Fatal Exudative Dermatitis (FED) in Island Populations of Red Squirrels (Sciurus vulgaris): Spillover of a Virulent Staphylococcus aureus Clone (ST49) From Reservoir Hosts.

Fatal exudative dermatitis (FED) is a significant cause of death of red squirrels (Sciurus vulgaris) on the island of Jersey in the Channel Islands where it is associated with a virulent clone of Staphylococcus aureus, ST49. S. aureus ST49 has been found in other hosts such as small mammals, pigs and humans, but the dynamics of carriage and disease of this clone, or any other lineage in red squirrels, is currently unknown. We used whole-genome sequencing to characterize 228 isolates from healthy red squirrels on Jersey, the Isle of Arran (Scotland) and Brownsea Island (England), from red squirrels showing signs of FED on Jersey and the Isle of Wight (England) and a small number of isolates from other hosts. S. aureus was frequently carried by red squirrels on the Isle of Arran with strains typically associated with small ruminants predominating. For the Brownsea carriage, S. aureus was less frequent and involved strains associated with birds, small ruminants and humans, while for the Jersey carriage S. aureus was rare but ST49 predominated in diseased squirrels. By combining our data with publicly available sequences, we show that the S. aureus carriage in red squirrels largely reflects frequent but facile acquisitions of strains carried by other hosts sharing their habitat ('spillover'), possibly including, in the case of ST188, humans. Genome-wide association analysis of the ruminant lineage ST133 revealed variants in a small number of mostly bacterial-cell-membrane-associated genes that were statistically associated with squirrel isolates from the Isle of Arran, raising the possibility of specific adaptation to red squirrels in this lineage. In contrast there is little evidence that ST49 is a common carriage isolate of red squirrels and infection from reservoir hosts such as bank voles or rats, is likely to be driving the emergence of FED in red squirrels

Improved characterisation of MRSA transmission using within-host bacterial sequence diversity

Methicillin-resistant Staphylococcus aureus (MRSA) transmission in the hospital setting has been a frequent subject of investigation using bacterial genomes, but previous approaches have not yet fully utilised the extra deductive power provided when multiple pathogen samples are acquired from each host. Here, we used a large dataset of MRSA sequences from multiply-sampled patients to reconstruct colonisation of individuals in a high-transmission setting in a hospital in Thailand. We reconstructed transmission trees for MRSA. We also investigated transmission between anatomical sites on the same individual, finding that this either occurs repeatedly or involves a wide transmission bottleneck. We examined the between-subject bottleneck, finding considerable variation in the amount of diversity transmitted. Finally, we compared our approach to the simpler method of identifying transmission pairs using single nucleotide polymorphism (SNP) counts. This suggested that the optimum threshold for identifying a pair is 39 SNPs, if sensitivities and specificities are equally weighted

Can differences in heat flow between east and southern Africa be easily interpreted?: Implications for understanding regional variability in continental heat flow

We address the extent to which regional variations in continental heat flow can be interpreted, making use of a heat flow data set from east and southern Africa. The first-order observation deriving from these heat flow measurements is a common pattern characterized in both regions by low heat flow in Archean cratons and higher heat flow in younger mobile belts. Two regional differences between east and southern Africa are superimposed on this common heat flow pattern: (1) heat flow in the Tanzania Craton is about 13 mW m-2 lower than in the Kalahari Craton, and (2) heat flow in the Mozambique Belt in east Africa is about 9 mW m-2 lower than in the southern African mobile belts, within about 250 km of the respective Archean cratons. The differences in heat flow between east and southern Africa suggest that the thermal structure of the lithosphere beneath these regions differs somewhat, and we attempt to resolve these differences in lithospheric thermal structure by examining four explanations that could account for the heat flow observations: (1) diminished heat flow in shallow boreholes in east Africa; (2) less crustal heat production in the regions of lower heat flow; (3) thicker lithosphere beneath the regions of lower heat flow; (4) cooler mantle beneath the areas of lower heat flow. We find it difficult to interpret uniquely the heat flow differences between east and southern Africa because available constraints on crustal heat production, crustal structure, lithospheric thickness and mantle temperatures are insufficient to discriminate among the possible explanations. Hence, extracting significant information about lithospheric thermal structure from regional heat flow variations requires more ancillary geochemical and geophysical information than Africa presently offers.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30899/1/0000568.pd

Eclogite-facies shear zones--deep crustal reflectors?

Strongly foliated eclogite-facies rocks in 30-150 m thick shear zones of Caledonian age occur within a Grenvillian garnet granulite-facies gabbro-anorthosite terrain in the Bergen Arcs of Norway. The predominant eclogite-facies mineral assemblages in the shear zones are omphacite + garnet + zoisite + kyanite in gabbroic anorthosite and omphacite + garnet in gabbro. Eclogite-facies rocks in shear zones are generally fine-grained; alternating omphacite/garnet- and kyanite/clinozoisite-rich layers define gneissic layering. A strong shape preferred orientation of omphacite, kyanite, and white mica (phengitic muscovite and/or paragonite) define the foliation. The anorthositic eclogites show omphacite b-axis maxima approximately normal to the foliation and c-axis girdles within the foliation plane. P-wave velocities (Vp) determined at confining pressures to 600 MPa for samples from eclogite-facies shear zones range from 8.3 to 8.5 km s-1 and anisotropy ranges from 1 to 7%. The few samples with more pronounced anisotropy tend to be approximately transversely isotropic with minimum velocities for propagation directions normal to foliation and maximum velocities for propagation directions parallel to foliation. The fast propagation direction lies within the c-axis girdles (parallel to foliation) and the slow propagation direction is parallel to the b-axis concentration (normal to foliation) in samples for which omphacite crystallographic preferred orientation was determined. Vp for the granulite-facies protoliths average about 7.5 km s-1. High calculated reflection coefficients for these shear zones, 0.04-0.14, indicate that they are excellent candidates for deep crustal reflectors in portions of crust that experienced high-pressure conditions but escaped thermal reactivation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31633/1/0000567.pd

A review of the impacts of degradation threats on soil properties in the UK

National governments are becoming increasingly aware of the importance of their soil resources and are shaping strategies accordingly. Implicit in any such strategy is that degradation threats and their potential effect on important soil properties and functions are defined and understood. In this paper, we aimed to review the principal degradation threats on important soil properties in the UK, seeking quantitative data where possible. Soil erosion results in the removal of important topsoil and, with it, nutrients, C and porosity. A decline in soil organic matter principally affects soil biological and microbiological properties, but also impacts on soil physical properties because of the link with soil structure. Soil contamination affects soil chemical properties, affecting nutrient availability and degrading microbial properties, whilst soil compaction degrades the soil pore network. Soil sealing removes the link between the soil and most of the ‘spheres’, significantly affecting hydrological and microbial functions, and soils on re-developed brownfield sites are typically degraded in most soil properties. Having synthesized the literature on the impact on soil properties, we discuss potential subsequent impacts on the important soil functions, including food and fibre production, storage of water and C, support for biodiversity, and protection of cultural and archaeological heritage. Looking forward, we suggest a twin approach of field-based monitoring supported by controlled laboratory experimentation to improve our mechanistic understanding of soils. This would enable us to better predict future impacts of degradation processes, including climate change, on soil properties and functions so that we may manage soil resources sustainably

Elective cancer surgery in COVID-19-free surgical pathways during the SARS-CoV-2 pandemic: An international, multicenter, comparative cohort study

PURPOSE As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19–free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19–free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19–free surgical pathways. Patients who underwent surgery within COVID-19–free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19–free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score–matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19–free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION Within available resources, dedicated COVID-19–free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks

Elective Cancer Surgery in COVID-19-Free Surgical Pathways During the SARS-CoV-2 Pandemic: An International, Multicenter, Comparative Cohort Study.

PURPOSE: As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19-free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS: This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19-free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS: Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19-free surgical pathways. Patients who underwent surgery within COVID-19-free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19-free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score-matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19-free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION: Within available resources, dedicated COVID-19-free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks

An introduction to scholarly open access

Workshop presented to the Library Faculty at Washington State University