Genomanalyse av Salmonella enterica subsp. enterica serovar Typhimurium i Norge

Salmonella enterica subspecies enterica serovar Typhimurium, referred to as S. Typhimurium in this master`s thesis, is one of the most common pathogenic serovariants of Salmonella spp. S. Typhimurium has been isolated in a wide range of hosts from the wild fauna. These hosts are believed to be responsible for several of the human cases of Salmonella infections in Norway. The main goal of this thesis is to test the hypothesis that wild animals are a potential source of infection from S. Typhimurium among production animals in Norway. In this project a totalt of 127 S. Typhimurium isolates taken between 2001 and 2021 from wild animals, production animals and sport- and family animals were selected from the laboratory inventory at the Norwegian Veterinary Institute. The information present in the genome sequences of the S. Typhimurium isolates were examined using whole genome sequencing (WGS). WGS of pathogens is an important tool to improve the understanding of how contagious diseases spread between hosts. Due to limitations in the sequencing technology, the DNA are fragmented and only up to 300 bp are sequenced, this is then called reads. Bioinformatic tools were used for quality check a large number of the raw data from the sequencing before the original genom was attempted reconstructed using de novo SPAdes assembly. ” Multilocus Sequence Typing” (MLST) were used in further analysis to determine allele- variations based on 7 housekeeping genes, and each bacterial isolate were assigned one sequence type where ST19 and ST34 were the most common. Then the evolutionary similarity between isolates within the same ST was assessed by SNP analysis. Using phylogenetic analysis we were able to observe clusters with evolutionary similarity between wild animals and production animals, which indicates that transmission of S. Typhimurium had taken place. Based on the results from the applied dataset we found several of these cases, which gives a strong indication that wild animals can be the source of infection for S. Typhimurium among production animals in Norway