Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of Staphylococcus aureus in an intensive care unit

BACKGROUND  Strategies to prevent Staphylococcus aureus infection in hospitals focus on patient-to-patient transmission. We used whole-genome sequencing to investigate the role of colonized patients as the source of new S. aureus acquisitions, and the reliability of identifying patient-to-patient transmission using the conventional approach of spa typing and overlapping patient stay. METHODS Over 14 months, all unselected patients admitted to an adult intensive care unit (ICU) were serially screened for S. aureus. All available isolates (n = 275) were spa typed and underwent whole-genome sequencing to investigate their relatedness at high resolution. RESULTS Staphylococcus aureus was carried by 185 of 1109 patients sampled within 24 hours of ICU admission (16.7%); 59 (5.3%) patients carried methicillin-resistant S. aureus (MRSA). Forty-four S. aureus (22 MRSA) acquisitions while on ICU were detected. Isolates were available for genetic analysis from 37 acquisitions. Whole-genome sequencing indicated that 7 of these 37 (18.9%) were transmissions from other colonized patients. Conventional methods (spa typing combined with overlapping patient stay) falsely identified 3 patient-to-patient transmissions (all MRSA) and failed to detect 2 acquisitions and 4 transmissions (2 MRSA). CONCLUSIONS Only a minority of S. aureus acquisitions can be explained by patient-to-patient transmission. Whole-genome sequencing provides the resolution to disprove transmission events indicated by conventional methods and also to reveal otherwise unsuspected transmission events. Whole-genome sequencing should replace conventional methods for detection of nosocomial S. aureus transmission

Electron-beam propagation in a two-dimensional electron gas

A quantum mechanical model based on a Green's function approach has been used to calculate the transmission probability of electrons traversing a two-dimensional electron gas injected and detected via mode-selective quantum point contacts. Two-dimensional scattering potentials, back-scattering, and temperature effects were included in order to compare the calculated results with experimentally observed interference patterns. The results yield detailed information about the distribution, size, and the energetic height of the scattering potentials.Comment: 7 pages, 6 figure

Evaluation of methods for detecting human reads in microbial sequencing datasets

Sequencing data from host-associated microbes can often be contaminated by the body of the investigator or research subject. Human DNA is typically removed from microbial reads either by subtractive alignment (dropping all reads that map to the human genome) or by using a read classification tool to predict those of human origin, and then discarding them. To inform best practice guidelines, we benchmarked eight alignment-based and two classification-based methods of human read detection using simulated data from 10 clinically prevalent bacteria and three viruses, into which contaminating human reads had been added. While the majority of methods successfully detected >99 % of the human reads, they were distinguishable by variance. The most precise methods, with negligible variance, were Bowtie2 and SNAP, both of which misidentified few, if any, bacterial reads (and no viral reads) as human. While correctly detecting a similar number of human reads, methods based on taxonomic classification, such as Kraken2 and Centrifuge, could misclassify bacterial reads as human, although the extent of this was species-specific. Among the most sensitive methods of human read detection was BWA, although this also made the greatest number of false positive classifications. Across all methods, the set of human reads not identified as such, although often representing 300 bp) bacterial reads, the highest performing approaches were classification-based, using Kraken2 or Centrifuge. For shorter (c. 150 bp) bacterial reads, combining multiple methods of human read detection maximized the recovery of human reads from contaminated short read datasets without being compromised by false positives. A particularly high-performance approach with shorter bacterial reads was a two-stage classification using Bowtie2 followed by SNAP. Using this approach, we re-examined 11 577 publicly archived bacterial read sets for hitherto undetected human contamination. We were able to extract a sufficient number of reads to call known human SNPs, including those with clinical significance, in 6 % of the samples. These results show that phenotypically distinct human sequence is detectable in publicly archived microbial read datasets

Can explicit convection improve modelled dust in summertime West Africa?

Global and regional models have large systematic errors in their modelled dust fields over West Africa. It is well established that cold-pool outflows from moist convection (haboobs) can raise over 50% of the dust over parts of the Sahara and Sahel in summer, but parameterised moist convection tends to give a very poor representation of this in models. Here, we test the hypothesis that an explicit representation of convection in the Met Office Unified Model (UM) improves haboob winds and so may reduce errors in modelled dust fields. The results show that despite varying both grid spacing and the representation of convection there are only minor changes in dust aerosol optical depth (AOD) and dust mass loading fields between simulations. In all simulations there is an AOD deficit over the observed central Saharan dust maximum and a high bias in AOD along the west coast: both features are consistent with many climate (CMIP5) models. Cold-pool outflows are present in the explicit simulations and do raise dust. Consistent with this, there is an improved diurnal cycle in dust-generating winds with a seasonal peak in evening winds at locations with moist convection that is absent in simulations with parameterised convection. However, the explicit convection does not change the AOD field in the UM significantly for several reasons. Firstly, the increased windiness in the evening from haboobs is approximately balanced by a reduction in morning winds associated with the breakdown of the nocturnal low-level jet (LLJ). Secondly, although explicit convection increases the frequency of the strongest winds, they are still weaker than observed, especially close to the observed summertime Saharan dust maximum: this results from the fact that, although large mesoscale convective systems (and resultant cold pools) are generated, they have a lower frequency than observed and haboob winds are too weak. Finally, major impacts of the haboobs on winds occur over the Sahel, where, although dust uplift is known to occur in reality, uplift in the simulations is limited by a seasonally constant bare-soil fraction in the model, together with soil moisture and clay fractions which are too restrictive of dust emission in seasonally varying vegetated regions. For future studies, the results demonstrate (1) the improvements in behaviour produced by the explicit representation of convection, (2) the value of simultaneously evaluating both dust and winds and (3) the need to develop parameterisations of the land surface alongside those of dust-generating winds

Short Communication Genetic parameters for cow weight at calving and at calf weaning in South African Simmental cattle

Abstract A study was conducted to compare mature cow weight in the South African Simmental population when defined as the weight of the cow at calving or the weight of the cow at weaning of the calf. Data included in the analysis were 14458 records for cow weight at calving (CWT-C) representing 6534 cows and 18871 records for cow weight at weaning (CWT-W) representing 8395 cows. All cows were born between 1968 and 1996, while all calves were born between 1977 and 1998. The following effects had a significant influence on the traits and were included in the genetic analysis: Cow age in years fitted as a covariate term (linear and quadratic) and contemporary group fitted as a fixed effect. Contemporary group was defined as the unique combination of herd, birth year of calf, month of weighing, breeder-defined management group code for the calf and supplementary feeding code for the cow (for CWT-W). All analyses were done using ASREML, first fitting uni-trait and then bi-variate animal models that made provision for up to four weights per cow. The estimated genetic correlation obtained between the two cow weight traits was 0.95 ± 0.03, with a residual correlation of 0.61 ± 0.02. The heritability estimates for CWT-C and CWT-W from this analysis were 0.29 ± 0.04 and 0.37 ± 0.04, respectively. From a breeding perspective, these results confirm that little benefit is to be gained from weighing cows at calving if cows are to be weighed at weaning. If cow weights are to be recorded for an indication of cow maintenance costs, then weight at weaning is the more reliable and practical measure to record

External and internal noise surveys of London primary schools

Internal and external noise surveys have been carried out around schools in London, UK, to provide information on typical levels and sources to which children are exposed while at school. Noise levels were measured outside 142 schools, in areas away from flightpaths into major airports. 86% of the schools surveyed were exposed to noise from road traffic, the average external noise level outside a school being 57 dB LAeq. Detailed internal noise surveys have been carried out in 140 classrooms in 16 schools, together with classroom observations. It was found that noise levels inside classrooms depend upon the activities in which the children are engaged, with a difference of 20 dB LAeq between the 'quietest' and 'noisiest' activities. The average background noise level in classrooms exceeds the level recommended in current standards. The number of children in the classroom was found to affect noise levels. External noise influenced internal noise levels only when children were engaged in the quietest classroom activities. The effects of the age of the school buildings and types of window upon internal noise were examined but results were inconclusive

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high- quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open- source software pipeline, ‘ResPipe’

Active flow control systems architectures for civil transport aircraft

Copyright @ 2010 American Institute of Aeronautics and AstronauticsThis paper considers the effect of choice of actuator technology and associated power systems architecture on the mass cost and power consumption of implementing active flow control systems on civil transport aircraft. The research method is based on the use of a mass model that includes a mass due to systems hardware and a mass due to the system energy usage. An Airbus A320 aircraft wing is used as a case-study application. The mass model parameters are based on first-principle physical analysis of electric and pneumatic power systems combined with empirical data on system hardware from existing equipment suppliers. Flow control methods include direct fluidic, electromechanical-fluidic, and electrofluidic actuator technologies. The mass cost of electrical power distribution is shown to be considerably less than that for pneumatic systems; however, this advantage is reduced by the requirement for relatively heavy electrical power management and conversion systems. A tradeoff exists between system power efficiency and the system hardware mass required to achieve this efficiency. For short-duration operation the flow control solution is driven toward lighter but less power-efficient systems, whereas for long-duration operation there is benefit in considering heavier but more efficient systems. It is estimated that a practical electromechanical-fluidic system for flow separation control may have a mass up to 40% of the slat mass for a leading-edge application and 5% of flap mass for a trailing-edge application.This work is funded by the Sixth European Union Framework Programme as part of the AVERT project (Contract No. AST5-CT-2006-030914

High-resolution characterisation of short-term temporal variability in the taxonomic and resistome composition of wastewater influent

Wastewater-based epidemiology (WBE) for population-level surveillance of antimicrobial resistance (AMR) is gaining significant traction, but the impact of wastewater sampling methods on results is unclear. In this study, we characterized taxonomic and resistome differences between single-timepoint-grab and 24 h composites of wastewater influent from a large UK-based wastewater treatment work [WWTW (population equivalent: 223435)]. We autosampled hourly influent grab samples (n=72) over three consecutive weekdays, and prepared additional 24 h composites (n=3) from respective grabs. For taxonomic profiling, metagenomic DNA was extracted from all samples and 16S rRNA gene sequencing was performed. One composite and six grabs from day 1 underwent metagenomic sequencing for metagenomic dissimilarity estimation and resistome profiling. Taxonomic abundances of phyla varied significantly across hourly grab samples but followed a repeating diurnal pattern for all 3days. Hierarchical clustering grouped grab samples into four time periods dissimilar in both 16S rRNA gene-based profiles and metagenomic distances. 24H-composites resembled mean daily phyla abundances and showed low variability of taxonomic profiles. Of the 122 AMR gene families (AGFs) identified across all day 1 samples, single grab samples identified a median of six (IQR: 5–8) AGFs not seen in the composite. However, 36/36 of these hits were at lateral coverage <0.5 (median: 0.19; interquartile range: 0.16–0.22) and potential false positives. Conversely, the 24H-composite identified three AGFs not seen in any grab with higher lateral coverage (0.82; 0.55–0.84). Additionally, several clinically significant human AGFs (blaVIM, blaIMP, blaKPC) were intermittently or completely missed by grab sampling but captured by the 24 h composite. Wastewater influent undergoes significant taxonomic and resistome changes on short timescales potentially affecting interpretation of results based on sampling strategy. Grab samples are more convenient and potentially capture low-prevalence/transient targets but are less comprehensive and temporally variable. Therefore, we recommend 24H-composite sampling where feasible. Further validation and optimization of WBE methods is vital for its development into a robust AMR surveillance approach

Imaging Inter-Edge State Scattering Centers in the Quantum Hall Regime

We use an atomic force microscope tip as a local gate to study the scattering between edge channels in a 2D electron gas in the quantum Hall regime. The scattering is dominated by individual, microscopic scattering centers, which we directly image here for the first time. The tip voltage dependence of the scattering indicates that tunneling occurs through weak links and localized states.Comment: 4 pages, 5 figure