A single missense mutation in hilD is responsible for further adaptation of a Salmonella Derby lineage to swine and reduced risk to human health

Salmonella enterica variants exhibit diverse host adaptation, outcome of infection, and associated risk to humans. Analysis of 6,335 Salmonella isolates recovered from integrated human-animal surveillance in Emilia Romagna region, Northern Italy, (human population ca 4,500,000), from 2012 to 2017 showed that Salmonella enterica serovar Derby constitutes a swine associated serovar in this epidemiological context while representing also a significant causative agent of human infections. Comparison of the distribution of subtypes of Salmonella Derby from human and swine identified isolates with a distinct PFGE profile that were significantly less isolated in human infections than in swine infections compared to all other subtypes. Here we show that isolates with this PFGE profile form a distinct phylogenetic sub-clade within Salmonella Derby and exhibit a marked reduction in invasion and replication in human epithelial cells but a relatively small reduction in swine epithelial cells, in line with the epidemiological evidence. A single missense mutation in hilD, that encodes the master-regulator of the Salmonella Pathogenicity Island 1 (SPI-1), was identified in this lineage of Salmonella Derby. Since SPI-1 encodes for a primary system of Salmonella invasion into epithelial cells, we investigated the role of the observed mutation in detail. We demonstrated that the missense mutation results in a loss of function of HilD that accounts for the reduced invasion and replication in human epithelial cells while showing a relatively small impact on the interaction with swine cells. This finding is suggestive of a mechanism of invasion alternative to SPI-1 in the Salmonella-swine combination Transcriptome analysis of Salmonella Derby ER1175, ER278 strains and their hilD mutants