Main menu

NCM 2022: WGS analysis of Salmonella enterica from VT backyard chickens using MinION: advantages and pitfalls


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.

Download the PDF

Getting started

Buy a MinION starter pack Nanopore store Sequencing service providers Channel partners

Quick links

Intellectual property Cookie policy Corporate reporting Privacy policy Terms & conditions Accessibility

About Oxford Nanopore

Contact us News Media resources & contacts Investor centre Careers BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
English flag