Risk Factors and Predictive Score for Bacteremic Biliary Tract Infections Due to Enterococcus faecalis and Enterococcus faecium: a Multicenter Cohort Study from the PROBAC Project

Biliary-tract bloodstream infections (BT-BSI) caused by Enterococcus faecalis and E. faecium are associated with inappropriate empirical treatment and worse outcomes compared to other etiologies. The objective of this study was to investigate the risk factors for enterococcal BT-BSI. Patients with BT-BSI from the PROBAC cohort, including consecutive patients with BSI in 26 Spanish hospitals between October 2016 and March 2017, were selected; episodes caused by E. faecalis or E. faecium and other causes were compared. Independent predictors for enterococci were identified by logistic regression, and a predictive score was developed. Eight hundred fifty episodes of BT-BSI were included; 73 (8.5%) were due to target Enterococcus spp. (48 [66%] were E. faecium and 25 [34%] E. faecalis). By multivariate analysis, the variables independently associated with Enterococcus spp. were (OR; 95% confidence interval): cholangiocarcinoma (4.48;1.32 to 15.25), hospital acquisition (3.58;2.11 to 6.07), use of carbapenems in the previous month (3.35;1.45 to 7.78), biliary prosthesis (2.19;1.24 to 3.90), and moderate or severe chronic kidney disease (1.55;1.07 to 2.26). The AUC of the model was 0.74 [95% CI0.67 to 0.80]. A score was developed, with 7, 6, 5, 4, and 2 points for these variables, respectively, with a negative predictive value of 95% for a score ? 6. A model, including cholangiocarcinoma, biliary prosthesis, hospital acquisition, previous carbapenems, and chronic kidney disease showed moderate prediction ability for enterococcal BT-BSI. Although the score will need to be validated, this information may be useful for deciding empirical therapy in biliary tract infections when bacteremia is suspected. IMPORTANCE Biliary tract infections are frequent, and a significant cause of morbidity and mortality. Bacteremia is common in these infections, particularly in the elderly and patients with cancer. Inappropriate empirical treatment has been associated with increased risk of mortality in bacteremic cholangitis, and the probability of receiving inactive empirical treatment is higher in episodes caused by enterococci. This is because many of the antimicrobial agents recommended in guidelines for biliary tract infections lack activity against these organisms. To the best of our knowledge, this is the first study analyzing the predictive factors for enterococcal BT-BSI and deriving a predictive score

Risk Factors and Predictive Score for Bacteremic Biliary Tract Infections Due to Enterococcus faecalis and Enterococcus faecium: a Multicenter Cohort Study from the PROBAC Project

Biliary-tract bloodstream infections (BT-BSI) caused by Enterococcus faecalis and E. faecium are associated with inappropriate empirical treatment and worse outcomes compared to other etiologies. The objective of this study was to investigate the risk factors for enterococcal BT-BSI. Patients with BT-BSI from the PROBAC cohort, including consecutive patients with BSI in 26 Spanish hospitals between October 2016 and March 2017, were selected; episodes caused by E. faecalis or E. faecium and other causes were compared. Independent predictors for enterococci were identified by logistic regression, and a predictive score was developed. Eight hundred fifty episodes of BT-BSI were included; 73 (8.5%) were due to target Enterococcus spp. (48 [66%] were E. faecium and 25 [34%] E. faecalis). By multivariate analysis, the variables independently associated with Enterococcus spp. were (OR; 95% confidence interval): cholangiocarcinoma (4.48;1.32 to 15.25), hospital acquisition (3.58;2.11 to 6.07), use of carbapenems in the previous month (3.35;1.45 to 7.78), biliary prosthesis (2.19;1.24 to 3.90), and moderate or severe chronic kidney disease (1.55;1.07 to 2.26). The AUC of the model was 0.74 [95% CI0.67 to 0.80]. A score was developed, with 7, 6, 5, 4, and 2 points for these variables, respectively, with a negative predictive value of 95% for a score # 6. A model, including cholangiocarcinoma, biliary prosthesis, hospital acquisition, previous carbapenems, and chronic kidney disease showed moderate prediction ability for enterococcal BT-BSI. Although the score will need to be validated, this information may be useful for deciding empirical therapy in biliary tract infections when bacteremia is suspected. IMPORTANCE Biliary tract infections are frequent, and a significant cause of morbidity and mortality. Bacteremia is common in these infections, particularly in the elderly and patients with cancer. Inappropriate empirical treatment has been associated with increased risk of mortality in bacteremic cholangitis, and the probability of receiving inactive empirical treatment is higher in episodes caused by enterococci. This is because many of the antimicrobial agents recommended in guidelines for biliary tract infections lack activity against these organisms. To the best of our knowledge, this is the first study analyzing the predictive factors for enterococcal BT-BSI and deriving a predictive score.8 página

Overview of recent TJ-II stellarator results

The main results obtained in the TJ-II stellarator in the last two years are reported. The most important topics investigated have been modelling and validation of impurity transport, validation of gyrokinetic simulations, turbulence characterisation, effect of magnetic configuration on transport, fuelling with pellet injection, fast particles and liquid metal plasma facing components. As regards impurity transport research, a number of working lines exploring several recently discovered effects have been developed: the effect of tangential drifts on stellarator neoclassical transport, the impurity flux driven by electric fields tangent to magnetic surfaces and attempts of experimental validation with Doppler reflectometry of the variation of the radial electric field on the flux surface. Concerning gyrokinetic simulations, two validation activities have been performed, the comparison with measurements of zonal flow relaxation in pellet-induced fast transients and the comparison with experimental poloidal variation of fluctuations amplitude. The impact of radial electric fields on turbulence spreading in the edge and scrape-off layer has been also experimentally characterized using a 2D Langmuir probe array. Another remarkable piece of work has been the investigation of the radial propagation of small temperature perturbations using transfer entropy. Research on the physics and modelling of plasma core fuelling with pellet and tracer-encapsulated solid-pellet injection has produced also relevant results. Neutral beam injection driven Alfvénic activity and its possible control by electron cyclotron current drive has been examined as well in TJ-II. Finally, recent results on alternative plasma facing components based on liquid metals are also presentedThis work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training programme 2014–2018 under Grant Agreement No. 633053. It has been partially funded by the Ministerio de Ciencia, Inovación y Universidades of Spain under projects ENE2013-48109-P, ENE2015-70142-P and FIS2017-88892-P. It has also received funds from the Spanish Government via mobility grant PRX17/00425. The authors thankfully acknowledge the computer resources at MareNostrum and the technical support provided by the Barcelona S.C. It has been supported as well by The Science and Technology Center in Ukraine (STCU), Project P-507F

Flash flood events recorded by air temperature changes in caves: A case study in Covadura Cave (SE Spain)

On 28th September 2012, more than 150 mm rain fell in just two hours in some points of southeastern Spain, triggering intense flash floods that resulted in the death of ten people and widespread material damage. In the gypsum karst of Sorbas, rainfall intensity reached 33 mm/h. Air temperature monitoring in different levels of Covadura Cave, down to 85 m depth, enabled the effect of this extreme episode on the cave microclimate to be evaluated in real time. The cave air temperature increased by between 0.9 and 4.1 °C as a result of water flow into the cavity and intense mixing of air masses, in addition to the displacement of deeper air masses toward shallower levels produced by fast recharge of the surrounding karst aquifer. The lag between peak rainfall intensity and the highest cave air temperature was 5–6 h, indicating the response time of the karst to this rainfall event. No trends with depth were observed, suggesting that water not only flowed in through the main cave entrance but also through secondary accesses and fractures. Furthermore, the size of the cave passages and the intensity of air turbulence generated by waterfalls in the cave played an important role in producing these temperature differences. Even though the rainfall event lasted 10 h, cave air temperature did not return to pre-flash flood values until more than 20 days later. This indicates that, while waterflow through the cave might stop a few hours after the rainfall event, cave air temperature can be affected over a longer period. This can be explained by slow groundwater level decreasing of the surrounding karst aquifer and latent heat liberation produced by moisture condensation on the cave walls. Our results show how continuous monitoring of air temperature in caves can be a useful tool for evaluating the short-term effects of flash floods in subterranean karst systems.Financial support was made available through funds from the Water Resources and Environmental Geology Research Group (University of Almería) and the ‘‘GLOCHARID’’ Project (852/2009/M/00) of the Junta de Andalucía Regional Government. Funding was also provided by the People Programme (Marie Curie Actions – Intra-European Fellowships, call 2013) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 624204 to Dr. Fernández-Cortés.Peer Reviewe

First assessment on the air CO2 dynamic in the show caves of tropical karst, Vietnam

In this study, air, water, and host rock in show caves in a Vietnam’s karst region was monitored and analyzed to identify the ventilation regime and track the cave air CO2 sources. In general, the studied caves are well ventilated. In dynamic – multiple entrance caves, air ventilation is described with the use of U shape model. In static – single entrance cave, air circulation is explained by cold air trap model. Both ventilation models suggest that air is more circulated in winter than in summer. Seasonally, the cave air CO2 increases from early spring to summer. Value in the deepest part of the single-entrance cave is approximately 1,000 ppmv and 8,000 ppmv in early spring and summer, respectively. In multiple-entrance and wet caves, CO2 level is fairly constant all over the show section, increasing from 500 ppmv in early spring to 2,000 ppmv in summer. Data of microclimate, CO2 content, and particularly δ13C show that cave air, particularly in single entrance cave, has higher CO2 concentration during summer due to a stagnation of cave air circulation and an elevated CO2 input from soil and epikarst. The cave air CO2 increase is also observed after intense rainfalls. A factor that increase cave air CO2 in show caves during the festive days could probably be huma n exhaling but the extent of human factor in these studied cave systems should be further investigated. Cave waters including cave pools and streams mediate CO2 level in wet caves. Above all, the atmospheric fraction of CO2 is always dominant (>60%) in all cave sections.Peer Reviewe

Geo-environmental evaluation for the preventive conservation of open-air archaeological sites: the case of the Roman Necropolis of Carmona (Spain)

The Necropolis of Carmona, which has more than 600 tombs carved in calcarenites, is among the most important Roman burial sites preserved in southern Spain. The tombs in the Necropolis show severe alteration and multiple weathering processes after being excavated at the end of the nineteenth century without a preventive conservation plan. The archaeological site shows strong anthropic modifications related to different excavation stages and in relation to the construction of facilities for the visiting public. In particular, the exposure of the buried tombs to meteoric conditions and anthropic modification of natural drainage have led to an important acceleration of the deterioration of the tombs. The conservation status of the Necropolis was defined through a comprehensive geo-environmental study that combined field observations and laboratory data, modelling and digital mapping and environmental monitoring. Results allow a methodology to be developed providing guidelines to minimize potential risks when excavating new tombs (now buried) in the future. Moreover, the most suitable prospective areas can be defined inside the Necropolis in terms of the environmental, geological and geomorphological conditions which will enhance the preservation of newly exhumed tombs. Geo-environmental preventive conservation methods that we propose can be entirely applied to other large archaeological sites completely exposed to open-air atmospheric conditions.This research was funded by the Consejería de Cultura, Junta de Andalucía (project CSIC-2007X0859)

On the role of cave-soil in the carbon cycle. A fist approach.

On-line, del 4 al 8 de mayo de 2020Karsts cover up to 25 % of the land surface and contain significant sedimentary deposits that become active cave-soils. Subterranean karst ecosystems play an active role in the global carbon cycle in terms of their contribution to the global GHG balance. They act alternately as a source or sink of CO2 and as a rapid sink of CH4. The most recent results indicate that microbiota must play a significant ecological role in the biogeochemical processes that control the subterranean atmosphere composition. Soils forming underneath the surface must host a large part of the subterranean microbiota. But to date, their behaviour concerning the production of gases and exchange with the ¿confined troposphere¿ has not been evaluated. Systematic direct estimates of CO2 and CH4 fluxes from cave-soils do not exist in literature. And they are needed before global generalizations can be made about the carbon budgets (emissions and sinks) of karstic ecosystems.Here we present pioneering research to evaluate the carbon fluxes from the cave soils directly exchanged with the cave atmosphere. This preliminary study is the first approach to systematically characterize the role of cave-soils in the production and transport of CO2 and CH4 in the subterranean environment. We carried out automatic in situ and real-time monitoring of CO2 and CH4 diffusive fluxes from a sedimentary alluvial soil in Pindal cave for one year (north Spain). We developed seasonal campaigns for CH4 and CO2 fluxes daily continuous monitoring by a LICOR closed chamber-based gas exchange system, in conjunction with a compatible Gasmet FTIR gas analyser. Moreover, autonomous equipment monitored the main micro-environmental parameters of the local subsurface-soil-atmosphere system. To interpret gas exchange processes and rates, and to understand the underlying mechanisms in soils, we also carried out seasonal ¿13C geochemical tracing by using Picarro cavity ring-down spectroscopy, through simultaneous cave atmosphere-soil-chamber air samplings. We also characterized the soil microbial communities related to the carbon cycle by meta-barcoding analyses of bacterial 16S rRNA genes and Shotgun Metagenomics. Preliminary results show net CO2 emissions from cave-soil on a daily scale, resulting from respiration by chemotrophic microorganisms. We detect significant magnitude variations along the day, reaching occasionally values close to zero. This is remarkable in such thermo-hygrometric stable environment and absence of light. Changes in the cave ventilation regime seems to be the determining factor just in some cases. Intrinsic microbial processes appear to be decisive in others. The results also reveal net CH4 uptake from cave-soil on a daily scale, with no significant magnitude variations along the day. It seems to be linked to the metabolism of Nitrate-dependent methanotrophs belonging to the phylum Rokubacteria. Additionally, we detected significant variations in magnitude and different flow patterns in the cave-soils colonized by biofilms, most prominent in the case of moonmilk deposits. These preliminary results confirm that cave-soil is playing an outstanding role in the processes of production, consumption and storage of CO2 and CH4 and may be partially determining the strong variations of these major GHGs in natural subterranean ecosystems

Insights on Climate-Driven Fluctuations of Cave 222Rn and CO2Concentrations Using Statistical and Wavelet Analyses

This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Understanding the fluctuations in cave air concentrations and their climatic control is substantial not only to preserve the quality of indoor atmospheres but also to avoid the risk related to the presence of hazardous substances. In this study, we investigated the most influential factors affecting 222Rn and CO2 concentrations, the nature of their dynamics, and their coupling with climatic variations. For this purpose, we combined a set of mathematical methods that included a statistical and wavelet analysis of a 6-year time series in Rull Cave (Spain). Generally, the 222Rn and CO2 dynamic in cave air showed similar patterns. However, the obtained results show that these gases have a different frequency response. Thus, the annual component of 222Rn and CO2 is controlled by the relationship between external and internal temperatures. At low frequencies, both gases are affected by the same variables when the cave atmosphere reaches a minimum concentration. However, when the cave atmosphere is isolated from the outdoors, 222Rn and CO2 behave differently and disturbance caused by the visitors is evidenced in terms of the CO2 concentration; the latter observation was confirmed by the wavelet analysis at high frequencies. In contrast, the 222Rn concentration shows important variations following rainfall, which was weakly identified in the CO2 concentration.This research was funded by the Spanish Ministry of Science, Innovation and Universities (projects CGL2016-78318-C2-1-R, CGL2016-78318-C2-2-R, and RTI2018-099052-B-I00) and the University of Alicante (project GRE17-12)

Climate-driven changes on storage and sink of carbon dioxide in subsurface atmosphere of karst terrains

A comprehensive environmental monitoring programme has been recently launched in Ojo Guareña cave system (Burgos, Spain), one of the longest caves in Europe, aimed to assess the magnitude of the spatiotemporal changes of CO2 (g), on daily and synoptic timescales in the cave–soil–atmosphere profile. CO2 concentration of cave air is usually close to atmospheric background but huge daily oscillations of CO2 levels, ranging 680–1,900 ppm/day on average, have registered during periods when exterior air temperature oscillates every day around cave air temperature. These daily variations of CO2 content are hidden once the air temperature outside is continuously below cave temperature and a prevailing advective-renewal of cave air is established, so that daily-averaged concentrations of CO2 reach minimum values close to 500 ppm. The spatiotemporal pattern of CO2(g) provides evidence that the amounts of carbon that might be sequestered and then emitted (CO2) from subsurface air located in the uppermost part of the vadose zone could be noticeable at local or regional scale by considering long subterranean systems as Ojo Guareña karst.Peer reviewe

Microbial role in N2O-NO2 production and CH4 oxidation under active hypogenic settings

On-line, del 4 al 8 de mayo de 2020The hydrothermal caves linked to active faulting have subterranean atmospheres with a distinctive gaseous composition containing deep endogenous gases, such as carbon dioxide, methane and nitrogen oxides (NOx). Ascending fluids through associated near-surface hydrothermal processes can mobilize endogenous gases into the Critical Zone and, ultimately, to the lower troposphere. Nitrogen oxides are polluting gases and can have adverse effects on human health, especially inhaled NO2. They also catalyse ozone (O3) production in the lower layers of the atmosphere and the greenhouse effect, when they react with volatile organic compounds. The largest source of NOx emissions is anthropogenic. The rest is produced naturally by microbial processes in soil and water, by lightning, volcanic activity, storms, etc. Production of N2O and NO2 is associated with soil and other active-geothermal ecosystems, far less is known about the sources and sinks of these gases within subterranean locations. Here, we report high N2O and NO2 concentrations detected along a hypogenic system associated with an active faulting (Vapour Cave, southern Spain), which enables direct gas exchange with the low-atmosphere. These anomalous concentrations of N2O and, NO2 are about ten and five times higher than the typical atmospheric background, respectively. Gaseous composition analyses of subterranean atmosphere were conducted by high precision field-deployable CRDS and FTIR spectrometers for measuring in situ the target tracer gases (NO2, N2O, CH4, CO2) and ¿13C of both carbon-GHGs. DNA extraction, sequencing and phylogenetic analyses were conducted to characterize the microbial community of cave sediments. The results showed that N2O and NO2 emission depends on the activity of nitrification by ammonia oxidizing microorganisms (such as members of the family Nitrosomonadaceae and phylum Thaumarchaeota) and/or as a result of incomplete denitrification by heterotrophic denitrifying bacteria (such as Bacillus, Acinetobacter and Cupriavidus) from this hydrothermal and hypoxic ecosystem. On the other hand, CH4 concentrations and 13CH4 vary along the cave (with the deep), in deepest cave locations CH4 values are higher with lighter 13C values in comparison with the more superficial areas, which indicates a deep endogenous origin of methane. However, in areas near the entrance we observe lower concentrations of methane and heavier 13C values (CH4<1 ppm and 13C close to 30), as a result of methane oxidation by denitrifying methanotrophs of the NC10 phylum during gas migration from the deepest areas to the surface. These new findings reveal the sourcing of these nitrogenous gases into the upper vadose zone of a hypogenic/geothermal ecosystem, and its potential release to the lower troposphere. A better understanding of biogeochemical processes controlling the production of nitrogenous gases in subterranean environments will be useful to identify and characterize new possible sources, reservoirs and sinks of greenhouse gases (CO2, CH4, N2O and NOx) in order to calculate more accurately the budgets and for the design of new mitigation strategies of these gases