An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics.

BACKGROUND: Effective surveillance of microbial communities in the healthcare environment is increasingly important in infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but are currently challenged by several limitations: (1) they are not powerful enough to extract valid signals out of the background noise for low-biomass samples, (2) they do not distinguish between viable and nonviable organisms, and (3) they do not reveal the microbial load quantitatively. An additional practical challenge towards a robust pipeline is the inability to efficiently allocate sequencing resources a priori. Assessment of sequencing depth is generally practiced post hoc, if at all, for most microbiome studies, regardless of the sample type. This practice is inefficient at best, and at worst, poor sequencing depth jeopardizes the interpretation of study results. To address these challenges, we present a workflow for metagenomics-based environmental surveillance that is appropriate for low-biomass samples, distinguishes viability, is quantitative, and estimates sequencing resources. RESULTS: The workflow was developed using a representative microbiome sample, which was created by aggregating 120 surface swabs collected from a medical intensive care unit. Upon evaluating and optimizing techniques as well as developing new modules, we recommend best practices and introduce a well-structured workflow. We recommend adopting liquid-liquid extraction to improve DNA yield and only incorporating whole-cell filtration when the nonbacterial proportion is large. We suggest including propidium monoazide treatment coupled with internal standards and absolute abundance profiling for viability assessment and involving cultivation when demanding comprehensive profiling. We further recommend integrating internal standards for quantification and additionally qPCR when we expect poor taxonomic classification. We also introduce a machine learning-based model to predict required sequencing effort from accessible sample features. The model helps make full use of sequencing resources and achieve desired outcomes. Video Abstract CONCLUSIONS: This workflow will contribute to more accurate and robust environmental surveillance and infection prevention. Lessons gained from this study will also benefit the continuing development of methods in relevant fields.

Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture.

Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.

Measurement of the Charge-Averaged Elastic Lepton-Proton Scattering Cross Section by the OLYMPUS Experiment.

We report the first measurement of the average of the electron-proton and positron-proton elastic scattering cross sections. This lepton charge-averaged cross section is insensitive to the leading effects of hard two-photon exchange, giving more robust access to the proton's electromagnetic form factors. The cross section was extracted from data taken by the OLYMPUS experiment at DESY, in which alternating stored electron and positron beams were scattered from a windowless gaseous hydrogen target. Elastic scattering events were identified from the coincident detection of the scattered lepton and recoil proton in a large-acceptance toroidal spectrometer. The luminosity was determined from the rates of Møller, Bhabha, and elastic scattering in forward electromagnetic calorimeters. The data provide some selectivity between existing form factor global fits and will provide valuable constraints to future fits.

Infectious Period of Severe Acute Respiratory Syndrome Coronavirus 2 in 17 Nursing Home Residents-Arkansas, June-August 2020.

BACKGROUND: To estimate the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in older adults with underlying conditions, we assessed duration of coronavirus disease 2019 (COVID-19) symptoms, reverse-transcription polymerase chain reaction (RT-PCR) positivity, and culture positivity among nursing home residents. METHODS: We enrolled residents within 15 days of their first positive SARS-CoV-2 test (diagnosis) at an Arkansas facility from July 7 to 15, 2020 and instead them for 42 days. Every 3 days for 21 days and then weekly, we assessed COVID-19 symptoms, collected specimens (oropharyngeal, anterior nares, and saliva), and reviewed medical charts. Blood for serology was collected on days 0, 6, 12, 21, and 42. Infectivity was defined by positive culture. Duration of culture positivity was compared with duration of COVID-19 symptoms and RT-PCR positivity. Data were summarized using measures of central tendency, frequencies, and proportions. RESULTS: We enrolled 17 of 39 (44%) eligible residents. Median participant age was 82 years (range, 58-97 years). All had ≥3 underlying conditions. Median duration of RT-PCR positivity was 22 days (interquartile range [IQR], 8-31 days) from diagnosis; median duration of symptoms was 42 days (IQR, 28-49 days). Of 9 (53%) participants with any culture-positive specimens, 1 (11%) severely immunocompromised participant remained culture-positive 19 days from diagnosis; 8 of 9 (89%) were culture-positive ≤8 days from diagnosis. Seroconversion occurred in 12 of 12 (100%) surviving participants with ≥1 blood specimen; all participants were culture-negative before seroconversion. CONCLUSIONS: Duration of infectivity was considerably shorter than duration of symptoms and RT-PCR positivity. Severe immunocompromise may prolong SARS-CoV-2 infectivity. Seroconversion indicated noninfectivity in this cohort.

Measurement of the Vector and Tensor Asymmetries at Large Missing Momentum in Quasielastic (e[over →],e

We report the measurement of the beam-vector and tensor asymmetries A_{ed}^{V} and A_{d}^{T} in quasielastic (e[over →],e^{'}p) electrodisintegration of the deuteron at the MIT-Bates Linear Accelerator Center up to missing momentum of 500 MeV/c. Data were collected simultaneously over a momentum transfer range 0.1

Surfactant utilization and short-term outcomes in an era of non-invasive respiratory support in Canadian neonatal intensive care units.

OBJECTIVE: Increased use of non-invasive respiratory support (NRS) in the delivery room management of preterm neonates has resulted in delayed surfactant treatment, yet the short-term effects of this change are unknown. The aim of this study was to comparatively evaluate the use of surfactant and the short-term outcomes prior to and after the implementation of early routine use of NRS. STUDY DESIGN: Eligible infants of <29 weeks gestational age (GA) admitted to a Canadian tertiary neonatal center during two time periods (2005 to 2008 and 2010 to 2013) were included in this retrospective cohort study. Timing of surfactant (prophylactic vs therapeutic) and short-term outcomes were compared between the two groups. Univariate and multivariate regression analysis was performed to determine the adjusted odds ratio (AOR) along with 95% confidence interval (CI) of receiving exogenous surfactant and developing bronchopulmonary dysplasia (BPD) using the later cohort as the reference group. Subgroup analyses were also performed for infants <26 and 26 to 286/7 weeks GA, respectively. RESULTS: A total of 3980 and 5137 infants were included in the first and second time periods, respectively. There was no significant difference in overall surfactant utilization between the two time periods (AOR 1.00, 95% CI 0.89, 1.13). However, between 2005 and 2008, a lower proportion of neonates received therapeutic surfactant compared with the later cohort (47.1% vs 56.9%, P<0.01) but were more likely to receive prophylactic surfactant (52.9% vs 43.1%, P<0.01). BPD overall was significantly higher in the earlier cohort (AOR 1.19, 95% CI 1.07, 1.33), particularly among the <26 weeks gestation subgroup (AOR 1.34, 95% CI 1.08, 1.66). CONCLUSION: Early routine use of NRS did not impact overall surfactant utilization rate, although therapeutic surfactant administration rates were higher with a concomitant decrease in BPD rates.

Hard Two-Photon Contribution to Elastic Lepton-Proton Scattering Determined by the OLYMPUS Experiment.

The OLYMPUS Collaboration reports on a precision measurement of the positron-proton to electron-proton elastic cross section ratio, R_{2γ}, a direct measure of the contribution of hard two-photon exchange to the elastic cross section. In the OLYMPUS measurement, 2.01 GeV electron and positron beams were directed through a hydrogen gas target internal to the DORIS storage ring at DESY. A toroidal magnetic spectrometer instrumented with drift chambers and time-of-flight scintillators detected elastically scattered leptons in coincidence with recoiling protons over a scattering angle range of ≈20° to 80°. The relative luminosity between the two beam species was monitored using tracking telescopes of interleaved gas electron multiplier and multiwire proportional chamber detectors at 12°, as well as symmetric Møller or Bhabha calorimeters at 1.29°. A total integrated luminosity of 4.5 fb^{-1} was collected. In the extraction of R_{2γ}, radiative effects were taken into account using a Monte Carlo generator to simulate the convolutions of internal bremsstrahlung with experiment-specific conditions such as detector acceptance and reconstruction efficiency. The resulting values of R_{2γ}, presented here for a wide range of virtual photon polarization 0.456<ε<0.978, are smaller than some hadronic two-photon exchange calculations predict, but are in reasonable agreement with a subtracted dispersion model and a phenomenological fit to the form factor data.

Retinopathy of prematurity: Risk factors and variability in Canadian neonatal intensive care units.

OBJECTIVE: To identify predictors of severe retinopathy of prematurity (ROP) in a large population-based cohort and to examine risk-adjusted variations across units. STUDY DESIGN: Retrospective analysis of Canadian Neonatal Network data on neonates with birth weight <1500 g who were screened for ROP between 2003 and 2010. Characteristics of infants with and without ROP were compared and a risk-adjusted model for severe ROP was developed. Rates of severe ROP were compared between sites. RESULTS: 1163 of 9187 (12.7%) infants developed severe ROP. Lower gestational age, male sex, small for gestational age, patent ductus arteriosus, late onset sepsis, more than two blood transfusions, inotrope use, and outborn status were associated with an increased risk of severe ROP. Severe ROP rates varied significantly between units. CONCLUSION: Younger, smaller and sicker male infants had higher adjusted risks of severe ROP and rates varied significantly among sites.

Focal seizures after instillation of cyclomydril to a neonate with congenital CMV infection.

We present the case of a term neonate who underwent a diagnostic eye examination on day one for possible genetic disorders. Five minutes after Cyclomydril (0.2% clyclopentolate and 1% phenylephrine) eye drops were instilled, a focal seizure lasting for approximately one hour occurred. The electroencephalograph (EEG) was normal but the magnetic resonance imaging (MRI) revealed calcifications in the bilateral periventricular regions. Urine CMV-DNA and maternal serum CMV-IgM were both positive. Auditory brainstem testing suggested severe sensoneural hearing loss. The baby was treated for congenital CMV infection and did not have further seizures. In this case the congenital CMV infection may have been the predisposing factor to central nervous system (CNS) toxicity induced by cyclopentolate. The exact mechanism is unknown but severe neurological impairment may be considered a contraindication for cyclopentolate eye drops in the neonate. To our knowledge, this is the first report of seizures occurring within the first week of life secondary to cyclomydril eye drops in a term neonate.

Views of parents and health-care providers regarding parental presence at bedside rounds in a neonatal intensive care unit.

OBJECTIVE: To examine the views of parents and health-care providers regarding parental presence during neonatal intensive care rounds. STUDY DESIGN: Cross-sectional survey of parents whose children were admitted to a tertiary-care neonatal intensive care unit (n=81). Medical trainees (n=67) and nurses (n=28) were also surveyed. RESULT: The majority of parents reported that attending rounds reduced their anxiety and increased their confidence in the health-care team. Nurses were more likely than medical trainees to support parental presence at rounds (P=0.02). About three-quarters of medical trainees and nurses thought discussion is inhibited and 69% of trainees felt teaching is decreased when parents attend rounds. CONCLUSION: Most parents who attended rounds found the experience beneficial, but medical trainees' views were mixed. The positive impact on parents, and the learning opportunities created in family-centered care and communication when parents are present on rounds, should be highlighted for trainees and other neonatal intensive care personnel.

Precise measurement of deuteron tensor analyzing powers with BLAST.

We report a precision measurement of the deuteron tensor analyzing powers T(20) and T(21) at the MIT-Bates Linear Accelerator Center. Data were collected simultaneously over a momentum transfer range Q=2.15-4.50 fm(-1) with the Bates Large Acceptance Spectrometer Toroid using a highly polarized deuterium internal gas target. The data are in excellent agreement with calculations in a framework of effective field theory. The deuteron charge monopole and quadrupole form factors G(C) and G(Q) were separated with improved precision, and the location of the first node of G(C) was confirmed at Q=4.19±0.05 fm(-1). The new data provide a strong constraint on theoretical models in a momentum transfer range covering the minimum of T(20) and the first node of G(C).

Charge form factor of the neutron at low momentum transfer from the 2H-->(e-->,e'n)1H reaction.

We report new measurements of the neutron charge form factor at low momentum transfer using quasielastic electrodisintegration of the deuteron. Longitudinally polarized electrons at an energy of 850 MeV were scattered from an isotopically pure, highly polarized deuterium gas target. The scattered electrons and coincident neutrons were measured by the Bates Large Acceptance Spectrometer Toroid (BLAST) detector. The neutron form factor ratio GEn/GMn was extracted from the beam-target vector asymmetry AedV at four-momentum transfers Q2=0.14, 0.20, 0.29, and 0.42 (GeV/c)2.

Corticotropin releasing hormone modulates endotoxin-induced inflammatory cytokine expression in human trophoblast cells.

Recent studies have suggested a significant increase in corticotropin releasing hormone (CRH) in maternal plasma and placenta during the course of maternal infection. The aim of this study was to examine the possible role of CRH in lipopolysaccharide (LPS)-induced pro-inflammatory cytokine expression using the well-established human extravillous trophoblast cell line HTR-8/SVneo. Exposure of the HTR-8/SVneo cells to LPS resulted in increased secretion of tumour necrosis factor alpha (TNF-alpha) and interleukin (IL)-8. Pre-treatment of the cells with CRH prior to LPS exposure significantly enhanced LPS induced TNF-alpha and IL-8 secretion. This effect was inhibited by the CRH antagonist astressin. Stimulation of the cells with CRH caused a rapid and transient phosphorylation of p38/MAPK while CRH had no effect on ERK1/2 activation. The effect of CRH on p38/MAPK activation was suppressed by astressin and by the p38/MAPK inhibitor SB203580. Exposure of the cells to CRH resulted in increased expression of TLR-4 and this effect was also inhibited by astressin. Taken together, these findings suggest that CRH augments LPS induced cytokine secretion in human trophoblast cells. Modulation of LPS induced immune responses by CRH may be mediated through regulation of TLR-4 and selective activation of the p38/MAPK signalling pathway.

-Measurement of the proton's electric to magnetic form factor ratio from 1H(over -->)(e(over -->),e'p).

We report the first precision measurement of the proton electric to magnetic form factor ratio from spin-dependent elastic scattering of longitudinally polarized electrons from a polarized hydrogen internal gas target. The measurement was performed at the MIT-Bates South Hall Ring over a range of four-momentum transfer squared Q2 from 0.15 to 0.65 (GeV/c)(2). Significantly improved results on the proton electric and magnetic form factors are obtained in combination with existing cross-section data on elastic electron-proton scattering in the same Q2 region.

Measurements of the generalized electric and magnetic polarizabilities of the proton at low Q2 using the virtual-compton-scattering reaction.

The mean square polarizability radii of the proton have been measured for the first time in a virtual-Compton-scattering experiment performed at the MIT-Bates out-of-plane scattering facility. Response functions and polarizabilities obtained from a dispersion analysis of the data at Q2 = 0.057 GeV2/c2 are in agreement with O(p3) heavy baryon chiral perturbation theory. The data support the dominance of mesonic effects in the polarizabilities.

Results of allergen-specific immunotherapy in 117 dogs with atopic dermatitis.

The success of the treatment of 117 dogs with atopic dermatitis with allergen-specific immunotherapy for up to 48 months was assessed. An excellent response (remission with exclusive immunotherapy) was recorded in 18 of the dogs, a good response (more than 50 per cent reduction in medication and improvement of clinical signs) was recorded in 57, a moderate response was recorded in 24 and a poor response in 18. The mould antigens in the allergen extract were stored in a separate vial before administration and the success rate of the immunotherapy including mould antigens was much higher than in an earlier study in which mould and pollen antigens had been stored in one vial. The success rate was not affected significantly by the age of the dogs when the disease developed, or by their age or the period for which they had shown clinical signs when the treatment began; it was also unaffected by whether pollens, moulds or dust mites were used as antigens, or by whether the offending allergens had been identified by intradermal testing or by serum testing for allergen-specific immunoglobulin E.

Investigation of the conjectured nucleon deformation at low momentum transfer.

We report new precise H(e,e(')p)pi(0) measurements at the Delta(1232) resonance at Q(2)=0.127 (GeV/c)(2) obtained at the MIT-Bates out-of-plane scattering facility which are particularly sensitive to the transverse electric amplitude (E2) of the gamma(*)N-->Delta transition. The new data have been analyzed together with those of earlier measurements to yield precise quadrupole to dipole amplitude ratios: Re(E(3/2)(1+)/M(3/2)(1+))=(-2.3+/-0.3(stat+syst)+/-0.6(model))% and Re(S(3/2)(1+)/M(3/2)(1+))=(-6.1+/-0.2(stat+syst)+/-0.5(model))% for M(3/2)(1+)=(41.4+/-0.3(stat+syst)+/-0.4(model))(10(-3)/m(pi(+))). The derived amplitudes give credence to the conjecture of deformation in hadrons favoring, at low Q2, the dominance of mesonic effects.

Parity-violating electron deuteron scattering and the proton's neutral weak axial vector form factor.

We report on a new measurement of the parity-violating asymmetry in quasielastic electron scattering from the deuteron at backward angles at Q2=0.038 (GeV/c)2. This quantity provides a determination of the neutral weak axial vector form factor of the nucleon, which can potentially receive large electroweak corrections. The measured asymmetry A=-3.51+/-0.57 (stat)+/-0.58 (syst) ppm is consistent with theoretical predictions. We also report on updated results of the previous experiment at Q2=0.091 (GeV/c)2, which are also consistent with theoretical predictions.

Relativistic effects and two-body currents in (H)((-->)e(')p)n using out-of-plane detection.

Measurements of the (2)H((-->)e,e(')p)n reaction were performed with the out-of-plane magnetic spectrometers (OOPS) at the MIT-Bates Linear Accelerator. The longitudinal-transverse, f(LT) and f(')(LT), and the transverse-transverse, f(TT), interference responses at a missing momentum of 210 MeV/c were simultaneously extracted in the dip region at Q2 = 0.15 (GeV/c)(2). In comparison to models of deuteron electrodisintegration, the data clearly reveal strong effects of relativity and final-state interactions and the importance of two-body meson-exchange currents and isobar configurations. We demonstrate that such effects can be disentangled by extracting these responses using the novel out-of-plane technique.