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.
Highlights
Derby sequence type (MLST) profile 71 (ST71) genomes were closely related, with an average of 82 single nucleotide polymorphism substitutions (SNPs) and a standard deviation (SD) of 64 SNPs even though the isolates came from different continents and origins
More strains from the United States and Asia would reinforce our conclusion, the study suggests that the three identified ST71 Derby groups were in accordance with the geographic distribution
The first group included two strains from the USA, the second grouped one strain study suggests that the three identified ST71 Derby groups were in accordance with the geographic distribution of the strains (Figure 1)
Summary
The European Union (EU) is a major producer of turkey meat worldwide with 80% of production supplied by six countries: Germany, France, Poland, Italy, Spain, and the United Kingdom (UK). 2014 the UK has consistently reported high occurrence of Salmonella enterica subsp. Derby) in the turkey sector compared to other countries [1,2,3]. Derby was identified in 64.4% of the pig isolates and 32% of the poultry isolates distributed in 21.0% from turkeys and 11.3% from broilers. The most frequent serovar detected in fattening turkey flocks was
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