Tell me if you prefer bovine or poultry sectors and I’ll tell you who you are: Characterization of Salmonella enterica subsp. enterica serovar Mbandaka in France

IntroductionIn north-western France, Salmonella enterica susp. enterica serovar Mbandaka (S. Mbandaka) is most frequently isolated from bovine and dairy samples. While this serovar most often results in asymptomatic carriage, for a number of years it has caused episodes of abortions, which have serious economic consequences for the sector. Interestingly, this serovar is also isolated from Gallus gallus in the same geographic zone. Despite its prevalence in bovines in north-western France, S. Mbandaka has not been broadly studied at the genomic level, and its prevalence and host adaptation are still not fully understood.MethodsIn this study, we analyzed the genomic diversity of 304 strains of S. Mbandaka isolated from the bovine and poultry sectors in this area over a period of 5 years. A phylogenetic analysis was carried out and two approaches were followed to identify conserved genes and mutations related to host associations. The first approach targeted the genes compiled in the MEGARESv2, Resfinder, VFDB and SPI databases. Plasmid and phage contents were also investigated. The second approach refers to an in-house algorithm developed for this study that computes sensitivity, specificity, and accuracy of accessory genes and core variants according to predefined genomes groups.Results and discussionAll the analyzed strains belong to the multi-locus sequence type profile ST413, and the phylogenomic analysis revealed main clustering by host (bovine and poultry), emphasizing the circulation of 12 different major clones, of which seven circulate in poultry and five in the bovine sector in France and a likely food production chain adaptation of these clones. All strains present resistance determinants including heavy metals and biocides that could explain the ability of this serovar to survive and persist in the environment, within herds, and in food processing plants. To explore the wild animal contribution to the spread of this serovar in north-western France, we retrieved S. Mbandaka genomes isolated from wild birds from EnteroBase and included them in the phylogenomic analysis together with our collection. Lastly, screening of accessory genes and major variants allowed us to identify conserved specific mutations characteristic of each major cluster. These mutations could be used to design useful probes for food safety surveillance

Phosphorus availability measurements using the diffusive gradients in thin films (DGT) technique in highly weathered soils

Phosphorus availability measurements using the diffusive gradients in thin films (DGT) technique in highly weathered soilsPhosphorus (P), next to nitrogen, is the most important limiting factor for crop production in many tropical and subtropical soils. Besides low total and/or available P contents, these soils are often highly P-fixing due to their high aluminium and iron oxide concentration (Norman et al. 1995; Sanchez et al. 1997). Essential for the evaluation of different plant-soil systems is the correct determination of plant-available P and profound knowledge about P dynamics. The starting point for correcting the soil fertility status is soil testing. Over the past century, many soil P tests have been established and put forward as being the ultimate index of P availability in soils. Unfortunately none of these techniques seems adequate to correctly assess the phosphorus status in strongly weathered acid soils as found in tropical areas. These established soil P tests are based on chemical extraction with a strong base, acid or complexing agent. Typically soil tests only give reliable results for the soils they were calibrated for (Degryse et al. 2009b). The research presented aims at investigating whether the diffusive gradients in thin films (DGT) technique allows a better prediction of available P compared to established soil P tests. The DGT technique is a passive sampling technique that has been successfully applied to aquatic systems for measurement of trace metal concentration (Zhang and Davison 1995; Zhang et al. 1998b), later for phosphorus measurements (Zhang et al. 1998a) and more recently for predicting crop response to applied P in a wide range of soils (Mason et al. 2010; McBeath et al. 2007; Menzies et al. 2005; Tandy et al. 2011). In contrast to previous studies, this study focuses on strongly weathered, acid, tropical soils. Similar to the anion exchange membrane methods (AEM), the DGT technique attempts to mimic the physico-chemical uptake of P by plant roots by providing a sink for free phosphate (Mason et al. 2010). The continuous removal of P from solution lowers the concentration of P in the soil solution (intensity factor, I), which in turn promotes resupply from the soil solid phase, depending on the labile P pool or P quantity of a soil (Q) and the resupply capacity, P buffering capacity (PBC). Provided that diffusion of P towards plant roots is the rate limiting step for P uptake under P deficient conditions, the DGT measured concentrations, which are a measure for such a diffusive flux and P intensity, have potential to be a better predictor for P availability to plant roots than established soil P tests, which are rather measures for P quantity in a soil.Firstly, it was hypothesized that soil P tests that extract P from the plant accessible pool, will predict availability and uptake more robustly than empirical tests, i.e. based on chemical extraction. This was tested by comparison of the isotope ratios (33P/31P, specific activity, SA) of P between plant shoot and the soil extract. When the SA of the plant shoot is not significantly different from the SA in the soil extract, the same P pool is most likely advocated. In contrast, when the SA in the soil test is smaller than that in the maize shoot, P was extracted from a P pool not accessible to maize. To this test we submitted the DGT technique, in comparison with conventional soil P tests viz. Olsen, Colwell, Bray-1, Mehlich-3, ammonium oxalate, AEM and 0.01 M CaCl2 solution. A pot trial was conducted with maize as a test crop, grown in two P deficient soils from western Kenya with contrasting P sorption characteristics, amended with a low and a high P rate and labelled with 33P. A close correspondence was found between the SA of the extracts of the different soil tests (except CaCl2 and ammonium oxalate extracts) and that of the plant, at the low P rate in the soil with low P sorption capacity. For the high P rate on this soil, differences in SA between maize shoot and soil test were small for all established soil tests, but significant for the Colwell, Bray-1, Mehlich-3 and AEM test. The SA in the soil extracts was significantly smaller than that in the maize shoot for the strongly P-sorbing soil at both P rates for all conventional tests, including AEM. This indicates that these tests extracted P from a pool that is not accessible to the plant. For the DGT test, however, there was no difference in SA between the maize shoot and the soil test, for any of the treatments. From this experiment, we could conclude that most conventional soil tests extract a fraction of P which is not available to maize. In contrast, the DGT technique samples only P from the plant-accessible pool. Secondly, a pot trial was conducted to test DGT relative to established soil P tests in predicting the growth response to P addition across nine different tropical soils marked by P deficiency, for two plant species with contrasting growth rate affecting P demand per dry matter unit, i.e. maize and upland or rainfed rice. Data from previous pot and field trials support our hypothesis that the predictive power of the DGT is superior compared to established soil P tests, because DGT provides a measure for the P supply to plant roots under P deficient conditions where the rate limiting step for P uptake is diffusional supply of P to the roots. We found that the DGT method and CaCl2 extractions explained relative yield (% of maximum yield) of maize among soils better (R² = 0.82 and 0.75 respectively) than P determined by Olsen, Colwell, Bray-1, Mehlich-3, ammonium oxalate and resin extractions (R² < 0.53). In strong contrast, relative yields of rice were best predicted by Mehlich-3, Bray-1, Olsen and resin P (R² ~ 0.7) compared to DGT (R² = 0.53) and CaCl2 (R² = 0.08). Moreover, modelling results by Degryse et al. (2009b) suggest that the critical DGT concentrations, i.e. the CDGT to obtain 80 % of the maximum yield, are plant specific rather than soil specific. Our results confirm this suggestion: the critical DGT P concentrations on this set of soils were 73 µg P L-1 for maize andonly 7 µg P L-1 for rice. The critical DGT value measured for maize is in correspondence with literature. In short, for tropical, P deficient soils, intensity-based indices of soil P availability such as DGT and CaCl2, are superior to quantity-based indices (i.e. the established soil P tests based on extraction) for maize with high P demand. However, the reverse is true for rice suggesting that diffusion of P in the soil as measured by DGT is not the main factor explaining P uptake for rice. We suggest, but do not prove, that this upland rice variety disposes of strategies to overcome P deficiency (e.g. exudation of organic acids or phosphatases, changing root architecture). Finally, our goal was to evaluate the potential of the DGT technique to predict bioavailable P in different soils amended with various qualities of OM. This was investigated since it is known that the P fertilizer value of organic materials (OM) such as plant residues or manure, can be larger than that of mineral fertilizers in weathered soils. In our final experiment, phosphorus was applied at various rates (deficient to adequate) as triple superphosphate (TSP) only or at one intermediate P dose, in a substitution trial with 4 different OMs: farmyard manure (FYM) or residues of Tithonia diversifolia, each at low or high P content. Results demonstrated that the combined application of TSP and OM increased, decreased or did not affect dry matter yields compared to single TSP application at corresponding total P dose, differences depending on soil and OM type. Relative yield to soil P test values correlated most strongly for DGT measured P concentrations, R² is 0.74, compared to Olsen (R² = 0.60) and AEM (R² = 0.62), when considering all treatments with a P-related effect. This selection was needed because also non P-related factors as a consequence of OM application, can have an effect on growth. Results of this study suggest that DGT performs better in detecting TSP × OM interactions in different soils than the established soil P tests (Olsen and AEM); although not all trends in DM yields can be fully understood using the DGT technique. In conclusion, this work demonstrated the strong prediction power of DGT in P deficient soils for maize yields, compared to established soil P tests. This strong prediction power is not surprising, given that DGT samples P from the plant accessible pool of P in the soils, while with the conventional soil P tests P was also extracted from a pool not accessible to plant roots, which must lead to an overestimation of plant available P. For rice the prediction power of quantity measures seems larger, which can most likely be related to their strategies to overcome P deficiency. Our results confirm that the critical DGT concentrations are not soil dependent, but rather are plant specific. Finally, the critical DGT concentrations for maize were constant over the two response experiments, even when different growing periods, growth conditions, P amendments or soils are used. Our work demonstrates that the DGT technique is a robust method to assess the P status of a soil and to correct it if required.status: publishe

Inorganic species of arsenic in soil solution determined by microcartridges and ferrihydrite-based diffusive gradient in thin films (DGT)

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The performance of DGT versus conventional soil phosphorus tests in tropical soils - an isotope dilution study

o Background and aims A soil test that samples nutrients only from fractions that are accessible to plants will predict availability and uptake more robustly than empirical tests. This can be tested by comparison of the isotope ratios (specific activity, SA) of the nutrient between plant and the soil extract. This study was set up to assess this requirement for the diffusive gradients in thin films technique (DGT), recently proposed as a soil P test, in comparison with conventional soil P tests viz. Olsen, Colwell, Bray-1, Mehlich-3, ammonium oxalate, anion exchange membranes (AEM) and 0.01 M CaCl2 solution. o Methods Maize (Zea mays L.) was grown in two P-deficient soils from western Kenya with contrasting P sorption characteristics, amended with a low and a high P rate and labelled with 33P. o Results The SA in the plant shoot corresponded with that of the extracts of the different soil tests, except CaCl2 and ammonium oxalate extracts, at the low P rate in the soil with low P sorption capacity. For the high P rate on this soil, differences in SA between maize shoot and soil test were small for all established soil tests, but significant for the Colwell, Bray-1, Mehlich-3 and AEM test. The SA in the soil extracts was significantly smaller than that in the maize shoot for the strongly P-sorbing soil at both P rates for all conventional tests, including AEM, This indicates that these tests extracted P from a pool that is not accessible to the plant. For the DGT test, however, there was no difference in SA between the maize shoot and the soil test, in any of the treatments. o Conclusions Most conventional soil tests can extract a fraction of P which is not available to maize. The DGT technique, however, only samples P from the plant-accessible pool.status: publishe

Countrywide multi-serotype outbreak of Salmonella Bovismorbificans ST142 and monophasic Salmonella Typhimurium ST34 associated with dried pork sausages in France, September 2020* to January 2021

Raw reads of the 34 genomes of S. Bovismorbificans and 12 genomes of S. Typhimurium from human and food origin in this study were submitted to the European Nucleotide Archive under project numbers PRJEB41645 and PRJEB49565.International audienceThe French National Reference Centre for Escherichia coli, Shigella and Salmonella (FNRC-ESS) detected two human clusters of 33 cases (median age: 10 years; 17 females) infected by Salmonella enterica serotype Bovismorbificans, ST142, HC5_243255 (EnteroBase HierCC‑cgMLST scheme) in September-November 2020 and of 11 cases (median age: 11 years; seven males) infected by S. enterica serotype 4,12:i:-, ST34, HC5_198125 in October-December 2020. Epidemiological investigations conducted by Santé publique France linked these outbreaks to the consumption of dried pork sausages from the same manufacturer. S. Bovismorbificans and S. 4,12:i:- were isolated by the National Reference Laboratory from different food samples, but both strains were identified in a single food sample only by qPCR. Three recalls and withdrawals of dried pork products were issued by the French general directorate of food of the French ministry for agriculture and food in November 2020, affecting eight supermarket chains. A notification on the European Rapid Alert System for Food and Feed and a European urgent enquiry on the Epidemic Intelligence Information System for Food and Waterborne Diseases and Zoonoses (EPIS-FWD) were launched. No cases were reported outside France. Outbreaks caused by multiple serotypes of Salmonella may go undetected by protocols in standard procedures in microbiology laboratories

Measles outbreak in a French Roma community in the Provence-Alpes-Cote d'Azur region, France, May to July 2017

International audience`Objectives: To analyse a measles outbreak in a Roma community. Methods: We describe a community-wide outbreak of genotype D8 measles that took place in southeastern France, between May and July 2017, along with the control measures adopted. Results: We identified a total of eighteen cases, between six months and 24 years old. All cases were unvaccinated or incompletely vaccinated and belonged to a sedentary French Roma community. Most of them (67%) were hospitalised, with three cases (17%) of severe measles including one death of a 16-year-old girl who had previously received oral corticosteroids. The latter was the only lethal case notified in France during theyear 2017. Control measures included intensification of surveillance, isolation of cases, and a large vaccination campaignin this Romacommunity. During the outbreak period, there was no caseof healthcareassociated measles transmission. A broad adherence to vaccination through the mediating role of both the chief of the community and the pastor allowed reaching completed vaccination coverage of 90%. Conclusions: Efforts should be concentrated to enhance access to health services for minorities such as the Roma community characterized by low vaccination coverage. A trustful relationship with leaders of the community is essential to ensure adherence to vaccination. In France, attributable mortality to measles is low and concerns mainly unvaccinated and immunodepressed patients. (c) 2018 Published by Elsevier Ltd on behalf of International Society for Infectious Diseases

Beyond target chemicals : updating the NORMAN prioritisation scheme to support the EU chemicals strategy with semi-quantitative suspect/non-target screening data

Background: Prioritisation of chemical pollutants is a major challenge for environmental managers and decision-makers alike, which is essential to help focus the limited resources available for monitoring and mitigation actions on the most relevant chemicals. This study extends the original NORMAN prioritisation scheme beyond target chemicals, presenting the integration of semi-quantitative data from retrospective suspect screening and expansion of existing exposure and risk indicators. The scheme utilises data retrieved automatically from the NORMAN Database System (NDS), including candidate substances for prioritisation, target and suspect screening data, ecotoxicological effect data, physico-chemical data and other properties. Two complementary workflows using target and suspect screening monitoring data are applied to first group the substances into six action categories and then rank the substances using exposure, hazard and risk indicators. The results from the ‘target’ and ‘suspect screening’ workflows can then be combined as multiple lines of evidence to support decision-making on regulatory and research actions. Results: As a proof-of-concept, the new scheme was applied to a combined dataset of target and suspect screening data. To this end, &gt; 65,000 substances on the NDS, of which 2579 substances supported by target wastewater monitoring data, were retrospectively screened in 84 effluent wastewater samples, totalling &gt; 11 million data points. The final prioritisation results identified 677 substances as high priority for further actions, 7455 as medium priority and 326 with potentially lower priority for actions. Among the remaining substances, ca. 37,000 substances should be considered of medium priority with uncertainty, while it was not possible to conclude for 19,000 substances due to insufficient information from target monitoring and uncertainty in the identification from suspect screening. A high degree of agreement was observed between the categories assigned via target analysis and suspect screening-based prioritisation. Suspect screening was a valuable complementary approach to target analysis, helping to prioritise thousands of substances that are insufficiently investigated in current monitoring programmes. Conclusions: This updated prioritisation workflow responds to the increasing use of suspect screening techniques. It can be adapted to different environmental compartments and can support regulatory obligations, including the identification of specific pollutants in river basins and the marine environments, as well as the confirmation of environmental occurrence levels predicted by modelling tools. Graphical Abstract: (Figure presented.