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International audience; Listeria monocytogenes can grow under stressful conditions and contaminate various food categories. Progresss in DNA sequencing-based identification methods, such as multi-locus sequence typing (MLST) now allow for more accurate characterization of pathogens. L. monocytogenes MLST genetic diversity is reflected by the different prevalence of the "clonal complexes" (CCs) in foods or infections. Better understanding of the growth potentials of L. monocytogenes is essential for quantitative risk assessment and efficient detection across CCs genetic diversity. Using optical density measurements taken with an automated spectrophotometer, we compared the maximal growth rate and lag phase of 39 strains from 13 different CCs and various food origins, in 3 broths mimicking stresful food conditions (8 °C, aw 0.95 and pH5) and in ISO Standard enrichment broths (Half Fraser and Fraser). This is important as growth could influence risk through pathogen multiplication in food. Besides, enrichment problems could lead to a lack of detection of some CCs. Despite small differences highlighting natural intraspecific variability, our results show that growth performances of L. monocytogenes strains under the conditions tested in selective and non-selective broth do not appear to be strongly correlated to CCs and cannot explain higher CC "virulence" or prevalence.

International audience; Tick-borne encephalitis (TBE) is a viral disease endemic in Eurasia. The virus is mainly transmitted to humans via ticks and occasionally via the consumption of unpasteurized milk products. The European Centre for Disease Prevention and Control reported an increase in TBE incidence over the past years in Europe as well as the emergence of the disease in new areas. To better understand this phenomenon, we investigated the drivers of TBE emergence and increase in incidence in humans through an expert knowledge elicitation. We listed 59 possible drivers grouped in eight domains and elicited forty European experts to: (i) allocate a score per driver, (ii) weight this score within each domain, and (iii) weight the different domains and attribute an uncertainty level per domain. An overall weighted score per driver was calculated, and drivers with comparable scores were grouped into three terminal nodes using a regression tree analysis. The drivers with the highest scores were: (i) changes in human behavior/activities; (ii) changes in eating habits or consumer demand; (iii) changes in the landscape; (iv) influence of humidity on the survival and transmission of the pathogen; (v) difficulty to control reservoir(s) and/or vector(s); (vi) influence of temperature on virus survival and transmission; (vii) number of wildlife compartments/groups acting as reservoirs or amplifying hosts; (viii) increase of autochthonous wild mammals; and (ix) number of tick species vectors and their distribution. Our results support researchers in prioritizing studies targeting the most relevant drivers of emergence and increasing TBE incidence.

This paper was prepared thanks to the collective expertise carried out by the ANSES emergency collective expert appraisal group (GECU) “Monkeypox – Food” (ANSES opinion no 2022-SA-0110), chaired by Nadia Haddad, and whose members are cited in the authors.; International audience; Monkeypox (MPX) is a zoonotic infectious disease caused by Monkeypox virus (MPXV), an enveloped DNA virus belonging to the Poxviridae family and the Orthopoxvirus genus. Since early May 2022, a growing number of human cases of Monkeypox have been reported in non-endemic countries, with no history of contact with animals imported from endemic and enzootic areas, or travel to an area where the virus usually circulated before May 2022. This qualitative risk assessment aimed to investigate the probability that MPXV transmission occurs through food during its handling and consumption. The risk assessment used “top-down” (based on epidemiological data) and “bottom-up” (following the agent through the food chain to assess the risk of foodborne transmission to human) approaches, which were combined. The “top-down” approach first concluded that bushmeat was the only food suspected as a source of contamination in recorded cases of MPXV, by contact or ingestion. The “bottom-up” approach then evaluated the chain of events required for a human to become ill after handling or consuming food. This approach involves several conditions: (i) the food must be contaminated with MPXV (naturally, by an infected handler or after contact with a contaminated surface); (ii) the food must contain viable virus when it reaches the handler or consumer; (iii) the person must be exposed to the virus and; (iv) the person must be infected after exposure. Throughout the risk assessment, some data gaps were identified and highlighted. The conclusions of the top-down and bottom-up approaches are consistent and suggest that the risk of transmission of MPXV through food is hypothetical and that such an occurrence was never reported. In case of contamination, cooking (e.g., 12 min at 70°C) could be considered effective in inactivating Poxviridae in foods. Recommendations for risk management are proposed. To our knowledge, this is the first risk assessment performed on foodborne transmission of MPXV.

Listeria monocytogenes (Lm) is a ubiquitous bacterium that causes the serious foodborne illness listeriosis. Although soil is a primary reservoir and a central habitat for Lm, little information is available on the genetic features underlying the fitness of Lm strains in this complex habitat. The aim of this study was to identify (i) correlations between the strains fitness in soil, their origin and their phylogenetic position (ii) identify genetic markers allowing Lm to survive in the soil. To this end, we assembled a balanced panel of 216 Lm strains isolated from three major ecological compartments (outdoor environment, animal hosts, and food) and from 33 clonal complexes occurring worldwide. The ability of the 216 strains to survive in soil was tested phenotypically. Hierarchical clustering identified three phenotypic groups according to the survival rate (SR): phenotype 1 “poor survivors” (SR < 2%), phenotype 2 “moderate survivors” (2% < SR < 5%) and phenotype 3 “good survivors” (SR > 5%). Survival in soil depended neither on strains’ origin nor on their phylogenetic position. Genome-wide-association studies demonstrated that a greater number of genes specifically associated with a good survival in soil was found in lineage II strains (57 genes) than in lineage I strains (28 genes). Soil fitness was mainly associated with variations in genes (i) coding membrane proteins, transcription regulators, and stress resistance genes in both lineages (ii) coding proteins related to motility and (iii) of the category “phage-related genes.” The cumulative effect of these small genomic variations resulted in significant increase of soil fitness.

International audience; Milk and milk products can harbor a multiple varieties of microorganisms. Therefore, they can be an important source of foodborne pathogens, including multidrug-resistant bacteria. Methicillin-resistant Staphylococcus aureus (MRSA) causes a wide spectrum of infections both in animals and humans. Over the last two decades, the presence of MRSA in foods and food-producing animals, including milk and milk products, has been frequently reported worldwide, raising public health concerns. In order to monitor and prevent foodborne MRSA contamination, it is necessary to understand their sources, the pheno/genotypic characteristics of the strains, and their transmission dynamics. In this review, studies conducted worldwide were summarized in order to assess the prevalence and diversity of MRSA circulating in milk and milk products. The risk factors for the occurrence of MRSA in milk and milk products were also discussed with preventive and control measures to avoid MRSA contamination in the dairy food chain.

The authors are grateful to collaborators of the SACADA consortium: Géraldine Boué, Steven Duret, Michel Federighi, Maxence Feher, Lisa Fourniol, Yvonnick Guillois, Pauline Kooh, Sophie Le Poder, Anne-Laure Maillard, Jean-Claude Manuguerra, Mathilde Pivette, Jessica Vanhomwegen, Prunelle Waldman; International audience; SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2), a virus causing severe acute respiratory disease in humans, emerged in late 2019. This respiratory virus can spread via aerosols, fomites, contaminated hands or surfaces as for other coronaviruses. Studying their persistence under different environmental conditions represents a key step for better understanding the virus transmission. This work aimed to present a reproducible procedure for collecting data of stability and inactivation kinetics from the scientific literature. The aim was to identify data useful for characterizing the persistence of viruses in the food production plants. As a result, a large dataset related to persistence on matrices or in liquid media under different environmental conditions is presented. This procedure, combining bibliographic survey, data digitalization techniques and predictive microbiological modelling, identified 65 research articles providing 455 coronaviruses kinetics. A ranking step as well as a technical validation with a Gage Repeatability & Reproducibility process were performed to check the quality of the kinetics. All data were deposited in public repositories for future uses by other researchers.

The foodborne pathogen, Listeria monocytogenes, (Lm), frequently undergoes selection pressure associated with the extensive use of disinfectants, such as quaternary ammonium compounds, which are widely used in food processing plants. The repeated exposure to sub-inhibitory biocide concentrations can induce increased tolerance to these compounds, but can also trigger the development of antibiotic resistance, and both increase the risk of food contamination and persistence in food production environments. Although the acquisition of genes can explain biocide tolerance, the genetic mechanisms underlying the adaptive cross-resistance to antibiotics remain unclear. We previously showed that repeated exposure to benzalkonium chloride (BC) and didecyldimethyl ammonium chloride (DDAC) led to reduced susceptibility to ciprofloxacin in Lm strains from diverse sources. Here, we compared the genomes of 16 biocide-adapted and 10 parental strains to identify the molecular mechanisms of fluoroquinolone cross-resistance. A core genome SNP analysis identified various mutations in the transcriptional regulator fepR (lmo2088) for 94% of the adapted strains and mutations in other effectors at a lower frequency. FepR is a local repressor of the MATE fluoroquinolone efflux pump FepA. The impact of the mutations on the structure and function of the protein was assessed by performing in silico prediction and protein homology modeling. Our results show that 75% of the missense mutations observed in fepR are located in the HTH domain of the protein, within the DNA interaction site. These mutations are predicted to reduce the activity of the regulator, leading to the overexpression of the efflux pump responsible for the ciprofloxacin-enhanced resistance.

International audience; Characterising pesticide residues from a qualitative and quantitative point of view is key to both risk assessment in the framework of pesticide approval and risk management. In the European Union (EU), these concerns are addressed during the evaluation of active substances at the European level prior to marketing authorisation. In the framework of this review, we will focus on one specific item of the residue section, namely the effect of process (industrial or domestic transformation of the raw commodities) on the nature of the residue in food. A limited number of hydrolysis conditions defined by three parameters (temperature, pH and time) are set to be “representative of the most widely used industrial and domestic food processing technologies”. These hydrolysis conditions, however, do not cover processes at temperatures higher than 120 °C, such as cooking with a conventional oven or in a pan, frying or using a microwave oven.

The ubiquitous and growing presence of microplastics (MPs) in all compartments of the environment raises concerns about their possible harmful effects on human health. Human exposure to MPs occurs largely through ingestion. Polyethylene (PE) is widely employed for reusable bags and food packaging and found to be present in drinking water and food. It is also one of the major polymers detected in human stool. The aim of this study was to characterize the effects of intestinal exposure to PE MPs on gut homeostasis. Mice were orally exposed for 6 weeks to PE microbeads of 2 different sizes, 36 and 116 μm, that correspond to those found in human stool. They were administrated either individually or as a mixture at a dose of 100 μg/g of food. Both PE microbead sizes were detected in mouse stool. Different parameters related to major intestinal functions were compared between control mice, mice exposed to each type of microbead, or co-exposed to the 2 types of microbeads. Intestinal disturbances were observed after individual exposure to each size of PE microbead, and the most marked deleterious effects were found in co-exposed mice. At the histomorphological level, crypt depth was increased throughout the intestinal tissues. Significant variations of gene expression related to epithelial, permeability, and inflammatory biomarkers were quantified. Defective recruitment of some intestinal immune cells was observed from the proximal portion of the small intestine to the colon. Several bacterial taxa at the order level were found to be affected by exposure to the MPs by metagenomic analysis of cecal microbiota. These results show that ingestion of PE microbeads induces significant alterations of crucial intestinal markers in mice and underscores the need to further study the health impact of MP exposure in humans.

International audience; Plastic food packaging represents 40 % of the plastic production worldwide and belongs to the 10 most commonly found items in aquatic environments. They are characterized by high additives contents with >4000 formulations available on the market. Thus they can release their constitutive chemicals (i.e. additives) into the surrounding environment, contributing to chemical pollution in aquatic systems and to contamination of marine organism up to the point of questioning the health of the consumer. In this context, the chemical and toxicological profiles of two types of polypropylene (PP) and polylactic acid (PLA) food packaging were investigated, using in vitro bioassays and target gas chromatography mass spectrometry analyses. Plastic additives quantification was performed both on the raw materials, and on the material leachates after 5 days of lixiviation in filtered natural seawater. The results showed that all samples (raw materials and leachates) contained additive compounds (e.g. phthalates plasticizers, phosphorous flame retardants, antioxidants and UV-stabilizers). Differences in the number and concentration of additives between polymers and suppliers were also pointed out, indicating that the chemical signature cannot be generalized to a polymer and is rather product dependent. Nevertheless, no significant toxic effects was observed upon exposure to the leachates in two short-term bioassays targeting baseline toxicity (Microtox® test) and Pacific oyster Crassostrea gigas fertilization success and embryo-larval development. Overall, this study demonstrates that both petrochemical and bio-based food containers contain harmful additives and that it is not possible to predict material toxicity solely based on chemical analysis. Additionally, it highlights the complexity to assess and comprehend the additive content of plastic packaging due to the variability of their composition, suggesting that more transparency in polymer formulations is required to properly address the risk associated with such materials during their use and end of life.

International audience; Chemical contaminant concentrations in wild organisms are used to assess environmental status under the Eu-ropean Marine Strategy Framework Directive. However, this approach is challenged by the complex intra- andinter-species variability, and the different regional features. In this study, concentrations in trace elements (As,Cd, Hg and Pb), polychlorinated biphenyls (PCBs), polychlorodibenzo-para-dioxines (PCDDs) and poly-chlorodibenzofuranes (PCDFs) were monitored in 8 fish species sampled on the continental shelf of three Frenchregions: the Eastern English Channel (EEC) and Bay of Biscay (BoB) in the Northeast Atlantic Ocean, and the Gulfof Lions (GoL) in Western Mediterranean Sea. Our objectives were to identify species or regions more likely to becontaminated and to assess how to take this variability into account in environmental assessment. While con-centrations were higher in benthic and demersal piscivores, PCB and PCDD/F concentrations (lipid-weight) weresimilar in most teleost species. For Cd, Hg and Pb, the trophic group accumulating the highest concentrationsdepended on the contaminant and region. Concentrations in Hg, PCBs and PCDD/Fs were higher in the EEC and/or GoL than in BoB. Cadmium and Pb concentrations were highest in the BoB. Lipid content accounted for 35%–84% of organic contaminant variability. Lipid normalisation was employed to enhance robustness in the iden-tification of spatial patterns. Contaminant patterns in chondrichthyans clearly differed from that in teleosts. Inaddition, trophic levels accounted for ≤1% and ≤33% of the contaminant variability in teleost fishes in the EECand BoB, respectively. Therefore, developing taxa-specific thresholds might be a more practical way forward forenvironmental assessment than normalisation to trophic levels

International audience; The interest of studying organic plastic additives (OPAs) is growing since many of them are considered as toxic for human beings, marine organisms and have been found in the ecosystem. The impact and the extent of this pollution is not fully understood because of the lack of methods able to comprehensively analyze the wide diversity of OPAs. This study aims at offering a quick and efficient way to identify specific harmful plastic additives in polymer materials. For this purpose, a general method, for identifying 49 OPAs, has been successfully developed using pyrolyzer/thermal desorption-gas chromatography coupled to a high-resolution mass spectrometer (Py/TD-GC-HRMS). The retention indices were calculated for each compound and a high-resolution mass spectra database for plastic additives was implemented. This method was then applied to characterize the OPAs included in food containers that are frequently found in the environment. Four samples made of polypropylene (PP) and polylactic acid (PLA) coming from two distinct suppliers were then selected. A total of 10 additives, which were plasticizers (phthalates and adipates), antioxidants (bisphenol B) and phosphorous flames retardants, were found in these food packaging. Generally, higher peak signals were detected in the PP samples in comparison to PLA samples, except for tributyl phosphate and bisphenol B that were exclusively found in PLA samples. Moreover, the experimentations pointed out additives differences between suppliers, for products intended for the same use and made of the same polymer, for both PP and PLA samples highlighting the complexity of identifying and generalizing the additive content of plastic materials.

To prevent health risks associated with the consumption of shellfish contaminated with BTXs in France, a working group was set up by the French Agency for Food, Environmental and Occupational Health & Safety (Anses). One of the aims of this working group was to propose a guidance level for the presence of BTXs in shellfish.; International audience; Brevetoxins (BTXs) are marine biotoxins responsible for neurotoxic shellfish poisoning (NSP) after ingestion of contaminated shellfish. NSP is characterized by neurological, gastrointestinal and/or cardiovascular symptoms. The main known producer of BTXs is the dinoflagellate Karenia brevis, but other microalgae are also suspected to synthesize BTX-like compounds. BTXs are currently not regulated in France and in Europe. In November 2018, they have been detected for the first time in France in mussels from a lagoon in the Corsica Island (Mediterranean Sea), as part of the network for monitoring the emergence of marine biotoxins in shellfish. To prevent health risks associated with the consumption of shellfish contaminated with BTXs in France, a working group was set up by the French Agency for Food, Environmental and Occupational Health & Safety (Anses). One of the aims of this working group was to propose a guidance level for the presence of BTXs in shellfish. Toxicological data were too limited to derive an acute oral reference dose (ARfD). Based on human case reports, we identified two lowest-observed-adverse-effect levels (LOAELs). A guidance level of 180 µg BTX-3 eq./kg shellfish meat is proposed, considering a protective default portion size of 400 g shellfish meat.

International audience; Salmonella enterica subsp. enterica serovars are considered major causes of food poisoning and we performed this study because Salmonella is a burden in Lebanon. The present study investigated the ability of genomic information to predict serovar using a collection of Salmonella isolates from infected humans (n = 24) and contaminated food (n = 63) in Lebanon. Further, the phylogenomic relationships of the serovar the predominated in Lebanon (i.e., S. Enteritidis; n = 25) were investigated in comparison with isolates from other countries (n = 130) based on coregenome single nucleotide polymorphisms (SNPs). Genetic elements, specifically Salmonella pathogenicity islands (SPIs), plasmid replicons, and antibiotic-resistance genes were screened in S. Enteritidis genomes (n = 155). Our results revealed that the Salmonella serovars identification by seroagglutination from the samples isolated in Lebanon (n = 87) was highly correlated with the genomic-based prediction of serovars (80.4-85.0% with SeqSero1 and 93.1-94.2% with SeqSero2). The Salmonella serovars isolated from human and food samples in Lebanon were mainly Enteritidis (28.7%) and Infantis (26%). To a rare extent, other serovars included Amager, Anatum, Bredeney, Chincol, Heidelberg, Hofit, Kentucky, Montevideo, Muenster, Newport, Schwarzengrund, Senftenberg and Typhimurium. In comparison with other countries, S. Enteritidis samples isolated in Lebanon (56 +/- 27 intra-group pairwise SNP differences) presented a strong phylogenomic relativeness at the coregenome level with samples, as for example with samples isolated from Syria (65 +/- 31 inter-group pairwise SNP differences). Most of the studied S. Enteritidis genomes encoded 10 SPIs involved in survival in immune cells (i.e. SPIs 1, 2, 3, 4, 5, 12, 13, 14, 16 and 17). The plasmid replicons IncFIB (S)_1 and IncFII (S)_1 encoding elements involved in virulence were identified in the majority of the S. Enteritidis genomes (94% and 96%, respectively), the majority exhibiting aminoglycosides (gene aac(6')-Iaa_1). The IncI_1_Alpha replicon responsible for ampicillin-resistance was only detected in 2 of 25 S. Enteritidis Lebanese strains. Genomic-based risk assessment of Salmonella serovars in Lebanon showed that food imported from Syria might be an origin of the S. Enteritidis human cases in Lebanon. The detection of several SPIs involved in the survival, plasmid replicons involved in virulence, and aminoglycoside-resistance genes, emphasizes that S. Enteritidis is of paramount importance for public health in Lebanon and other countries.

International audience; By now the polymeric nature of microparticles has to be demonstrated before their classification as microplastics. Pyrolysis coupled to gas chromatography and mass spectrometry (Py-GC/MS) has been used for years to characterize polymers. Thanks to three distinct steps, destructuring, separation, and identification, this chapter explains how this technique allows the analyst to ascertain the polymeric composition of different plastic materials and much more. Far from being used as much as vibrational spectroscopy methods for the study of microplastics, Py-GC/MS nevertheless has advantages which will be presented in this chapter, through the presentation of the contributions of this technique in terms of identification and quantification of microplastics. All of the studies presented here allow to outline some good laboratory practices relative to this technique. The last part of this chapter is dedicated to the future of microplastics analysis by Py-GC/MS, including the need of method normalization and the contribution of this technology for the research of nanoplastics and additives.

International audience; Plasmids are genetic elements that enable rapid adaptation and evolution by transferring genes conferring selective advantages to their hosts. Conjugative plasmids are predominantly responsible for the global dissemination of antimicrobial resistance, representing an important threat to global health. As the number of plasmid sequences grows exponentially, it becomes critical to depict the global diversity and decipher the distribution of circulating plasmids in the bacterial community. To this end, we created COMPASS, a novel and comprehensive database compiling 12,084 complete plasmids with associated metadata from 1571 distinct species isolated worldwide over more than 100 years. The curation of the database allowed us to identify identical plasmids across different bacteria revealing mainly intraspecies dissemination and rare cases of horizontal transmission. We outlined and analyzed all relevant features, plasmid properties, host range and characterized their replication and mobilization systems. After an exhaustive comparison of PlasmidFinder and MOB-typer, the MOB-typer-based analysis revealed that the current knowledge embedded in the current typing schemes fails to classify all the plasmid sequences collected in COMPASS. We were able to categorize 6828 and 5229 plasmids by replicon and MOB typing, respectively, mostly associated with Proteobacteria and Firmicutes. We then searched for the presence of multiple core genes involved in replication and propagation. Our results showed that 2403 plasmids carried multiple replicons that were distributed in 206 bacterial species. The co-integration of replicon types from different incompatibility (Inc) groups is an adaptive mechanism, which plays an important role in plasmid survival and dissemination by extending their host range. Our results highlight the crucial role of IncF alleles (present in 56% of all multireplicons) and revealed that IncH, IncR, and IncU replicons were also frequently carried in multireplicons. Here, we provided a comprehensive picture of the different IncF subtypes by identifying 20 different profiles in 849 IncF multireplicons, which were mostly associated with Enterobacteriaceae. These results could provide the basis for a novel IncF plasmid nomenclature based on different allelic profiles.

The starry smooth-houndMustelus asteriasis a near-threatened coastal shark in Europe, whose parasitofauna is largely unknown. We studied metazoan parasites of 20 immature sharks (13 males and seven females) from the English Channel and we examined their relationships with host condition and their use as host bioindicators. All the sharks were parasitized by one to six metazoan taxa among the twelve recorded in the whole sampling (one trematode, six cestodes and two nematodes trophically-transmitted; one monogenean, one copepod and one myxosporean on gills), with a mean abundance of 30.5 ± 21.4 parasites per fish (myxosporeans not included). The three major taxa were in decreasing order: the nematodeAcanthocheilus rotundatus(prevalence: 75%, Confidence Interval 53–89%), the cestodeEutetrarhynchussp. (70%, CI 48–85%), and the monogeneanErpocotyle laevis(60%, CI 39–78%). The gill copepodKroyeria lineataand the gut nematodeProleptus obtususwere identified as significant pathogens. Parasite community differed between males and females despite their immature stage, suggesting early spatial sex-segregation, withE. laevis,Eutetrarhynchussp. andAnthobothriumsp. proposed as tags. We discuss results in terms of host fitness loss and information given by parasites on diet ecology and stock discrimination. We recommend incorporating parasitology in further research to improve shark conservation and management.

International audience; Consumers generally considered organic products to be healthier and safer but data regarding the contamination of organic products are scarce. This study evaluated the impact of the farming system on the levels of ochratoxin A (OTA) in the tissues of French pigs (muscle and liver) reared following three different types of production (organic, Label Rouge and conventional). Because OTA is present at trace levels in animal products, a sensitive ultra-high performance liquid chromatography-tandem mass spectrometry method using stable isotope dilution assay was developed and validated. OTA was detected or quantified (LOQ of 0.10 mu g kg(-1)) in 67% (n = 47) of the 70 pig liver samples analysed, with concentrations ranging from < 0.10 to 3.65 mu g kg(-1). The maximum concentration was found in a sample from organic production but there were no significant differences in the content of OTA between farming systems. OTA was above the LOQ in four out of 25 samples of the pork muscles. A good agreement was found between OTA levels in muscle and liver (liver concentration = 2.9 x OTA muscle concentration, r = 0.981).

As for many opportunistic pathogens, the virulence potential of Listeria monocytogenes is highly heterogeneous between isolates and correlated, to some extent, with phylogeny and gene repertoires. In sharp contrast with copious data on intraspecies genome diversity, little is known about transcriptome diversity despite the role of complex genetic regulation in pathogenicity. The current study implemented RNA sequencing to characterize the transcriptome profiles of 33 isolates under optimal in vitro growth conditions. Transcript levels of conserved single-copy genes were comprehensively explored from several perspectives, including phylogeny, in silico-predicted virulence category based on epidemiological multilocus sequence typing (MLST) data, and in vivo virulence phenotype assessed in Galleria mellonella. Comparing baseline transcriptomes between isolates was intrinsically more complex than standard genome comparison because of the inherent plasticity of gene expression in response to environmental conditions. We show that the relevance of correlation analyses and their statistical power can be enhanced by using principal-component analysis to remove the first level of irrelevant, highly coordinated changes linked to growth phase. Our results highlight the major contribution of transcription factors with key roles in virulence to the diversity of transcriptomes. Divergence in the basal transcript levels of a substantial fraction of the transcriptome was observed between lineages I and II, echoing previously reported epidemiological differences. Correlation analysis with in vivo virulence identified numerous sugar metabolism-related genes, suggesting that specific pathways might play roles in the onset of infection in G. mellonella. IMPORTANCEListeria monocytogenes is a multifaceted bacterium able to proliferate in a wide range of environments from soil to mammalian host cells. The accumulated genomic data underscore the contribution of intraspecies variations in gene repertoire to differential adaptation strategies between strains, including infection and stress resistance. It seems very likely that the fine-tuning of the transcriptional regulatory network is also a key component of the phenotypic diversity, albeit more difficult to investigate than genome content. Some studies reported incongruity in the basal transcriptome between isolates, suggesting a putative relationship with phenotypes, but small isolate numbers hampered proper correlation analyses with respect to their characteristics. The present study is the embodiment of the promising approach that consists of analyzing correlations between transcriptomes and various isolate characteristics. Statistically significant correlations were found with phylogenetic groups, epidemiological evidence of virulence potential, and virulence in Galleria mellonella larvae used as an in vivo model.

International audience; Plastics are found to be major debris composing marine litter; microplastics (MP, < 5 mm) are found in all marine compartments. The amount of MPs tends to increase with decreasing size leading to a potential misidentification when only visual identification is performed. These last years, pyrolysis coupled with gas chromatography/mass spectrometry (Py-GC/MS) has been used to get information on the composition of polymers with some applications on MP identification. The purpose of this work was to optimize and then validate a Py-GC/MS method, determine limit of detection (LOD) for eight common polymers, and apply this method on environmental MP. Optimization on multiple GC parameters was carried out using polyethylene (PE) and polystyrene (PS) microspheres. The optimized Py-GC/MS method require a pyrolysis temperature of 700 °C, a split ratio of 5 and 300 °C as injector temperature. Performance assessment was accomplished by performing repeatability and intermediate precision tests and calculating limit of detection (LOD) for common polymers. LODs were all below 1 μg. For performance assessment, identification remains accurate despite a decrease in signal over time. A comparison between identifications performed with Raman micro spectroscopy and with Py-GC/MS was assessed. Finally, the optimized method was applied to environmental samples, including plastics isolated from sea water surface, beach sediments, and organisms collected in the marine environment. The present method is complementary to μ-Raman spectroscopy as Py-GC/MS identified pigment containing particles as plastic. Moreover, some fibers and all particles from sediment and sea surface were identified as plastic.

International audience; This study assesses the impact of the farming system on the levels of copper, zinc, arsenic, cadmium, lead and mercury in pig tissues from three types of production (Organic (n = 28), Label Rouge (n = 12) and Conventional (n = 30)) randomly sampled in different slaughterhouses. All the concentrations were below regulatory limits. In muscles, Cu, Zn and As were measured at slightly higher levels in organic samples but no differences between organic and Label Rouge was observed. Livers from conventional and Label Rouge pig farms exhibited higher Zn and Cd contents than the organic ones, probably due to different practice in zinc or phytase supplementation of fattening diets. Principal component analysis indicated a correlation between Cu and As concentrations in liver and carcass weight, and between Zn and Cd liver levels and lean meat percentage. The linear discriminant analysis succeeded in predicting the farming process on the basis of the lean meat percentage and the liver Cd level.

International audience; To reduce the exposure of the French West Indies population to the organochlorine insecticide chlordecone (Kepone; CLD), the contamination of currently consumed foodstuffs must be reduced. Depuration of contaminated animals before slaughter could be a strategy to obtain safe animal products. The aim of this study was to characterize and quantify CLD elimination in contaminated ewes during depuration process. Experiments A and B consisted in a single intravenous (i.v.) administration of CLD (n = 5) and CLDOH (chlordecol; n = 3) followed by a 84-d and 3-d depuration period respectively with collection of blood, faeces and urine samples. After CLD administration, CLD and conjugated-CLDOH (CLDOH-C) were quantified in serum and urine and CLD and CLDOH were quantified in faeces. Based on calculations of faecal, urinary and body clearances of CLD and CLDOH-C, faeces appeared as the major route of CLD excretion with 86 % of the CLD administered dose eliminated in faeces, either as CLD (51 %) or as CLDOH (35 %).

O80:H2 enterohemorrhagic Escherichia coli (EHEC) of sequence type ST301 is one of the main serotypes causing European hemolytic and uremic syndrome, but also invasive infections, due to extra-intestinal virulence factors (VFs). Here, we determined whether other such heteropathotypes exist among ST301. EnteroBase was screened for ST301 strains that were included in a general SNP-phylogeny. French strains belonging to a new heteropathotype clone were sequenced. ST, hierarchical clusters (HC), serotype, resistome, and virulome were determined using EnteroBase, the CGE website, and local BLAST. The ST301 general phylogeny shows two groups. Group A (n = 25) is mainly composed of enteropathogenic E. coli, whereas group B (n = 55) includes mostly EHEC. Three serotypes, O186:H2, O45:H2 and O55:H9, share the same virulome as one of the O80:H2 sub-clones from which they derive subsequent O-antigen switches. The O55:H9 clone, mainly present in France (n = 29), as well as in the UK (n = 5) and Germany (n = 1), has a low background of genetic diversity (four HC20), although it has three Stx subtypes, an H-antigen switch, and genes encoding the major extra-intestinal VF yersiniabactin, and extended-spectrum beta-lactamases. Diverse heteropathotype clones genetically close to the O80:H2 clone are present among the ST301, requiring close European monitoring, especially the virulent O55:H9 clone.

International audience; Predicting chromatographic retention times of pesticides has become more and more important for suspect and non-target screening. Indeed, high-resolution mass spectrometry hyphenated (HRMS) to liquid chromatography (LC) are of growing interest for research and monitoring of pesticides, their metabolites and transformation products. The development of quantitative structure-retention relationship models require selecting the most adequate and best set of molecular descriptors and the best machine-learning algorithm. Here, we used seven molecular descriptor sets extracted from four well-known studies and applied them to roughly 800 pesticides and their chromatographic reversed-phase retention times. We used and optimized five different machine-learning algorithms with these descriptor sets to carry out predictions. Our results show that a support-vector machine regression algorithm with only eight molecular descriptors gave the best compromise between the number of molecular descriptors, processing time and model complexity to optimize prediction performance for this specific gradient LC method.

A total diet study (TDS) was undertaken to estimate the chronic dietary exposure to pesticide residues and health risks for the French infants and young children below 3 years old. As a whole, 516 pesticides and metabolites were analysed in 309 food composite samples including 219 manufactured baby foods and 90 common foods, which cover 97% of infants and young children's diet. These composite samples were prepared using 5,484 food products purchased during all seasons from 2011 to 2012 and processed as consumed. Pesticide residues were detected in 67% of the samples and quantified in 27% of the baby food samples and in 60% of the common foods. Seventy-eight different pesticides were detected and 37 of these quantified at levels ranging from 0.02 to 594 µg/kg. The most frequently detected pesticides (greater than 5% samples) were (1) the fungicides 2-phenylphenol, azoxystrobin, boscalid, captan and its metabolite tetrahydrophthalimide, carbendazim, cyprodinil, difenoconazole, dodine, imazalil, metalaxyl, tebuconazole, thiabendazole, (2) the insecticides acetamiprid, pirimiphos-methyl and thiacloprid, (3) the herbicide metribuzin and (4) the synergist piperonyl butoxide. Dietary intakes were estimated for each of the 705 individuals studied and for 431 pesticides incl. 281 with a toxicological reference value (TRV). In the lower-bound scenario, which tends to underestimate the exposure, the TRV were never exceeded. In the upper-bound scenario that overestimates exposure, the estimated intakes exceeded the TRV for dieldrin and lindane (two persistent organic pollutants) and propylene thiourea, a metabolite of propineb. For these three substances, more sensitive analyses are needed to refine the assessment. For 17 other detected and/or prioritised pesticides, the risk could not be characterised due to the lack of a valid TRV, of certain food analyses or the absence of analytical standards for their metabolites. Keywords: Food safety, Infants and young children, Pesticide residues, Total diet study, Exposure assessment, Risk characterization

Salmonella enterica serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S. e nterica serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) S. enterica serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylogeographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase (gyrA) and DNA topoisomerase IV (parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. e nterica serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS26-mediated insertions and deletions, which appear to have hampered previous attempts to trace the clone’s evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results indicate that most MDR S. e nterica serotype Kentucky circulating globally result from the clonal expansion of a single lineage that acquired chromosomal AMR genes 30 years ago, and has continued to diversify and accumulate additional resistances to last-line oral antimicrobials. This article contains data hosted by Microreact.

International audience; We present the LiSEQ (Listeria SEQuencing) project, funded by the European Food Safety Agency (EFSA) to compare Listeria monocytogenes isolates collected in the European Union from ready-to-eat foods, compartments along the food chain (e.g. food-producing animals, food-processing environments) and humans. In this article, we report the molecular characterization of a selection of this data set employing whole-genome sequencing analysis. We present an overview of the strain diversity observed in different sampled sources, and characterize the isolates based on their virulence and resistance profile. We integrate into our analysis the global L. monocytogenes genome collection described by Moura and colleagues in 2016 to assess the representativeness of the LiSEQ collection in the context of known L. monocytogenes strain diversity. DATA SUMMARY All FASTQ reads from this study have been deposited in the National Center for Biotechnology Information short-read archive (SRA) under the BioProject PRJNA475189.

International audience; Plastic pollution is a source of chemical to the environment and wildlife. Despite the ubiquity of plastic pollution and thus plastic additive in the environment, plastic additives have been studied to a limited extend. As a prerequisite to a study aiming to evaluate the leaching of a common additive used as an antioxidant (Irgafos® 168) from polyethylene microparticles, an inventory of the potential background contamination of the laboratory workplace was done. In this study, Irgafos® 168 (tris(2,4-ditert-butylphenyl) phosphite) and its oxidized form (tris (2,4-ditert-butylphenyl) phosphate) were quantified in different laboratory reagents, including the plastic packaging and the powders, using Pyrolysis-GC/MS. At least one form of Irgafos® 168 was detected in all tested laboratory reagents with higher concentrations in caps and bottles as compared to the powders. Additionally, oxidized Irgafos® 168 was also found in the reverse osmosed and deionized water container used in the laboratory. The same profile of contamination, i.e. higher concentration of the oxidized form and higher concentrations in acidic reagents, was observed when comparing the reagent and their respective containers suggesting that the additive is leaching from the container into the powder. Overall, this study demonstrates that the antioxidant additive Irgafos® 168 is ubiquitous in the laboratory workplace. Plastic additives such as Irgafos® 168 can therefore largely interfere and biased ecotoxicological and toxicological studies especially using environmentally relevant concentrations of microplastics. The source, fate and effects of plastic additive from plastic debris should be carefully considered in future studies that require setting up methods to overcome these contaminations

International audience; Microplastics (MPs), plastics with particles smaller than 5 mm, have been found almost in every corner of the world, especially in the ocean. Due to the small size, MPs can be ingested by animals and enter the marine trophic chain. MPs can affect animal health by physically causing damage to the digestive tract, leaking plastic chemical components, and carrying environmental pollutants and pathogens into animals. In this study, impacts of MPs ingestion on gut microbiota were investigated. Filter feeding mussels were exposed to “virgin” and “weathered” MPs at relatively realistic concentration 0.2 mg L−1 (“low”) and exaggerated concentration 20 mg L−1 (“high”) for 6 weeks. Influence in mussel gut microbiota was investigated with 16S rRNA gene high-throughput sequencing. As compared with non-exposed mussels, alteration of gut microbiota was observed after mussels were exposed to MPs for 1 week, 3 weeks, 6 weeks, and even after 8-day post-exposure depuration. Potential human pathogens were found among operational taxonomic units (OTUs) with increased abundance induced by MP-exposure. Faecal pellets containing microorganisms from altered gut microbiota and MPs might further influence microbiota of surrounding environment. Our results have demonstrated impacts of MP-exposure on mussel gut microbiota and suggested possible consequent effects on food quality, food safety, and the well-being of marine food web in the ecosystem for future studies.

International audience; Among the enteric viruses implicated in waterborne outbreaks, human norovirus and hepatitis A virus (HAV) are a serious public health issue. Most foodborne viruses are difficult or currently unlikely to cultivate. Because of the lack of a cell culture method, real-time reverse transcriptase PCR is commonly used for the detection of norovirus in foodstuffs and environmental samples. Due to low infectious doses in humans and low virus concentration in water sample, filter adsorption methods were used for concentrating viruses from water. The ISO (Anonymous, ISO 15216-1, 2017) describes standardized molecular methods for detecting HAV and norovirus in bottled water. This method includes a two-step procedure: concentrating the virus using a microporous electropositive filter (47 mm diameter, 0.45 μm pore size) then molecular detection. The Zetapor filter, which had a charged membrane with a pore size of 0.45 μm, was commonly used in the past to concentrate viruses from water or from salad leaves following virus elution. But, unfortunately, the Zetapor filter is no longer marketed and it is therefore necessary to assess an alternative filter. The aim of this study was to compare the ability of two electropositive filters with a pore size of 0.45 μm or 0.22 μm and one uncharged filter (0.45 μm) to recover norovirus and HAV from two different types of drinking water (bottled water and tap water) with the adsorption-elution method proposed by ISO (Anonymous, ISO 15216-1, 2017) (method A) and with direct viral extraction using filters (method B). The mean extraction yields for norovirus and HAV calculated with RNA extracts ranged from 0.2 % - 4.81 % with method A and from 5.05 % - 53.58 % with method B, and did not differ significantly between the two types of drinking water tested. For method B, the mean extraction yields for HAV and norovirus were evaluated according to results from the three filters used. The recovery rate of HAV and norovirus ranged between 3.47 % and 62.41 % with the 0.45 μm electropositive filter and were higher than the other filters. The 0.45 μm electropositive filter could be used to concentrate viruses for routine viral monitoring of drinking water for researchers who want to adopt the method in their lab routine.

From January 2011 to March 2018, 26 patients aged from 20 to 80 years old reported being sick in France after eating sea figs of the genus Microcosmus. The patients had symptoms evoking a cerebellar syndrome: blurred or double vision, ataxia and dizziness, asthenia, headache, muscle cramps, paresthesia and digestive disorders (nausea, vomiting and diarrhea). Three of the 18 food poisoning events recorded by the Poison Control Center in Marseille and involving four patients were further investigated as the meal leftovers were collected and analyzed. A previous study ruled out the presence of the regulated lipophilic marine toxins after high-resolution mass spectrometry, but further analyses were required to look for hydrophilic cyanotoxins. The sea fig leftovers from food poisoning case Numbers 1 (January 2011), 6 (December 2012) and 17 (March 2018) of this published case series were analyzed by hydrophilic interaction liquid chromatography coupled to low- and high-resolution mass spectrometry to investigate the presence of hydrophilic cyanotoxins. The sea fig samples showed anatoxin-a (ATX-a) concentrations ranging from 193.7 to 1240.2 &micro, g/kg. The sea fig control sample analyzed was also contaminated with ATX-a but in a much smaller concentration (22.5 &micro, g/kg). To the best of our knowledge, this is the first report of human food poisoning involving ATX-a as the possible causative toxin where the cyanotoxin could be unequivocally identified.

Despite the high burden of vector-borne disease in (sub)tropical areas, few information are available regarding the diversity of tick and tick-borne pathogens circulating in the Caribbean. Management and control of vector-borne disease require actual epidemiological data to better assess and anticipate the risk of (re)emergence of tick-borne diseases in the region. To simplify and reduce the costs of such large-scale surveys, we implemented a high-throughput microfluidic real-time PCR system suitable for the screening of the main bacterial and parasitic genera involved in tick-borne disease and potentially circulating in the area. We used the new screening tool to perform an exploratory epidemiological study on 132 adult specimens of Amblyomma variegatum and 446 of Rhipicephalus microplus collected in Guadeloupe and Martinique. Not only the system was able to detect the main pathogens of the area&mdash, Ehrlichia ruminantium, Rickettsia africae, Anaplasma marginale, Babesia bigemina and Babesia bovis&mdash, but the system also provided evidence of unsuspected microorganisms in Caribbean ticks, belonging to the Anaplasma, Ehrlichia, Borrelia and Leishmania genera. Our study demonstrated how high-throughput microfluidic real-time PCR technology can assist large-scale epidemiological studies, providing a rapid overview of tick-borne pathogen and microorganism diversity, and opening up new research perspectives for the epidemiology of tick-borne pathogens.

Foodborne transmission of HEV is a growing public health concern in industrialised countries, where the disease is mainly autochthonous, caused by zoonotic HEV of either genotype 3 or 4. Foodstuffs containing pig's liver were suspected on several occasions to be the cause of autochthonous cases of HEV infection, while the transmission was associated with animal contact and the ingestion of raw or uncooked meat, especially liver. In assessing the risk related to the presence of HEV in food, detection methods were previously developed but HEV detection rates seem to vary with the type of samples and methods. As foodstuff containing pig liver can be contaminated with HEV internally, an efficient virus extraction procedure is required. The aim of this study was to evaluate six methods for their efficiency in releasing HEV viral particles from figatelli, pig liver sausages and liver samples previously tested positive for the presence of HEV. The ratio weight to volume of elution buffer (1:5) and the FastPrep®-24 homogeniser showed to significantly improve the quantity of HEV genomes released per gram of figatelli and pig liver sausages. To our knowledge, this study is the first to evaluate several methods for elution of HEV particles from naturally contaminated pig liver products, and may be extended for quantifying other viral genomes from food of animal origin.

International audience; Estuaries serve as nursery grounds for many marine fish species. However, increasing human activities within estuaries and surrounding areas lead to significant habitat quality degradation for the juveniles. In recent years, plastic pollution has become a global environmental issue as plastic debris are found in all aquatic environments with potential adverse impacts on marine biota. Given the important ecological role of estuaries and implications of microplastics (MP) in ecosystems, here we assess the occurrence, number, size and polymer types of MP ingested by wild and caged juveniles European flounder (Platichthys flesus). We deployed caged fish for one month at five sites in three estuaries in the Eastern English Channel. The Seine estuary, heavily impacted by manmade modifications and one of the most contaminated estuaries in Europe, was compared to two smaller estuaries (Canche and Liane) less impacted by industrial activities. We found that juvenile flounders (7- 9 cm) were vulnerable to plastic ingestion. 75% of caged fish and 58% of wild caught fish had the presence of MP items in their digestive tract. Fibers (69%) dominated in the fish’s digestive tract at all sites. An average of 2.04 ± 1.93 MP items were ingested by feral juveniles flounder and 1.67 ± 1.43 by caged juveniles flounder. For the caged fish, the three sites impacted by wastewater treatment plant (Liane, Le Havre Harbor and Rouen) were those with the highest percentage of individuals that have ingested MP items. Most of the isolated items were fibers and blue in color. Polymers identified by micro Raman spectroscopy were Polycaprolactam, Polyethylene Terephtalate and Polyurethane. Although other environmental factors may have affected caged fish condition and mortality, we found no significant correlation with the number of ingested MP. However, the high occurrence of MP ingested by juvenile fish on nursery grounds raises concerns on their potential negative effects for fish recruitment success and population renewal. Finally, this study describes, for the first time, the feasibility of using caged juvenile fish as an assessing tool of MP contamination in estuarine nursery grounds.

International audience

[Departement_IRSTEA]Ecotechnologies [TR1_IRSTEA]SPEE; The aim of this manuscript is to apply the methodology proposed in an accompanying part I describing the different sources of variability in the apple cold chain allowing the identification of significant factors on the evolution of apple quality. The methodology uses a deterministic model to predict the evolution of quality (firmness, colour) and stochastic models to account for the variability of product time temperature history, biological properties and initial quality. Hereto, a dedicated field test to obtain a realistic set of time temperature data for the long term controlled atmosphere (CA) storage of apple was conducted. The apple cold chain under consideration in this study comprises the following links: pre-cooling, CA storage, non-refrigerated transport and wholesale. Then, the simulation results, using kinetic models for describing the evolution of firmness and colour as influenced by the time temperature profiles, and following the method presented in part I (global sensitivity analysis and an accept-and-reject algorithm) are analysed. Our research indicated that the product time temperature profile along the cold chain was the most influencing factor on the final apple quality. A refined analysis by the accept-and-reject algorithm revealed the impact of CA storage and pre-cooling.

[Departement_IRSTEA]Ecotechnologies [TR1_IRSTEA]SPEE; High product and air temperatures and moistures are often observed in certain positions of a cold room leading to deterioration of food quality and safety. To reduce food losses, it is necessary to understand heat and mass transfers. However, these transfers are complex phenomena because of the presence of the product (airflow obstacle, heat of respiration...) and the coupling between the transfers and airflow. Temperature and velocity measurements were carried out in a ventilated cold room filled with four apple pallets. Because of the room small dimensions (3.4 x 3.4 x 2.5 m), the cold supply air headed directly to the rear part of the room. Therefore, the rear pallets were submitted to lower air temperatures compared to the front ones. This leads to more rapid product cooling rate and lower product final temperature at the rear. A simplified model was developed. It describes the evolution of product and air temperatures at different zones in the cold room. Good agreement between the predicted and experimental results was found for both product cooling rate and final product temperature.

International audience; Shells fired during World War I exhibited different explosive compounds and some of these weapons also contained a wide variety of chemical warfare agents. At the end of the war, for safety purposes, the large quantity of weapons remaining on the former front needed to be dismantled and destroyed. A large amount of the remaining shells was destroyed in specific sites which led to the contamination of the surroundings in Belgium and France.In the 1920s, 1.5 million chemical shells and 30,000 explosive shells were destroyed in a place close to the city of Verdun, in the East of France. In this paper, the risk for human health related to the consumption of foodstuffs produced on this site was assessed. To this end, food products of plant and animal origin were sampled in 2015-2016 and contaminant analyses were conducted. Human exposure was assessed using a specifically built methodology. The contaminants considered in this study were trace elements (TEs - primarily Zn, As, Pb and Cd), nitroaromatic explosives (trinitrotoluene, 2,4-dinitrotoluene, 2,6-dinitrotoluene, 2-amino-4,6-dinitroluene and 4-amino-2,6-dinitrotoluene), phenylarsenic compounds including diphenylarsinic acid and triphenylarsine, perchlorate, tetrabromoethane and vinyl bromide. Depending on the compound, different approaches were used to assess the risk for both adults and children.Exposure to these contaminants through the consumption of foodstuffs produced locally on the considered site was unlikely to be a health concern. However, as for inorganic arsenic, given the presence of highly contaminated zones, it was suggested that cereals should not be grown on certain plots.

UNLABELLED Four strains were isolated from a spoiled whiting (Merlangius merlangus). All of them were able to grow aerobically from 4 to 30°C and also able to develop anaerobically in the presence of trimethylamine N-Oxide (TMAO) at 25°C. Biochemical characterization did not allow identification of the strains species but showed that one of the four strains was unable to produce H2 S. Two strains synthetized an ornithine decarboxylase being potential putrescine producers. Results of carbon source use highlighted that the four strains were able to use citrate and d-sucrose and one strain was not able to use l-arabinose. Genotypic characterization of the strains thanks to 16S rRNA and gyrB partial gene sequencing led to their identification as members of Shewanella baltica species. These observations suggest that H2 S production may not be the most appropriate screening parameter for Shewanella species and further to monitor the development of spoilage flora. SIGNIFICANCE AND IMPACT OF THE STUDY Shewanella is a complex genus composed of numerous and heterogeneous species. One of them Shewanella baltica has previously been described as one of the most important H2 S-producing bacterial species in iced stored fish and may act as spoilage organism through the reduction of trimethylamine N-Oxide (TMAO). Four strains of S. baltica were isolated from spoiled whiting (Merlangius merlangus), and description of three H2 S-positive strains and one H2 S-negative strain of S. baltica is highlighted in this short paper. Consequently, H2 S production might not be the most appropriate screening parameter to assess the development of spoilage organisms.

Aims Rapid detection of enterohaemorrhagic E. coli O157:H7 in large range of stress conditions occurring in food processing. Methods and Results Detection of E. coli O157:H7 in various food processing stress conditions using surface plasmon resonance imaging (SPRi) technique on an antibody microarray was evaluated. The direct detection method based on the culture/capture/measure (CCM) process consists of detecting bacteria during an enrichment step, which significantly decreases the overall assay duration. In optimized culture conditions, this method allows the specific detection of low CFU ml−1 in

International audience; This work presents the effects of pan cooking on PCBs, PCDD/Fs, pesticides and trace elements in meat from a risk assessment perspective. Three different realistic cooking intensities were studied. A GC_GC-TOF/MS method was set up for the multiresidue analysis of 189 PCBs, 17 PCDD/Fs and 16 pesticides whereas Cd, As, Pb and Hg were assayed by ICP-MS. In terms of quantity, average PCB losses after cooking were 18 ± 5% for rare, 30 ± 3% for medium, and 48 ± 2% for well-done meat. In contrast, average PCDD/F losses were not significant. For pesticides, no loss occurred for aldrin, lindane, DDE or DDD, whereas losses exceeding 80% were found for dieldrin, sulfotep or phorate. Losses close to the margin of error were observed for trace elements. These results are discussed in light of the physicochemical properties of the micropollutants as well as of water and fat losses into cooking juice.

International audience; The aim of this study was to characterize the Listeria monocytogenes biofilm and particularly the nature of the carbohydrates in the biofilm extracellular matrix and culture supernatant versus to cell wall carbohydrates. Listeria monocytogenes serotype 1/2a and 4b strains were able to form complex biofilms embedded in an extracellular matrix. The soluble carbohydrates from biofilm extracellular matrix and culture supernatant were identified as teichoic acids, structurally identical to cell wall teichoic acids. In addition, the DSS 1130 BFA2 strain had a serotype 1/2a teichoic acid lacking N-acetyl glucosamine glycosylation due to a mutation in the lmo2550 gene. Consequently, we hypothesized that the extracellular teichoic acids in L. monocytogenes biofilms have the same origin as cell wall teichoic acid.

Surfaces in industrial settings provide a home for resident biofilms that are likely to interact with the attachment, growth and survival of pathogens such as Listeria monocytogenes. Experimental results have indicated that L. monocytogenes cells were inhibited by the presence of a model resident flora (Lactococcus lactis) in dual-species continuous flow-biofilms, and are spatially restricted to the lower biofilm layers. Using a new, simplified individual-based model (IBM) that simulates bacterial cell growth in a three-dimensional space, the spatial arrangements of the two species were reconstructed and their cell counts successfully predicted. This model showed that the difference in generation times between L. monocytogenes and L. lactis cells during the initial stages of dual-species biofilm formation was probably responsible for the species spatialization observed and the subsequent inhibition of growth of the pathogen.

L'acide rumenique (AR), 18:2 9c,11t, est le principal acide linoleique conjugue (ALC) present dans les produits laitiers. Pour completer les tables de composition des aliments editees par le CIQUAL, l'AFSSA a entrepris plusieurs etudes pour determiner les teneurs en acide rumenique de la matiere grasse laitiere afin d'evaluer la consommation en AR de la population francaise. Lors d'une premiere etude, nous avons analyse 54 beurres francais de fabrications locales sur 7 regions, a differentes saisons de l'annee. Les beurres analyses contiennent en moyenne 0,45 g AR/100 g beurre en hiver, 0,58 au printemps, et 0,80 en ete. Des variations dans les teneurs en AR ont egalement ete constatees entre les differentes regions productrices de beurre. Les beurres issus de laits de regions de collines et de montagnes, et les beurres de Normandie, presentent les taux moyens annuels d'acide rumenique les plus eleves et les variations de plus grandes amplitudes d'une saison a l'autre. Pour completer ces donnees, une deuxieme etude a ete mise en place tout au long d'une annee sur plusieurs produits laitiers. Pendant douze mois, du lait, de la creme issue de ce lait, et du beurre fabrique avec cette creme, ont ete preleves mensuellement dans 5 cooperatives laitieres francaises et analyses pour leurs teneurs en acide rumenique. Globalement, les taux moyens annuels d'acide rumenique en France sont de 0,59 g AR/100 g de matiere grasse pour le lait (s = 0,219, n = 54), de 0,62 g AR/100 g de matiere grasse pour la creme (s = 0,223, n = 57), et de 0,60 g AR/100 g de matiere grasse pour le beurre (s = 0,202, n = 57), toutes saisons et toutes regions confondues. Ces taux d'acide rumenique presentent des differences significatives entre saisons et regions. Les taux d'acide rumenique montrent un minimum en hiver (0,38 AR/100 g de matiere grasse) et un maximum en ete (0,96 g AR/100 g). Les teneurs en acide rumenique varient egalement d'une region a l'autre de 0,48 a 0,69 g AR/100 g de matiere grasse (moyennes annuelles des 2 regions extremes). En revanche, aucune difference significative n'a ete observee entre echantillons de lait, de creme, et de beurre de meme origine (meme region, meme mois). Ces resultats suggerent l'implication de divers parametres sur la production d'acide rumenique par les vaches laitieres, parametres incluant l'alimentation, le mode d'elevage, la race de bovin, etc., qui different d'une region a l'autre. Cependant, l'ecremage du lait, la maturation de la creme, et le barattage lors de la fabrication du beurre ne semblent pas modifier les taux d'acide rumenique de la matiere grasse laitiere.

As a preliminary for recommended trans fatty acid (TFA) consumption levels as regards health, it was essential to estimate the TFA intake level. Recent results of TFA content of foods were collected, and the total TFA, 18:1 TFA, 18:2 TFA and total conjugated linoleic acid (CLA) compositions were recorded for around 900 food items. These results were combined with the latest consumption data in France in order to update the TFA intake level in France. Average daily total TFA intake was about 3.0 and 3.4 g/ day in boys and men, and about 2.7 and 2.8 g/day in girls and women, respectively. The same tendency was observed for TFA 18:1 intake (boys 2.1 g/day, men 2.4 g/day, girls 1.9 g/day, women 2.0 g/day) and for TFA 18:2 (boys 0.2 g/day, men 0.24 g/day, girls 0.18 g/day, women 0.18 g/day). For CLA, the mean daily intake was higher in males than in females for both adults (0.21 g/day vs. 0.18 g/day) and children (0.18 g/ day vs. 0.17 g/day). Foods of animal origin (dairy products and meat from ruminants) were the main contributors of total TFA, accounting for 60% of the identified TFA. Dairy products were the main contributors of total CLA, accounting for 70% of the identified CLA. In other words, manufactured pastries, biscuits, ready meals and chocolate bars accounted for 40% of total TFA and 30% of CLA.

International audience; During the summer of 2010, 31 species including fish, echinoderms, gastropods, crustaceans, cephalopods and sponges were sampled in the Bay of Villefranche on the French Mediterranean coast and screened for the presence of PLTX-group toxins using the haemolytic assay. Liquid chromatography tandem mass spectrometry (LC-MS/MS) was used for confirmatory purposes and to determine the toxin profile. The mean toxin concentration in the whole flesh of all sampled marine organisms, determined using the lower- (LB) and upper-bound (UB) approach was 4.3 and 5.1 µg·kg−1, respectively, with less than 1% of the results exceeding the European Food Safety Authority (EFSA) threshold of 30 µg·kg−1and the highest values being reported for sea urchins (107.6 and 108.0 µg·kg−1). Toxins accumulated almost exclusively in the digestive tube of the tested species, with the exception of octopus, in which there were detectable toxin amounts in the remaining tissues (RT). The mean toxin concentration in the RT of the sampled organisms (fishes, echinoderms and cephalopods) was 0.7 and 1.7 µg·kg−1 (LB and UB, respectively), with a maximum value of 19.9 µg·kg−1 for octopus RT. The herbivorous and omnivorous organisms were the most contaminated species, indicating that diet influences the contamination process, and the LC-MS/MS revealed that ovatoxin-a was the only toxin detected.

International audience; Liver is a reliable matrix for laboratory confirmation of avian botulism using real-time PCR. Here, we developed, optimized, and validated the analytical steps preceding PCR to maximize the detection of Clostridium botulinum group III in avian liver. These pre-PCR steps included enrichment incubation of the whole liver (maximum 25 g) at 37°C for at least 24 h in an anaerobic chamber and DNA extraction using an enzymatic digestion step followed by a DNA purification step. Conditions of sample storage before analysis appear to have a strong effect on the detection of group III C. botulinum strains and our results recommend storage at temperatures below -18°C. Short-term storage at 5°C is possible for up to 24 h, but a decrease in sensitivity was observed at 48 h of storage at this temperature. Analysis of whole livers (maximum 25 g) is required and pooling samples before enrichment culturing must be avoided. Pooling is however possible before or after DNA extraction under certain conditions. Whole livers should be 10-fold diluted in enrichment medium and homogenized using a Pulsifier® blender (Microgen, Surrey, UK) instead of a conventional paddle blender. Spiked liver samples showed a limit of detection of 5 spores/g liver for types C and D and 250 spores/g for type E. Using the method developed here, the analysis of 268 samples from 73 suspected outbreaks showed 100% specificity and 95.35% sensitivity compared with other PCR-based methods considered as reference. The mosaic type C/D was the most common neurotoxin type found in examined samples, which included both wild and domestic birds.

International audience; Nanosized titanium dioxide (TiO2) is one of the most interesting and valuable nanomaterials for the construction industry but also in health care applications, food, and consumer goods, e.g., cosmetics. Therefore, the properties associated with this material are described in detail. Despite its widespread use, the analytical determination and characterization of nanosized metal oxides is not as straightforward as the comparatively easy-to-detect metallic nanoparticles (e.g., silver or gold). This study presents the method development and the results of the determination of tissue titanium (Ti) levels after treatment of rats with the nanosized TiO2. Total Ti levels were chosen to evaluate the presence and distribution of TiO2 nanoparticles. A procedure consisting of incubation with a mixture of nitric acid (HNO3) and hydrofluoric acid (HF), and heating was developed to digest tissues and TiO2 nanomaterials in order to determine the total Ti content by inductively coupled plasma mass spectrometry (ICPMS). For the inter-laboratory comparison, altogether four laboratories analyzed the same samples upon digestion using the available ICPMS equipment. A major premise for any toxicokinetic study is the possibility to detect the chemical under investigation in biological samples (tissues). So, the study has to be performed with a dose high enough to allow for subsequent tissue level measurement of the chemical under investigation. On the other hand, dose of the chemical applied should not induce over toxicity in the animal as this may affect its absorption, distribution, metabolism, and excretion. To determine a non-toxic TiO2 dosage, an acute toxicity study in rats was performed, and the organs obtained were evaluated for the presence of Ti by ICPMS. Despite the differences in methodology and independent of the sample preparation and the ICPMS equipment used, the results obtained for samples with Ti concentrations >4 µg Ti/g tissue agreed well.

This review describes analytical methods developed for the separation, identification and quantitation of trans-isomers of unsaturated fatty acids. Although these methods are applicable to a wide variety of food matrices, we have particularly emph a- sised the analysis of trans unsaturated fatty acids in milk fat. Various methods are described such as infrared spectroscopy, direct gas chromatography, gas chromatography in combination with either thin-layer chromatography or liquid chromatography both impregnated with silver nitrate and gas chromatography coupled with mass spectrometry. The field of application, the advantages and the drawbacks of each method are evaluated and discussed.

International audience; An outbreak of the monophasic variant of Salmonella enterica serotype 4,[5],12:i:- occurred in November and December 2011 in France. Epidemiological investigation and food investigation with the help of supermarket loyalty cards suggested dried pork sausage from one producer as the most likely source of the outbreak. Despite the absence of positive food samples, control measures including withdrawal and recall were implemented.