Microevolution during the emergence of the monophasic Salmonella Typhimurium epidemic. Microevolution during the emergence of the monophasic Salmonella Typhimurium epidemic

Microevolutionary events associated with the emergence and clonal expansion of new epidemic clones of bacterial pathogens hold the key to understanding the drivers of epidemiological success. We describe a comparative whole genome sequence and phylogenomic analysis of S. Typhimurium and monophasic Typhimurium strains from the UK associated with an epidemic over the past decade. The monophasic Typhimurium strains from the UK isolated since 2005 are not part of other recent epidemics reported in Spain and North America. Whole genome sequence revealed a large novel genomic island encoding resistance to heavy metals (SGI-3) is characteristic of the monophasic epidemic strains from other Typhimurium isolates in the current epidemic and may have contributed to the epidemiological success. We report a remarkable degree of genotypic variation that accumulated during clonal expansion of an epidemic including acquisition of the virulence-asscoiated sopE effector protein and novel prophage and hyper variability in the phase II flagellum locus.