Development of a new molecular typing method of Salmonella spp. based on SNPs detection

The aim of this study was to develop a new molecular typing method of Salmonella spp. based on the detection of point mutations (Single Nucleotide Polymorphisms or SNPs) in the genome. Several genomic regions (ManB, InvA, pduF) were sequenced in strains isolated from pig, the sequences were aligned and 49 point mutations were identified. A panel of 12 SNPs giving a genotype characteristic of a particular serotype was selected. Until now, thes selected SNPs were unable to distinguish the all strains. Therefore, additional SNPs must be selected

Bifidobacterium mongoliense genome seems particularly adapted to milk oligosaccharide digestion leading to production of antivirulent metabolites

Background: Human milk oligosaccharides (HMO) could promote the growth of bifidobacteria, improving young children's health. In addition, fermentation of carbohydrates by bifidobacteria can result in the production of metabolites presenting an antivirulent activity against intestinal pathogens. Bovine milk oligosaccharides (BMO), structurally similar to HMO, are found at high concentration in cow whey. This is particularly observed for 3′-sialyllactose (3′SL). This study focused on enzymes and transport systems involved in HMO/BMO metabolism contained in B. crudilactis and B. mongoliense genomes, two species from bovine milk origin. The ability of B. mongoliense to grow in media supplemented with whey or 3′SL was assessed. Next, the effects of cell-free spent media (CFSM) were tested against the virulence expression of Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium. Results: Due to the presence of genes encoding β-galactosidases, β-hexosaminidases, α-sialidases and α-fucosidases, B. mongoliense presents a genome more sophisticated and more adapted to the digestion of BMO/HMO than B. crudilactis (which contains only β-galactosidases). In addition, HMO/BMO digestion involves genes encoding oligosaccharide transport systems found in B. mongoliense but not in B. crudilactis. B. mongoliense seemed able to grow on media supplemented with whey or 3′SL as main source of carbon (8.3 ± 1.0 and 6.7 ± 0.3 log cfu/mL, respectively). CFSM obtained from whey resulted in a significant under-expression of ler, fliC, luxS, stx1 and qseA genes (- 2.2, - 5.3, - 2.4, - 2.5 and - 4.8, respectively; P < 0.05) of E. coli O157:H7. CFSM from 3′SL resulted in a significant up-regulation of luxS (2.0; P < 0.05) gene and a down-regulation of fliC (- 5.0; P < 0.05) gene. CFSM obtained from whey resulted in significant up-regulations of sopD and hil genes (2.9 and 3.5, respectively; P < 0.05) of S. Typhimurium, while CFSM obtained from 3′SL fermentation down-regulated hil and sopD genes (- 2.7 and - 4.2, respectively; P < 0.05). Conclusion: From enzymes and transporters highlighted in the genome of B. mongoliense and its potential ability to metabolise 3′SL and whey, B. mongoliense seems well able to digest HMO/BMO. The exact nature of the metabolites contained in CFSM has to be identified still. These results suggest that BMO associated with B. mongoliense could be an interesting synbiotic formulation to maintain or restore intestinal health of young children

Exploring the risk factors for Salmonella in the ten biggest Belgian pig slaughterhouses

The goal of this work is to identify the risk factors related to Salmonella in the porcine die at the stage of the slaughterhouse. Thanks to investigations carried out into the ten biggest Belgian slaughterhouses, data concerning the manufacturing process and the working methods were gathered. Moreover, an access to the microbiological results carried out on these companies within the framework of the official plans of monitoring was asked to the Belgian Food Agency. A data base allowing to test the influence of risk factors on the presence of Salmonella was established. To quantify a relation between a risk factor and the presence of Salmonella, statistical methods such as the logistic regressions were used

Degrees of algorithmic equivalence between the brain and its DNN models

Deep neural networks (DNNs) have become powerful and increasingly ubiquitous tools to model human cognition, and often produce similar behaviors. For example, with their hierarchical, brain-inspired organization of computations, DNNs apparently categorize real-world images in the same way as humans do. Does this imply that their categorization algorithms are also similar? We have framed the question with three embedded degrees that progressively constrain algorithmic similarity evaluations: equivalence of (i) behavioral/brain responses, which is current practice, (ii) the stimulus features that are processed to produce these outcomes, which is more constraining, and (iii) the algorithms that process these shared features, the ultimate goal. To improve DNNs as models of cognition, we develop for each degree an increasingly constrained benchmark that specifies the epistemological conditions for the considered equivalence

Total column CO_2 measurements at Darwin, Australia – site description and calibration against in situ aircraft profiles

An automated Fourier Transform Spectroscopic (FTS) solar observatory was established in Darwin, Australia in August 2005. The laboratory is part of the Total Carbon Column Observing Network, and measures atmospheric column abundances of CO_2 and O_2 and other gases. Measured CO_2 columns were calibrated against integrated aircraft profiles obtained during the TWP-ICE campaign in January–February 2006, and show good agreement with calibrations for a similar instrument in Park Falls, Wisconsin. A clear-sky low airmass relative precision of 0.1% is demonstrated in the CO2 and O2 retrieved column-averaged volume mixing ratios. The 1% negative bias in the FTS X_(CO_2) relative to the World Meteorological Organization (WMO) calibrated in situ scale is within the uncertainties of the NIR spectroscopy and analysis

Exposure assessment of foodborne pathogens in pork in Belgium

The aim of this study was to assess the exposure of the most incident foodborne pathogens in the Belgian meat production chain. The prevalence of Salmonella, Campylobacter and Listeria monocytogenes were evaluated in carcasses (swabs), retail cuts, minced meat and meat products of pork. The investigation was made each year since 1997, using official methods from the Ministry of Public Health for Salmonella and Campylobacter and the Vidas Listeria monocytogenes method. More than 10 % of each matrix were contaminated with Salmonella. For minced meat and meat products, the contamination rate were respectively round 20 % and 3 – 6 % for Listeria monocytogenes. Under 5 % of minced meat samples were positive for Campylobacter. For minced meat, the contamination has also been assessed according to the location of sampling (agreed, low capacity establishments or retail level). The characterisation of bacterial species allows the comparison between meat and human isolates

Clostridium difficile beyond stools : dog nasal discharge as a possible new vector of bacterial transmission

Zoonotic transmission of Clostridium difficile has been largely hypothesised to occur after direct or indirect contact with contaminated animal faeces. Recent studies have reported the presence of the bacterium in the natural environment, including in soils and rivers. If C. difficile spores are scattered in the environment, they can easily enter the respiratory tract of dogs, and therefore, dog nasal discharge could be a direct route of transmission not previously investigated. This study reports for the first time the presence of C. difficile in the respiratory tracts of dogs. The bacterium was isolated from 6 (17.1%) out of 35 nasal samples, with a total of 4 positive dogs (19%). C. difficile was recovered from both proximal and distal nasal cavities. All isolates were toxigenic and belonged to PCR- ribotype 014, which is one of the most predominant types in animals and in community- acquired C. difficile infections in recent years. The findings of this study demonstrate that the nasal cavity of dogs is contaminated with toxigenic C. difficile, and therefore, its secretions could be considered as a new route by which bacteria are spread and transmitted.Peer reviewe

Using airborne HIAPER Pole-to-Pole Observations (HIPPO) to evaluate model and remote sensing estimates of atmospheric carbon dioxide

In recent years, space-borne observations of atmospheric carbon dioxide (CO_2) have been increasingly used in global carbon-cycle studies. In order to obtain added value from space-borne measurements, they have to suffice stringent accuracy and precision requirements, with the latter being less crucial as it can be reduced by just enhanced sample size. Validation of CO_2 column-averaged dry air mole fractions (XCO_2) heavily relies on measurements of the Total Carbon Column Observing Network (TCCON). Owing to the sparseness of the network and the requirements imposed on space-based measurements, independent additional validation is highly valuable. Here, we use observations from the High-Performance Instrumented Airborne Platform for Environmental Research (HIAPER) Pole-to-Pole Observations (HIPPO) flights from 01/2009 through 09/2011 to validate CO_2 measurements from satellites (Greenhouse Gases Observing Satellite – GOSAT, Thermal Emission Sounder – TES, Atmospheric Infrared Sounder – AIRS) and atmospheric inversion models (CarbonTracker CT2013B, Monitoring Atmospheric Composition and Climate (MACC) v13r1). We find that the atmospheric models capture the XCO_2 variability observed in HIPPO flights very well, with correlation coefficients (r^2) of 0.93 and 0.95 for CT2013B and MACC, respectively. Some larger discrepancies can be observed in profile comparisons at higher latitudes, in particular at 300 hPa during the peaks of either carbon uptake or release. These deviations can be up to 4 ppm and hint at misrepresentation of vertical transport. Comparisons with the GOSAT satellite are of comparable quality, with an r^2 of 0.85, a mean bias μ of −0.06 ppm, and a standard deviation σ of 0.45 ppm. TES exhibits an r^2 of 0.75, μ of 0.34 ppm, and σ of 1.13 ppm. For AIRS, we find an r^2 of 0.37, μ of 1.11 ppm, and σ of 1.46 ppm, with latitude-dependent biases. For these comparisons at least 6, 20, and 50 atmospheric soundings have been averaged for GOSAT, TES, and AIRS, respectively. Overall, we find that GOSAT soundings over the remote Pacific Ocean mostly meet the stringent accuracy requirements of about 0.5 ppm for space-based CO_2 observations

Carbon dioxide column abundances at the Wisconsin Tall Tower site

We have developed an automated observatory for measuring atmospheric column abundances of CO_2 and O_2 using near-infrared spectra of the Sun obtained with a high spectral resolution Fourier Transform Spectrometer (FTS). This is the first dedicated laboratory in a new network of ground-based observatories named the Total Carbon Column Observing Network. This network will be used for carbon cycle studies and validation of spaceborne column measurements of greenhouse gases. The observatory was assembled in Pasadena, California, and then permanently deployed to northern Wisconsin during May 2004. It is located in the heavily forested Chequamegon National Forest at the WLEF Tall Tower site, 12 km east of Park Falls, Wisconsin. Under clear sky conditions, ∼0.1% measurement precision is demonstrated for the retrieved column CO_2 abundances. During the Intercontinental Chemical Transport Experiment–North America and CO_2 Boundary Layer Regional Airborne Experiment campaigns in summer 2004, the DC-8 and King Air aircraft recorded eight in situ CO_2 profiles over the WLEF site. Comparison of the integrated aircraft profiles and CO_2 column abundances shows a small bias (∼2%) but an excellent correlation