Cross-Border Transmission of Salmonella Choleraesuis var. Kunzendorf in European Pigs and Wild Boar: Infection, Genetics, and Evolution

Abstract

Salmonella enterica subspecies enterica serotype Choleraesuis is a swine adapted serovar. S. Choleraesuis variant Kunzendorf is responsible for the majority of outbreaks among pigs. S. Choleraesuis is rare in Europe, although there have been serious outbreaks in pigs including two outbreaks in Denmark in 1999–2000 and 2012–2013. Here, we elucidate the epidemiology, possible transmission routes and sources, and clonality of European S. Choleraesuis isolates including the Danish outbreak isolates. A total of 102 S. Choleraesuis isolates from different European countries and the United States, covering available isolates from the last two decades were selected for whole genome sequencing. We applied a temporally structured sequence analysis within a Bayesian framework to reconstruct a temporal and spatial phylogenetic tree. MLST type, resistance genes, plasmid replicons, and accessory genes were identified using bioinformatics tools. Fifty-eight isolates including 11 out of 12 strains from wild boars were pan-susceptible. The remaining isolates carried multiple resistance genes. Eleven different plasmid replicons in eight plasmids were determined among the isolates. Accessory genes were associated to the identified resistance genes and plasmids. The European S. Choleraesuis was estimated to have emerged in ∼1837 (95% credible interval, 1733–1983) with the mutation rate of 1.02 SNPs/genome/year. The isolates were clustered according to countries and neighbor countries. There were transmission events between strains from the United States and European countries. Wild boar and pig isolates were genetically linked suggesting cross-border transmission and transmission due to a wildlife reservoir. The phylogenetic tree shows that multiple introductions were responsible for the outbreak of 2012–2013 in Denmark, and suggests that poorly disinfected vehicles crossing the border into Denmark were potentially the source of the outbreak. Low levels of single nucleotide polymorphisms (SNPs) differences (0–4 SNPs) can be observed between clonal strains isolated from different organs of the same animal. Proper disinfection of livestock vehicles and improved quality control of livestock feed could help to prevent future spread of S. Choleraesuis or other more serious infectious diseases such as African swine fever (ASF) in the European pig production system.

Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany

“…The evolution rates of certain Salmonella serovars over time have been estimated recently to be approximately 1 to 5 bases per year per genome ( Hawkey et al, 2013 ; Deng et al, 2014 ; Phillips et al, 2016 ; Leekitcharoenphon et al, 2019 ). Such mutation rates are calculated by temporally structured sequence analyses within a Bayesian framework based on sets of isolates giving an indication for the rate of mutational changes within a population over the time ( Leekitcharoenphon et al, 2019 ). Nevertheless, recognizing the dimension of an outbreak, possibly running over years and consisting of several WGS subclusters, requires extensive consideration of epidemiological data and an understanding of the biology of the pathogen itself, as well as the environmental conditions in which the pathogen persists.…”

Re-Emergence of Salmonellosis in Hog Farms: Outbreak and Bacteriological Characterization

“…The emergence and amplification of the illness may be related to factors such as the introduction of carrier animals, neglected biosafety, contaminated feed, failure of protocol, or inadequate cleaning and disinfection [ 4 ]. Wild boars have been described as Salmonella and antimicrobial resistance reservoirs [ 16 , 17 , 18 , 19 ], and could be a vector if biosafety protocols are not followed. Although the disease is uncommon in an early stage due to the transfer of maternal immunoglobulin, it was observed in atypical cases of salmonellosis in the suckling period (6.15%) with both septicemic and enteric clinical-pathological presentations.…”

“…However, its prevalence has decreased over the years. Recent reports have associated S. choleraesuis with outbreaks in Japanese pig herds during 2001 and 2005 and in Danish pig herds during 2012 and 2013 [ 14 , 15 ] and in wild boar populations in several European countries [ 16 , 17 , 18 , 19 ].…”

Evaluation of Nanopore sequencing technology to differentiateSalmonellaserotypes and serotype variants with the same or closely related antigenic formulae

“…Choleraesuis is a serotype adapted to swine. This serotype has caused serious disease outbreaks in swine, including two in Denmark in 1999 – 2000 and 2012 – 2013 (Leekitcharoenphon et al, 2019). It also has a propensity to cause extraintestinal infections in humans (Chiu et al, 2004; Sirichote et al, 2010).…”

“…Choleraesuis var. Kunzendorf is responsible for the majority of outbreaks among swine (Leekitcharoenphon et al, 2019). Serotype Orion has two closely related variants, Orion var.…”