High-Resolution Comparative Genomics of Salmonella Kentucky Aids Source Tracing and Detection of ST198 and ST152 Lineage-Specific Mutations

Abstract

Non-typhoidal Salmonella (NTS) is a major cause of foodborne illness globally. Salmonella Kentucky is a polyphyletic NTS serovar comprised of two predominant multilocus sequence types (STs): ST152 and ST198. Epidemiological studies have revealed that ST152 is most prevalent in US poultry whereas ST198 is more prevalent in international poultry. Interestingly, ST152 is sporadically associated with human illness, whereas ST198 is more commonly associated with human disease. The goal of this study was to develop a better understanding of the epidemiology of ST198 and ST152 in WA State. We compared the antimicrobial resistance phenotypes and genetic relationship, using pulsed-field gel electrophoresis, of 26 clinical strains of S. Kentucky isolated in Washington State between 2004 and 2014, and 140 poultry-associated strains of S. Kentucky mostly recovered from the northwestern USA between 2004 and 2014. We also sequenced whole genomes of representative human clinical and poultry isolates from the northwestern USA. Genome sequences of these isolates were compared with a global database of S. Kentucky genomes representing 400 ST198 and 50 ST152 strains. The results of the phenotypic, genotypic, and case report data on food consumption and travel show that human infections caused by fluoroquinolone-resistant (FluR) S. Kentucky ST198 in WA State originated from outside of North America. In contrast, fluoroquinolone-susceptible (FluS) S. Kentucky ST198 and S. Kentucky ST152 infection have a likely domestic origin, with domestic cattle and poultry being the potential sources. We also identified lineage-specific non-synonymous single nucleotide polymorphisms (SNPs) that distinguish ST198 and ST152. These SNPs may provide good targets for further investigations on lineage-specific traits such as variation in virulence, metabolic adaptation to different environments, and potential for the development of intervention strategies to improve the safety of food.

Ciprofloxacin‐resistantST198SalmonellaKentucky in a hospitalized American black bear (Ursus americanus), with evidence of subsequent nosocomial transmission

“…According to that study, Clade ST198.2 in the United States has been associated with humans and imported foods, whereas Clade ST198.1 has been isolated from domestically produced food animal products in addition to humans and imported foods (Tate et al, 2022). Among most human clinical cases of Clade ST198.2 Salmonella Kentucky infection in the United States, there is a history of recent travel to Africa, Asia, or Europe (Haley et al, 2019; Soltys et al, 2021). Imported foods from which Clade ST198.2 has been isolated include spices and seafood (Tate et al, 2022).…”

Genomic and phenotypic characterization of Salmonella enterica serovar Kentucky

“…For many years, it has been the number one serovar isolated from broiler chickens at processing [28, 29] and studies have shown that these are typically isolates belonging to the Kentucky-I lineage [24, 27]. Despite broilers being the largest single reservoir for human cases of Salmonella [30], serovar Kentucky is rarely associated with human clinical cases in the USA [31]. This suggests that humans come into contact frequently with serovar Kentucky-I but that this contact does not result in significant illness.…”