PCR for the detection of pathogens in neonatal early onset sepsis.

BACKGROUND: A large proportion of neonates are treated for presumed bacterial sepsis with broad spectrum antibiotics even though their blood cultures subsequently show no growth. This study aimed to investigate PCR-based methods to identify pathogens not detected by conventional culture. METHODS: Whole blood samples of 208 neonates with suspected early onset sepsis were tested using a panel of multiplexed bacterial PCRs targeting Streptococcus pneumoniae, Streptococcus agalactiae (GBS), Staphylococcus aureus, Streptococcus pyogenes (GAS), Enterobacteriaceae, Enterococcus faecalis, Enterococcus faecium, Ureaplasma parvum, Ureaplasma urealyticum, Mycoplasma hominis and Mycoplasma genitalium, a 16S rRNA gene broad-range PCR and a multiplexed PCR for Candida spp. RESULTS: Two-hundred and eight samples were processed. In five of those samples, organisms were detected by conventional culture; all of those were also identified by PCR. PCR detected bacteria in 91 (45%) of the 203 samples that did not show bacterial growth in culture. S. aureus, Enterobacteriaceae and S. pneumoniae were the most frequently detected pathogens. A higher bacterial load detected by PCR was correlated positively with the number of clinical signs at presentation. CONCLUSION: Real-time PCR has the potential to be a valuable additional tool for the diagnosis of neonatal sepsis

Exploring the Effect of G6PC2 Single Nucleotide Polymorphisms on Enzyme Activity and Human Health

G6PC2 encodes a glucose-6-phosphatase catalytic subunit that is highly expressed in pancreatic islet beta cells. Genome wide association studies (GWAS) have shown that single nucleotide polymorphisms (SNPs) in the G6PC2 gene are associated with variations in fasting blood glucose (FBG), a parameter linked with risk for type 2 diabetes (T2D). Studies in mice have complemented these GWAS data by showing that deletion of G6pc2 abolishes islet glucose-6-phosphatase activity and lowers FBG. We hypothesize that G6pc2 forms a substrate cycle with glucokinase that determines the sensitivity of glucose-stimulated insulin secretion (GSIS) to glucose. In support of this hypothesis we have previously shown that deletion of G6pc2 enhances GSIS at sub-maximal glucose concentrations and abolishes glucose cycling in isolated islets. More recently we have demonstrated that deletion of G6pc2 enhances glycolysis in isolated mouse islets, and that high rates of glucose cycling are also detected in human islets. Our broad hypothesis is that the results of these studies will strongly suggest that G6PC2 inhibition should be considered as a novel therapeutic strategy for lowering FBG and thereby preventing T2D. To extend these observations we have developed a novel intact cell assay for G6PC2 activity. This assay relies on the observation that CREB and ChREBP bound to the rat G6PC1 promoter are highly glucose responsive in the rat islet-derived 832/13 cell line and the fact that endogenous G6PC2 is absent. In the presence of catalytically-dead G6PC2, glucose stimulates G6PC1-luciferase fusion gene expression. However, this induction is blunted in the presence of wild type G6PC2. We are using this assay to determine the effect of non-synonymous G6PC2 SNPs on G6PC2 activity and then examining the association between SNPs that markedly affect G6PC2 activity with their effects on human health as assessed using Vanderbilt’s BioVU biobank. These data will reveal whether SNPs in G6PC2 are associated with only altered FBG or whether G6PC2 affects other aspects of human health

Natural ventilation for the prevention of airborne contagion.

BACKGROUND: Institutional transmission of airborne infections such as tuberculosis (TB) is an important public health problem, especially in resource-limited settings where protective measures such as negative-pressure isolation rooms are difficult to implement. Natural ventilation may offer a low-cost alternative. Our objective was to investigate the rates, determinants, and effects of natural ventilation in health care settings. METHODS AND FINDINGS: The study was carried out in eight hospitals in Lima, Peru; five were hospitals of "old-fashioned" design built pre-1950, and three of "modern" design, built 1970-1990. In these hospitals 70 naturally ventilated clinical rooms where infectious patients are likely to be encountered were studied. These included respiratory isolation rooms, TB wards, respiratory wards, general medical wards, outpatient consulting rooms, waiting rooms, and emergency departments. These rooms were compared with 12 mechanically ventilated negative-pressure respiratory isolation rooms built post-2000. Ventilation was measured using a carbon dioxide tracer gas technique in 368 experiments. Architectural and environmental variables were measured. For each experiment, infection risk was estimated for TB exposure using the Wells-Riley model of airborne infection. We found that opening windows and doors provided median ventilation of 28 air changes/hour (ACH), more than double that of mechanically ventilated negative-pressure rooms ventilated at the 12 ACH recommended for high-risk areas, and 18 times that with windows and doors closed (p < 0.001). Facilities built more than 50 years ago, characterised by large windows and high ceilings, had greater ventilation than modern naturally ventilated rooms (40 versus 17 ACH; p < 0.001). Even within the lowest quartile of wind speeds, natural ventilation exceeded mechanical (p < 0.001). The Wells-Riley airborne infection model predicted that in mechanically ventilated rooms 39% of susceptible individuals would become infected following 24 h of exposure to untreated TB patients of infectiousness characterised in a well-documented outbreak. This infection rate compared with 33% in modern and 11% in pre-1950 naturally ventilated facilities with windows and doors open. CONCLUSIONS: Opening windows and doors maximises natural ventilation so that the risk of airborne contagion is much lower than with costly, maintenance-requiring mechanical ventilation systems. Old-fashioned clinical areas with high ceilings and large windows provide greatest protection. Natural ventilation costs little and is maintenance free, and is particularly suited to limited-resource settings and tropical climates, where the burden of TB and institutional TB transmission is highest. In settings where respiratory isolation is difficult and climate permits, windows and doors should be opened to reduce the risk of airborne contagion

Surveillance of congenital Zika syndrome in England and Wales: methods and results of laboratory, obstetric and paediatric surveillance.

The spread of the Zika virus (ZIKV) in the Americas led to large outbreaks across the region and most of the Southern hemisphere. Of greatest concern were complications following acute infection during pregnancy. At the beginning of the outbreak, the risk to unborn babies and their clinical presentation was unclear. This report describes the methods and results of the UK surveillance response to assess the risk of ZIKV to children born to returning travellers. Established surveillance systems operating within the UK - the paediatric and obstetric surveillance units for rare diseases, and national laboratory monitoring - enabled rapid assessment of this emerging public health threat. A combined total of 11 women experiencing adverse pregnancy outcomes after possible ZIKV exposure were reported by the three surveillance systems; five miscarriages, two intrauterine deaths and four children with clinical presentations potentially associated with ZIKV infection. Sixteen women were diagnosed with ZIKV during pregnancy in the UK. Amongst the offspring of these women, there was unequivocal laboratory evidence of infection in only one child. In the UK, the number and risk of congenital ZIKV infection for travellers returning from ZIKV-affected countries is very small

Factors controlling rare earth element plus yttrium enrichment in Fe–Mn crusts from Canary Islands Seamounts (NE Central Atlantic)

Marine minerals are important because concentrate in their structure high contents of strategic and critical elements as rare earth elements. Forty-two samples from eight seamounts of Canary Islands Seamount Province (CISP) have been analyzed in order to evaluate their rare earth elements plus yttrium contents (REY). Highest contents of REY are related to hydrogenetic minerals and essentially Fe-vernadite (on average 3000 μg/g). Diagenetic minerals, on the other hand, show the lowest REY contents with an average content of 260 μg/g. These differences also depend on the growth rates, hydrogenetic minerals with growth rates between 0.5 and 5 mm/Ma allow the incorporation of more REY in their structure. REY contents in studied samples varies depending several factors associated with depth and location, shallowest samples presumably growth near or within the oxygen minimum zone are the most enriched with up to 3800 μg/g due to local enrichment of these elements and the slowest growth rate promoted by the reduced ambient conditions while deeper samples around 3000 m water depth show 2800 μg/g. Location also has a role in REY contents essentially due to the presence of different currents. Samples faced to north are exposed to the more oxygenated waters of the North Atlantic Deep Water and are depleted in REY if compared with deeper samples facing to south to the more oxic Antarctic Bottom Water. Finally, the case of study made on three different seamounts of the CISP show that Fe–Mn crusts from this area could provide on average 130 tons of hydrometallurgical recovered REY (based on 1 km2 areal crust coverage) together with interesting quantity of several other strategic and base elements as Mn, Co, Ni, Cu, V, Mo between others

The detection of airborne transmission of tuberculosis from HIV-infected patients, using an in vivo air sampling model

Background. Nosocomial transmission of tuberculosis remains an important public health problem. We created an in vivo air sampling model to study airborne transmission of tuberculosis from patients coinfected with human immunodeficiency virus (HIV) and to evaluate environmental control measures. Methods. An animal facility was built above a mechanically ventilated HIV‐tuberculosis ward in Lima, Peru. A mean of 92 guinea pigs were continuously exposed to all ward exhaust air for 16 months. Animals had tuberculin skin tests performed at monthly intervals, and those with positive reactions were removed for autopsy and culture for tuberculosis. Results. Over 505 consecutive days, there were 118 ward admissions by 97 patients with pulmonary tuberculosis, with a median duration of hospitalization of 11 days. All patients were infected with HIV and constituted a heterogeneous group with both new and existing diagnoses of tuberculosis. There was a wide variation in monthly rates of guinea pigs developing positive tuberculin test results (0%–53%). Of 292 animals exposed to ward air, 159 developed positive tuberculin skin test results, of which 129 had laboratory confirmation of tuberculosis. The HIV‐positive patients with pulmonary tuberculosis produced a mean of 8.2 infectious quanta per hour, compared with 1.25 for HIV‐negative patients with tuberculosis in similar studies from the 1950s. The mean monthly patient infectiousness varied greatly, from production of 0–44 infectious quanta per hour, as did the theoretical risk for a health care worker to acquire tuberculosis by breathing ward air. Conclusions. HIV‐positive patients with tuberculosis varied greatly in their infectiousness, and some were highly infectious. Use of environmental control strategies for nosocomial tuberculosis is therefore a priority, especially in areas with a high prevalence of both tuberculosis and HIV infection

Li–Na interdiffusion and diffusion-driven lithium isotope fractionation in pegmatitic melts

In this study, we investigate the diffusion of Li and its stable isotopes (6Li and 7Li) in flux-rich (1.8 % Li2O, 2.6 % B2O3, 2.3 % P2O5 and 3 % F) pegmatitic melts in order to contribute to the understanding of Li enrichment in such systems. Two glasses were synthesized with a model pegmatitic composition, one of which is highly enriched in Li (&gt; 1 wt %, PEG2-blue) and the other one essentially Li-free (PEG2-Li-free). Diffusion couple experiments were performed to determine the chemical diffusivity of Li in dry pegmatitic melts. Experiments were conducted using rapid-heat and rapid-quench cold-seal pressure vessels in a temperature range of 650–940 ∘C at 100 MPa with Ar as the pressure medium. We observed rapidly formed diffusion profiles, driven by an interdiffusive exchange of the monovalent alkalis Li and Na, while the other elements are immobile on the timescale of experiments (1–30 min). From these experiments, activation energies for Li–Na interdiffusion were determined as 99 ± 7 kJ mol−1 with a pre-exponential factor of log D0 = −5.05 ± 0.33 (D0 in m2 s−1). Li and Na partitioning between the stronger depolymerized PEG2-blue and the less depolymerized PEG2-Li-free leads to a concentration jump at the interface; i.e. Na is enriched in the more depolymerized PEG2-blue. Li–Na interdiffusion coefficients in the studied melt composition are in a similar range as Li and Na tracer diffusivities in other dry aluminosilicate melts, confirming little to no effect of aluminosilicate melt composition on Li diffusivity. Thus, added fluxes do not enhance the Li diffusivity in the same way as observed for H2O (Holycross et al., 2018; Spallanzani et al., 2022). Using melt viscosity as a proxy for the polymerization of the melt shows that water has a stronger potential to depolymerize a melt compared to other fluxing elements. Faster diffusion of 6Li compared to 7Li leads to a strong Li isotope fractionation along the diffusion profile, resulting in δ7Li as low as −80 ‰ relative to the diffusion-unaffected regions. This diffusive isotope fractionation can be quantified with an empirical isotope fractionation factor (β) of 0.20 ± 0.04, similar to previously observed β values for Li diffusion in melts. This suggests in accordance with previously published data that a β value of ca. 0.2 seems to be universally applicable to diffusive Li isotope fractionation in aluminosilicate melts.</p

Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared t