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

Abstract

The cattle-adapted serovar Salmonella Dublin (S. Dublin) causes enteritis and systemic diseases in animals. In the German federal state Schleswig-Holstein, S. Dublin is the most important serovar in cattle indicating an endemic character of the infection. To gain information on dissemination and routes of infection, whole-genome sequencing (WGS) was used to explore the genetic traits of 78 S. Dublin strains collected over a period of six years. The phylogeny was analysed using core-genome single nucleotide polymorphisms (cgSNPs). Genomic clusters at 100, 15 and 1 cgSNPs were selected for molecular analysis. Important specific virulence determinants were detected in all strains but multidrug resistance in S. Dublin organisms was not found. Using 15 cgSNPs epidemiological links between herds were identified, clusters at 1 cgSNPs provided clear evidence on both persistence of S. Dublin at single farms in consecutive years and transmission of the organisms between herds in different distances. A possible risk factor for the repeated occurrence of S. Dublin in certain districts of Schleswig-Holstein might be the spreading of manure on pastures and grassland. Effective control of S. Dublin requires farm-specific analysis of the management supplemented by WGS of outbreak causing S. Dublin strains to clearly identify routes of infection.

Semi-Quantitative Biosecurity Assessment Framework Targeting Prevention of the Introduction and Establishment of Salmonella Dublin in Dairy Cattle Herds

“…Furthermore, cow pats may act as a reservoir for Salmonella transmission between grassing seasons [ 76 ]. Pasture areas used by other foreign cows, application of manure from infected herds close to or directly on pastures without an adequate resting period is, therefore, thought to be an important S. Dublin transmission route and an efficient pathway for the establishment of the bacteria within a herd [ 35 ]. The probability of establishment was highlighted by Fossler et al, who identified a significant risk of shedding of Salmonella bacteria in cows in dairy herds with previous Salmonella history if their own manure was applied to owned or rented land or if cows ate roughage or grassed fields where manure had been applied to the ground surface without additional ploughing [ 78 ].…”

“…This is supported by epidemiological studies conducted in comparable cattle populations in other countries [ 32 , 33 ]. Additionally, whole-genome sequencing analysis has identified the geographical clustering of S. Dublin genetic groups [ 34 , 35 , 36 , 37 , 38 ]. Together, this suggests that indirect spread mechanisms are the drivers for the local spread of S. Dublin between herds.…”

Oxford nanopore technologies—a valuable tool to generate whole-genome sequencing data for in silico serotyping and the detection of genetic markers in Salmonella

“…In addition to serotyping, the WGS approach opens the opportunity to perform further bioinformatics analysis to study Salmonella strains in detail ( 44 ). Especially the detection of genetic markers for virulence and AMR as well as plasmid characterization and SPI detection are important steps in outbreak analysis.…”