AIMS: (i) Evaluation of delayed time to blood culture extraction by the Sepsityper kit and impact of shipping pellets off‐site for MALDI‐TOF MS analysis. (ii) Comparison of Sepsityper and ...laboratory‐developed extraction methods from a literature review. METHODS AND RESULTS: Using two blood culture systems (BD BACTEC and VersaTREK), we extracted 411 positive blood cultures using the Sepsityper kit to mimic a potential protocol for institutions without a MALDI‐TOF MS. Extracted pellets were shipped and analysed on the Bruker UltraflexIII. Successful extraction of 358 (87·1%) samples was determined by the presence of detectable proteins. MALDI‐TOF MS correctly identified 332 (80·8%) samples. CONCLUSIONS: Delayed time to extraction did not affect Sepsityper extraction or MALDI‐TOF MS accuracy. The extracted pellets remain stable and provide accurate results by MALDI‐TOF MS when shipped at room temperature to off‐site reference laboratories. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study to show that institutions without a MALDI‐TOF MS can take advantage of this innovative technology by shipping a volume of blood to an off‐site laboratory for extraction and MALDI‐TOF MS analysis. We also performed a literature review to compare various extraction methods.
1. The role of phenotypic plasticity in evolution has historically been a contentious issue because of debate over whether plasticity shields genotypes from selection or generates novel opportunities ...for selection to act. Because plasticity encompasses diverse adaptive and non-adaptive responses to environmental variation, no single conceptual framework adequately predicts the diverse roles of plasticity in evolutionary change. 2. Different types of phenotypic plasticity can uniquely contribute to adaptive evolution when populas are faced with new or altered environments. Adaptive plasticity should promote establishment and persistence in a new environment, but depending on how close the plastic response is to the new favoured phenotypic optimum dictates whether directional selection will cause adaptive divergence between populations. Further, non-adaptive plasticity in response to stressful environments can result in a mean phenotypic response being further away from the favoured optimum or alternatively increase the variance around the mean due to the expression of cryptic genetic variation. The expression of cryptic genetic variation can facilitate adaptive evolution if by chance it results in a fitter phenotype. 3. We conclude that adaptive plasticity that places populations close enough to a new phenotypic optimum for directional selection to act is the only plasticity that predictably enhances fitness and is most likely to facilitate adaptive evolution on ecological timescales in new environments. However, this type of plasticity is likely to be the product of past selection on variation that may have been initially non-adaptive. 4. We end with suggestions on how future empirical studies can be designed to better test the importance of different kinds of plasticity to adaptive evolution.
Background. Clostridium difficile is the leading cause of infectious diarrhea among hospitalized patients and is a major concern for patients undergoing hematopoietic stem cell transplantation ...(HSCT). Risk factors and the natural history of C. difficile infection (CDI) are poorly understood in this population. Methods. We performed a retrospective nested case-control study to describe the epidemiology, timing, and risk factors for CDI among adult patients who received HSCTs at our center from January 2003 through December 2008. Results. The overall 1-year incidence of CDI was 9.2% among HSCTs performed (n = 999). The median time to diagnosis of CDI was short among both autologous and allogeneic HSCT recipients (6.5 days and 33 days, respectively). Risk factors for CDI in allogeneic HSCT recipients included receipt of chemotherapy prior to conditioning for HSCT, broad-spectrum antimicrobial use, and acute graft-versus-host disease (GVHD; adjusted odds ratio AOR, 4.45; 95% confidence interval CI, 1.54—12.84; P = .006). There was a strong relationship between early CDI and subsequent development of gastrointestinal tract GVHD in the year following allogeneic HSCT (P < .001). Gastrointestinal GVHD was also strongly associated with an increased risk for recurrent CDI (AOR, 4.23 95% CI, 1.20—14.86; P = .02). Conclusions. These results highlight the high incidence and early timing of CDI after HSCT. Early timing, coupled with the noted risk of pretransplant chemotherapy, suggests that the natural history of disease in some patients may involve colonization prior to HSCT. A potentially important interplay between CDI and GVHD involving the gastrointestinal tract was observed.
ABSTRACT
We have previously reported on the susceptibility and epidemiology of
Clostridioides difficile
isolates from six geographically dispersed medical centers in the United States. This current ...survey was conducted with isolates collected in 2020–2021 from six geographically dispersed medical centers in the United States, with specific attention to susceptibility to ridinilazole as well as nine comparators.
C. difficile
isolates or stools from patients with
C. difficile
antibiotic-associated diarrhea were collected and referred to a central laboratory. After species confirmation of 300 isolates at the central laboratory, antibiotic susceptibilities were determined by the agar dilution method M11-A9, Clinical and Laboratory Standards Institute (CLSI) against the 10 agents. Ribotyping was performed by PCR capillary gel electrophoresis on all isolates. Ridinilazole had a minimum inhibitory concentration (MIC) 90 of 0.25 mcg/mL, and no isolate had an MIC greater than 0.5 mcg/mL. In comparison, fidaxomicin had an MIC 90 of 0.5 mcg/mL. The vancomycin MIC 90 was 2 mcg/mL with a 0.7% resistance rate both CLSI and European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. The metronidazole MIC 90 was 1 mcg/mL, with none resistant by CLSI criteria, and a 0.3% resistance rate by EUCAST criteria. Among the 50 different ribotypes isolated in the survey, the most common ribotype was 014–020 (14.0%) followed by 106 (10.3%), 027 (10%), 002 (8%), and 078–126 (4.3%). Ridinilazole maintained activity against all ribotypes and all strains resistant to any other agent tested. Ridinilazole showed excellent
in vitro
activity against
C. difficile
isolates collected between 2020 and 2021 in the United States, independent of ribotype.
Cost-effective yet safe creation of high-permeability reservoirs within deep bedrock is the primary challenge for the viability of enhanced geothermal systems (EGS) and unconventional oil/gas ...recovery. Although fracturing fluids are commonly used for oil/gas, standard fracturing methods are not developed or proven for EGS temperatures and pressures. Furthermore, the environmental impacts of currently used fracturing methods are only recently being determined. Widespread concerns about the environmental contamination have resulted in a number of regulations for fracturing fluids advocating for greener fracturing processes. To enable EGS feasibility and lessen environmental impact of reservoir stimulation, an environmentally benign, CO sub(2)-activated, rheoreversible fracturing fluid that enhances permeability through fracturing due to in situ volume expansion and gel formation is investigated herein. The chemical mechanism, stability, phase-change behavior, and rheology for a novel polyallylamine (PAA)-CO sub(2) fracturing fluid was characterized at EGS temperatures and pressures. Hydrogel is formed upon reaction with CO sub(2), and this process is reversible (via CO sub(2) depressurization or solubilizing with a diluted acid) allowing potential removal from the formation and recycling, decreasing environmental impact. Rock obtained from the Coso geothermal field was fractured in laboratory-scale experiments under various EGS temperatures and pressures at significantly (at least an order of magnitude) lower effective stress than standard fracturing fluids, and the fractures were characterized with imaging, permeability measurement, and flow modeling. Although additional work is required to further understand the fluid properties, potential and limitations, this novel fracturing fluid and process represent a potential alternative to conventional fracturing fluids to vastly reduce water usage and the environmental impact of fracturing practices and effectively make EGS production and unconventional oil/gas exploitation cost-effective and cleaner.
Hyporheic exchange in streams is critical to ecosystem functions such as nutrient cycling along river corridors, especially for slowly moving or small stream systems. The transient storage model ...(TSM) has been widely used for modeling of hyporheic exchange. TSM calibration, for hyporheic exchange, is typically used to estimate four parameters, including the mass exchange rate coefficient, the dispersion coefficient, stream cross‐sectional area, and hyporheic zone cross‐sectional area. Prior studies have raised concerns regarding the non‐uniqueness of the inverse problem for the TSM, that is, the occurrence of different parameter vectors resulting in TSM solution that reproduces the observed in‐stream tracer break through curve (BTC) with the same error. This leads to practical non‐identifiability in determining the unknown parameter vector values even when global‐optimal values exist, and the parameter optimization becomes practically non‐unique. To address this problem, we applied the simulated annealing method to calibrate the TSM to BTCs, because it is less susceptible to local minima‐induced non‐identifiability. A hypothetical (or synthetic) tracer test data set with known parameters was developed to demonstrate the capability of the simulated annealing method to find the global minimum parameter vector, and it identified the “hypothetically‐true” global minimum parameter vector even with input data that were modified with up to 10% noise without increasing the number of iterations required for convergence. The simulated annealing TSM was then calibrated using two in‐stream tracer tests conducted in East Fork Poplar Creek, Tennessee. Simulated annealing was determined to be appropriate for quantifying the TSM parameter vector because of its search capability for the global minimum parameter vector.
Plain Language Summary
Hyporheic exchange is critical for biogeochemical and ecological processes in river corridors, and in‐stream tracer testing and modeling are commonly used for exchange characterization. Non‐uniqueness of inverse modeling parameter estimation is a concern for the transient storage model (TSM) for hyporheic exchange as gradient‐based parameter estimation methods tend to get trapped in local minima of the difference between observation and model results, which limits our ability to locate global minimum parameters that provide the closest match between model and data. We used a hypothetical (or synthetic) tracer test data set with known parameters to test simulated annealing as an alternative inverse modeling approach, which was also compared to the results of the commonly used TSM code, OTIS‐P, a modified version of one‐dimensional transport with inflow and storage (OTIS) code, couples the solution of the governing equation of OTIS with a nonlinear regression package (Runkel, 1998a). The simulated annealing method identified the “hypothetically‐true” global minimum parameter vector even with variations in initial guesses of the parameter vector values and input observation data that were modified to include up to 10% noise to account for experimental error. The simulated annealing inverse TSM was also able to identify reasonable/comparable parameters for two tracer tests conducted in East Fork Poplar Creek, Tennessee, which suggests that simulated annealing is a reasonable approach for TSM inverse modeling.
Key Points
Simulated annealing with random initial guesses was able to identify correct parameter values for synthetic case with known parameter vector
Acceptable parameter estimation (without increased iteration requirement) for Transient Storage Model (TSM) even with 5 and 10% noise was added
Simulated annealing method was successfully applied with random initial guesses of the parameter vector for model calibration of two in‐stream tracer test data sets
Sulfate is ubiquitous in groundwater, with both natural and anthropogenic sources. Sulfate reduction reactions play a significant role in mediating redox conditions and biogeochemical processes for ...subsurface systems. They also serve as the basis for innovative in situ methods for groundwater remediation. An overview of sulfate reduction in subsurface environments is provided, along with a brief discussion of characterization methods and applications for addressing acid mine drainage. We then focus on two innovative, in situ methods for remediating sulfate-contaminated groundwater, the use of zero-valent iron and the addition of electron-donor substrates. The advantages and limitations associated with the methods are discussed, with examples of prior applications.
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