Whole genome sequences of two Salmonella Dublin strains harbour viaA, viaB and ompB loci of the Vi antigen

Here we report the genome sequence of two Salmonella enterica serovar Dublin, 03EB8736SAL and 03EB8994SAL, isolated from raw milk cheese and filter of milk respectively. Analysis of draft genomes of the two isolates reveals the presence of viaA, viaB and ompB loci of the Vi capsular polysaccharide antigen (Vi antigen)

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

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

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

Halogenase Genes in Nonribosomal Peptide Synthetase Gene Clusters of Microcystis (Cyanobacteria): Sporadic Distribution and Evolution

Cyanobacteria of the genus Microcystis are known to produce secondary metabolites of large structural diversity by nonribosomal peptide synthetase (NRPS) pathways. For a number of such compounds, halogenated congeners have been reported along with nonhalogenated ones. In the present study, chlorinated cyanopeptolin- and/or aeruginosin-type peptides were detected by mass spectrometry in 17 out of 28 axenic strains of Microcystis. In these strains, a halogenase gene was identified between 2 genes coding for NRPS modules in respective gene clusters, whereas it was consistently absent when the strains produced only nonchlorinated corresponding congeners. Nucleotide sequences were obtained for 12 complete halogenase genes and 14 intermodule regions of gene clusters lacking a halogenase gene or containing only fragments of it. When a halogenase gene was found absent, a specific, identical excision pattern was observed for both synthetase gene clusters in most strains. A phylogenetic analysis including other bacterial halogenases showed that the NRPS-related halogenases of Microcystis form a monophyletic group divided into 2 subgroups, corresponding to either the cyanopeptolin or the aeruginosin peptide synthetases. The distribution of these peptide synthetase gene clusters, among the tested Microcystis strains, was found in relative agreement with their phylogeny reconstructed from 16S–23S rDNA intergenic spacer sequences, whereas the distribution of the associated halogenase genes appears to be sporadic. The presented data suggest that in cyanobacteria these prevalent halogenase genes originated from an ancient horizontal gene transfer followed by duplication in the cyanobacterial lineage. We propose an evolutionary scenario implying repeated gene losses to explain the distribution of halogenase genes in 2 NRPS gene clusters that subsequently defines the seemingly erratic production of halogenated and nonhalogenated aeruginosins and cyanopeptolins among Microcystis strains

Lack of Phylogeographic Structure in the Freshwater Cyanobacterium Microcystis aeruginosa Suggests Global Dispersal

Background : Free-living microorganisms have long been assumed to have ubiquitous distributions with little biogeographic signature because they typically exhibit high dispersal potential and large population sizes. However, molecular data provide contrasting results and it is far from clear to what extent dispersal limitation determines geographic structuring of microbial populations. We aimed to determine biogeographical patterns of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa. Being widely distributed on a global scale but patchily on a regional scale, this prokaryote is an ideal model organism to study microbial dispersal and biogeography. Methodology/Principal Findings : The phylogeography of M. aeruginosa was studied based on a dataset of 311 rDNA internal transcribed spacer (ITS) sequences sampled from six continents. Richness of ITS sequences was high (239 ITS types were detected). Genetic divergence among ITS types averaged 4% (maximum pairwise divergence was 13%). Preliminary analyses revealed nearly completely unresolved phylogenetic relationships and a lack of genetic structure among all sequences due to extensive homoplasy at multiple hypervariable sites. After correcting for this, still no clear phylogeographic structure was detected, and no pattern of isolation by distance was found on a global scale. Concomitantly, genetic differentiation among continents was marginal, whereas variation within continents was high and was mostly shared with all other continents. Similarly, no genetic structure across climate zones was detected. Conclusions/Significance : The high overall diversity and wide global distribution of common ITS types in combination with the lack of phylogeographic structure suggest that intercontinental dispersal of M. aeruginosa ITS types is not rare, and that this species might have a truly cosmopolitan distribution

A propos de quelques métabolites remarquables de cynobactéries (cyanopeptoline, aéruginosine et anatoxine-a)

Les cyanobactéries sont des organismes procaryotes photosynthétiques capables de produire de nombreux métabolites secondaires. Cette thèse s intéresse à la caractérisation moléculaire de cyanobactéries productrices de neurotoxines (anatoxine-a et homoanatoxine-a) ainsi qu à la mise en évidence d un gène codant pour une activité halogénase dans les clusters de gènes de biosynthèse des métabolites : cyanopeptoline et aéruginosine. De nombreux cas d'intoxications neurotoxiques d'animaux sauvages et domestiques sont régulièrement reportés en France. Nous avons mis en évidence sur deux sites pour lesquels des épisodes mortels ont été rapportés la présence de neurotoxines de cyanobactéries. Les cyanobactéries productrices d anatoxine-a ont été isolées et déposées dans la collection de cyanobactéries de l Institut Pasteur PCC. La caractérisation phénotypique et génétique des souches axéniques obtenues montre qu il s agit de souches du genre Oscillatoria. Sur la base des séquences codant pour les ARNr16S et ITS (Internal Transcribed Spacer) les relations phylogénétiques des nouvelles souches neurotoxiques au sein du genre Oscillatoria ont été étudiées. Une étude du contenu métabolique en cyanopeptoline et aéruginosine et de la présence des leur clusters de gènes de biosynthèse a été entreprise chez une trentaine de souches de Microcystis. Elle a permis de mettre en évidence la présence d halométabolites et d identifier les gènes portant l activité halogénase au sein des clusters aer et mcn. L histoire évolutive des clusters aer et mcn au sein du genre Microcystis a été reconstituée par analyse des séquences ITS. Le gène halogénase semble avoir été acquis par la cyanobactérie probablement d'une protéobactérie ancestrale par transfert horinzontal.PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

24 - Distribution spatiale journalière du corégone lors d'un bloom de Planktothrix rubescens : une voie directe d'accumulation de microcystine

National audienceDepuis les années 90, le lac du Bourget connaît des efflorescences de la cyanobactérie Planktothrix rubescens. Cette espèce est capable de produire une hépatotoxine, la microcystine. Dans de nombreux milieux, lors d’épisodes de blooms, cette toxine est retrouvée dans divers organes de nombreuses espèces de poissons, induisant des dommages physiologiques notables et des mortalités parfois importantes en cas de sénescence du bloom. Toutefois, les données sur l'exposition des poissons à cette toxine en milieu naturel sont peu nombreuses. La comparaison de la distribution spatiale de P. rubescens et des espèces piscicoles exploitées sur le lac (Perches et Corégones) est donc nécessaire pour déterminer si les poissons évitent ou se concentrent dans les zones touchées par les cyanobactéries. De Juin à Novembre 2009, les distributions spatiales diurnes de P. rubescens et des corégones (Coregonus lavaretus) ont été suivies à l’aide d’une sonde BBE et d’un échosondeur. Ainsi, les distributions verticales et horizontales ont été comparées pour toutes les dates d’échantillonnages. Les résultats montrent que les abondances de P. rubescens ont été maximales entre la fin du mois de juillet et le début du mois de Septembre. Durant cette période, P. rubescens se stratifie verticalement dans la colonne d’eau avec un maximum d’abondance situé entre 14 et 22 mètres en fonction des stations d’échantillonnages. A l’échelle horizontale, la distribution de P .rubescens est hétérogène sur l’ensemble du lac. Les données sur la distribution du corégone indiquent que pendant la journée, cette espèce est présente dans la couche d’eau située entre 15 et 30 mètres, couche d’eau où était également présent le pic de P. rubescens. De plus, le corégone ne semble ni éviter, ni au contraire être plus présent dans les zones de fortes abondances en P. rubescens. Les efflorescences de P. rubescens, aux concentrations observées, n’exercent donc pas de pression sur le schéma de répartition spatiale du corégone Par ailleurs, des filaments de P. rubescens ont été trouvés dans les contenus stomacaux de plusieurs corégones capturés par la pêche professionnelle et des toxines ont été mesurées dans divers organes. Ces derniers résultats indiquent qu’en raison du contact direct entre les poissons et les algues, la toxine peut facilement être accumulée dans le corégone par cette ingestion directe de filaments de P. rubescens, et donc conduire à des risques physiologiques pour cette espèce