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Maisons-Alfort, France

Knutsson R.,SVA National Veterinary Institute | van Rotterdam B.,RIVM National Institute for Public Health and the Environment | Fach P.,AFSSA French Food Safety Agency | De Medici D.,National Reference Center for Botulism | And 10 more authors.
International Journal of Food Microbiology | Year: 2011

A next frontier of the global food safety agenda has to consider a broad spectrum of bio-risks, such as accidental and intentional contaminations in the food and feed chain. In this article, the background for the research needs related to biotraceability and response to bioterrorism incidents are outlined. Given the current scale of international trade any response need to be considered in an international context. Biotraceability (e.g. the ability to use downstream information to point to processes or within a particular food chain that can be identified as the source of undesirable agents) is crucial in any food-born outbreak and particular in the response to bioterrorism events. In the later case, tested and proven biotraceability improves the following: (i) international collaboration of validated tracing tools and detection methods, (ii) multi-disciplinary expertise and collaboration in the field of food microbiology and conceptual modeling of the food chain, (iii) sampling as a key step in biotracing (iv) optimized sample preparation procedures, including laboratory work in Biosafety level 3 (BSL-3) laboratories, (v) biomarker discovery for relevant tracing and tracking applications, and (vi) high-throughput sequencing using bio-informatic platforms to speed up the characterization of the biological agent. By applying biotraceability, the response phase during a bioterrorism event may be shortened and is facilitated for tracing the origin of biological agent contamination. © 2010 Elsevier B.V.

Segerman B.,National Veterinary Institute SVA | De Medici D.,University of Veterinary Medicine Vienna | Ehling Schulz M.,National Reference Center for Botulism | Fach P.,AFSSA French Food Safety Agency | And 5 more authors.
International Journal of Food Microbiology | Year: 2011

The rapid technological development in the field of parallel sequencing offers new opportunities when tracing and tracking microorganisms in the food and feed chain. If a bioterror organism is deliberately spread it is of crucial importance to get as much information as possible regarding the strain as fast as possible to aid the decision process and select suitable controls, tracing and tracking tools. A lot of efforts have been made to sequence multiple strains of potential bioterror organisms so there is a relatively large set of reference genomes available. This study is focused on how to use parallel sequencing for rapid phylogenomic analysis and screen for genetic modifications. A bioinformatic methodology has been developed to rapidly analyze sequence data with minimal post-processing. Instead of assembling the genome, defining genes, defining orthologous relations and calculating distances, the present method can achieve a similar high resolution directly from the raw sequence data. The method defines orthologous sequence reads instead of orthologous genes and the average similarity of the core genome (ASC) is calculated. The sequence reads from the core and from the non-conserved genomic regions can also be separated for further analysis. Finally, the comparison algorithm is used to visualize the phylogenomic diversity of the bacterial bioterror organisms Bacillus anthracis and Clostridium botulinum using heat plot diagrams. © 2010 Elsevier B.V.

Freisling H.,International Agency for Research on Cancer | Fahey M.T.,University of Cambridge | Moskal A.,International Agency for Research on Cancer | Ocke M.C.,National Institute for Public Health and the Environment | And 39 more authors.
Journal of Nutrition | Year: 2010

Until recently, the study of nutrient patterns was hampered at an international level by a lack of standardization of both dietary methods and nutrient databases. We aimed to describe the diversity of nutrient patterns in the European Prospective Investigation into Cancer and Nutrition (EPIC) study at population level as a starting point for future nutrient pattern analyses and their associations with chronic diseases in multi-center studies. In this cross-sectional study, 36,034 persons aged 35-74 y were administered a single, standardized 24-h dietary recall. Intake of 25 nutrients (excluding intake from dietary supplements) was estimated using a standardized nutrient database. We used a graphic presentation of mean nutrient intakes by region and sex relative to the overall EPIC means to contrast patterns within and between 10 European countries. In Mediterranean regions, including Greece, Italy, and the southern centers of Spain, the nutrient pattern was dominated by relatively high intakes of vitamin E and monounsaturated fatty acids (MUFA), whereas intakes of retinol and vitamin D were relatively low. In contrast, in Nordic countries, including Norway, Sweden, and Denmark, reported intake of these same nutrients resulted in almost the opposite pattern. Population groups in Germany, The Netherlands, and the UK shared a fatty acid pattern of relatively high intakes of PUFA and SFA and relatively low intakes of MUFA, in combination with a relatively high intake of sugar. We confirmed large variability in nutrient intakes across the EPIC study populations and identified 3 main region-specific patterns with a geographical gradient within and between European countries. © 2010 American Society for Nutrition.

Bugarel M.,AFSSA French Food Safety Agency | Beutin L.,Federal Institute for Risk Assessment BfR | Fach P.,AFSSA French Food Safety Agency
Applied and Environmental Microbiology | Year: 2010

Rapid and specific detection of Shiga toxin-producing Escherichia coli (STEC) strains with a high level of virulence for humans has become a priority for public health authorities. This study reports on the development of a low-density macroarray for simultaneously testing the genes stx1, stx2, eae, and ehxA and six different nie genes issued from genomic islands OI-122 (ent, nleB, and nleE) and OI-71 (nleF, nleH1-2, and nleA). Various strains of E. coli isolated from the environment, food, animals, and healthy children have been compared with clinical isolates of various seropathotypes. The eae gene was detected in all enteropathogenic E. coli (EPEC) strains as well as in enterohemorrhagic E. coli (EHEC) strains, except in EHEC 091:1121 and EHEC O113:H21. The gene ehxA was more prevalent in EHEC (90%) than in STEC (42.66%) strains, in which it was unequally distributed. The nie genes were detected only in some EPEC and EHEC strains but with various distributions, showing that nie genes are strain and/or serotype specific, probably reflecting adaptation of the strains to different hosts or environmental niches. One characteristic nie gene distribution in EHEC O157: [H7], 0111:[H8], O26:[H11], 0103:H25, 0118:[H16], O121:[H19], 05:H-, 055:H7, 0123:H11, 0172:H25, and O165:1125 was ent/espL2, nleB, nleE, nleF, nleH1-2, nleA. (Brackets indicate genotyping of tne flic or rfb genes.) A second nie pattern (ent/espL2, nleB, nleE, nleH1-2) was characteristic of EHEC O103:H2,0145:[H28], 045:H2, and O15:H2. The presence of eae, ent/espL2, nleB, nleE, and nleH1-2 genes is a clear signature of STEC strains with high virulence for humans. Copyright © 2010, American Society for Microbiology. All Rights Reserved.

Schultz A.C.,Technical University of Denmark | Perelle S.,AFSSA French Food Safety Agency | Di Pasquale S.,Istituto Superiore di Sanita | Kovac K.,University of Ljubljana | And 4 more authors.
International Journal of Food Microbiology | Year: 2011

Enteric viruses, including norovirus (NoV) and hepatitis A virus (HAV), have emerged as a major cause of waterborne outbreaks worldwide. Due to their low infectious doses and low concentrations in water samples, an efficient and rapid virus concentration method is required for routine control. Three newly developed methods, A, B and C, for virus concentration in bottled water were compared against the reference method D: (A) Convective Interaction Media (CIM) monolithic chromatography; filtration of viruses followed by (B) direct lysis of viruses on membrane; (C) concentration of viruses by ultracentrifugation; and (D) concentration of viruses by ultrafiltration, for each methods' (A, B and C) efficacy to recover 10-fold dilutions of HAV and feline calicivirus (FCV) spiked in bottles of 1.5L of mineral water. Within the tested characteristics, all the new methods showed better performance than method D. Methods A, B and C shared a limit of detection (LOD50) of nine 50%-tissue culture infectious dose (TCID50) of FCV/1.5L, but differed with regard to the LOD50's of HAV with 45, 361 and 3607 TCID50/1.5L, respectively, and the percentage of recoveries of HAV/FCV with 34/6, 32/25 and 0.3/0.5, respectively. Method B resulted in significantly (p<0.0001) lower Ct-values for both HAV and FCV relative to the reference method D than any of the other methods. The most efficient method (B) was evaluated through a collaborative trial by five laboratories for the detection of HAV, FCV and NoV genogroup I and II (GI and GII), which resulted in the corresponding average LOD50's and percentage of recoveries: 211 TCID50/1.5L and 51% for HAV; 66 TCID50/1.5L and 34% for FCV; 9 reverse transcriptase-PCR Units (RT-PCR U)/1.5L and 61% for NoV GI and 286 RT-PCR U/1.5L and 35% for NoV GII. The results indicate that method B could be considered robust enough for routine control and useful for harmonized data generation. © 2010 Elsevier B.V.

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