Overview: direct-from-colony microbial sequencing (rapid Salmonella serotyping)

Direct-from-colony microbial sequencing: rapid Salmonella serotyping with nanopore sequencing

Salmonella species are one of the leading causes of food poisoning. Outbreaks of foodborne salmonellosis can originate from many kinds of foods, meaning that testing and tracing of contamination and/or outbreaks is of great importance to food safety and public health.

Whole-genome sequencing to identify isolated Salmonella organisms from contaminated food is becoming the gold standard for molecular typing. This protocol overview describes how to perform whole-genome amplification and rapid serotyping directly from a single Salmonella colony in 10–20 hours by using PCR and multiplexed nanopore sequencing. This protocol eliminates the need for subculture into liquid broth and DNA extraction — offering a rapid, simple, flexible end-to-end workflow.