Whole-Genome Investigation of Salmonella Dublin Considering Mountain Pastures as Reservoirs in Southern Bavaria, Germany

Abstract

Worldwide, Salmonella Dublin (S. Dublin) is responsible for clinical disease in cattle and also in humans. In Southern Bavaria, Germany, the serovar was identified as a causative agent for 54 animal disease outbreaks in herds between 2017 and 2021. Most of these emerged from cattle herds (n = 50). Two occurred in pig farms and two in bovine herds other than cattle. Genomic analysis of 88 S. Dublin strains isolated during these animal disease outbreaks revealed 7 clusters with 3 different MLST-based sequence types and 16 subordinate cgMLST-based complex types. Antimicrobial susceptibility investigation revealed one resistant and three intermediate strains. Furthermore, only a few genes coding for bacterial virulence were found among the isolates. Genome analysis enables pathogen identification and antimicrobial susceptibility, serotyping, phylogeny, and follow-up traceback analysis. Mountain pastures turned out to be the most likely locations for transmission between cattle of different herd origins, as indicated by epidemiological data and genomic traceback analyses. In this context, S. Dublin shedding was also detected in asymptomatic herding dogs. Due to the high prevalence of S. Dublin in Upper Bavaria over the years, we suggest referring to this administrative region as “endemic”. Consequently, cattle should be screened for salmonellosis before and after mountain pasturing.

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

“…Classical MLST (based on seven genes) typed all S. Dublin organisms in this study as ST 10, only one strain belonged to ST 3734. 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 ].…”

“…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.…”