Performance of Methicillin-Resistant Staphylococcus aureus Polymerase Chain Reaction Nasal Screening for Ruling Out MRSA Pneumonia in Hospitalized, Immunocompromised Patients.

Background: Recent literature demonstrates support for using methicillin-resistant Staphylococcus aureus (MRSA) nasal swab polymerase chain reaction (NaPCR) screening as an antimicrobial stewardship tool aiding early de-escalation of anti-MRSA antimicrobials. However, immunocompromised patients have been underrepresented in previous studies despite increased risk of morbidity and mortality from multidrug-resistant organisms (MDRO). Objective: The purpose of this study was to determine the negative predictive value (NPV) of the MRSA NaPCR in hospitalized, immunocompromised adult patients with suspected pneumonia. Methods: A single-center, retrospective, observational review was conducted of hospitalized, immunocompromised adult patients that had an MRSA NaPCR obtained between March 1, 2020 and January 10, 2021. For inclusion, bacterial cultures must have been collected within 2 weeks after MRSA NaPCR. The primary outcome was the NPV of MRSA NaPCR in hospitalized, immunocompromised patients with suspected pneumonia. Secondary outcomes include NPV in other infections. Results: Between March 1, 2020 and January 10, 2021, 59 patients with 78 unique cultures, including 28 respiratory cultures, were included in the study. The NPV of the MRSA NaPCR for pneumonia was 91.7%. The NPV for bloodstream infections was 100% and for urinary tract infections was 100%, but interpretation of these results should be cautioned due to the small sample sizes. Conclusion: The NPV of MRSA NaPCR in pneumonia remains high in this study. The MRSA NaPCR has utility as a de-escalation tool in hospitalized, immunocompromised adult patients, but larger studies are warranted to evaluate all immunocompromised patient populations.

Relationships Between Aquatic Toxicity, Chemical Hydrophobicity, and Mode of Action: Log Kow Revisited.

Relationships between toxicity and chemical hydrophobicity have been known for nearly 100 years in mammals and fish, typically using the log of the octanol:water partition coefficient (Kow). The current study reassessed the influence of mode of action (MOA) on acute aquatic toxicity-log Kow relationships using a comprehensive database of 617 organic chemicals with curated and standardized acute toxicity data that did not exceed solubility limits, their consensus log Kow values, and weight of evidence-based MOA classifications (including 6 broad and 26 specific MOAs). A total of 166 significant (p < 0.05) log Kow-toxicity models were developed across six taxa groups that included QSARs for 5 of the broad and 13 of the specific MOAs. In this study, we demonstrate that QSARs based on MOAs can significantly increase LC50 prediction accuracy for specific acting chemicals. Prediction accuracy increases when QSARs are built based on highly specific MOAs, rather than broad MOA classifications. Additionally, we demonstrate that building QSAR models with chemicals in specific MOA groupings, rather than broader MOA groups leads to significantly better estimates. We also evaluated the differences between models developed from mass-based (µg/L) and mole-based (µmol/L) toxicity data and demonstrate that both are suitable for QSAR development with no clear trend in greater model accuracy. Overall, the results reveal that, despite high variance in all taxa and MOA groups, specific MOA-based models can improve the accuracy of aquatic toxicity predictions over more general groupings.Please check and confirm that the authors and their respective affiliations have been correctly identified and amend if necessary.The affiliations are correct.

Environmental Fate of Cl-PFPECAs: Predicting the Formation of PFAS Transformation Products in New Jersey Soils.

Although next-generation per- and polyfluorinated substances (PFAS) were designed and implemented as safer and environmentally degradable alternatives to "forever" legacy PFAS, there is little evidence to support the actual transformation of these compounds and less evidence of the safety of transformed products in the environment. Multiple congeners of one such PFAS alternative, the chloro-perfluoropolyether carboxylates (Cl-PFPECAs), have been found in New Jersey soils surrounding a manufacturing facility. These compounds are ideal candidates for investigating environmental transformation due to the existence of potential reaction centers including a chlorinated carbon and ether linkages. Transformation products of the chemical structures of this class of compounds were predicted based on analogous PFAS transformation pathways documented in peer-reviewed literature. Potential reaction products were used as the basis for high-resolution mass-spectrometric suspect screening of the soils. Suspected transformation products of multiple congeners, the Cl-PFPECAs, including H-PFPECAs, epox-PFPECAs, and diOH-PFPECAs, were tentatively observed in these screenings. Although ether linkages have been hypothesized as potential reaction centers under environmental conditions, to date, no documentation of ether scission has been identified. Despite exhaustive scrutiny of the high-resolution data for our Cl-PFPECA-laden soils, we found no evidence of ether scission.

Development of a PFAS reaction library: identifying plausible transformation pathways in environmental and biological systems.

Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are used in many consumer applications due to their stain repellency, surfactant properties, ability to form water-proof coatings and use in fire suppression. The production, application, transport, use and disposal of PFAS and PFAS-treated products have resulted in their wide-spread occurrence in environmental and biological systems. Concern over exposure to PFAS and their transformation products and metabolites has necessitated the development of tools to predict the transformation of PFAS in environmental systems and metabolism in biological systems. We have developed reaction libraries for predicting transformation products and metabolites in a variety of environmental and biological reaction systems. These reaction libraries are based on generalized reaction schemes that encode the process science of PFAS reported in the peer-reviewed literature. The PFAS reaction libraries will be executed through the Chemical Transformation Simulator, a web-based tool that is available to the public. These reaction libraries are intended for predicting the environmental transformation and metabolism of PFAS only.

Per- and polyfluoroalkyl substances in the environment.

Over the past several years, the term PFAS (per- and polyfluoroalkyl substances) has grown to be emblematic of environmental contamination, garnering public, scientific, and regulatory concern. PFAS are synthesized by two processes, direct fluorination (e.g., electrochemical fluorination) and oligomerization (e.g., fluorotelomerization). More than a megatonne of PFAS is produced yearly, and thousands of PFAS wind up in end-use products. Atmospheric and aqueous fugitive releases during manufacturing, use, and disposal have resulted in the global distribution of these compounds. Volatile PFAS facilitate long-range transport, commonly followed by complex transformation schemes to recalcitrant terminal PFAS, which do not degrade under environmental conditions and thus migrate through the environment and accumulate in biota through multiple pathways. Efforts to remediate PFAS-contaminated matrices still are in their infancy, with much current research targeting drinking water.

Prioritizing Direct Photolysis Products Predicted by the Chemical Transformation Simulator: Relative Reasoning and Absolute Ranking.

The United States Environmental Protection Agency's Chemical Transformation Simulator (CTS) platform implemented the first freely available reaction library to predict direct photolysis products of organic contaminants in aquatic systems. However, the initial version of the reaction library did not differentiate the formation likelihood of each predicted product, and therefore, the number of predicted products that are not observed tended to exponentially increase with the prediction generation. To alleviate this problem, we first employed relative reasoning algorithms to remove unlikely products. We then ranked different reaction schemes according to their transformation kinetics and removed slowly forming products. Applying the two strategies improved the precision (the percentage of correctly predicted products over all predicted products) by 34% and 53% for the internal evaluation set and the external evaluation set, respectively, when products from three generations were considered. This improved library also revealed new research directions to improve predictions of the dominant phototransformation products.

Reaction Library to Predict Direct Photochemical Transformation Products of Environmental Organic Contaminants in Sunlit Aquatic Systems.

Cheminformatics-based applications to predict transformation pathways of environmental contaminants are useful to quickly prioritize contaminants with potentially toxic/persistent products. Direct photolysis can be an important degradation pathway for sunlight-absorbing compounds in aquatic systems. In this study, we developed the first freely available direct phototransformation pathway predictive tool, which uses a rule-based reaction library. Journal publications studying diverse contaminants (such as pesticides, pharmaceuticals, and energetic compounds) were systematically compiled to encode 155 reaction schemes into the reaction library. The execution result of this predictive tool was internally evaluated against 390 compounds from the compiled journal publications and externally evaluated against 138 compounds from the regulatory reports. The recall (sensitivity) and precision (selectivity) were 0.62 and 0.35, respectively, for internal evaluation, and 0.56 and 0.20, respectively, for external evaluation, when only the products formed from the first reaction step were counted. This predictive tool could help to narrow the data gaps in chemical registration/evaluation and inform future experimental studies.

A Workflow for Identifying Metabolically Active Chemicals to Complement in vitro Toxicity Screening.

The new paradigm of toxicity testing approaches involves rapid screening of thousands of chemicals across hundreds of biological targets through use of in vitro assays. Such assays may lead to false negatives when the complex metabolic processes that render a chemical bioactive in a living system are unable to be replicated in an in vitro environment. In the current study, a workflow is presented for complementing in vitro testing results with in silico and in vitro techniques to identify inactive parents that may produce active metabolites. A case study applying this workflow involved investigating the influence of metabolism for over 1,400 chemicals considered inactive across18 in vitro assays related to the estrogen receptor (ER) pathway. Over 7,500 first-generation and second-generation metabolites were generated for these in vitro inactive chemicals using an in silico software program. Next, a consensus model comprised of four individual quantitative structure activity relationship (QSAR) models was used to predict ER-binding activity for each of the metabolites. Binding activity was predicted for ~8-10% of metabolites in each generation, with these metabolites linked to 259 in vitro inactive parent chemicals. Metabolites were enriched in substructures consisting of alcohol, aromatic, and phenol bonds relative to their inactive parent chemicals, suggesting these features are potentially favorable for ER-binding. The workflow presented here can be used to identify parent chemicals that can be potentially bioactive, to aid confidence in high throughput risk screening.

Demonstration of a consensus approach for the calculation of physicochemical properties required for environmental fate assessments.

Eight software applications are compared for their performance in estimating the octanol-water partition coefficient (Kow), melting point, vapor pressure and water solubility for a dataset of polychlorinated biphenyls, polybrominated diphenyl ethers, polychlorinated dibenzodioxins, and polycyclic aromatic hydrocarbons. The predicted property values are compared against a curated dataset of measured property values compiled from the scientific literature with careful consideration given to the analytical methods used for property measurements of these hydrophobic chemicals. The variability in the predicted values from different calculators generally increases for higher values of Kow and melting point and for lower values of water solubility and vapor pressure. For each property, no individual calculator outperforms the others for all four of the chemical classes included in the analysis. Because calculator performance varies based on chemical class and property value, the geometric mean and the median of the calculated values from multiple calculators that use different estimation algorithms are recommended as more reliable estimates of the property value than the value from any single calculator.

High-throughput in-silico prediction of ionization equilibria for pharmacokinetic modeling.

Chemical ionization plays an important role in many aspects of pharmacokinetic (PK) processes such as protein binding, tissue partitioning, and apparent volume of distribution at steady state (Vdss). Here, estimates of ionization equilibrium constants (i.e., pKa) were analyzed for 8132 pharmaceuticals and 24,281 other compounds to which humans might be exposed in the environment. Results revealed broad differences in the ionization of pharmaceutical chemicals and chemicals with either near-field (in the home) or far-field sources. The utility of these high-throughput ionization predictions was evaluated via a case-study of predicted PK Vdss for 22 compounds monitored in the blood and serum of the U.S. population by the U.S. Centers for Disease Control and Prevention National Health and Nutrition Examination Survey (NHANES). The chemical distribution ratio between water and tissue was estimated using predicted ionization states characterized by pKa. Probability distributions corresponding to ionizable atom types (IATs) were then used to analyze the sensitivity of predicted Vdss on predicted pKa using Monte Carlo methods. 8 of the 22 compounds were predicted to be ionizable. For 5 of the 8 the predictions based upon ionization are significantly different from what would be predicted for a neutral compound. For all but one (foramsulfuron), the probability distribution of predicted Vdss generated by IAT sensitivity analysis spans both the neutral prediction and the prediction using ionization. As new data sets of chemical-specific information on metabolism and excretion for hundreds of chemicals are being made available (e.g., Wetmore et al., 2015), high-throughput methods for calculating Vdss and tissue-specific PK distribution coefficients will allow the rapid construction of PK models to provide context for both biomonitoring data and high-throughput toxicity screening studies such as Tox21 and ToxCast.

Developing and applying metamodels of high resolution process-based simulations for high throughput exposure assessment of organic chemicals in riverine ecosystems.

As defined by Wikipedia (https://en.wikipedia.org/wiki/Metamodeling), "(a) metamodel or surrogate model is a model of a model, and metamodeling is the process of generating such metamodels." The goals of metamodeling include, but are not limited to (1) developing functional or statistical relationships between a model's input and output variables for model analysis, interpretation, or information consumption by users' clients; (2) quantifying a model's sensitivity to alternative or uncertain forcing functions, initial conditions, or parameters; and (3) characterizing the model's response or state space. Using five models developed by the US Environmental Protection Agency, we generate a metamodeling database of the expected environmental and biological concentrations of 644 organic chemicals released into nine US rivers from wastewater treatment works (WTWs) assuming multiple loading rates and sizes of populations serviced. The chemicals of interest have log n-octanol/water partition coefficients (logKOW) ranging from 3 to 14, and the rivers of concern have mean annual discharges ranging from 1.09 to 3240m3/s. Log-linear regression models are derived to predict mean annual dissolved and total water concentrations and total sediment concentrations of chemicals of concern based on their logKOW, Henry's Law Constant, and WTW loading rate and on the mean annual discharges of the receiving rivers. Metamodels are also derived to predict mean annual chemical concentrations in fish, invertebrates, and periphyton. We corroborate a subset of these metamodels using field studies focused on brominated flame retardants and discuss their application for high throughput screening of exposures to human and ecological populations and for analysis and interpretation of field data.

Prediction of Hydrolysis Products of Organic Chemicals under Environmental pH Conditions.

Cheminformatics-based software tools can predict the molecular structure of transformation products using a library of transformation reaction schemes. This paper presents the development of such a library for abiotic hydrolysis of organic chemicals under environmentally relevant conditions. The hydrolysis reaction schemes in the library encode the process science gathered from peer-reviewed literature and regulatory reports. Each scheme has been ranked on a scale of one to six based on the median half-life in a data set compiled from literature-reported hydrolysis rates. These ranks are used to predict the most likely transformation route when more than one structural fragment susceptible to hydrolysis is present in a molecule of interest. Separate rank assignments are established for pH 5, 7, and 9 to represent standard conditions in hydrolysis studies required for registration of pesticides in Organisation for Economic Co-operation and Development (OECD) member countries. The library is applied to predict the likely hydrolytic transformation products for two lists of chemicals, one representative of chemicals used in commerce and the other specific to pesticides, to evaluate which hydrolysis reaction pathways are most likely to be relevant for organic chemicals found in the natural environment.

Runoff water quality during drought in a zero-order georgia piedmont pasture: nitrogen and total organic carbon.

Approximately 11% of the Southern Piedmont (1.8 million ha) is used for pasture and hay production, mostly under low-input management. Few studies have investigated in the region long-term nitrogen and carbon losses in surface runoff, which can be significant. We present 1999 to 2009 hydrologic and water quality data from a rotationally grazed, 7.8-ha, zero-order pasture (W1) near Watkinsville in the Georgia Piedmont. Annual rainfall was 176 to 463 mm below the long-term average (1240 mm) in 7 of the 11 yr. There were 20 runoff events during 86 mo of below-average rainfall (deficit period), compared with 54 events during 46 mo of nondeficit period. Mean event flow-weighted concentration (in mg L) was 0.96 for nitrate-nitrogen (NO-N), 0.97 for ammonium-nitrogen (NH-N), 3.70 for total nitrogen (TN), and 9.12 for total organic carbon (TOC) ( = 43-47; limited due to instrument problem). Nutrient loads (in kg ha per event) averaged 0.04 for NO-N, 0.03 for NH-N, 0.19 for TN, and 0.54 for TOC. Total loads for N and TOC were 6 to 11 times greater from nondeficit than from deficit periods. The observed N concentrations, while well below maximum drinking water standard limits, could pose risk for eutrophication, which can be stimulated at lower concentrations. However, the ability of headwater streams, such as the one downstream of W1, to reduce nutrient concentrations might partially alleviate this concern. The results of this study point to the need to use a long-term dataset that includes measurements made in drought and wet years when evaluating the efficacy of water quality standards.

Feasibility of a new concept for measuring actual functional performance in daily life of transfemoral amputees.

OBJECTIVE: Determining the feasibility of implementing a new concept to objectively evaluate actual functional abilities of transfemoral amputees into a new measuring tool called "Assessment of Daily Activity Performance in Transfemoral amputees" (ADAPT). DESIGN: Study 1: cross-sectional design. Study 2: repeated measures design. SUBJECTS: Study 1 comprised two groups of 10 participants, age range 19-72 years. One group used microprocessor-controlled knee joints and the other group used mechanically controlled knee joints. Study 2 comprised 20 participants, age range 31-68 years. METHODS: Two versions of ADAPT were assessed in the separate studies. In study 1 performance times on version 1 of ADAPT were compared between groups. In study 2 participants completed version 2 of ADAPT twice with a 1 h rest between trials. The Locomotor Capabilities Index was administered. Reliability was determined by calculating correlation coefficients and by Bland-Altman analyses. RESULTS: In study 1, ADAPT version 1 proved to be sensitive in detecting differences in performance between groups. In study 2, 75% of all correlation coefficients exceeded 0.90 in version 2 of ADAPT. Bland-Altman analyses showed high test-retest agreement. CONCLUSION: It is feasible to reliably assess actual functional abilities of transfemoral amputees using standardized simulations of daily activities. This ADAPT concept is able to differentiate between different functional performance levels.

In vitro metabolism of the fungicide and environmental contaminant trans-bromuconazole and implications for risk assessment.

trans-Bromuconazole is a chiral chemical representative of a class of triazole derivatives known to inhibit specific fungal cytochrome P-450 (CYP) reactions. Kinetic measurements and delineation of metabolic pathways for triazole chemicals within in vitro hepatic microsomes are needed for accurate risk assessment and predictive in vivo physiological modeling. The studies described here were conducted with rat liver microsomes to determine Michaelis-Menten saturation kinetic parameters (Vmax and KM) for trans-bromuconazole using both substrate depletion and product formation reaction velocities. Kinetic parameters determined for trans-bromuconazole depletion at varying protein levels incubated at physiological temperature 37 degrees C resulted in a KM value of 1.69 microM and a Vmax value of 1398 pmol/min/mg protein. The concomitant linear formation of two metabolites identified using liquid chromatography/time-of-flight mass spectrometry (LC/MS-TOF) and LC-MS/MS indicated hydroxylation of the trans-bromuconazole dichlorophenyl ring moiety. KM values determined for the hydroxylated metabolites were 0.87 and 1.03 microM, with Vmax values of 449 and 694 pmol/min/mg protein, respectively. Chemical inhibition assays and studies conducted with individual purified human recombinant enzymes indicated the CYP3A subfamily was primarily responsible for biotransformation of the parent substrate. Additionally, trans-bromuconazole was found to undergo stereoselective metabolism as evidenced by a change in the enantiomeric ratio (trans-/trans+) with respect to time.

Estimation of microbial reductive transformation rates for chlorinated benzenes and phenols using a quantitative structure-activity relationship approach.

A set of literature data was used to derive several quantitative structure-activity relationships (QSARs) to predict the rate constants for the microbial reductive dehalogenation of chlorinated aromatics. Dechlorination rate constants for 25 chloroaromatics were corrected for the effects of hydrophobic partitioning and adjusted for the observed distribution of product species. A number of physicochemical properties and molecular parameters were considered for inclusion in the QSARs. Multivariate statistical analyses were used to select the optimal set of descriptors to minimize multicollinearity between the descriptors, as well as to minimize the p-value of the regression coefficients. The final QSAR included four descriptors: The logarithm of the octanol-water partition coefficient (Kow), the summation of the Hammett sigma constants, and the sigma induction constants in the ortho and meta positions relative to the transformation reaction center. The predictive ability of this QSAR was evaluated using 24 site-specific rate constants that were measured in five separate studies and were not used to derive the expression. The peer-reviewed literature was screened carefully to ensure that all rate constant data were representative of environmentally relevant conditions.

H2 consumption during the microbial reductive dehalogenation of chlorinated phenols and tetrachloroethene.

Competition for molecular hydrogen exists among hydrogen-utilizing microorganisms in anoxic environments, and evidence suggests that lower hydrogen concentrations are observed with more energetically favorable electron-accepting processes. The transfer of electrons to organochlorines via reductive dehalogenation reactions plays an important role in hydrogen dynamics in impacted systems. We studied the flux of aqueous hydrogen concentrations in methanogenic sediment microcosms prior to and during reductive dehalogenation of a variety of substituted chlorophenols (CP) and tetrachloroethene (perchloroethylene, PCE). Mean hydrogen concentrations during reductive dehalogenation of 2,4-CP, 2,3,4-CP, and PCP were 3.6 nM, 4.1 nM, and 0.34 nM, respectively. Sediment microcosms that were not dosed with chlorophenols yet were actively methanogenic maintained a significantly higher mean hydrogen concentration of 9.8 nM. During active PCE dehalogenation, sediment microcosms maintained a mean hydrogen concentration of 0.82 nM. These data indicate that during limiting hydrogen production, the threshold ecosystem hydrogen concentration is controlled by microbial populations that couple hydrogen oxidation to thermodynamically favorable electron accepting reactions, including reductive dehalogenation of chloroaromatic and chloroaliphatic compounds. We also present revised estimates for the Gibbs free energy available from the reductive dehalogenation of a variety of substituted chlorophenols based on recently published values of vapor pressure, solubility, and pKa for these compounds.