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We propose two explicit expressions to calculate the settling speed of solid atmospheric particles with prolate spheroidal shapes under the hypothesis of horizontal and vertical orientation. The first formulation is based on theoretical arguments only. The second method, valid for particles with mass median diameter up to 1000 µm, is based on recent heuristic drag expressions based on numeric simulations. We show that these two formulations show equivalent results within 2 % for deq≤100 µm and within 10 % for particles with deq≤500 µm falling with a horizontal orientation, showing that the first, more simple, method is suitable for virtually all atmospheric aerosols, provided their shape can be adequately described as a prolate spheroid. Finally, in order to facilitate the use of our results in chemistry transport models, we provide an implementation of the first of these methods in AerSett v2.0.2, a module written in Fortran.

A new version of the CHIMERE model is presented. This version contains both computational and physico-chemical changes. The computational changes make it easy to choose the variables to be extracted as a result, including values of maximum sub-hourly concentrations. Performance tests show that the model is 1.5 to 2 times faster than the previous version for the same setup. Processes such as turbulence, transport schemes and dry deposition have been modified and updated. Optimization was also performed for the management of emissions such as anthropogenic and mineral dust. The impact of fires on wind speed, soil properties and leaf area index (LAI) was added. Pollen emissions, transport and deposition were added for birch, ragweed, olive and grass. The model is validated with a simulation covering Europe with a 60 km × 60 km resolution and the entire year of 2019. Results are compared to various measurements, and statistical scores show that the model provides better results than the previous versions.

Meteorological and chemical modelling at the regional scale often involve the nudging of the modelled meteorology towards reanalysis fields and meteo-chemical coupling to properly consider the interactions between aerosols, clouds and radiation. Both types of processes can change the meteorology, but not for the same reasons and not necessarily in the same way. To assess the possible interactions between nudging and online coupling, several simulations are carried out with the WRF–CHIMERE (Weather Research and Forecasting) model in its offline and online configurations. Through comparison with measurements, we show that the use of nudging significantly improves the model performances. We also show that coupling changes the results much less than nudging. Finally, we show that when nudging is used, it limits the variability in the results due to coupling.

This study presents a novel method to estimate the performance of advection schemes in numerical experiments along with a semi-realistic, non-linear, stiff chemical system. This method is based on the examination of the “signature function”, an invariant of the advection equation. Apart from exposing this concept in a particular numerical test case, we show that a new numerical scheme based on a combination of the piecewise parabolic method (PPM) with the flux adjustments of Walcek outperforms both the PPM and the Walcek schemes for inert tracer advection as well as for advection of chemically active species. From a fundamental point of view, we think that our evaluation method, based on the invariance of the signature function under the effect of advection, offers a new way to evaluate objectively the performance of advection schemes in the presence of active chemistry. More immediately, we show that the new PPM + W (“piecewise parabolic method + Walcek”) advection scheme offers chemistry-transport modellers an alternative, high-performance scheme designed for Cartesian-grid Eulerian chemistry-transport models, with improved performance over the classical PPM scheme. The computational cost of PPM + W is not higher than that of PPM. With improved accuracy and controlled computational cost, this new scheme may find applications in other fields such as ocean models or atmospheric circulation models.

The atypical huge forest fires observed in France during the summer of 2022 are modeled using the CHIMERE model. The impact of these emissions is quantified on ozone, aerosols and aerosol optical depth (AOD). The fires also influence the surface by destroying the vegetation and creating new erodible surfaces. This increases the mineral dust emissions but also reduces the leaf area index (LAI), and then it decreases the biogenic emissions and the dry deposition of gases such as ozone. Results show that the fires induce numerous increases in surface ozone and particulate matter (PM) concentrations close to the sources but also in downwind remote sites such as the Paris area. During the period of the most intense fires in July, the impact of concentrations is mainly due to emissions themselves, and later, in August, ozone and PM concentrations continue to increase but this time due to changes in the burned surfaces.

This study introduces AerSett v1.0 (AERosol SETTling version 1.0), a model giving the settling speed of big spherical aerosols in the atmosphere without going through an iterative equation resolution. We prove that, for all spherical atmospheric aerosols with diameter D up to 1000 µm, this direct and explicit method including the drag coefficient formulation of Clift and Gauvin (1971) and the Davies (1945) slip correction factor gives results within 2 % of the exact solution obtained from the numerical resolution of a non-linear fixed-point equation. This error is acceptable considering the uncertainties on the drag coefficient formulations themselves. For D, the error is below 0.5 %. We provide a Fortran implementation of this simple and straightforward model, hoping that more chemistry–transport models (CTMs) and general circulation models will be able to take into account large-particle drag correction to the settling speed of big spherical aerosol particles in the atmosphere, without performing an iterative and time-consuming calculation.

Air pollution in the central zone of Chile is not only a public health concern but also threatens water resources and climate, in connection with the transport and deposition of black carbon (BC) from urban centers onto the glaciers of the Andes. Chemistry-transport simulations reveal a seasonal dichotomy in the flux and latitudinal pattern of BC deposition on glaciers of the central Chilean Andes. The average deposition flux of BC on glaciers between 30 and 37∘ S is 4 times larger in winter, affecting mostly low-elevation glaciers, whereas the smaller summertime flux affects glaciers evenly, irrespective of their elevation. The contribution of emissions from the city of Santiago is dominant in summertime with more than 50 % along the Andes but minor in wintertime with less than 20 % even close to the capital city. Transport at larger scales and more local sources likely account for the remaining flux. The superimposition of synoptic-scale circulation and local mountain-valley circulation along the Andes drives the differences between summertime and wintertime deposition fluxes and generates a greater meteorological export potential during summer months. Future emissions and climate projections suggest that under the RCP8.5 scenario the gap between summertime and wintertime BC export and deposition flux could decrease, thereby pointing to summertime emission control gaining relevance. The chemistry-transport modeling approach for BC deposition on the Andes sheds light on the importance of the often disregarded summertime emissions on the radiative balance of its glaciers, particularly in the vicinity of Santiago.

Volcanic activity is an important source of atmospheric sulfur dioxide (SO2), which, after conversion into sulfuric acid, induces impacts on rain acidity, human health, meteorology and the radiative balance of the atmosphere, among others. This work focuses on the conversion of SO2 into sulfates (SO4(p)2-, S(+VI)) in the mid-tropospheric volcanic plume emitted by the explosive eruption of Mount Etna (Italy) on 12 April 2012, using the CHIMERE chemistry transport model. As the volcanic plume location and composition depend on several often poorly constrained parameters, using a chemistry transport model allows us to study the sensitivity of SO2 oxidation to multiple aspects, such as volcanic water emissions, transition metal emissions, plume diffusion and plume altitude. Our results show that two pathways contribute to sulfate production in the mid-troposphere: (1) the oxidation of SO2 by OH in the gaseous phase (70 %) and (2) aqueous oxidation by O2 catalysed by Mn2+ and Fe3+ ions (25 %). Oxidation in the aqueous phase is the faster process, but liquid water is scarce in the mid-troposphere; therefore, the relative share of gaseous oxidation can be important. After 1 d in the mid-troposphere, about 0.5 % of the volcanic SO2 was converted to sulfates via the gaseous process. Because of the nonlinear dependency of the kinetics in the aqueous phase on the amount of volcanic water emitted and on the availability of transition metals in the aqueous phase, several experiments have been designed to determine the prominence of different parameters. Our simulations show that, during the short time that liquid water remains in the plume, around 0.4 % of sulfates manage to quickly enter the liquid phase. Sensitivity tests regarding the advection scheme have shown that this scheme must be chosen wisely, as dispersion will impact both of the oxidation pathways explained above.

The CHIMERE chemistry-transport model v2020r1 replaces the v2017r5 version and provides numerous novelties. The most important of these is the online coupling with the Weather Research and Forecasting (WRF) meteorological model via the OASIS3 – Model Coupling Toolkit (MCT) external coupler. The model can still be used in offline mode; the online mode enables us to take into account the direct and indirect effects of aerosols on meteorology. This coupling also enables using the meteorological parameters with sub-hourly time steps. Some new parameterizations are implemented to increase the model performance and the user's choices: dimethyl sulfide (DMS) emissions, additional schemes for secondary organic aerosol (SOA) formation with volatility basis set (VBS) and H2O, improved schemes for mineral dust, biomass burning, and sea-salt emissions. The NOx emissions from lightning are added. The model also includes the possibility to use the operator-splitting integration technique. The subgrid-scale variability calculation of concentrations due to emission activity sectors is now possible. Finally, a new vertical advection scheme has been implemented, which is able to simulate more correctly long-range transport of thin pollutant plumes.

Central Chile faces atmospheric pollution issues all year long as a result of elevated concentrations of fine particulate matter during the cold months and tropospheric ozone during the warm season. In addition to public health issues, environmental problems regarding vegetation growth and water supply, as well as meteorological feedback, are at stake. Sharp spatial gradients in regional emissions, along with a complex geographical situation, make for variable and heterogeneous dynamics in the localization and long-range transport of pollutants, with seasonal differences. Based on chemistry–transport modeling with Weather Research Forecasting (WRF)–CHIMERE, this work studies the following for one winter period and one summer period: (i) the contribution of emissions from the city of Santiago to air pollution in central Chile, and (ii) the reciprocal contribution of regional pollutants transported into the Santiago basin. The underlying 3-dimensional advection patterns are investigated. We find that, on average for the winter period, 5 to 10 µg m−3 of fine particulate matter in Santiago come from regional transport, corresponding to between 13 % and 15 % of average concentrations. In turn, emissions from Santiago contribute between 5 % and 10 % of fine particulate matter pollution as far as 500 km to the north and 500 km to the south. Wintertime transport occurs mostly close to the surface. In summertime, exported precursors from Santiago, in combination with mountain–valley circulation dynamics, are found to account for most of the ozone formation in the adjacent Andes cordillera and to create a persistent plume of ozone of more than 50 ppb (parts per billion), extending along 80 km horizontally and 1.5 km vertically, and located slightly north of Santiago, several hundred meters above the ground. This work constitutes the first description of the mechanism underlying the latter phenomenon. Emissions of precursors from the capital city also affect daily maxima of surface ozone hundreds of kilometers away. In parallel, cutting emissions of precursors in the Santiago basin results in an increase in surface ozone mixing ratios in its western area.

The potential of the antidiffusive transport scheme proposed by Després and Lagoutière (1999) for resolving vertical transport in chemistry-transport models is investigated in an idealized framework with very encouraging results. We show that, compared to classical higher-order schemes, the Després and Lagoutière (1999) scheme reduces numerical diffusion and improves accuracy in idealized cases that are typical of atmospheric transport of tracers in chemistry-transport models. The increase in accuracy and the reduction in diffusion are substantial when, and only when, vertical resolution is insufficient to properly resolve vertical gradients, which is very frequent in chemistry-transport models. Therefore, we think that this scheme is an extremely promising solution for reducing numerical diffusion in chemistry-transport models.

Excessive numerical diffusion is one of the major limitations in the representation of long-range transport by chemistry transport models. In the present study, we focus on excessive diffusion in the vertical direction, which has been shown to be a major issue, and we explore three possible ways of addressing this problem: increasing the vertical resolution, using an advection scheme with anti-diffusive properties and more accurately representing the vertical wind. This study was carried out using the CHIMERE chemistry transport model for the 18 March 2012 eruption of Mount Etna, which released about 3 kt of sulfur dioxide into the atmosphere in a plume that was observed by satellite instruments (the Infrared Atmospheric Sounding Interferometer instrument, IASI, and the Ozone Monitoring Instrument, OMI) for several days. The change from the classical Van Leer (1977) scheme to the Després and Lagoutière (1999) anti-diffusive scheme in the vertical direction was shown to provide the largest improvement to model outputs in terms of preserving the thin plume emitted by the volcano. To a lesser extent, the improved representation of the vertical wind field was also shown to reduce plume dispersion. Both of these changes helped to reduce vertical diffusion in the model as much as a brute-force approach (increasing vertical resolution).

Biomass burning emissions are a major source of trace gases and aerosols. Wildfires being highly variable in time and space, calculating emissions requires a numerical tool able to estimate fluxes at the kilometer scale and with an hourly time step. Here, the APIFLAME model version 2.0 is presented. It is structured to be modular in terms of input databases and processing methods. The main evolution compared to version 1.0 is the possibility of merging burned area and fire radiative power (FRP) satellite observations to modulate the temporal variations of fire emissions and to integrate small fires that may not be detected in the burned area product. Accounting for possible missed detection due to small fire results in an increase in burned area ranging from ∼5 % in Africa and Australia to ∼30 % in North America on average over the 2013–2017 time period based on the Moderate-Resolution Imaging Spectroradiometer (MODIS) Collection 6 fire products. An illustration for the case of southwestern Europe during the summer of 2016, marked by large wildfires in Portugal, is presented. Emissions calculated using different possible configurations of APIFLAME show a dispersion of 80 % on average over the domain during the largest wildfires (8–14 August 2016), which can be considered as an estimate of uncertainty of emissions. The main sources of uncertainty studied, by order of importance, are the emission factors, the calculation of the burned area, and the vegetation attribution. The aerosol (PM10) and carbon monoxide (CO) concentrations simulated with the CHIMERE regional chemistry transport model (CTM) are consistent with observations (good timing for the beginning and end of the events, ±1 d for the timing of the peak values) but tend to be overestimated compared to observations at surface stations. On the contrary, vertically integrated concentrations tend to be underestimated compared to satellite observations of total column CO by the Infrared Atmospheric Sounding Interferometer (IASI) instrument and aerosol optical depth (AOD) by MODIS. This underestimate is lower close to the fire region (5 %–40 % for AOD depending on the configuration and 8 %–18 % for total CO) but rapidly increases downwind. For all comparisons, better agreement is achieved when emissions are injected higher into the free troposphere using a vertical profile as estimated from observations of aerosol plume height by the Multi-angle Imaging SpectroRadiometer (MISR) satellite instrument (injection up to 4 km). Comparisons of aerosol layer heights to observations by the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) show that some parts of the plume may still be transported at too low an altitude. The comparisons of the different CTM simulations to observations point to uncertainties not only on emissions (total mass and daily variability) but also on the simulation of their transport with the CTM and mixing with other sources. Considering the uncertainty of the emission injection profile and of the modeling of the transport of these dense plumes, it is difficult to fully validate emissions through comparisons between model simulations and atmospheric observations.

Aerosols may impact precipitation in a complex way involving their direct and indirect effects. In a previous numerical study, the overall microphysical effect of aerosols was found to weaken precipitation through reduced precipitable water and convective instability. The present study aims to quantify the relative importance of these two processes in the reduction of summer precipitation using temperature–precipitation scaling. Based on a numerical sensitivity experiment conducted in central Europe aiming to isolate indirect effects, the results show that, all others effects being equal, the scaling of hourly convective precipitation with temperature follows the Clausius–Clapeyron (CC) relationship, whereas the decrease in convective precipitation does not scale with the CC law since it is mostly attributable to increased stability with increased aerosol concentration rather than to decreased precipitable water content. This effect is larger at low surface temperatures at which clouds are statistically more frequent and optically thicker. At these temperatures, the increase in stability is mostly linked to the stronger reduction in temperature in the lower troposphere compared to the upper troposphere, which results in lower lapse rates.

In wintertime, high concentrations of atmospheric fine particulate matter (PM2.5) are commonly observed in the metropolitan area of Santiago, Chile. Hourly peaks can be very strong, up to 10 times above average levels, but have barely been studied so far. Based on atmospheric composition measurements and chemistry-transport modeling (WRF-CHIMERE), the chemical signature of sporadic skyrocketing wintertime PM2.5 peaks is analyzed. This signature and the timing of such extreme events trace their origin back to massive barbecue cooking by Santiago's inhabitants during international soccer games. The peaks end up evacuated outside Santiago after a few hours but trigger emergency plans for the next day. Decontamination plans in Santiago focus on decreasing emissions from traffic, industry, and residential heating. Thanks to the air quality network of Santiago, this study shows that cultural habits such as barbecue cooking also need to be taken into account. For short-term forecast and emergency management, cultural events such as soccer games seem a good proxy to prognose possible PM2.5 peak events. Not only can this result have an informative value for the Chilean authorities but also a similar methodology could be reproduced for other cases throughout the world in order to estimate the burden on air quality of cultural habits.

During the monsoon season, pollutants emitted by large coastal cities and biomass burning plumes originating from central Africa have complex transport pathways over southern West Africa (SWA). The Dynamics–Aerosol–Chemistry–Cloud Interactions in West Africa (DACCIWA) field campaign has provided numerous dynamical and chemical measurements in and around the super-site of Savè in Benin ( ≈ 185 km away from the coast), which allows quantification of the relative contribution of advected pollutants. Through the combination of in situ ground measurements with aircraft, radio-sounding, satellite, and high-resolution chemistry-transport modeling with the CHIMERE model, the source attribution and transport pathways of pollutants inland (here, NOx and CO) are carefully analyzed for the 1–7 July 2016 period. The relative contributions of different sources (i.e., emissions from several large coastal cities) to the air quality in Savè are characterized. It is shown that a systematic diurnal cycle exists with high surface concentrations of pollutants from 18:00 to 22:00 UTC. This evening peak is attributed to pollution transport from the coastal city of Cotonou (Benin). Numerical model experiments indicate that the anthropogenic pollutants are accumulated during the day close to the coast and transported northward as soon as the daytime convection in the atmospheric boundary layer ceases after 16:00 UTC, reaching 8° N at 21:00 UTC. When significant biomass burning pollutants are transported into continental SWA, they are mixed with anthropogenic pollutants along the coast during the day, and this mixture is then transported northward. At night, most of the coastal anthropogenic plumes are transported within the planetary boundary layer (below about 500 m above ground level), whereas the biomass burning pollutants are mostly transported above it, thus generally not impacting ground level air quality.

Aerosols affect atmospheric dynamics through their direct and semi-direct effects as well as through their effects on cloud microphysics (indirect effects). The present study investigates the indirect effects of aerosols on summer precipitation in the Euro-Mediterranean region, which is located at the crossroads of air masses carrying both natural and anthropogenic aerosols. While it is difficult to disentangle the indirect effects of aerosols from the direct and semi-direct effects in reality, a numerical sensitivity experiment is carried out using the Weather Research and Forecasting (WRF) model, which allows us to isolate indirect effects, all other effects being equal. The Mediterranean hydrological cycle has often been studied using regional climate model (RCM) simulations with parameterized convection, which is the approach we adopt in the present study. For this purpose, the Thompson aerosol-aware microphysics scheme is used in a pair of simulations run at 50 km resolution with extremely high and low aerosol concentrations. An additional pair of simulations has been performed at a convection-permitting resolution (3.3 km) to examine these effects without the use of parameterized convection. While the reduced radiative flux due to the direct effects of the aerosols is already known to reduce precipitation amounts, there is still no general agreement on the sign and magnitude of the aerosol indirect forcing effect on precipitation, with various processes competing with each other. Although some processes tend to enhance precipitation amounts, some others tend to reduce them. In these simulations, increased aerosol loads lead to weaker precipitation in the parameterized (low-resolution) configuration. The fact that a similar result is obtained for a selected area in the convection-permitting (high-resolution) configuration allows for physical interpretations. By examining the key variables in the model outputs, we propose a causal chain that links the aerosol effects on microphysics to their simulated effect on precipitation, essentially through reduction of the radiative heating of the surface and corresponding reductions of surface temperature, resulting in increased atmospheric stability in the presence of high aerosol loads.

Carbon monoxide, CO, and fine atmospheric particulate matter, PM2.5, are analyzed over the Guinean Gulf coastal region using the WRF-CHIMERE modeling system and observations during the beginning of the monsoon 2006 (from May to July), corresponding to the Africa Multidisciplinary Monsoon Analysis (AMMA) campaign period. Along the Guinean Gulf coast, the contribution of long-range pollution transport to CO or PM2.5 concentrations is important. The contribution of desert dust PM2.5 concentration decreases from ∼ 38 % in May to ∼ 5 % in July. The contribution of biomass burning PM2.5 concentration from Central Africa increases from ∼ 10 % in May to ∼ 52 % in July. The anthropogenic contribution is ∼ 30 % for CO and ∼ 10 % for PM2.5 during the whole period. When focusing only on anthropogenic pollution, frequent northward transport events from the coast to the Sahel are associated with periods of low wind and no precipitation. In June, anthropogenic PM2.5 and CO concentrations are higher than in May or July over the Guinean coastal region. Air mass dynamics concentrate pollutants emitted in the Sahel due to a meridional atmospheric cell. Moreover, a part of the pollution emitted remotely at the coast is transported and accumulated over the Sahel. Focusing the analysis on the period 8–15 June, anthropogenic pollutants emitted along the coastline are exported toward the north especially at the beginning of the night (18:00 to 00:00 UTC) with the establishment of the nocturnal low level jet. Plumes originating from different cities are mixed for some hours at the coast, leading to high pollution concentration, because of specific disturbed meteorological conditions.

CHIMERE is a chemistry-transport model designed for regional atmospheric composition. It can be used at a variety of scales from local to continental domains. However, due to the model design and its historical use as a regional model, major limitations had remained, hampering its use at hemispheric scale, due to the coordinate system used for transport as well as to missing processes that are important in regions outside Europe. Most of these limitations have been removed in the CHIMERE-2017 version, allowing its use in any region of the world and at any scale, from the scale of a single urban area up to hemispheric scale, with or without polar regions included. Other important improvements have been made in the treatment of the physical processes affecting aerosols and the emissions of mineral dust. From a computational point of view, the parallelization strategy of the model has also been updated in order to improve model numerical performance and reduce the code complexity. The present article describes all these changes. Statistical scores for a model simulation over continental Europe are presented, and a simulation of the circumpolar transport of volcanic ash plume from the Puyehue volcanic eruption in June 2011 in Chile provides a test case for the new model version at hemispheric scale.

A simple and complementary model evaluation technique for regional chemistry transport is discussed. The methodology is based on the concept that we can learn about model performance by comparing the simulation results with observational data available for time periods other than the period originally targeted. First, the statistical indicators selected in this study (spatial and temporal correlations) are computed for a given time period, using colocated observation and simulation data in time and space. Second, the same indicators are used to calculate scores for several other years while conserving the spatial locations and Julian days of the year. The difference between the results provides useful insights on the model capability to reproduce the observed day-to-day and spatial variability. In order to synthesize the large amount of results, a new indicator is proposed, designed to compare several error statistics between all the years of validation and to quantify whether the period and area being studied were well captured by the model for the correct reasons.

The presence of airborne aerosols affects the meteorology as it induces a perturbation in the radiation budget, the number of cloud condensation nuclei and the cloud micro-physics. Those effects are difficult to model at regional scale as regional chemistry-transport models are usually driven by a distinct meteorological model or data. In this paper, the coupling of the CHIMERE chemistry-transport model with the WRF meteorological model using the OASIS3-MCT coupler is presented. WRF meteorological fields along with CHIMERE aerosol optical properties are exchanged through the coupler at a high frequency in order to model the aerosol–radiation interactions. The WRF-CHIMERE online model has a higher computational burden than both models run separately in offline mode (up to 42 % higher). This is mainly due to some additional computations made within the models such as more frequent calls to meteorology treatment routines or calls to optical properties computation routines. On the other hand, the overall time required to perform the OASIS3-MCT exchanges is not significant compared to the total duration of the simulations. The impact of the coupling is evaluated on a case study over Europe, northern Africa, the Middle East and western Asia during the summer of 2012, through comparisons of the offline and two online simulations (with and without the aerosol optical properties feedback) to observations of temperature, aerosol optical depth (AOD) and surface PM10 (particulate matter with diameters lower than 10 µm) concentrations. The result shows that using the optical properties feedback induces a radiative forcing (average forcing of −4.8 W m−2) which creates a perturbation in the average surface temperatures over desert areas (up to 2.6° locally) along with an increase in both AOD and PM10 concentrations.

The aerosol speciation and size distribution is modeled during the summer 2013 and over a large area encompassing Africa, Mediterranean and western Europe. The modeled aerosol is compared to available measurements such as the AERONET aerosol optical depth (AOD) and aerosol size distribution (ASD) and the EMEP network for surface concentrations of particulate matter PM2.5, PM10 and inorganic species (nitrate, sulfate and ammonium). The main goal of this study is to quantify the model ability to realistically model the speciation and size distribution of the aerosol. Results first showed that the long-range transport pathways are well reproduced and mainly constituted by mineral dust: spatial correlation is ≈ 0.9 for AOD and Ångström exponent, when temporal correlations show that the day-to-day variability is more difficult to reproduce. Over Europe, PM2.5 and PM10 have a mean temporal correlation of ≈ 0.4 but the lowest spatial correlation ( ≈ 0.25 and 0.62, respectively), showing that the fine particles are not well localized or transported. Being short-lived species, the uncertainties on meteorology and emissions induce these lowest scores. However, time series of PM2.5 with the speciation show a good agreement between model and measurements and are useful for discriminating the aerosol composition. Using a classification from the south (Africa) to the north (northern Europe), it is shown that mineral dust relative mass contribution decreases from 50 to 10 % when nitrate increases from 0 to 20 % and all other species, sulfate, sea salt, ammonium, elemental carbon, primary organic matter, are constant. The secondary organic aerosol contribution is between 10 and 20 % with a maximum at the latitude of the Mediterranean Sea (Spanish stations). For inorganic species, it is shown that nitrate, sulfate and ammonium have a mean temporal correlation of 0.25, 0.37 and 0.17, respectively. The spatial correlation is better (0.25, 0.5 and 0.87), showing that the mean values may be biased but the spatial localization of sulfate and ammonium is well reproduced. The size distribution is compared to the AERONET product and it is shown that the model fairly reproduces the main values for the fine and coarse mode. In particular, for the fine mode, the model overestimates the aerosol mass in Africa and underestimates it in Europe.

The Mediterranean basin is characterized by large concentrations of aerosols from both natural and anthropogenic sources. These aerosols affect tropospheric photochemistry by modulating the photolytic rates. Three simulations of the atmospheric composition at basin scale have been performed with the CHIMERE chemistry-transport model for the period from 6 June to 15 July 2013 covered by the ADRIMED campaign, a campaign of intense measurements in the western Mediterranean basin. One simulation takes into account the radiative effect of the aerosols on photochemistry, the second one does not, and the third one is designed to quantify the model sensitivity to a bias in the ozone column. These simulations are compared to satellite and ground-based measurements, with a particular focus on the area of Lampedusa. Values of the aerosol optical depth (AOD) are obtained from the MODIS instrument on the AQUA and TERRA satellites as well as from stations in the AERONET network and from the MFRSR sun photometer deployed at Lampedusa. Additional measurements from instruments deployed at Lampedusa either permanently or exceptionally are used for other variables: MFRSR sun photometer for AOD, diode array spectrometer for actinic fluxes, LIDAR for the aerosol backscatter, sequential sampler for speciation of aerosol and Brewer spectrophotometer for the total ozone column. It is shown that CHIMERE has a significant ability to reproduce observed peaks in the AOD, which in Lampedusa are mainly due to dust outbreaks during the ADRIMED period, and that taking into account the radiative effect of the aerosols in CHIMERE considerably improves the ability of the model to reproduce the observed day-to-day variations of the photolysis rate of ozone to O2 and O(1D), J(O1D), and that of NO2 to NO and O(3P), J(NO2). While in the case of J(O1D) other variation factors such as the stratospheric ozone column are very important in representing correctly the day-to-day variations, the day-to-day variations of J(NO2) are captured almost completely by the model when the optical effects of the aerosols are taken into account. Finally, it is shown that the inclusion of the direct radiative effect of the aerosols in the CHIMERE model leads to reduced J(O1D) and J(NO2) values over all the simulation domain, which range from a few percents over continental Europe and the north-east Atlantic Ocean to about 20 % close to and downwind from Saharan dust sources. The effect on the modelled ozone concentration is 2-fold: the effect of aerosols leads to reduced ozone concentrations over the Mediterranean Sea and continental Europe, close to the sources of NOx, but it also leads to increased ozone concentrations over remote areas such as the Sahara and the tropical Atlantic Ocean.

The Chemistry-Aerosol Mediterranean Experiment (ChArMEx; http://charmex.lsce.ipsl.fr) is a collaborative research program federating international activities to investigate Mediterranean regional chemistry-climate interactions. A special observing period (SOP-1a) including intensive airborne measurements was performed in the framework of the Aerosol Direct Radiative Impact on the regional climate in the MEDiterranean region (ADRIMED) project during the Mediterranean dry season over the western and central Mediterranean basins, with a focus on aerosol-radiation measurements and their modeling. The SOP-1a took place from 11 June to 5 July 2013. Airborne measurements were made by both the ATR-42 and F-20 French research aircraft operated from Sardinia (Italy) and instrumented for in situ and remote-sensing measurements, respectively, and by sounding and drifting balloons, launched in Minorca. The experimental setup also involved several ground-based measurement sites on islands including two ground-based reference stations in Corsica and Lampedusa and secondary monitoring sites in Minorca and Sicily. Additional measurements including lidar profiling were also performed on alert during aircraft operations at EARLINET/ACTRIS stations at Granada and Barcelona in Spain, and in southern Italy. Remote-sensing aerosol products from satellites (MSG/SEVIRI, MODIS) and from the AERONET/PHOTONS network were also used. Dedicated meso-scale and regional modeling experiments were performed in relation to this observational effort. We provide here an overview of the different surface and aircraft observations deployed during the ChArMEx/ADRIMED period and of associated modeling studies together with an analysis of the synoptic conditions that determined the aerosol emission and transport. Meteorological conditions observed during this campaign (moderate temperatures and southern flows) were not favorable to producing high levels of atmospheric pollutants or intense biomass burning events in the region. However, numerous mineral dust plumes were observed during the campaign, with the main sources located in Morocco, Algeria and Tunisia, leading to aerosol optical depth (AOD) values ranging between 0.2 and 0.6 (at 440 nm) over the western and central Mediterranean basins. One important point of this experiment concerns the direct observations of aerosol extinction onboard the ATR-42, using the CAPS system, showing local maxima reaching up to 150 M m−1 within the dust plume. Non-negligible aerosol extinction (about 50 M m−1) has also been observed within the marine boundary layer (MBL). By combining the ATR-42 extinction coefficient observations with absorption and scattering measurements, we performed a complete optical closure revealing excellent agreement with estimated optical properties. This additional information on extinction properties has allowed calculation of the dust single scattering albedo (SSA) with a high level of confidence over the western Mediterranean. Our results show a moderate variability from 0.90 to 1.00 (at 530 nm) for all flights studied compared to that reported in the literature on this optical parameter. Our results underline also a relatively low difference in SSA with values derived near dust sources. In parallel, active remote-sensing observations from the surface and onboard the F-20 aircraft suggest a complex vertical structure of particles and distinct aerosol layers with sea spray and pollution located within the MBL, and mineral dust and/or aged North American smoke particles located above (up to 6–7 km in altitude). Aircraft and balloon-borne observations allow one to investigate the vertical structure of the aerosol size distribution showing particles characterized by a large size (> 10 µm in diameter) within dust plumes. In most of cases, a coarse mode characterized by an effective diameter ranging between 5 and 10 µm, has been detected above the MBL. In terms of shortwave (SW) direct forcing, in situ surface and aircraft observations have been merged and used as inputs in 1-D radiative transfer codes for calculating the aerosol direct radiative forcing (DRF). Results show significant surface SW instantaneous forcing (up to −90 W m−2 at noon). Aircraft observations provide also original estimates of the vertical structure of SW and LW radiative heating revealing significant instantaneous values of about 5° K per day in the solar spectrum (for a solar angle of 30°) within the dust layer. Associated 3-D modeling studies from regional climate (RCM) and chemistry transport (CTM) models indicate a relatively good agreement for simulated AOD compared with observations from the AERONET/PHOTONS network and satellite data, especially for long-range dust transport. Calculations of the 3-D SW (clear-sky) surface DRF indicate an average of about −10 to −20 W m−2 (for the whole period) over the Mediterranean Sea together with maxima (−50 W m−2) over northern Africa. The top of the atmosphere (TOA) DRF is shown to be highly variable within the domain, due to moderate absorbing properties of dust and changes in the surface albedo. Indeed, 3-D simulations indicate negative forcing over the Mediterranean Sea and Europe and positive forcing over northern Africa. Finally, a multi-year simulation, performed for the 2003 to 2009 period and including an ocean–atmosphere (O–A) coupling, underlines the impact of the aerosol direct radiative forcing on the sea surface temperature, O–A fluxes and the hydrological cycle over the Mediterranean.

The ADRIMED (Aerosol Direct Radiative Impact on the regional climate in the MEDiterranean region) project was dedicated to study the atmospheric composition during the summer 2013 in the European Mediterranean region. During its campaign experiment part, the WRF (Weather Research and Forecast Model) and CHIMERE models were used in the forecast mode in order to decide whether intensive observation periods should be triggered. Each day, a simulation of 4 days was performed, corresponding to (D-1) to (D+2) forecast leads. The goal of this study was to determine whether the model forecast spread is lower or greater than the model biases compared to observations. It is shown that the differences between observations and the model are always higher than those between the forecasts. Among all forcing types used in the chemistry-transport model, it is shown that the strong bias and other related low forecast scores are mainly due to the forecast accuracy of the wind speed, which is used both for the mineral dust emissions (a threshold process) and for the long-range transport of aerosol: the surface wind speed forecast spread can reach 50%, leading to mineral dust emission forecast spread of up to 30%. These variations are responsible for a moderate forecast spread of the surface PM10 (a few percentage points) and for a large spread (more than 50%) in the mineral dust concentration at higher altitudes, leading to a mean AOD (aerosol optical depth) forecast spread of ±10%.

In the Mediterranean area, aerosols may originate from anthropogenic or natural emissions (biogenic, mineral dust, fire and sea salt) before undergoing complex chemistry. In case of a huge pollution event, it is important to know whether European pollution limits are exceeded and, if so, whether the pollution is due to anthropogenic or natural sources. In this study, the relative contribution of emissions to surface PM10, surface PM2.5 and total aerosol optical depth (AOD) is quantified. For Europe and the Mediterranean regions and during the summer of 2012, the WRF and CHIMERE models are used to perform a sensitivity analysis on a 50 km resolution domain (from −10° W to 40° E and from 30° N to 55° N): one simulation with all sources (reference) and all others with one source removed. The reference simulation is compared to data from the AirBase network and two ChArMEx stations, and from the AERONET network and the MODIS satellite instrument, to quantify the ability of the model to reproduce the observations. It is shown that the correlation ranges from 0.19 to 0.57 for surface particulate matter and from 0.35 to 0.75 for AOD. For the summer of 2012, the model shows that the region is mainly influenced by aerosols due to mineral dust and anthropogenic emissions (62 and 19 %, respectively, of total surface PM10 and 17 and 52 % of total surface PM2.5). The western part of the Mediterranean is strongly influenced by mineral dust emissions (86 % for surface PM10 and 44 % for PM2.5), while anthropogenic emissions dominate in the northern Mediterranean basin (up to 75 % for PM2.5). Fire emissions are more sporadic but may represent 20 % of surface PM2.5, on average, during the period near local sources. Sea salt mainly contributes for coastal sites (up to 29 %) and biogenic emissions mainly in central Europe (up to 20 %). The same analysis was undertaken for the number of daily exceedances of the European Union limit of 50 μg m−3 for PM10 (over the stations), and for the number of daily exceedances of the WHO recommendation for PM2.5 (25 μg m−3), over the western part of Europe and the central north. This number is generally overestimated by the model, particularly in the northern part of the domain, but exceedances are captured at the right time. Optimized contributions are computed with the observations, by subtracting the background bias at each station and the specific peak biases from the considered sources. These optimized contributions show that if natural sources such as mineral dust and fire events are particularly difficult to estimate, they were responsible exclusively for 35.9 and 0.7 %, respectively, of the exceedances for PM10 during the summer of 2012. The PM25 recommendation of 25 μg m−3 is exceeded in 21.1 % of the cases because of anthropogenic sources exclusively and in 0.02 % because of fires. The other exceedances are induced by a mixed contribution between mainly mineral dust (49.5–67 % for PM10 exceedance contributions, 4.4–13.8 % for PM2.5), anthropogenic sources (14.9–24.2 % and 46.3–80.6 %), biogenic sources (4.1–15.7 % and 12.6–30 %) and fires (2.2–7.2 % and 1.6–12.4 %).

During the months of June and July 2013, over the Euro–Mediterranean area, the ADRIMED (Aerosol Direct Radiative Impact on the regional climate in the MEDiterranean region) project was dedicated to characterize the ozone and aerosol concentrations in the troposphere. It is first shown that this period was not highly polluted compared to previous summers in this region, with a moderate ozone production, no significant vegetation fire events and several precipitation periods scavenging the aerosol. The period is modeled with the WRF (Weather Research and Forecasting) and CHIMERE models, and their ability to quantify the observed pollution transport events is presented. The CHIMERE model simulating all kinds of sources (anthropogenic, biogenic, mineral dust, vegetation fires); the aerosol speciation, not available with the measurements, is presented: during the whole period, the aerosol was mainly constituted by mineral dust, sea salt and sulfates close to the surface and mainly by mineral dust in the troposphere. Compared to the AERONET (Aerosol Robotic Network) size distribution, it is shown that the model underestimates the coarse mode near mineral dust sources and overestimates the fine mode in the Mediterranean area, highlighting the need to improve the model representation of the aerosol size distribution both during emissions, long-range transport and deposition.

Tropospheric trace gas and aerosol pollutants have adverse effects on health, environment and climate. In order to quantify and mitigate such effects, a wide range of processes leading to the formation and transport of pollutants must be considered, understood and represented in numerical models. Regional scale pollution episodes result from the combination of several factors: high emissions (from anthropogenic or natural sources), stagnant meteorological conditions, kinetics and efficiency of the chemistry and the deposition. All these processes are highly variable in time and space, and their relative contribution to the pollutants budgets can be quantified with chemistry-transport models. The CHIMERE chemistry-transport model is dedicated to regional atmospheric pollution event studies. Since it has now reached a certain level a maturity, the new stable version, CHIMERE 2013, is described to provide a reference model paper. The successive developments of the model are reviewed on the basis of published investigations that are referenced in order to discuss the scientific choices and to provide an overview of the main results.

Five one-year air quality simulations over a domain covering Europe have been performed using the CHIMERE chemistry transport model and the EMEP emission dataset for Europe. These five simulations differ only by the representation of the effective emission heights for anthropogenic emissions: one has been run using the EMEP standard recommendations, three others with vertical injection profiles derived from the EMEP recommendations but multiplying the injection height by 0.75, 0.50 and 0.25, respectively, while the last one uses vertical profiles derived from the recent literature. It is shown that using injection heights lower than the EMEP recommendations leads to significantly improved simulation of background SO2, NO2 and O3 concentrations when compared to the Airbase station measurements.

In September 2017, numerous measurement stations recorded large surface concentrations of Ru106 in Europe. This event was well recorded by various monitoring stations worldwide and offer a valuable framework to compare the modelling strategies deployed to quickly evaluate where the plume goes and with what concentrations. In general, the source and its intensity are not known and hypotheses have to be done. Models have to be fast and accurate: Lagrangian and Eulerian are often used but rarely compared. In this study, the FLEXPART Lagrangian model and the WRF-CHIMERE Eulerian models are used to simulate the emissions, transport and deposition of this source of Ru106. First, it is shown that the hypothesis of location, timing and intensity of the source is realistic, by comparison to surface measurements. Second, sensitivity analysis performed with the Eulerian model and several transport scheme showed that this model may provide better results than the Lagrangian one. It opens the door to further development, including chemistry and mixing with other pollutants during these specific events., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Ice and snow in the Central Andes contain significant amounts of light-absorbing particles such as black carbon. The consequent accelerated melting of the cryosphere is not only a threat from a climate perspective but also for water resources and snow-dependent species and activities, worsened by the mega-drought affecting the region since the last decade. Given its proximity to the Andes, emissions from the Metropolitan Area of Santiago, Chile, are believed to be among the main contributors to deposition on glaciers. However, no evidence backs such an assertion, especially given the usually subsident and stable conditions in wintertime, when the snowpack is at its maximum extent. Based on high-resolution chemistry-transport modeling with WRF-CHIMERE, the present work shows that, for the month of July 2015, up to 40% of black carbon dry deposition on snow or ice covered areas in the Central Andes downwind from the Metropolitan area can be attributed to emissions from Santiago. Through the analysis of aerosol tracers we determine (i) that the areas of the Metropolitan Area where emissions matter most when it comes to export towards glaciers are located in Eastern Santiago near the foothills of the Andes, (ii) the crucial role of the network of Andean valleys that channels pollutants up to remote locations near glaciers, following gentle slopes. A direct corollary is that severe urban pollution, and deposition of impurities on the Andes, are anti-correlated phenomena. Finally, a two-variable meteorological index is developed that accounts for the dynamics of aerosol export towards the Andes, based on the zonal wind speed over the urban area, and the vertical diffusion coefficient in the valleys close to ice and snow covered terrain. Numerous large urban areas are found along the Andes so that the processes studied here can shed light on similar investigations for other glaciers-dependent Andean regions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Recent studies based on observations have shown the impact of lockdown measures taken in various European countries to contain the Covid-19 pandemic on air quality. However, these studies are often limited to compare situations without and with lockdown measures, which correspond to different time periods and then under different meteorological conditions. We propose a modelling study with the WRF-CHIMERE modelling suite for March 2020, an approach allowing to compare atmospheric composition with and without lockdown measures without the biases of meteorological conditions. This study shows that the lockdown effect on atmospheric composition, in particular through massive traffic reductions, has been important for several short-lived atmospheric trace species, with a large reduction in NO 2 concentrations, a lower reduction in Particulate Matter (PM) concentrations and a mitigated effect on ozone concentrations due to non-linear chemical effects., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

Purpose: Diagnostic criteria for fibromyalgia have been subject to debate and controversy for many years. The preliminary diagnostic criteria introduced in 2010 and 2011 have been criticized for different reasons, including questionable diagnostic specificity and a lack of an etiopathogenetic foundation. The "ABC indicators" presented in this study reflect a further development of the 2011 criteria and refer to (A) algesia, (B) bilateral, axial-symmetric pain distribution, and (C) chronic distress., Patients and Methods: We compared the diagnostic performance of the ABC indicators with that of the 2011 criteria by analyzing the data of 409 inpatients with chronic functional pain divided into two subgroups of pain patients: Those with whole-body pain and those with pain not involving the whole body. Under the premise that FM phenotypically represents a whole-body pain disorder, sensitivity, specificity, correct classification and diagnostic odds ratios were calculated., Results: The 2011 criteria demonstrated a specificity of 68.1%, a sensitivity of 75.5%, a correct classification of 71.0% and a diagnostic odds ratio of 6.56 (CI: 4.17-10.31). The ABC indicators achieved a specificity of 88.3%, a sensitivity of 62.3%, a correct classification of 78.6%, and a diagnostic odds ratio of 12.47 (CI: 7.30-21.28)., Conclusion: The ABC fibromyalgia indicators demonstrated better specificity, lower sensitivity, and better overall diagnostic effectiveness than the original 2011 criteria., Competing Interests: NE has developed a method of peg algometry. Importantly, the here implemented method is not patentable (since the peg existed beforehand) and is replicable anywhere without extensive technical effort.43 The authors report no other conflicts of interest in this work.

We here show adequate species identification for bacterial isolates of the genus Nocardia spp. through VITEK mass spectrometry. Application of a specific sample preparation method in combination with a robust matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) database leads to 94% accurate identification to the species level on a set of 164 isolates. The possibility to identify Nocardia spp. using MALDI-TOF MS will be available in the next release of VITEK MS update (IVD Version 3.0)., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Identification of microorganisms by MALDI-TOF MS has been widely accepted in clinical microbiology. However, for Mycobacterium spp. and Nocardia spp. such identification has not yet reached the optimal level of routine testing. Here we describe the development of an identification tool for 49 and 15 species of Mycobacterium spp. and Nocardia spp., respectively. During database construction, a number of ambiguous reference identifications were revealed and corrected via molecular analyses. Eventually, more than 2000 individual mass spectra acquired from 494 strains were included in a reference database and subjected to bio-statistical analyses. This led to correct species identification and correct combination of species into several complexes or groups, such as the Mycobacterium tuberculosis complex. With the Advanced Spectrum Classifier algorithm, class-specific bin weights were determined and tested by cross-validation experiments with good results. When challenged with independent isolates, overall identification performance was 90% for identification of Mycobacterium spp. and 88% for Nocardia spp. However, for a number of Mycobacterium sp. isolates, no identification could be achieved and in most cases, this could be attributed to the production of polymers that masked the species-specific protein peak patterns. For the species where >20 isolates were tested, correct identification reached 95% or higher. With the current spectral database, the identification of Mycobacterium spp. and Nocardia spp. by MALDI-TOF MS can be performed in routine clinical diagnostics although in some complicated cases verification by sequencing remains mandatory., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Candida auris is an emerging antifungal resistant yeast species causing nosocomial and invasive infections, emphasising the need of improved diagnostics and epidemiological typing methods. We show that MALDI-TOF VITEK-MS followed by amplified length polymorphisms allows for accurate species identification and subsequent epidemiological characterisation of strains encountered during potential outbreaks., (© 2016 Blackwell Verlag GmbH.)

Trepanation is defined as the intentional perforation of the cranial vault with removal of a piece of skull bone. In Europe, trepanation is known to have been practiced at least since the Neolithic, and it can still be found today in East African native tribes. Two skulls with lesions from the Late Iron Age site Münsingen-Rain (420-240 BC) were investigated. The aim of this study was to analyse the lesions and to determine whether they were caused by surgical interventions. Both individuals were analysed by current morphologic-anthropological methods and radiological examinations were performed with a multislice CT-scanner. Additionally, this work surveys trepanations reported in Switzerland and calculates survival rates. In Switzerland, 34 individuals with trepanations have been published. As a tendency, the survival rate appears to be relatively high from the Neolithic to Late Antiquity but then decreases until Pre-Modern times. The 78% survival rate in Late Iron Age Switzerland indicates that the surgery was often performed successfully. Skull injuries sustained in conflicts could have been a reason for trepanation during the Iron Age., (Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.)

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-ToF MS) has been introduced in clinical routine microbiology laboratories. For the rapid diagnosis of urinary tract infections, culture-independent methods prior MALDI-mediated identification have been described. Here, we describe a comparison of three of these methods based on their performance of bacterial identification and their potential as a routine tool for microbiology labs : (i) differential centrifugation, (ii) urine filtration and (iii) a 5-h bacterial cultivation on solid culture media. For 19 urine samples, all methods were directly compared and correct bacterial species identification by MALDI was used as performance indicator. A higher percentage of correct MALDI identification was obtained after filtration (78.9 %) and the growth-based method (84.2 %) as compared to differential centrifugation (68.4 %). Additional testing of 76 mono-microbial specimens (bacteriuria > 10(5) CFU/mL) confirmed the good performance of short growth with a 90.8 % correct MALDI score, with a potentially better fit to the routine workflow of microbiology labs.

The identification of mycobacteria outside biocontainment facilities requires that the organisms first be rendered inactive. Exposure to 70% ethanol (EtOH) either before or after mechanical disruption was evaluated in order to establish a safe, effective, and rapid inactivation protocol that is compatible with identification of Mycobacterium and Nocardia species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). A combination of 5 min of bead beating in 70% EtOH followed by a 10-min room temperature incubation period was found to be rapidly bactericidal and provided high-quality spectra compared to spectra obtained directly from growth on solid media. The age of the culture, the stability of the refrigerated or frozen lysates, and freeze-thaw cycles did not adversely impact the quality of the spectra or the identification obtained., (Copyright © 2014, American Society for Microbiology. All Rights Reserved.)

Motivation: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has been broadly adopted by routine clinical microbiology laboratories for bacterial species identification. An isolated colony of the targeted microorganism is the single prerequisite. Currently, MS-based microbial identification directly from clinical specimens can not be routinely performed, as it raises two main challenges: (i) the nature of the sample itself may increase the level of technical variability and bring heterogeneity with respect to the reference database and (ii) the possibility of encountering polymicrobial samples that will yield a 'mixed' MS fingerprint. In this article, we introduce a new method to infer the composition of polymicrobial samples on the basis of a single mass spectrum. Our approach relies on a penalized non-negative linear regression framework making use of species-specific prototypes, which can be derived directly from the routine reference database of pure spectra., Results: A large spectral dataset obtained from in vitro mono- and bi-microbial samples allowed us to evaluate the performance of the method in a comprehensive way. Provided that the reference matrix-assisted laser desorption/ionization time-of-flight mass spectrometry fingerprints were sufficiently distinct for the individual species, the method automatically predicted which bacterial species were present in the sample. Only few samples (5.3%) were misidentified, and bi-microbial samples were correctly identified in up to 61.2% of the cases. This method could be used in routine clinical microbiology practice.

Enterobacter sakazakii is regarded as a ubiquitous organism that can be isolated from a wide range of foods and environments. Infection in at-risk infants has been epidemiologically linked to the consumption of contaminated powdered infant formula. Preventing the dissemination of this pathogen in a powdered infant formula manufacturing facility is an important step in ensuring consumer confidence in a given brand together with the protection of the health status of a vulnerable population. In this study we report the application of a repetitive sequence-based PCR typing method to subtype a previously well-characterized collection of E. sakazakii isolates of diverse origin. While both methods successfully discriminated between the collection of isolates, repetitive sequence-based PCR identified 65 types, whereas pulsed-field gel electrophoresis identified 110 types showing > or =95% similarity. The method was quick and easy to perform, and our data demonstrated the utility and value of this approach to monitor in-process contamination, which could potentially contribute to a reduction in the transmission of E. sakazakii.

The development of reliable and rapid methods for the identification of patients colonized with vancomycin-resistant enterococci (VRE) is central to the containment of this agent within a hospital environment. To this end, we evaluated a prototype chromogenic agar medium (VRE-BMX; bioMérieux, Marcy l'Etoile, France) used to recover VRE from clinical specimens. This medium can also identify isolated colonies as either vancomycin-resistant Enterococcus faecium or Enterococcus faecalis, based on distinct colony colors. We compared the performance of VRE-BMX with bile esculin azide agar supplemented with vancomycin (BEAV). For this study, 147 stool samples were plated on each test medium and examined after 24 and 48 h of incubation. At 24 h, the sensitivity and specificity of each medium were as follows: BEAV, 90.9% and 89.9%, respectively; VRE-BMX, 96.4% and 96.6%, respectively. The positive predictive values (PPV) of VRE-BMX and BEAV at 24 h were 89.8% and 80.7%, respectively. VRE-BMX provided the identification of 10 isolates of vancomycin-resistant E. faecalis and 4 isolates of vancomycin-resistant E. faecium that were not recovered by BEAV. Further, VRE-BMX was capable of identifying patients colonized with both E. faecium and E. faecalis, a feature useful for infection control purposes that is not a function of BEAV. In terms of the recovery of vancomycin-resistant E. faecium and E. faecalis, the sensitivity and PPV were as follows: BEAV, 75.7% and 74.6%, respectively; VRE-BMX, 95.5% and 91.3%, respectively. In this initial evaluation, we found that VRE-BMX provided improved recovery of VRE from stool specimens, with the added advantage of being able to differentiate between vancomycin-resistant E. faecalis and E. faecium. Extending the incubation period beyond 24 h did not significantly improve the recovery of VRE and resulted in decreased specificity.