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To conduct a pilot study implementing combined genomic and epidemiologic surveillance for hospital-acquired multidrug-resistant organisms (MDROs) to predict transmission between patients and to estimate the local burden of MDRO transmission.
Pilot prospective multicenter surveillance study.
The study was conducted in 8 university hospitals (2,800 beds total) in Melbourne, Australia (population 4.8 million), including 4 acute-care, 1 specialist cancer care, and 3 subacute-care hospitals.
All clinical and screening isolates from hospital inpatients (April 24 to June 18, 2017) were collected for 6 MDROs: vanA VRE, MRSA, ESBL Escherichia coli (ESBL-Ec) and Klebsiella pneumoniae (ESBL-Kp), and carbapenem-resistant Pseudomonas aeruginosa (CRPa) and Acinetobacter baumannii (CRAb). Isolates were analyzed and reported as routine by hospital laboratories, underwent whole-genome sequencing at the central laboratory, and were analyzed using open-source bioinformatic tools. MDRO burden and transmission were assessed using combined genomic and epidemiologic data.
In total, 408 isolates were collected from 358 patients; 47.5% were screening isolates. ESBL-Ec was most common (52.5%), then MRSA (21.6%), vanA VRE (15.7%), and ESBL-Kp (7.6%). Most MDROs (88.3%) were isolated from patients with recent healthcare exposure.
Combining genomics and epidemiology identified that at least 27.1% of MDROs were likely acquired in a hospital; most of these transmission events would not have been detected without genomics. The highest proportion of transmission occurred with vanA VRE (88.4% of patients).
Genomic and epidemiologic data from multiple institutions can feasibly be combined prospectively, providing substantial insights into the burden and distribution of MDROs, including in-hospital transmission. This analysis enables infection control teams to target interventions more effectively.
Alzheimer’s disease (AD) studies are increasingly targeting earlier (pre)clinical populations, in which the expected degree of observable cognitive decline over a certain time interval is reduced as compared to the dementia stage. Consequently, endpoints to capture early cognitive changes require refinement. We aimed to determine the sensitivity to decline of widely applied neuropsychological tests at different clinical stages of AD as outlined in the National Institute on Aging – Alzheimer’s Association (NIA-AA) research framework.
Amyloid-positive individuals (as determined by positron emission tomography or cerebrospinal fluid) with longitudinal neuropsychological assessments available were included from four well-defined study cohorts and subsequently classified among the NIA-AA stages. For each stage, we investigated the sensitivity to decline of 17 individual neuropsychological tests using linear mixed models.
1103 participants (age = 70.54 ± 8.7, 47% female) were included: n = 120 Stage 1, n = 206 Stage 2, n = 467 Stage 3 and n = 309 Stage 4. Neuropsychological tests were differentially sensitive to decline across stages. For example, Category Fluency captured significant 1-year decline as early as Stage 1 (β = −.58, p < .001). Word List Delayed Recall (β = −.22, p < .05) and Trail Making Test (β = 6.2, p < .05) became sensitive to 1-year decline in Stage 2, whereas the Mini-Mental State Examination did not capture 1-year decline until Stage 3 (β = −1.13, p < .001) and 4 (β = −2.23, p < .001).
We demonstrated that commonly used neuropsychological tests differ in their ability to capture decline depending on clinical stage within the AD continuum (preclinical to dementia). This implies that stage-specific cognitive endpoints are needed to accurately assess disease progression and increase the chance of successful treatment evaluation in AD.
We undertook a strengths, weaknesses, opportunities, and threats (SWOT) analysis of Northern Hemisphere tree-ring datasets included in IntCal20 in order to evaluate their strategic fit with the demands of archaeological users. Case studies on wiggle-matching single tree rings from timbers in historic buildings and Bayesian modeling of series of results on archaeological samples from Neolithic long barrows in central-southern England exemplify the archaeological implications that arise when using IntCal20. The SWOT analysis provides an opportunity to think strategically about future radiocarbon (14C) calibration so as to maximize the utility of 14C dating in archaeology and safeguard its reputation in the discipline.
Terrestrial plant macrofossils from the sedimentary record of Lake Suigetsu, Japan, provide the only quasi-continuous direct atmospheric record of radiocarbon (14C) covering the last 50 ka cal BP (Bronk Ramsey et al. 2012). Since then, new high precision data have become available on U-Th dated speleothems from Hulu Cave China, covering the same time range (Cheng et al. 2018). In addition, an updated varve-based chronology has also been published for the 2006 core from Lake Suigetsu (SG06) based on extended microscopic analysis of the sediments and improved algorithms for interpolation (Schlolaut et al. 2018). Here we reanalyze the radiocarbon dataset from Suigetsu based on the new varve counting information and the constraints imposed by the speleothem data. This enables the new information on the calendar age scale of the Suigetsu dataset to be used in the construction of the consensus IntCal calibration curve. Comparison of the speleothem and plant macrofossil records provides insight into the mechanisms underlying the incorporation of carbon into different types of record and the relative strengths of different types of archive for calibration purposes.
Clinical Enterobacteriacae isolates with a colistin minimum inhibitory concentration (MIC) ≥4 mg/L from a United States hospital were screened for the mcr-1 gene using real-time polymerase chain reaction (RT-PCR) and confirmed by whole-genome sequencing. Four colistin-resistant Escherichia coli isolates contained mcr-1. Two isolates belonged to the same sequence type (ST-632). All subjects had prior international travel and antimicrobial exposure.
In late summer, sometime between cal a.d. 340–405, a hoard of tightly packed, stacked copper-alloy vessels was deposited in the Vale of Pewsey, Wiltshire. The corrosion of the vessels allowed for the preservation of delicate plant macrofossils and pollen. Analysis of this material has provided insights into the date, season and context of this act of structured deposition. A second hoard of similar vessels was deposited in the fourth or fifth century only a few miles away at Wilcot. The hoards and their deposition relate to Romano-British lifeways, at a time when the region was on the cusp of a dramatic period of change. The distribution of late Roman coins and belt fittings offers further insights into the social and economic character of Wiltshire at their times of deposition.
In Scotland, the base of the Ballagan Formation has traditionally been placed at the first grey mudstone within a contiguous Late Devonian to Carboniferous succession. This convention places the Devonian–Carboniferous boundary within the Old Red Sandstone (ORS) Kinnesswood Formation. The consequences of this placement are that tetrapods from the Ballagan Formation were dated as late Tournaisian in age and that the ranges of typically Devonian fish found in the Kinnesswood Formation continued into the Carboniferous. The Pease Bay specimen of the fish Remigolepis is from the Kinnesswood Formation. Comparisons with its range in Greenland, calibrated against spores, show it was Famennian in age. Detailed palynological sampling at Burnmouth from the base of the Ballagan Formation proves that the early Tournaisian spore zones (VI and HD plus Cl 1) are present. The Schopfites species that occurs through most of the succession is Schopfites delicatus rather than Schopfites claviger. The latter species defines the late Tournaisian CM spore zone. The first spore assemblage that has been found in Upper ‘ORS' strata underlying the Ballagan Formation (Preston, Whiteadder Water), contains Retispora lepidophyta and is from the early latest Famennian LL spore zone. The spore samples are interbedded with volcaniclastic debris, which shows that the Kelso Volcanic Formation is, in part, early latest Famennian in age. These findings demonstrate that the Ballagan Formation includes most of the Tournaisian with the Devonian–Carboniferous boundary positioned close to the top of the Kinnesswood Formation. The Stage 6 calcrete at Pease Bay can be correlated to the equivalent section at Carham, showing that it represents a time gap equivalent to the latest Famennian glaciation(s). Importantly, some of the recently described Ballagan Formation tetrapods are older than previously dated and now fill the key early part of Romer's Gap.
The lower Mississippian Ballagan Formation of northern Britain is one of only two successions worldwide to yield the earliest known tetrapods with terrestrial capability following the end-Devonian mass extinction event. Studies of the sedimentary environments and habitats in which these beasts lived have been an integral part of a major research project into how, why and under what circumstances this profound step in the evolution of life on Earth occurred. Here, a new palaeogeographic map is constructed from outcrop data integrated with new and archived borehole material. The map shows the extent of a very low-relief coastal wetland developed along the tropical southern continental margin of Laurussia. Coastal floodplains in the Midland Valley and Tweed basins were separated from the marginal marine seaway of the Northumberland–Solway Basin to the south by an archipelago of more elevated areas. A complex mosaic of sedimentary environments was juxtaposed, and included fresh and brackish to saline and hypersaline lakes, a diverse suite of floodplain palaeosols and a persistent fluvial system in the east of the region. The strongly seasonal climate led to the formation of evaporite deposits alternating with flooding events, both meteoric and marine. Storm surges drove marine floods from the SW into both the western Midland Valley and Northumberland–Solway Basin; marine water also flooded into the Tweed Basin and Tayside in the east. The Ballagan Formation is a rare example in the geological record of a tropical, seasonal coastal wetland that contains abundant, small-scale evaporite deposits. The diverse sedimentary environments and palaeosol types indicate a network of different terrestrial and aquatic habitats in which the tetrapods lived.
Stonehenge is a site that continues to yield surprises. Excavation in 2009 added a new and unexpected feature: a smaller, dismantled stone circle on the banks of the River Avon, connected to Stonehenge itself by the Avenue. This new structure has been labelled ‘Bluestonehenge’ from the evidence that it once held a circle of bluestones that were later removed to Stonehenge. Investigation of the Avenue closer to Stonehenge revealed deep periglacial fissures within it. Their alignment on Stonehenge's solstitial axis (midwinter sunset–midsummer sunrise) raises questions about the early origins of this ritual landscape.
To examine the use of vitamin D supplements during infancy among the participants in an international infant feeding trial.
Information about vitamin D supplementation was collected through a validated FFQ at the age of 2 weeks and monthly between the ages of 1 month and 6 months.
Infants (n 2159) with a biological family member affected by type 1 diabetes and with increased human leucocyte antigen-conferred susceptibility to type 1 diabetes from twelve European countries, the USA, Canada and Australia.
Daily use of vitamin D supplements was common during the first 6 months of life in Northern and Central Europe (>80 % of the infants), with somewhat lower rates observed in Southern Europe (>60 %). In Canada, vitamin D supplementation was more common among exclusively breast-fed than other infants (e.g. 71 % v. 44 % at 6 months of age). Less than 2 % of infants in the USA and Australia received any vitamin D supplementation. Higher gestational age, older maternal age and longer maternal education were study-wide associated with greater use of vitamin D supplements.
Most of the infants received vitamin D supplements during the first 6 months of life in the European countries, whereas in Canada only half and in the USA and Australia very few were given supplementation.
The Gemini Planet Imager (GPI) is a high contrast coronagraph designed to directly image exoplanets and circumstellar disks. GPI includes a polarimetry mode designed to characterize dust grains and enhance the contrast of scattered, polarized light by a factor of 100. Reflections and birefringence of optics within the optical train induce a polarization signature that needs to be measured a priori and calibrated out during data reduction. Here we report on the results of an extensive laboratory characterization campaign of the polarimetry mode. The linear instrumental polarization has been measured in 4 GPI passbands and found to be between 3.5 ± 0.3 % at 1.0 micron and 1.1 ± 0.3 % at 2.0 microns. Modulation efficiency has been measured to be 94% at 1.0 micron increasing to 97% at 2.0 microns. Stability has been shown to better than 0.6% over timescales of ~ 3 months and over cool down cycles. The tests show that GPI passes all polarimetry design requirements and should be able to measure circumstellar disk linear polarization to 1% accuracy.
We present an update of the ‘key points’ from the Antarctic Climate Change and the Environment (ACCE) report that was published by the Scientific Committee on Antarctic Research (SCAR) in 2009. We summarise subsequent advances in knowledge concerning how the climates of the Antarctic and Southern Ocean have changed in the past, how they might change in the future, and examine the associated impacts on the marine and terrestrial biota. We also incorporate relevant material presented by SCAR to the Antarctic Treaty Consultative Meetings, and make use of emerging results that will form part of the Intergovernmental Panel on Climate Change (IPCC) Fifth Assessment Report.
Although overall outcomes for children undergoing heart surgery have improved, there is a significant variation in outcomes across hospitals. This review discusses the variation in cost and outcomes across centres performing congenital heart surgery, potential underlying mechanisms, and efforts to reduce variation and improve outcome.
Excavations at Tinney's Lane, Sherborne in 2002 uncovered extensive evidence for Late Bronze Age settlement and pottery production, dating from a short time period probably within the 12th or 11th century cal bc. Well-preserved deposits of burnt stone, broken vessels, and burnt sherds, together with resulting debris redeposited in associated pits, were accompanied by a series of post-hole structures interpreted as round-houses and four-post settings. Environmental evidence in the form of charcoal, charred plant remains, and molluscs has provided important information concerning sources of fuel and water for pottery production as well as allowing a reconstruction of the local vegetation. Finds of fired clay, metal, stone, shale, flint, and bone include items from distant sources, informing topics such as site status and exchange, and include many categories of tools and equipment that would have been used within the pottery-making processes. Analysis of the spatial distribution of these finds amongst the structures and surviving layers of burning has allowed the definition of a series of industrial activity areas, each comprising one or more round-houses, a four-post structure, bonfire bases or pits used for firing, and other pits with specific related functions. Altogether the site has provided some of the best evidence for pottery production within prehistoric Britain.
This paper describes the results of two seasons of excavation and associated palaeoenvironmental analyses of a wetland site on Beccles Marshes, Beccles, Suffolk. The site has been identified as a triple post alignment of oak timbers (0.6–2.0 m long), over 100 m in length, and 3–4 m wide, running north-west to south-east towards the River Waveney. It was constructed in a single phase which has been dated dendrochronologically to 75 BC, although discrete brushwood features identified as possible short trackways have been dated by radiocarbon to both before and after the alignment was built. It is unclear if the posts ever supported a superstructure but notches (‘halving lap joints’) in some of the posts appear to have held timbers to support the posts and/or aid in their insertion. In addition, fragments of both Iron Age and Romano-British pottery were recovered. A substantial assemblage of worked wooden remains appears to reflect the construction of the post row itself and perhaps the on-site clearance of floodplain vegetation. This assemblage also contains waste material derived from the reduction splitting of timbers larger than the posts of the alignment, but which have not been recovered from the site. Environmental analyses indicate that the current landscape context of the site with respect to the River Waveney is probably similar to that which pertained in prehistory. The coleoptera (beetle) record illustrates a series of changes in the on-site vegetation in the period before, during and after the main phase of human activity which may be related to a range of factors including floodplain hydrology and anthropogenic utilisation of Beccles Marshes. The possible form and function of the site is discussed in relation to the later prehistoric period in Suffolk.