A multiplex real-time PCR assay targeting virulence and resistance genes in Salmonella enterica serotype Typhimurium

<p>Abstract</p> <p>Background</p> <p>Typhimurium is the main serotype of <it>Salmonella enterica </it>subsp. <it>enterica </it>implicated in food-borne diseases worldwide. This study aimed to detect the prevalence of ten markers combined in a macro-array based on multiplex real-time PCR. We targeted characteristic determinants located on pathogenicity islands (SPI-2 to -5, virulence plasmid <it>pSLT </it>and <it>Salmonella </it>genomic island 1 (SGI1)) as well as a specific 16S-23S rRNA intergenic spacer sequence of definitive type 104 (DT104). To investigate antimicrobial resistance, the study also targeted the presence of genes involved in sulfonamide (<it>sul1</it>) and beta-lactam (<it>bla</it>_TEM) resistance. Finally, the <it>intI1 </it>determinant encoding integrase from class 1 integron was also investigated.</p> <p>Results</p> <p>A total of 538 unrelated <it>S</it>. Typhimurium strains isolated between 1999 and 2009 from various sources, including food animals, food products, human and environmental samples were studied. Based on the combined presence or absence of these markers, we distinguished 34 different genotypes, including three major genotypes encountered in 75% of the studied strains, Although SPI determinants were almost always detected, SGI1, <it>intI1</it>, <it>sul1 </it>and <it>bla</it>_TEMdeterminants were found 47%, 52%, 54% and 12% of the time respectively, varying according to isolation source. Low-marker patterns were most often detected in poultry sources whereas full-marker patterns were observed in pig, cattle and human sources.</p> <p>Conclusion</p> <p>The GeneDisc^®assay developed in this study madeit easier to explore variability within serotype Typhimurium by analyzing ten relevant gene determinants in a large collection of strains. This real-time multiplex method constitutes a valuable tool for strains characterization on epidemiological purposes.</p

Comment inciter les entreprises à afficher les impacts environnementaux sur les produits de grande consommation ?:Les leviers d’une politique publique « d’affichage volontaire encadré »

Ce policy brief analyse la politique publique française en matière d’affichage environnemental. Cette politique publique a été initiée en 2009 à la suite du Grenelle de l’Environnement et a été réactivée en 2018 dans le cadre d’une action de déploiement sur cinq secteurs économiques. L’objectif de cette politique publique est d’encourager les entreprises à afficher les impacts environnementaux des produits qu’elles mettent en marché. Elle se heurte à d’importantes résistances du monde économique qui se montre réticent à s’engager dans des actions d’évaluation des impacts environnementaux jugées à la fois coûteuses à mettre en œuvre et insuffisamment stabilisées sur un plan technique. A l’heure où les politiques d’affichage sur les produits tendent à se multiplier (affichage nutritionnel, affichage énergie, affichage carbone, affichage sur la durée de vie), nous revenons sur les spécificités d’une action publique, faiblement dotée en ressources financières, politiques ou légales, qui cherche à inciter les entreprises à plus de responsabilité. Nous montrons que cette politique publique repose sur un socle législatif faiblement coercitif mais susceptible de faire évoluer les intérêts de certains acteurs privés. Nous suggérons que les pouvoirs publics construisent des alliances stratégiques avec certains acteurs privés afin d’activer des leviers au sein des rapports de concurrence ou des rapports de force marchands susceptibles de produire des effets d’entrainement. C’est précisément la co-construction publique-privée de cette politique publique qui la rend acceptable pour le monde économique. Nous revenons sur les enjeux et points critiques d'une politique publique, qui, même si elle n'est pas encore généralisée, a montré une certaine efficacité dans sa capacité à mobiliser les entreprises.The present policy brief analyses a French public policy aiming at encouraging companies to display on labels the environmental impacts of their products. This public policy was initiated in 2009 after President Sarkozy’s election but has recently been reactivated in 2018 when the government decided a national implementation within five industries. The public policy was seriously contested by economic actors, which considered product environmental assessment as too costly and based on insufficiently stabilized knowledge. Today, consumer information public policies are becoming increasingly common: nutritional labelling, environmental footprint labelling, energy labels, product lifetime labelling. How can these public policies, which have limited financial, political and legal resources, achieve any efficiency to convince corporations to engage in changes they are reluctant to make? We demonstrate that this public policy relies on a weak coercive legislative basis but with strong capacity to modify the interests of some of the private actors. We also show how public deciders make strong allies within different types of economic actors, in order to activate levers through competition dynamics or supply chains relationships. This public-private public policy instrument building process contributes to strengthen the capacity of the public policy. Finally, we question the stakes and critical points of this public policy, which has not achieved a widespread implementation so far, but has demonstrated its ability to engage companies in environmental improvements

Genetic Diversity of Salmonella Derby from the Poultry Sector in Europe

International audienceSalmonella Derby (S. Derby) is emerging in Europe as a predominant serovar in fattening turkey flocks. This serovar was recorded as being predominant in the turkey sector in 2014 in the United Kingdom (UK). Only two years later, in 2016, it was also recorded in the turkey and broiler sectors in Ireland and Spain. These S. Derby isolates were characterised as members of the multilocus sequence type (MLST) profile 71 (ST71). For the first time, we characterise by whole genome sequencing (WGS) analysis a panel of 90 S. Derby ST71 genomes to understand the routes of transmission of this emerging pathogen within the poultry/turkey food trade. Selected panel included strains isolated as early as 2010 in five leading European g countries for turkey meat production. Twenty-one of the 90 genomes were extracted from a public database-Enterobase. Five of these originated from the United States (n=3), China (n=1) and Taiwan (n=1) isolated between 1986 and 2016. A phylogenomic analysis at the core-genome level revealed the presence of three groups. The largest group contained 97.5% of the European strains and included both, turkey and human isolates that were genetically related by an average of 35 ± 15 single nucleotide polymorphism substitutions (SNPs). To illustrate the diversity, the presence of antimicrobial resistance genes and phages were characteised in 30, S. Derby ST71 genomes, including 11 belonging to this study This study revealed an emergent turkey-related S. Derby ST71 clone circulating in at least five European countries (the UK, Germany, Poland, Italy, and France) since 2010 that causes human gastroenteritis. A matter of concern is the identification of a gyrA mutation involved in resistance to quinolone, present in the Italian genomes. Interestingly, the diversity of phages seems to be related to the geographic origins. These results constitute a baseline for following the spread of this emerging pathogen and identifying appropriate monitoring and prevention measures

Carbapenem-Resistant Bacteria Recovered from Faeces of Dairy Cattle in the High Plains Region of the USA

OBJECTIVE:A study was conducted to recover carbapenem-resistant bacteria from the faeces of dairy cattle and identify the underlying genetic mechanisms associated with reduced phenotypic susceptibility to carbapenems. METHODS:One hundred and fifty-nine faecal samples from dairy cattle were screened for carbapenem-resistant bacteria. Phenotypic screening was conducted on two media containing ertapenem. The isolates from the screening step were characterised via disk diffusion, Modified Hodge, and Carba NP assays. Carbapenem-resistant bacteria and carbapenemase-producing isolates were subjected to Gram staining and biochemical testing to include Gram-negative bacilli. Whole genome sequencing was performed on bacteria that exhibited either a carbapenemase-producing phenotype or were not susceptible to ertapenem and were presumptively Enterobacteriaceae. RESULTS:Of 323 isolates collected from the screening media, 28 were selected for WGS; 21 of which were based on a carbapenemase-producing phenotype and 7 were presumptively Enterobacteriaceae and not susceptible to ertapenem. Based on analysis of WGS data, isolates included: 3 Escherichia coli harbouring blaCMY-2 and truncated ompF genes; 8 Aeromonas harbouring blacphA-like genes; 1 Acinetobacter baumannii harbouring a novel blaOXA gene (blaOXA-497); and 6 Pseudomonas with conserved domains of various carbapenemase-producing genes. CONCLUSIONS:Carbapenem resistant bacteria appear to be rare in cattle. Nonetheless, carbapenem-resistant bacteria were detected across various genera and were found to harbour a variety of mechanisms conferring reduced susceptibility. The development and dissemination of carbapenem-resistant bacteria in livestock would have grave implications for therapeutic treatment options in human medicine; thus, continued monitoring of carbapenem susceptibility among enteric bacteria of livestock is warranted

Chapitre 3. Les activités

I- Gestion de l’eau (Frédéric Marty, Brice Chevaux, Sophie Ledrole, Jean-Marc Féménias) L’approvisionnement en eau est assuré par cinq puits. Leur localisation et leur faible diamètre permettent de leur attribuer un statut privé. Deux sont clairement localisés dans l’angle d’une cour (bât. 1 : 2196 ; bât. 11 : 185). Le puits 3082 se trouve coincé entre le hangar 52 et la pièce 54, dans un espace ouvert étroit correspondant à la cour du bâtiment 16, considérablement réduite après la constructi..

Establishing Streptomycin Epidemiological Cut-Off Values for Salmonella and Escherichia coli

This study was conducted to elucidate the accuracy of the current streptomycin epidemiological cut-off value (ECOFF) for Escherichia coli and Salmonella spp. A total of 236 Salmonella enterica and 208 E. coli isolates exhibiting MICs between 4 and 32¿mg/L were selected from 12 countries. Isolates were investigated by polymerase chain reaction for aadA, strA, and strB streptomycin resistance genes. Out of 236 Salmonella isolates, 32 (13.5%) yielded amplicons for aadA (n¿=¿23), strA (n¿=¿9), and strB (n¿=¿11). None of the 60 Salmonella isolates exhibiting MIC 4¿mg/L harbored resistance genes. Of the Salmonella isolates exhibiting MICs 8¿mg/L, 16¿mg/L, and 32¿mg/L, 1.6%, 15%, and 39%, respectively, tested positive for one or more genes. For most monitoring programs, the streptomycin ECOFF for Salmonella is wild type (WT) =32 or =16¿mg/L. A cut-off value of WT =32¿mg/L would have misclassified 13.5% of the strains as belonging to the WT population, since this proportion of strains harbored resistance genes and exhibited MICs =32¿mg/L. Out of 208 E. coli strains, 80 (38.5%) tested positive for aadA (n¿=¿69), strA (n¿=¿18), and strB (n¿=¿31). Of the E. coli isolates exhibiting MICs of 4¿mg/L, 8¿mg/L, 16¿mg/L, and 32¿mg/L, 3.6%, 17.6%, 53%, and 82.3%, respectively, harbored any of the three genes. Based on the European Committee on Antimicrobial Susceptibility Testing guidelines (ECOFF =16¿mg/L), 25% of the E. coli strains presenting MIC =16¿mg/L would have been incorrectly categorized as belonging to the WT population. The authors recommend an ECOFF value of WT =16¿mg/L for Salmonella and WT =8¿mg/L for E. coli

Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes

International audiencePlasmid-mediated colistin resistance mechanisms have been identified worldwide in the past years. A multiplex polymerase chain reaction (PCR) protocol for detection of all currently known transferable colistin resistance genes (mcr-1 to mcr-5, and variants) in Enterobacteriaceae was developed for surveillance or research purposes. Methods: We designed four new primer pairs to amplify mcr-1, mcr-2, mcr-3 and mcr-4 gene products and used the originally described primers for mcr-5 to obtain a stepwise separation of ca 200 bp between amplicons. The primer pairs and amplification conditions allow for single or multiple detection of all currently described mcr genes and their variants present in Enterobacteriaceae. The protocol was validated testing 49 European Escherichia coli and Salmonella isolates of animal origin. Results: Multiplex PCR results in bovine and porcine isolates from Spain, Germany, France and Italy showed full concordance with whole genome sequence data. The method was able to detect mcr-1, mcr-3 and mcr-4 as singletons or in different combinations as they were present in the test isolates. One new mcr-4 variant, mcr-4.3, was also identified. Conclusions: This method allows rapid identification of mcr-positive bacteria and overcomes the challenges of phenotypic detection of colistin resistance. The multiplex PCR should be particularly interesting in settings or laboratories with limited resources for performing genetic analysis as it provides information on the mechanism of colistin resistance without requiring genome sequencing

Une agglomération rurale gallo-romaine des rives de l’Étang de Berre

En 2011, une fouille archéologique préventive réalisée à Istres, au pied de la colline du Castellan n, a mis au jour les vestiges d’une agglomération rurale gallo-romaine, qui prend la suite d’une agglomération de hauteur des premier et second âges du fer, avant d’être démantelée par des récupérateurs de matériaux à la fin du IVe siècle ou au début du Ve siècle. Idéalement située dans l’environnement varié à proximité de l’étang de Berre, de la plaine de la Crau, des zones humides de Camargue et de la Méditerranée, cette agglomération a su tirer parti des ressources naturelles disponibles et de sa proximité avec le port antique de Fos, lieu d’échange des produits du commerce maritime. Les bâtiments, leurs aménagements et le mobilier révèlent la vie quotidienne et les pratiques culturelles d’une population gauloise rurale. La découverte de deux sépultures et d’un bûcher placés au plus près des vivants témoigne également des coutumes funéraires locales. Au total, ces investigations renouvellent profondément notre vision de l’occupation du territoire et des modes de peuplement à l’ouest de l’étang de Berte. Aux villae, établissements et bergeries viennent désormais s’ajourer de petites agglomérations qui trouvent leur place dans le maillage territorial