of the ecological implications of the tropicalization of temperate ecosystems in North America.

Co-Designing a New Yoga-Based Mindfulness Intervention for Survivors of Stroke: A Formative Evaluation.

Movement-based mindfulness interventions (MBI) are complex, multi-component interventions for which the design process is rarely reported. For people with stroke, emerging evidence suggests benefits, but mainstream programs are generally unsuitable. We aimed to describe the processes involved and to conduct a formative evaluation of the development of a novel yoga-based MBI designed for survivors of stroke. We used the Medical Research Council complex interventions framework and principles of co-design. We purposefully approached health professionals and consumers to establish an advisory committee for developing the intervention. Members collaborated and iteratively reviewed the design and content of the program, formatted into a training manual. Four external yoga teachers independently reviewed the program. Formative evaluation included review of multiple data sources and documentation (e.g., formal meeting minutes, focus group discussions, researcher observations). The data were synthesized using inductive thematic analysis. Three broad themes emerged: (a) MBI content and terminology; (b) manual design and readability; and (c) barriers and enablers to deliver the intervention. Various perspectives and feedback on essential components guided finalizing the program. The design phase of a novel yoga-based MBI was strengthened by interdisciplinary, consumer contributions and peer review. The 12-week intervention is ready for testing among survivors of stroke.

Spatial and temporal scales of variability for indoor air constituents.

Historically air constituents have been assumed to be well mixed in indoor environments, with single point measurements and box modeling representing a room or a house. Here we demonstrate that this fundamental assumption needs to be revisited through advanced model simulations and extensive measurements of bleach cleaning. We show that inorganic chlorinated products, such as hypochlorous acid and chloramines generated via multiphase reactions, exhibit spatial and vertical concentration gradients in a room, with short-lived ⋅OH radicals confined to sunlit zones, close to windows. Spatial and temporal scales of indoor constituents are modulated by rates of chemical reactions, surface interactions and building ventilation, providing critical insights for better assessments of human exposure to hazardous pollutants, as well as the transport of indoor chemicals outdoors.

Contrasting Reactive Organic Carbon Observations in the Southeast United States (SOAS) and Southern California (CalNex).

Despite the central role of reactive organic carbon (ROC) in the formation of secondary species that impact global air quality and climate, our assessment of ROC abundance and impacts is challenged by the diversity of species that contribute to it. We revisit measurements of ROC species made during two field campaigns in the United States: the 2013 SOAS campaign in forested Centreville, AL, and the 2010 CalNex campaign in urban Pasadena, CA. We find that average measured ROC concentrations are about twice as high in Pasadena (73.8 µgCsm-3) than in Centreville (36.5 µgCsm-3). However, the OH reactivity (OHR) measured at these sites is similar (20.1 and 19.3 s-1). The shortfall in OHR when summing up measured contributions is 31%, at Pasadena and 14% at Centreville, suggesting that there may be a larger reservoir of unmeasured ROC at the former site. Estimated O3 production and SOA potential (defined as concentration × yield) are both higher during CalNex than SOAS. This analysis suggests that the ROC in urban California is less reactive, but due to higher concentrations of oxides of nitrogen and hydroxyl radicals, is more efficient in terms of O3 and SOA production, than in the forested southeastern U.S.

Cooking, Bleach Cleaning, and Air Conditioning Strongly Impact Levels of HONO in a House.

The relative importance of common activities on indoor nitrous acid (HONO) mixing ratios was explored during high time resolution, month-long measurements by chemical ionization mass spectrometry in a previously unoccupied house. Indoor HONO varied from 0.2 to 84.0 ppb (mean: 5.5 ppb; median 3.8 ppb), an order of magnitude higher than simultaneously measured outdoor values, indicating important indoor sources. They agree well with simultaneous measurements of HONO by Laser-Photofragmentation/Laser-Induced Fluorescence. Before any combustion activities, the mixing ratio of 3.0 ± 0.3 ppb is indicative of secondary sources such as multiphase formation from NO2. Cooking (with propane gas), especially the use of an oven, led to significant enhancements up to 84 ppb, with elevated mixing ratios persisting for a few days due to slow desorption from indoor surface reservoirs. Floor bleach cleaning led to prolonged, substantial decreases of up to 71-90% due to reactive processes. Air conditioning modulated HONO mixing ratios driven by condensation to wet surfaces in the AC unit. Enhanced ventilation also significantly lowered mixing ratios. Other conditions including human occupancy, ozone addition, and cleaning with terpene, natural product, and vinegar cleaners had a much smaller influence on HONO background levels measured following these activities.

Coastal restoration evaluated using dominant habitat characteristics and associated fish communities.

Increasing coastal populations and urban development have led to the loss of estuarine habitats for fish and wildlife. Specifically, a decline in complexity and heterogeneity of tidal marshes and creeks is thought to negatively impact fish communities by altering the function of nursery grounds, including predator refuge and prey resources. To offset these impacts, numerous agencies are restoring degraded habitats while also creating new ones where habitat has been lost. To improve understanding of what contributes to a successful restoration, six quarterly sampling events using two gear types to collect small- and large-bodied fishes were conducted to compare the fish community structure and habitat characteristics at three natural, three restored, and three impacted (i.e. ditched) areas along the coast of Tampa Bay, Florida. Overall, impacted sites had significantly lower small-bodied and juvenile fish diversity than natural and restored areas, while restored sites harbored a greater number of fish species than impacted sites for both large- and small-bodied fish. Habitat features such as shoreline slope differentiated impacted and restored from natural areas. Although we did not find a direct correlation, habitat heterogeneity likely played a role in structuring fish communities. These findings provide guidance for future coastal restoration or modification of existing projects. Specifically, the habitat mosaic approach of creating a geographically compact network of heterogenous habitat characteristics is likely to support fish diversity, while decreasing shoreline slope in a greater amount of area within coastal wetland restorations would more closely mimic natural areas.

Rapid Next-Generation Sequencing-Based Diagnostics of Bacteremia in Septic Patients.

The increasing incidence of bloodstream infections including sepsis is a major challenge in intensive care units worldwide. However, current diagnostics for pathogen identification mainly depend on culture- and molecular-based approaches, which are not satisfactory regarding specificity, sensitivity, and time to diagnosis. Herein, we established a complete diagnostic workflow for real-time high-throughput sequencing of cell-free DNA from plasma based on nanopore sequencing for the detection of the causative agents, which was applied to the analyses of eight samples from four septic patients and three healthy controls, and subsequently validated against standard next-generation sequencing results. By optimization of library preparation protocols for short fragments with low input amounts, a 3.5-fold increase in sequencing throughput could be achieved. With tailored bioinformatics workflows, all eight septic patient samples were found to be positive for relevant pathogens. When considering time to diagnosis, pathogens were identified within minutes after start of sequencing. Moreover, an extrapolation of real-time sequencing performance on a cohort of 239 septic patient samples revealed that more than 90% of pathogen hits would have also been detected using the optimized MinION workflow. Reliable identification of pathogens based on circulating cell-free DNA sequencing using optimized workflows and real-time nanopore-based sequencing can be accomplished within 5 to 6 hours following blood draw. Therefore, this approach might provide therapy-relevant results in a clinically critical timeframe.

Enhanced Performance of Next-Generation Sequencing Diagnostics Compared With Standard of Care Microbiological Diagnostics in Patients Suffering From Septic Shock.

OBJECTIVES: Culture-based diagnostics represent the standard of care in septic patients, but are highly insensitive and in many cases unspecific. We recently demonstrated the general feasibility of next-generation sequencing-based diagnostics using free circulating nucleic acids (cell-free DNA) in plasma samples of septic patients. Within the presented investigation, higher performance of next-generation sequencing-based diagnostics was validated by comparison to matched blood cultures. DESIGN: A secondary analysis of a prospective, observational, single-center study. SETTING: Surgical ICU of a university hospital and research laboratory. PATIENTS: Fifty patients with septic shock, 20 uninfected patients with elective surgery as control cohort. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: From 256 plasma samples of 48 septic patients at up to seven consecutive time points within the 28-day observation period, cell-free DNA was isolated and analyzed by next-generation sequencing and relevance scoring. In parallel, results from culture-based diagnostics (e.g., blood culture) were obtained. Plausibility of blood culture and next-generation sequencing results as well as adequacy of antibiotic therapy was evaluated by an independent expert panel. In contrast to blood culture with a positivity rate of 33% at sepsis onset, the positivity rate for next-generation sequencing-based pathogen identification was 72%. Over the whole study period, blood culture positivity was 11%, and next-generation sequencing positivity was 71%. Ninety-six percent of positive next-generation sequencing results for acute sepsis time points were plausible and would have led to a change to a more adequate therapy in 53% of cases as assessed by the expert evaluation. CONCLUSIONS: Our results show that next-generation sequencing-based analyses of bloodstream infections provide a valuable diagnostic platform for the identification of clinically relevant pathogens with higher sensitivity and specificity than blood culture, indicating that patients might benefit from a more appropriate therapy based on next-generation sequencing-based diagnosis.