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

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

Spatial match between Planktothrix rubescens and whitefish in a mesotrophic peri-alpine lake : Evidence of toxins accumulation

International audienceLake Bourget (France) provides drinking water and is a place for professional and recreational fishing. Since the mid 1990s, the lake has been exhibiting blooms of the filamentous cyanobacterium Planktothrix rubescens. This species is able to produce microcystin-LR and RR, toxins that contaminate different fish tissues and, if concentrated in the liver, can induce fish mortality. However, data on fish exposure to these toxins in a natural environment are scare and comparisons of spatial distribution between P. rubescens and exploited fish are needed to determine whether these fish avoid or converge in zones affected by the cyanobacteria. From June to November 2009, diurnal data on P. rubescens and whitefish (Coregonus lavaretus) spatial distributions have been monitored by hydroacoustic and BBE probe sampling. For all water samples, intracellular microcystin concentration of P. rubescens was quantified by HPLC/PDA. Furthermore, an arbitrary sample of eight whitefish captured at the moment of highest P. rubescens concentration in the lake were analyzed to investigate both the presence of this cyanobacterium in the gastrointestinal tract by optical microscopy and the possible bioaccumulation of the microcystin in their tissues by liquid chromatography–tandem mass spectrometry. Results show that P. rubescens abundance was at a maximum between the end of July and the beginning of September. During this period, P. rubescens abundance was vertically stratified with a maximum around 14–22 m, depending on the sampling station. The horizontal distributions of P. rubescens were heterogeneous at the scale of the lake. Results indicate that the presence of P. rubescens, for the observed cyanobacterial abundance, does not exert a significant pressure on the distribution pattern of the whitefish. Whitefish were present in the same areas as P. rubescens maxima during daytime, and they do not avoid or seek out the zone of high P. rubescens abundance. Filaments of P. rubescens have been observed in intestinal tracts of whitefish and the presence of microcystin-LR has been detected in their intestine and liver. Consequently, because of a direct contact between these organisms, toxins can be incorporated into whitefish by ingestion of P. rubescens filaments, leading to potential adverse effects on the health of this species

Identification of a Polyketide Synthase Coding Sequence Specific for Anatoxin-a-Producing Oscillatoria Cyanobacteria▿ †

We report the identification of a sequence from the genome of Oscillatoria sp. strain PCC 6506 coding for a polyketide synthase. Using 50 axenic cyanobacteria, we found this sequence only in the genomes of Oscillatoria strains producing anatoxin-a or homoanatoxin-a, indicating its likely involvement in the biosynthesis of these toxins

Different Genotypes of Anatoxin-Producing Cyanobacteria Coexist in the Tarn River, France▿ †

Repeated dog deaths occurred in 2002, 2003, and 2005 after the animals drank water from the shoreline of the Tarn River in southern France. Signs of intoxication indicated acute poisoning due to a neurotoxin. Floating scum and biofilms covering pebbles were collected in the summers of 2005 and 2006 from six different sites along 30 km from the border of this river. The cyanobacterial neurotoxic alkaloid anatoxin-a and/or its methyl homolog, homoanatoxin-a, was detected in the extracts of most samples examined by gas chromatography-mass spectrometry. Fifteen filamentous cyanobacteria of the order Oscillatoriales were isolated and displayed four distinct phenotypes based on morphological characteristics and pigmentation. Three of the phenotypes can be assigned to the genus Oscillatoria or Phormidium, depending on the taxonomic treatises (bacteriological/botanical) employed for identification. The fourth phenotype is typical of the genus Geitlerinema Anagnostidis 1989. Eight strains rendered axenic were analyzed for production of anatoxin-a and homoanatoxin-a, and all strains of Oscillatoria/Phormidium proved to be neurotoxic. The genetic relatedness of the new isolates was evaluated by comparison of the intergenic transcribed spacer sequences with those of six oscillatorian strains from the Pasteur Culture Collection of Cyanobacteria. These analyses showed that the neurotoxic representatives are composed of five different genotypes, three of which correspond to phenotypes isolated in this study. Our findings prove that neurotoxic oscillatorian cyanobacteria exist in the Tarn River and thus were most likely implicated in the reported dog poisonings. Furthermore, they reemphasize the importance of monitoring benthic cyanobacteria in aquatic environments to fully assess the health risks associated with these organisms

Source Attribution Study of Sporadic Salmonella Derby Cases in France

International audienceSalmonella enterica subsp. enterica serovar Derby is one of the most frequent causes of gastroenteritis in humans. In Europe, this pathogen is one of the top five most commonly reported serovars in human cases. In France, S. Derby has been among the ten most frequently isolated serovars in humans since the year 2000. The main animal hosts of this serovar are pigs and poultry, and white meat is the main source of human contamination. We have previously shown that this serovar is polyphyletic and that three distinct genetic lineages of S. Derby cohabit in France. Two of them are associated with pork and one with poultry. In this study, we conducted a source attribution study based on single nucleotide polymorphism analysis of a large collection of 440 S. Derby human and non-human isolates collected in 2014-2015, to determine the contribution of each lineage to human contamination. In France, the two lineages associated with pork strains, and corresponding to the multilocus sequence typing (MLST) profiles ST39-ST40 and ST682 were responsible for 94% of human contaminations. Interestingly, the ST40 profile is responsible for the majority of human cases (71%). An analysis of epidemiologic data and the structure of the pork sector in France allowed us to explain the spread and the sporadic pattern of human cases that occurred in the studied period