Emergence of multi-drug resistant Salmonella Enteritidis strains harbouring novel virulence plasmid in Korea

The Salmonella enterica subspecies serovar Enteritidis is the one of main serovars isolated from human patients with food poisoning and poultry without clinical signs. Consumption of poultry products contaminated with Salmonella Enteritidis is a common source of human salmonellosis. This study was aimed to determine the genetic relationships between Salmonella Enteritidis strains isolated from human patients and those isolated from poultry sources using whole-genome sequencing analysis. Seven of multi-drug resistant (MDR) strains of Salmonella Enteritidis were isolated from 234 retail chicken meats, internal organs of chicken, and straw bedding samples at chicken farms. Whole genome sequences of the MDR strains were determined using the Oxford Nanopore sequencing and compared with available whole genome sequences of the Salmonella Enteritidis strains previously isolated in Korea. Single-nucleotide polymorphism analysis of the whole genomes showed that all MDR Salmonella Enteritidis strains were genetically close and related to the FORC_019 strain isolated from human blood in 2015 in Korea. All of the MDR Salmonella Enteritidis strains contained a 110 kb of plasmid, and comparative plasmid analysis showed that all of the MDR Salmonella Enteritidis strains carried a novel fusion plasmid with genes coding virulence factors and antibiotic resistance proteins. The almost identical plasmid, with an extra 7.5-kb insertion sequence was also found in the FORC_019 strain. These results suggested that the single genetic lineage of MDR Salmonella Enteritidis that can cause salmonellosis in human is currently contaminating the Korean poultry industry.