Spectral characteristics of soil dissolved organic matter: Long-term effects of exogenous organic matter on soil organic matter and spatial-temporal changes.

The aim of this study was to evaluate the long-term effect of urban and green waste compost exogenous organic matter (EOM) on soil dissolved organic matter (DOM). A luvic cambisol was amended 7 years before the study. DOM was investigated along a soil profile down to 1 m depth regarding seasonal variations (autumn and spring). DOM sampled by suction cups was characterized using dissolved organic carbon (DOC) content and excitation emission matrix (EEM) fluorescence. The variability of DOM concentrations was pronounced but no major change in composition was determined. The results obtained, reinforced by statistical analysis, showed that the DOM quality was mainly influenced by soil management (organic matter amendment) whereas the quantity mainly depended on the season (heavy precipitation event). DOM humic characteristics were strongly dependent on amendment and changed with depth but was not affected by the season. Long term effect of compost organic matter was highlighted after a 7-years amendment.

Differential DNA methylation in experienced meditators after an intensive day of mindfulness-based practice: Implications for immune-related pathways.

The human methylome is dynamically influenced by psychological stress. However, its responsiveness to stress management remains underexplored. Meditation practice has been shown to significantly reduce stress level, among other beneficial neurophysiological outcomes. Here, we evaluated the impact of a day of intensive meditation practice (t2-t1 = 8 h) on the methylome of peripheral blood mononuclear cells in experienced meditators (n = 17). In parallel, we assessed the influence of a day of leisure activities in the same environment on the methylome of matched control subjects with no meditation experience (n = 17). DNA methylation profiles were analyzed using the Illumina 450 K beadchip array. We fitted for each methylation site a linear model for multi-level experiments which adjusts the variation between t1 and t2 for baseline differences. No significant baseline differences in methylation profiles was detected between groups. In the meditation group, we identified 61 differentially methylated sites (DMS) after the intervention. These DMS were enriched in genes mostly associated with immune cell metabolism and ageing and in binding sites for several transcription factors involved in immune response and inflammation, among other functions. In the control group, no significant change in methylation level was observed after the day of leisure activities. These results suggest that a short meditation intervention in trained subjects may rapidly influence the epigenome at sites of potential relevance for immune function and provide a better understanding of the dynamics of the human methylome over short time windows.

[Description and role of bacteriological techniques in the management of lung infections]. / Description et place des techniques bactériologiques dans la prise en charge des infections pulmonaires.

Acute pneumonias occur in a variety of clinical settings and accurate identification of bacterial causes is extremely important. No microbiological tool is either 100 % sensitive or 100 % specific, and despite investigations, aetiology remains unanswered in more than 30 % of pneumonia. No sample may be necessary for patients treated as outpatients, non invasive respiratory specimens are preferred in hospitalised individuals (community or healthcare associated), while invasive specimens are used as second line for community acquired pneumonia (CAP) in intensive care, and in the first line where pneumonia occurs in immunosuppressed patients. Bacterial cultures have an important place, if the sample is taken before the introduction of antibiotic therapy. Some contexts may justify the use of blood cultures, testing for urinary antigens or serology. PCR is already becoming available as a daily service but the short-term future probably belongs to molecular multiplex panels capable of detecting many microorganisms within hours, especially in severe CAP resuscitation and in pneumonia in the immunosuppressed. High-throughput sequencing nucleotide techniques will soon revolutionize microbiological diagnosis in respiratory medicine, as in other areas of infectious diseases.

[Infections in cystic fibrosis: Up-to-date]. / Actualités en infectiologie dans la mucoviscidose.

This review focused on the news in CF airways infection. International guidelines were provided for the care of non tuberculous mycobacteria, and recent studies stressed on the benefit effect of azithromycin or combined antibiotics. The identification of multiresistant environmental bacteria in airways made to account for little-known consequences. Early diagnosis and eradication of Pseudomonas aeruginosa and Staphylococcus aureus methi-R were still a concern, and reports were proposed. However, the studies on staphylococcus methi-R should be interpreted as regards the European or American continent. Thus, levofloxacine has demonstrated its efficacy without enhancing the efficiency. This drug will increase the choice for treating the patient, but no study were provided on the expected modification of the patient microbiota and the known risk of emergent resistance to antibiotics. Lastly, this review underlined that the CF practitioner was encouraged to search and not underestimate the presence of fungus, of which the not so well studied Aspergillus fumigatus.

Unique blood culture for diagnosis of bloodstream infections in emergency departments: a prospective multicentre study.

Detection of microorganisms by blood cultures (BCs) is essential in managing patients with bacteraemia. Rather than the number of punctures, the volume of blood drawn is considered paramount in efficient and reliable detection of microorganisms. We performed a 1-year prospective multicentre study in adult emergency departments of three French university hospitals comparing two methods for BCs: a unique blood culture (UBC) collecting a large volume of blood (40 mL) and the standard method of multiple blood cultures (MBC). The performances of both methods for bacterial contamination and efficient microbial detection were compared, each patient serving as his own control. Amongst the 2314 patients included, three hundred were positive for pathogens (n=245) or contaminants (n=55). Out of the 245 patients, 11 were positive for pathogens by UBC but negative by MBC and seven negative by UBC but positive by MBC (p 0.480). In the subgroup of 137 patients with only two BCs, UBC was superior to MBC (p 0.044). Seven and 17 patients had contaminated BCs by UBC and MBC only, respectively (p 0.062). Considering the sums of pathogens missed and contaminants, UBC significantly outperformed MBC (p 0.045). Considering the complete picture of cost savings, efficient detection of microorganisms and decrease in contaminations, UBC offers an interesting alternative to MBC.

Bio oil synthesis by coupling biological biomass pretreatment and catalytic hydroliquefaction process.

The bio-oil synthesis from a mixture of wastes (7wt.% straw, 38wt.% wood, and 45wt.% grass) was carried out by direct liquefaction reaction using Raney Nickel as catalyst and tetralin as solvent. The green wastes were biologically degraded during 3 months. Longer the destructuration time; higher the yield into oil is. Biological pretreatment of green wastes promotes the liquefaction process. Among the components of degraded biomass, Humin, the major fraction (60-80wt.%) that was favored by the biological treatment, yields to a bio oil extremely energetic with a HHV close to biopetroleum (40MJ kg(-1)), contrariwise, Fulvic acids (2-12wt.%), the minor fraction is refractory to liquefaction reaction.

Evaluation of humic fractions potential to produce bio-oil through catalytic hydroliquefaction.

Humic substances were extracted from biodegraded lignocellulosic biomass (LCBb) and submitted to catalytic hydroliquefaction. The resulting bio-oils were compared with those of the initial biomass. Compared to fulvic and humic acids, humin presented a high conversion rate (74 wt.%) and the highest amount of liquid fraction (66 wt.%). Moreover it represented 78% of LCBb. Humin produced 43 wt.% of crude oil and 33 wt.% of hexane soluble fraction containing hydrocarbons which is a higher yield than those from other humic substances as well as from the initial biomass. Hydrocarbons were mainly aromatics, but humin produces the highest amount of aliphatics. Considering the quantity, the quality and the molecular composition of the humic fractions, a classification of the potential of the latter to produce fuel using hydroliquefaction process can be assess: Hu>AF>AH. The higher heating value (HHV) and oxygen content of HSF from humin were fully compatible with biofuel characteristics.

Meningococcal carriage during a clonal meningococcal B outbreak in France.

The aim of this study performed in Normandy, France, was to analyze the pharyngeal meningococcal carriage at the peak of a clonal meningococcal B outbreak, which was subsequently controlled using an outer membrane vesicle vaccination. This cross-sectional study included randomly selected subjects aged 1-25 years. Carriers and non carriers were compared using unconditional logistic regression. Among the 3,522 volunteers, there were 196 (standardized rate: 6.46 %) Neisseria meningitidis carriers, of which there were only five with the outbreak strain (B:14:P1.7,16/ST-32; standardized rate: 0.18 %). From the multivariate analysis, older age, smoking, higher degree of socialization, and social deprivation appear to favor the carriage of all the strains included. Prior antibiotic treatment up to 12 months before swabbing, even with ß-lactam, was protective against carriage. Our data indicate a low overall meningococcal carriage rate with a surprising protective effect of prior antibiotic exposure. The observed low carriage rate of the epidemic strain (B:14:P1.7,16/ST-32) contrasts with the high incidence of invasive meningococcal diseases (IMD) due to this strain. Hence, our data underline the high virulence of the strain and suggest a low level of natural immunity of the population against this strain. Although highly resource-consuming, carriage studies are helpful in guiding the implementation of control measures of IMD, such as mass vaccination or chemoprophylaxis.

Alternative fuel production by catalytic hydroliquefaction of solid municipal wastes, primary sludges and microalgae.

An alternative fuel production was investigated through catalytic hydroliquefaction of three different carbonaceous sources: solid municipal wastes (MW), primary sludges (PS), and microalgae (MA). The reaction was carried out under hydrogen pressure, at different temperatures (330, 380 and 450°C), with a Raney nickel catalyst and two different hydrogen donor solvents: a "fossil solvent" (tetralin) and a "green solvent" (2-methyl-hydro-furan). The feeds analyses (TDA-TGA, ICP-AES, lipids quantification) showed that MW and PS had similar characteristics and physico-chemical properties, but different from those of MA. The hydroliquefaction of these feeds allowed to obtain high oil yields, with a significant energetic value, similar to that of a bio-petroleum. 2-methyl-hydro-furan was more efficient than tetralin for the treatment of the strongly bio-degraded biomasses MW and PS, while better results were obtained with tetralin in the case of MA.

Biological pretreatment for production of lignocellulosic biofuel.

Lignocellulosic biomass was submitted to a biological pretreatment prior to a catalytic hydroliquefaction in order to produce biofuel. The biodegradation process was conducted over 3 months in a reactor under controlled conditions. During the biodegradation process the organic matter was characterised and its evolution was correlated with physico-chemical parameters. In parallel with the analysis of the lipidic fraction, analytical pyrolysis was used to monitor bacterial activity. The alterations of branched to linear fatty acids ratio and of mono- to diacids ratio were compared when determined by thermochemolysis and observed in the directly extractable lipids. The evolution of the phytol to the corresponding isoprenoic ketone ratio was observed to be dependent on the desorption technique since it decreases using headspace while it increases using pyrolysis. "Humic"/"fulvic acids" ratio, infrared spectroscopy and thermodifferential analysis were used to determine the degree of OM complexification.

Hydroliquefaction of green wastes to produce fuels.

The direct liquefaction of a biomass composed of a mixture of wastes (straw, wood and grass) was studied using Nickel Raney as catalyst and tetralin as a solvent. Tetralin allows to solubilize green waste from 330°C at relatively low hydrogen pressure, and avoids the recondensation of the intermediate products. The green waste deoxygenation results mainly from a decarboxylation reaction. The addition of Raney Ni in the feed, increases the gas yield due to methane formation, without diminishing the yield in solvolysis oil. The catalyst hydrogenolyses the small molecules present in the light fraction. Moreover, it improves the quality of the oil by increasing the hydrogen transfer between the solvent and the solvolysis oil. As a consequence, the oxygen content decreases and the yield of oil soluble in hexane strongly increases. The catalyst allows to obtain straight long chain alkanes (C(13)-C(26)), which result from the hydrogenation of the extractives compounds of the green waste.

Stability and maturity of a green waste and biowaste compost assessed on the basis of a molecular study using spectroscopy, thermal analysis, thermodesorption and thermochemolysis.

The organic matter (OM) of a green waste and bio waste compost was characterised over 8months and the observed evolution was correlated with physico-chemical parameters (temperature, pH, carbon content, C/N ratio). Thermochemolysis and thermodesorption were used to monitor bacterial activity (stability) whereas diffuse reflectance infrared fourier transform spectroscopy (DRIFTS) and thermodifferential analysis (TDA) permitted to determine the degree of OM humification (maturity). DRIFT spectroscopy and TDA provide two indicators of maturity since, with these two techniques, the signals associated with the biodegradable organic matter decrease relatively to the signals associated with refractory organic matter. This increase in R(TG) and R(IR) ratios between aromatic to aliphatic signals constitutes a proof for OM complexification. It correlates with humic acids/fulvic acids ratio known to be a maturity index. Pyrolysates are mainly constituted of lignin moieties, terpenoids, nitrogen containing compounds, carbohydrates (furanosic moiety), mono- and diacids (as methyl esters), and methoxyesters. The R(branched/linear) ratio between branched to linear acids traduces the evolution of the bacterial activity during composting. Moreover the R(di/mono) ratio between aliphatic mono to diacids correlates with the latter showing that diacids can occur from the biological oxidation of monoacids. These two ratios determined by thermochemolysis are useful to monitor the stability of compost. VOC, observed by thermodesorption are mainly constituted of terpenes, light acids, aldehydes and ketone. An unexpected result was obtained since the amount of phytol increases relatively to the isoprenoid ketone considered to originate from the latter.

[Evaluation of a new E-test method for antimicrobial sensitivity testing of Pseudomonas aeruginosa isolates from cystic fibrosis]. / Etude multicentrique portant sur l'évaluation d'une méthode simplifiée d'analyse bactériologique dans la surveillance des infections bronchiques à Pseudomonas aeruginosa survenant au cours de la mucoviscidose.

BACKGROUND: Sputum bacteriological analysis of cystic fibrosis (CF) patients colonised by Pseudomonas aeruginosa is difficult. The bronchial persistence of these bacteria involves phenotypical modifications and the many antibiotic treatments result in emergence of multiresistant strains. The aim of this study is to evaluate a new fast identification and sensitivity testing method of P. aeruginosa and other pathogenic bacteria in sputum of CF patients. It is based on applying a gradient of antibiotic (E-test strip) onto an agar plate inoculated with the sputum. OBSERVATIONS: 310 sputum, collected from adults and children colonised by P. aeruginosa, were analysed by this new method. This method allowed a direct reading of the minimal concentration of antibiotic that inhibited the totality of Gram-negative strains and the detection of resistant pathogenic bacteria inside the ellipse of inhibition. Results obtained by this new method were compared with the conventional method for identification and antimicrobial sensitivity. CONCLUSION: This new method, studying with CF patient colonised by P. aeruginosa, appears interesting, with a sensibility equal or higher than 89% in detection of the bacteria and their sensitivity to antibiotics. Furthermore it allows a saving of time and simplified results.

Changes in lipids and sterols during composting.

Pyrolysis-gas (Py-GC) chromatography was used to characterize organic [(diethyl ether (DEE) and chloroform (CHCl3)] extracts of raw and composted duck excreta enriched wood shavings from two finishing cycles (C1 and C2). Materials were collected on days 0, 8 and 23. C1 contained 1.7 % total N while C2 contained 0.9 % total N. Py-GC-MS (mass spectrometry) showed that the extracts contained n-alkanes (C12 to C32), alkenes (C12:1 to C33:1), n-fatty acids (C12 to C28), unsaturated fatty acids (C18:1 and C18:2), and sterols (cholestene, cholestadiene, stigmastene, stigmastadiene, stigmastatriene, cholesterol, stigmastanol, stigmastanone, stigmastadienone, 17-methyl dialkylsulfanyl decahydro-1H-cyclopenta [a] phenanthrene, 17-methyl dialkylsulfanyl dodecahydro-1H-cyclopenta [a] phenanthrene, and 17-methyl-17-dialkylsulfanyl decahydro-1H-cyclopenta [a] phenanthrene). Other components identified were prystene, squalene (precursor of cholesterol), phthalic acid, diphenylpropane, diphenylbut-2-ene and 1,3,6 triphenyl hex-4-ene. Our data showed significant changes in the lipid composition of duck excreta enriched wood shavings during composting, which appeared to be related to the total N content of the system.

Comparison of ATB staph, rapid ATB staph, Vitek, and E-test methods for detection of oxacillin heteroresistance in staphylococci possessing mecA.

The performance characteristics of the E-test (AB Biodisk, Solna, Sweden), the ATB Staph, the Rapid ATB Staph, and the Vitek GPS-503 card (bioMérieux, La Balme Les Grottes, France) methods for the detection of oxacillin resistance in a collection of staphylococci with a high proportion of troublesome strains were evaluated. Sixty-four Staphylococcus aureus strains and 76 coagulase-negative staphylococcal strains were tested. All strains were mecA positive and were characterized by the oxacillin agar screen plate test; 75 (53.6%) were found to be heterogeneous by a large-inoculum oxacillin disk diffusion assay, and oxacillin MICs for 89 (63.6%) were < or = 32 microg/ml. Three (4.7%) S. aureus strains and 25 (32.9%) coagulase-negative strains were classified as susceptible by the E-test, as defined by the National Committee for Clinical Laboratory Standards (NCCLS) oxacillin breakpoint (MIC < or = 2 microg/ml). The ATB Staph method failed to detect oxacillin resistance in 7 (11%) S. aureus isolates and 32 (42.1%) coagulase-negative isolates. The MICs for all but six of these discrepant isolates were < or = 16 microg/ml. The Rapid ATB Staph method was tested against S. aureus strains only and yielded 15 (23.4%) false-susceptible results for strains for which the MICs were < or = 32 microg/ml. The Vitek system was the best-performing system, since it failed to detect oxacillin resistance in only 3 (4.7%) S. aureus strains and 15 (19.7%) coagulase-negative strains, the MICs for all of which were < or = 2 microg/ml. These data indicate that (i) the performance of the two ATB Staph systems can be limited when the prevalence of borderline-heteroresistant staphylococci is high and (ii) the unreliability of the E-test and the Vitek methods for detecting resistant coagulase-negative strains might be reduced by the potential revision of the oxacillin breakpoint currently recommended by the NCCLS.