Phylogenetic analyses of Salmonella detected along the broiler production chain in Trinidad and Tobago

This study was conducted to determine the phylogenies of Salmonella strains isolated from crosssectional studies conducted at hatcheries, broiler farms, processing plants, and retail outlets (broiler production chain) in Trinidad and Tobago over 4 yr (2016-2019). Whole-genome sequencing (WGS) was used to characterize Salmonella isolates. Core genome phylogenies of 8 serovars of public health significance were analyzed for similarities in origin and relatedness. In addition, Salmonella strains isolated from human salmonellosis cases in Trinidad were analyzed for their relatedness to the isolates detected along the broiler production chain. The common source of these isolates of diverse serovars within farms, within processing plants, between processing plants and retail outlets, and among farm-processing plant-retail outlet continuum was well-supported (bootstrap value >70%) by the core genome phylogenies for the respective serovars. Also, genome analyses revealed clustering of Salmonella serovars of regional (intra-Caribbean) and international (extra-Caribbean) origin. Similarly, strains of S. Enteritidis and S. Infantis isolated from human clinical salmonellosis in 2019 from Trinidad and Tobago clustered with our processing plant isolates recovered in 2018. This study is the first phylogenetic analysis of Salmonella isolates using WGS from the broiler industry in the Caribbean region. The use of WGS confirmed the genetic relatedness and transmission of Salmonella serovars contaminating chickens in broiler processing, and retailing in the country, with zoonotic and food safety implications for humans.

Automated summary

This study conducted cross-sectional studies over 4 years to determine the phylogenies of Salmonella strains isolated from various stages of broiler production chain in Trinidad and Tobago. With the use of whole-genome sequencing, genetic relatedness and transmission of Salmonella serovars were confirmed. The results highlighted the presence of a common source of diverse serovar isolates within farms, processing plants, and retail outlets. The study also identified regional and international clustering of Salmonella serovars.