A retrospective and regional approach assessing the genomic diversity ofSalmonellaDublin

Abstract

From a historically rare serotype, Salmonella enterica subsp. enterica Dublin slowly became one of the most prevalent Salmonella in cattle and raw milk cheese in some regions of France. We present a retrospective genomic analysis of 480 S. Dublin isolates to address the context, evolutionary dynamics, local diversity and the genesis processes of regional S. Dublin outbreaks events between 2015 and 2017. Samples were clustered and assessed for correlation against metadata including isolation date, isolation matrices, geographical origin and epidemiological hypotheses. Significant findings can be drawn from this work. We found that the geographical distance was a major factor explaining genetic groups in the early stages of the cheese production processes (animals, farms) while down-the-line transformation steps were more likely to host genomic diversity. This supports the hypothesis of a generalised local persistence of strains from animal to finished products, with occasional migration. We also observed that the bacterial surveillance is representative of diversity, while targeted investigations without genomics evidence often included unrelated isolates. Combining both approaches in phylogeography methods allows a better representation of the dynamics, of outbreaks.

Epidemiological Analysis on the Occurrence of Salmonella enterica Subspecies enterica Serovar Dublin in the German Federal State Schleswig-Holstein Using Whole-Genome Sequencing

“…The only exceptional occurrence of others than ST 10 was also found in recent studies examining S. Dublin organisms from other German federal states [ 4 , 7 ] and is in line with the observation that ST 10 accounts for more than 90% of S. Dublin strains worldwide [ 32 ]. Therefore, regarding their antimicrobial resistance pattern, their pathogenic virulence potential but also their MLST profile the outbreak-causing S. Dublin strains from Schleswig-Holstein represent a homogeneous population which confirms findings from other European WGS-based S. Dublin analyses [ 4 , 5 , 6 , 7 , 8 ]. As the most strains of S. Dublin belong to ST 10, MLST is not an appropriate tool to further distinguish the strains.…”

“…Therefore, in this study cgSNP typing and hierarchical clustering served as discriminatory tools to analyse the S. Dublin epidemiology in the cattle population of Schleswig-Holstein. SNP-typing based on whole-genome-sequencing has been proven to be a powerful tool to study S. Dublin phylogeny in Europe [ 4 , 5 , 6 , 7 , 8 , 9 , 10 ]. While a threshold of 15 SNPs was shown to cluster strains from the same herds [ 6 ], 40 and 100 SNPs were used to detect intermediate and general clusters [ 4 ].…”

“…Therefore, in regions with repeated occurrence of S. Dublin outbreaks also the manure management should be considered in the analysis of the infection. Apart from effective biosecurity procedures to control Salmonella infections at cattle farms [ 1 , 3 , 7 ], WGS is an valuable tool to analyse outbreak-causing S. Dublin organisms and also strains from other serovars [ 6 , 8 , 10 , 30 , 32 ]. The identification of both, strains with a link between farms and identical strains in different herds using various thresholds for cgSNPs analysis is highly important to detect routes of infection and represents the basis for effective intervention measures.…”

“…To enhance information on the routes of infection as a prerequisite for better control, genetic traits of the outbreak causing S. Dublin strains in different regions over a period of six years in the federal state Schleswig-Holstein should be analysed. Whole-genome sequencing (WGS) has been successfully applied for the characterisation of S. Dublin organisms from different origin [ 4 , 5 , 6 , 7 , 8 , 9 ]. Core-genome single nucleotide polymorphisms (cgSNPs)-based typing has shown a high discriminatory potential to identify closely related and non-related isolates [ 4 , 5 , 6 , 7 , 8 , 9 , 10 ].…”

“…Whole-genome sequencing (WGS) has been successfully applied for the characterisation of S. Dublin organisms from different origin [ 4 , 5 , 6 , 7 , 8 , 9 ]. Core-genome single nucleotide polymorphisms (cgSNPs)-based typing has shown a high discriminatory potential to identify closely related and non-related isolates [ 4 , 5 , 6 , 7 , 8 , 9 , 10 ]. WGS data also give information on virulence genes and antimicrobial resistance determinants of the isolates.…”