Genetic Diversity of Salmonella Derby from the Poultry Sector in Europe

Abstract

Salmonella 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.

Source Attribution Study of Sporadic Salmonella Derby Cases in France

“…As demonstrated in our previous study (Sévellec et al, 2019) within the poultry sector, we were able to group separately two human strains (201402459 and 201507219) from the other FIGURE 2 | Phylogenetic tree of the French Salmonella Derby isolates belonging to ST40. (A) Complete phylogenetic tree: two clades can be identified within Cluster ST40.…”

“…These strains are all characterized by a particular antibacterial resistance gene profile (STR SMX TET TMP) ( Supplementary Figure S1). As already highlighted in a previous study (Sévellec et al, 2019), the analysis of the accessory genome (i.e., via the antimicrobial resistance gene profiles) is complementary to coregenome analysis, and is highly recommended when the objective is to establish links between food and human isolates within low-diversity clades.…”

“…CP029486) (Sévellec et al, 2018a) was used as a reference for the ST40 and ST39 analysis (average breath coverage of 99.9 and 96.4%, respectively) and the genome of strain 2014LSAL01779 (NCBI no. CP026609) (Sévellec et al, 2019) was used as a reference for the ST71 analysis (average breath coverage of 99.9%). In the absence of a complete genome for ST682, S. Typhimurium LT2 (NCBI NC_003197.1) was used as a reference (average breath coverage of 91.6%).…”

“…Salmonella enterica subsp. enterica serovar Derby (S. Derby) is one of the serovars that mainly affects at-risk populations, such as children and the elderly (Rubbo, 1948;Sanders et al, 1963; (ST71) (Sévellec et al, 2018b(Sévellec et al, , 2019. The high prevalence of S. Derby in these two sectors, which account for two-thirds of meat consumption in France, highlights the need to clarify the source of sporadic human cases of S. Derby.…”

AB_SA: Tracing the source of bacterial strains based on accessory genes. Application toSalmonellaTyphimurium environmental strains

“…Indeed, closely related strains can be found in multiple hosts challenging the association to a specific source by phylogenetic clustering (7). A particular case showing the utility of phylogenetic methods in the attribution of human salmonellosis to specific sources (e.g., turkey), by using epidemiological and genomic data, has been reported through the investigation of Salmonella Derby genetic diversity (8).…”