Genomic analysis of Salmonella enterica serovar Typhimurium DT56 variant in New Zealand

Salmonella enterica serovar Typhimurium DT160 was the predominant cause of notified human salmonellosis cases in New Zealand from 2000-2010, before it was superseded by another S. Typhimurium strain identified as DT56 variant. Whole genome sequencing was used to compare 109 DT160 isolates with eight DT56 variant isolates from animal and human New Zealand source groups to determine the time of common ancestor of both strains, and identify potential genomic reasons for the decline in DT160 and emergence of DT56 variant. Phylogenetic analysis provided evidence that DT160 and DT56 variant strains were distantly related with an estimated date of common ancestor around the 16th Century CE. Genomic comparisons confirmed that all DT160 isolates contained the ST160 phage and a plasmid similar to the pSTUK-100 plasmid, whilst the DT56 variant isolates contained the BTP1 phage, which may have contributed to its emergence. It also identified a pBSSB1 plasmid in one of the DT56 variant isolates analysed. Our study demonstrates how comparative genomics can help identify strain-specific elements and factors that may have influenced the emergence and decline of bacterial strains of public health importance.