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Diversité génomique de Salmonella Derby en France

Abstract : Salmonella enterica is the leading cause of human zoonosis in the European Union and represents a major public health issue. Salmonella enterica subsp. enterica serovar Derby (S. Derby) is one of the most frequently isolated serovar in food and more particularly in the pig and poultry sectors. It also belongs to the 5 most frequently isolated serovars from human clinical cases in Europe. Despite the threat posed by Derby serovar to human health, the genetic structure of the S. Derby population is poorly understood. This is due to the low discriminating power of the reference technique (PFGE) used for the Salmonella subtyping against Derby serovar but also to the lack of representatively of the collections that have been selected in previous studies.The objectives of my study are: 1/ to study the genetic diversity and structure of the Salmonella Derby population in France by sequencing the entire genome 2/ to use genomic data to conduct effective and accurate subtyping of sporadic cases attributed to S. Derby and 3/ to advance the understanding of S. Derby transmission from animal to human and its host specificity for pig and poultry.A collection of strains representative of the genetic diversity of S. Derby has been compiled with a one health approach, including both human clinical strains and strains isolated in the two animal sectors where Salmonella Derby has a higher prevalence. From the strain Collections of LSAl and Institut Pasteur, 140 food and 302 human strains of S. Derby respectively, have been selected for the years 2014 and 2015.The genomes of 442 strains were sequenced and the analysis of variants of the core genome (SNP, single nucleotide substitution) allowed us to study their genetic diversity. The results demonstrate the polyphyletic nature of the Derby serovar with 3 genetically distant lineages. Four different MLST profiles were identified within the strains analysed (ST39, ST40, ST71 and ST682).In France, S. Derby is divided into 3 lineages that we chose to call ST39-40, ST71 and ST682 with reference to the MLST profiles identified. These lineages are separated by an average of 15k SNP. The ST40, associated with the pork industry, accounts for 71% of human cases. On the other hand, ST71, associated with the poultry sector, accounts for only 2% of human cases. This study enabled us to attribute 93% of human clinical cases to S. Derby to the pig sector.To explain these results, a bioinformatics study of the pangenome of the strains in the collection was conducted. The genetic diversity of key Salmonella virulence factors as well as antibiotic resistance profiles were studied to determine the virulence potential of each lineage and to propose molecular hypotheses on their adaptation to the two hosts: pig and poultry. These genomic investigations were supplemented by cell invasion tests on human, porcine and avian epithelial cells.Pangenome analysis confirms significant differences in the presence or absence of virulence genes, and highlights allelic differences for genes associated with host specificity and intracellular survival. A major antibiotic resistance profile is present within the ST40 strains and ST39-40 lineage is characterized by a unique pathogenicity island, the SPI-23, known to facilitate invasion in pigs. Cell invasion tests confirm a limited ability of ST71 strains to invade human epithelial cells.
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Yann Sévellec. Diversité génomique de Salmonella Derby en France. Microbiologie et Parasitologie. Institut agronomique, vétérinaire et forestier de France, 2018. Français. ⟨NNT : 2018IAVF0022⟩. ⟨tel-03392473⟩

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