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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Antimicrobial resistance of enteric pathogens in the Military Health System, 2009 – 2019

Abstract Background Acute diarrhea (AD) can have significant impacts on military troop readiness. Medical providers must understand current trends of enteropathogen antimicrobial resistance (AMR) in service members (SMs) to inform proper, timely treatment options. However, little is known of enteric pathogen profiles across the Military Health System (MHS). The primary objectives of this study were to identify gaps in enteric pathogen surveillance within the MHS, describe the epidemiology of AMR in enteric pathogens, and identify trends across the MHS both within the Continental United States (CONUS) and outside of the Continental United States (OCONUS). Methods Health Level 7 (HL7)-formatted laboratory data were queried for all specimens where Salmonella , Shigella , and Campylobacter species, as well as Shiga toxin-producing Escherichia coli ( E. coli ) (STEC) were isolated and certified between 1 January 2009 - 31 December 2019. Antibiotic susceptibility testing (AST) results were queried and summarized where available. Descriptive statistics were calculated for each organism by specimen source, year, and susceptibility testing availability. Results Among a total of 13,852 enteric bacterial isolates, 11,877 (86%) were submitted from CONUS locations. Out of 1479 Shigella spp. and 6755 Salmonella spp. isolates, 1221 (83%) and 5019 (74%), respectively, reported any susceptibility results through the MHS. Overall, only 15% of STEC and 4% of Campylobacter spp. specimens had AST results available. Comparing AST reporting at CONUS versus OCONUS locations, AST was reported for 1175 (83%) and 46 (78%) of Shigella isolates at CONUS and OCONUS locations, respectively, and for 4591 (76%) and 428 (63%) of Salmonella isolates at CONUS and OCONUS locations, respectively. Conclusions This study revealed inconsistent enteropathogen AST conducted across the MHS, with differing trends between CONUS and OCONUS locations. Additional work is needed to assess pathogen-specific gaps in testing and reporting to develop optimal surveillance that supports the health of the force.

Ashbaugh, Hayley↗
DOE OSTI2023

Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics

Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of average nucleotide identity using MUMmer (ANIm) software, which calculates the percent bases aligned between two bacterial genomes and their corresponding ANI values, to set threshold values for determining species consistent with the conventional identification methods of known species. The performance of species identification was evaluated using two datasets: the Reference Genome Dataset v2 (RGDv2), consisting of 43 enteric genome assemblies representing 32 species, and the Test Genome Dataset (TGDv1), comprising 454 genome assemblies which is designed to represent all species needed to query for identification, as well as rare and closely related species. The RGDv2 contains six Campylobacter spp., three Escherichia/Shigella spp., one Grimontia hollisae, six Listeria spp., one Photobacterium damselae, two Salmonella spp., and thirteen Vibrio spp., while the TGDv1 contains 454 enteric bacterial genomes representing 42 different species. The analysis showed that, when a standard minimum of 70% genome bases alignment existed, the ANI threshold values determined for these species were ≥95 for Escherichia/Shigella and Vibrio species, ≥93% for Salmonella species, and ≥92% for Campylobacter and Listeria species. Using these metrics, the RGDv2 accurately classified all validation strains in TGDv1 at the species level, which is consistent with the classification based on previous gold standard methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

In silico analyses of diversity and dissemination of antimicrobial resistance genes and mobile genetics elements, for plasmids of enteric pathogens

The antimicrobial resistance (AMR) mobilome plays a key role in the dissemination of resistance genes encoded by mobile genetics elements (MGEs) including plasmids, transposons (Tns), and insertion sequences (ISs). These MGEs contribute to the dissemination of multidrug resistance (MDR) in enteric bacterial pathogens which have been considered as a global public health risk. To further understand the diversity and distribution of AMR genes and MGEs across different plasmid types, we utilized multiple sequence-based computational approaches to evaluate AMR-associated plasmid genetics. A collection of 1,309 complete plasmid sequences from Gammaproteobacterial species, including 100 plasmids from each of the following 14 incompatibility (Inc) types: A/C, BO, FIA, FIB, FIC, FIIA, HI1, HI2, I1, K, M, N, P except W, where only 9 sequences were available, was extracted from the National Center for Biotechnology Information (NCBI) GenBank database using BLAST tools. The extracted FASTA files were analyzed using the AMRFinderPlus web-based tools to detect antimicrobial, disinfectant, biocide, and heavy metal resistance genes and ISFinder to identify IS/Tn MGEs within the plasmid sequences. In silico prediction based on plasmid replicon types showed that the resistance genes were diverse among plasmids, yet multiple genes were widely distributed across the plasmids from enteric bacterial species. These findings provide insights into the diversity of resistance genes and that MGEs mediate potential transmission of these genes across multiple plasmid replicon types. This notion was supported by the observation that many IS/Tn MGEs and resistance genes known to be associated with them were common across multiple different plasmid types. Our results provide critical insights about how the diverse population of resistance genes that are carried by the different plasmid types can allow for the dissemination of AMR across enteric bacteria. The results also highlight the value of computational-based approaches and in silico analyses for the assessment of AMR and MGEs, which are important elements of molecular epidemiology and public health outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Novel Insights Into the Spread of Enteric Pathogens Using Genomics

Diarrheal diseases continue to be a leading cause of mortality and morbidity across the globe. The use of next-generation sequencing data has provided major insights into understanding epidemiological spread, antimicrobial resistance, vaccine effects, and basic mechanisms of bacterial and viral evolution. Furthermore, we discuss how genomic data have informed investigations across enteric pathogens, such as Shigella, Vibrio cholerae, Salmonella Typhi, rotavirus, and norovirus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

The effect of enrofloxacin on enteric Escherichia coli : Fitting a mathematical model to in vivo data

Antimicrobial drugs administered systemically may cause the emergence and dissemination of antimicrobial resistance among enteric bacteria. To develop logical, research-based recommendations for food animal veterinarians, we must understand how to maximize antimicrobial drug efficacy while minimizing risk of antimicrobial resistance. Our objective is to evaluate the effect of two approved dosing regimens of enrofloxacin (a single high dose or three low doses) on Escherichia coli in cattle. We look specifically at bacteria above and below the epidemiological cutoff (ECOFF), above which the bacteria are likely to have an acquired or mutational resistance to enrofloxacin. We developed a differential equation model for the antimicrobial drug concentrations in plasma and colon, and bacteria populations in the feces. The model was fit to animal data of drug concentrations in the plasma and colon obtained using ultrafiltration probes. Fecal E. coli counts and minimum inhibitory concentrations were measured for the week after receiving the antimicrobial drug. We predict that the antimicrobial susceptibility of the bacteria above the ECOFF pre-treatment strongly affects the composition of the bacteria following treatment. Faster removal of the antimicrobial drugs from the colon throughout the study leads to improved clearance of bacteria above the ECOFF in the low dose regimen. If we assume a fitness cost is associated with bacteria above the ECOFF, the increased fitness costs leads to reduction of bacteria above the ECOFF in the low dose study. These results suggest the initial E. coli susceptibility is a strong indicator of how steers respond to antimicrobial drug treatment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Synthesis and Characterization of a Novel pH-Sensitive Aluminum Crosslinked Carboxymethyl Tragacanth Beads for Extended and Enteric Drug Delivery

Carboxymethyl tragacanth (CM-TG) with a DS of 1.2 was synthesized and characterized for drug delivery using diclofenac sodium as a model drug. The mixture of CM-TG and drug was ionically crosslinked using aluminum chloride to form drug-loaded beads. The concentrations of 10 and 20% w/w solution of CM-TG were found to produce beads with acceptable qualities. The beads exhibited pH-dependent swelling. The highest swelling was observed at pH 6.8 which evidences the possibility to release the drug in the colon. FT-IR and TGA confirmed carboxymethylation of tragacanth and the absence of drug-polymer interaction. The diclofenac sodium entrapment efficiency was 30–35% while the loading varies from 4.5 to 18% w/w based upon the drug-polymer ratio. The beads could extend the drug release up to 180 min at pH 6.8. The pH-responsive CM-TG hydrogel beads are biocompatible and could be exploited as a new excipient in developing enteric release formulations.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Thermally Significant Fluid Seepage Through Thick Sediment on the Juan de Fuca Plate Entering the Cascadia Subduction Zone

We use heat flux measurements colocated with seismic reflection profiles over a buried basement high on the Juan de Fuca plate ∼25 km seaward of the deformation front offshore Oregon to test for the presence of hydrothermal circulation in the oceanic crust. We also revisit heat flux data crossing a buried basement high ∼25 km seaward of the deformation front ∼150 km north, offshore Washington. Seafloor heat flux is inversely correlated with sediment thickness, consistent with vigorous hydrothermal circulation in the basement aquifer homogenizing temperatures at the top of the basement. Heat flux immediately above the summit of the basement highs is greater than expected solely from conduction. Fluid seepage at rates of ∼2.6–5.4 cm yr −1 in a 1–1.5 km-wide conduit through ∼800–1,300 m thick sediment sections above these basement highs can explain these observations. Observations of thermally significant fluid seepage through sediment >225 m thick on oceanic crust are unprecedented. High sediment permeability, high fluid overpressure in the basement, or a combination of both is required to drive fluid seepage at the observed rates. We infer that rapid seepage occurs because the basement highs rise above the low permeability basal sediment with their tops protruding into the base of high permeability Nitinat or Astoria Fan sediment. Seepage from basement highs penetrating into the submarine fans can affect the thermal state of crust entering the subduction zone.

58 GEOSCIENCES↗
DOE OSTI2024

Genotypic analyses of IncHI2 plasmids from enteric bacteria

Incompatibility (Inc) HI2 plasmids are large (typically > 200 kb), transmissible plasmids that encode antimicrobial resistance (AMR), heavy metal resistance (HMR) and disinfectants/biocide resistance (DBR). To better understand the distribution and diversity of resistance-encoding genes among IncHI2 plasmids, computational approaches were used to evaluate resistance and transfer-associated genes among the plasmids. Complete IncHI2 plasmid (N - 667) sequences were extracted from GenBank and analyzed using AMRFinderPlus, IntegronFinder and Plasmid Transfer Factor database. The most common IncHI2-carrying genera included Enterobacter (N = 209), Escherichia (N = 208), and Salmonella (N = 204). Resistance genes distribution was diverse, with plasmids from Escherichia and Salmonella showing general similarity in comparison to Enterobacter and other taxa, which grouped together. Plasmids from Enterobacter and other taxa had a higher prevalence of multiple mercury resistance genes and arsenic resistance gene, arsC, compared to Escherichia and Salmonella. For sulfonamide resistance, sul1 was more common among Enterobacter and other taxa, compared to sul2 and sul3 for Escherichia and Salmonella. Similar gene diversity trends were also observed for tetracyclines, quinolones, β-lactams, and colistin. Over 99% of plasmids carried at least 25 IncHI2-associated conjugal transfer genes. These findings highlight the diversity and dissemination potential for resistance across different enteric bacteria and value of computational-based approaches for the resistance-gene assessment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Disturbance of hibernating bats due to researchers entering caves to conduct hibernacula surveys

Estimating population changes of bats is important for their conservation. Population estimates of hibernating bats are often calculated by researchers entering hibernacula to count bats; however, the disturbance caused by these surveys can cause bats to arouse unnaturally, fly, and lose body mass. We conducted 17 hibernacula surveys in 9 caves from 2013 to 2018 and used acoustic detectors to document cave-exiting bats the night following our surveys. We predicted that cave-exiting flights (i.e., bats flying out and then back into caves) of Townsend’s big-eared bats (Corynorhinus townsendii) and western small-footed myotis (Myotis ciliolabrum) would be higher the night following hibernacula surveys than on nights following no surveys. Those two species, however, did not fly out of caves more than predicted the night following 82% of surveys. Nonetheless, the activity of bats flying out of caves following surveys was related to a disturbance factor (i.e., number of researchers × total time in a cave). We produced a parsimonious model for predicting the probability of Townsend’s big-eared bats flying out of caves as a function of disturbance factor and ambient temperature. That model can be used to help biologists plan for the number of researchers, and the length of time those individuals are in a cave to minimize disturbing bats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Magnetization around mix jets entering inertial confinement fusion fuel

Engineering features are known to cause jets of ablator materials to enter the fuel hot-spot in inertial confinement fusion implosions. The Biermann battery mechanism wraps them in a self-generated magnetic field. Here we show that higher-Z jets have an additional thermoelectric magnetic source term that is not present for hydrogen jets, verified here through a kinetic simulation. It has similar magnitude to the Biermann term. We then include this in an extended magneto-hydrodynamic approach to post process an xRAGE radiation-hydrodynamic implosion simulation. The simulation includes an accurate model for the capsule fill tube, producing a dense carbon jet that becomes wrapped in a 4000 T magnetic field. A simple spherical carbon mix model shows that this insulates the electron heat conduction enough to cause contraction of the jet to an optically thick equilibrium. The denser magnetized jet hydrodynamics could change its core penetration and therefore the final mix mass, which is known to be well correlated with fusion yield degradation. Fully exploring this will require self-consistent magneto-hydrodynamic simulations. Experimental signatures of this self-magnetization may emerge in the high energy neutron spectrum.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Detection of a Space Capsule Entering Earth’s Atmosphere with Distributed Acoustic Sensing (DAS)

On 24 September 2023, the Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer sample return capsule (SRC) entered Earth’s atmosphere after successfully collecting samples from an asteroid. The known trajectory and timing of this return provided a rare opportunity to strategically instrument sites to record geophysical signals produced by the capsule because it travelled at hypersonic speeds through the atmosphere. For this work, we deployed two distributed acoustic sensing (DAS) interrogators to sample over 12 km of surface-draped fiber-optic cables, as well as six collocated seismometer-infrasound sensor pairs, spread across two sites near Eureka, Nevada. This campaign-style rapid deployment is the first reported recording of an SRC re-entry with any distributed fiber-optic sensing technology. The DAS interrogators recorded an impulsive arrival with an extended coda which had features that were similar to recordings from both the seismometers and infrasound sensors. While the signal-to-noise ratio of the DAS data was lower than the seismic-infrasound data, the extremely dense spacing of fiber-optic sensors allowed for more phases to be clearly distinguished and the visualization of the continuous transformation of the wavefront as it impacted the ground. Unexpectedly, the DAS recordings contain less low-frequency content than is present in both the seismic and infrasound data. The deployment conditions strongly affected the recorded DAS data; in particular, we observed that fiber selection and placement exert strong controls on data quality.

58 GEOSCIENCES↗
DOE OSTI2023

Gender Gaps in Mode Usage, Vehicle Ownership, and Spatial Mobility When Entering Parenthood: A Life Course Perspective

Entry into parenthood is a major disruptive event to travel behavior, and gender gaps in mobility choices are often widened during parenthood. The exact timing of gender gap formation and their long-term effects on different subpopulations are less studied in the literature. Leveraging a longitudinal dataset from the 2018 WholeTraveler Study, this paper examines the effects of parenthood on a diverse set of short- to long-term outcomes related to the three hierarchical domains of mobility biography: mode choice, vehicle ownership, spatial mobility, and career decisions. The progress of the effects is evaluated over a sequential set of parenting stages and differentiated across three subpopulations. We find that individuals classified as “Have-it-alls”, who start their careers, partner up, and have children concurrently and early, significantly increase their car uses two years prior to childbirth (“nesting period”), and they then relocate to less transit-accessible areas and consequently reduce their reliance on public transportation while they have children in the household. In contrast, individuals categorized as “Couples”, who start careers and partnerships early but delay parenthood, and “Singles”, who postpone partnership and parenthood, have less pronounced changes in travel behavior throughout the parenting stages. The cohort-level effects are found to be driven primarily by women, whose career development is on average more negatively impacted by parenting events than men, regardless of their life course trajectory. Early career decisions made by women upon entering parenthood contribute to gender gaps in mid- to longer-term mobility decisions, signifying the importance of early intervention.

Yang, Hung-Chia (ORCID:0000000161439904)↗
DOE OSTI2020

The Preservation of Super-Earths and the Emergence of Gas Giants after Their Progenitor Cores Have Entered the Pebble-isolation Phase

The omnipresence of super-Earths suggests that they are able to be retained in natal disks around low-mass stars, whereas exoplanets' mass distributions indicate that some cores have transformed into gas giants through runaway gas accretion at ≳1 au from solar-type stars. In this paper, we show that transition to runaway gas accretion by cores may be self-impeded by an increase of the grain opacity in their envelope after they have acquired sufficient mass (typically ~ 10M ⊕ ) to enter a pebble-isolation phase. The accumulation of approximately millimeter- to meter-sized pebbles in their migration barriers enhances their local fragmentation rates. The freshly produced submillimeter grains pass through the barrier, elevate the effective dust opacity, and reduce the radiative flux in the core's envelope. These effects alone are adequate to suppress the transition to runaway accretion and preserve super-Earths in the stellar proximity (~0.1 au), albeit entropy advection between the envelope and the disk can further reduce the accretion rate. At an intermediate distance (~1 au) from their host stars, the escalation in the dust opacity dominates over entropy advection in stalling the transition to runaway accretion for marginally pebble-isolated cores. Beyond a few astronomical unit, the transformation of more-massive cores to gas giants is reachable before severe depletion of disk gas. This requirement can be satisfied either in extended disks with large scale height via orderly accretion of migrating pebbles or through the mergers of oligarchic protoplanetary embryos, and can account for the correlated occurrence of long-period gas giants and close-in super-Earths.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Entering the Nickel Age of Superconductivity.

After a 30-year quest, researchers found a nickel-based analog of copper oxide superconductors. The discovery motivates the search for other nickelates and should provide new insights into the origin of high-temperature superconductivity.

Norman, Michael R.↗