NCM 2022: WGS analysis of Salmonella enterica from VT backyard chickens using MinION: advantages and pitfalls
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In 2016, there were over 46,000 cases of culture-confirmed Salmonella infections reported to the Laboratory-based Enteric Disease Surveillance system, and this is a small fraction of the 1.3 million estimated cases per year. Salmonella is the foremost foodborne pathogen in terms of cost of illness and mortality – $3.3 billion and 378 deaths. Backyard poultry ownership has been increasing across Vermont and the United States, which also increases contact with zoonotic pathogens such as Salmonella. In 2020, the number of reported illnesses linked to backyard flock outbreaks was higher than any year previously investigated (CDC, 2020). Next-generation sequencing techniques, such as the Oxford Nanopore MinION platform, allow for investigation of smaller and more dispersed foodborne outbreaks such as salmonellosis in backyard poultry flocks. We chose the Oxford Nanopore MinION platform for our sequencing due to apparent lower initial cost, accessibility, and the de novo assembly possibilities stemming from its long reads. Purpose: The purpose of this study is to determine the serovars and genomic traits, such as antimicrobial resistance, that are found in Salmonella enterica isolates from backyard poultry flocks across Vermont.