Public Health England (PHE) has released information about how it uses the developing science of genomics to identify and characterise Salmonella isolates and detect related clusters of illness that could signify foodborne outbreaks.
The PHE Gastrointestinal Bacteria Reference Unit has been implementing genomic techniques since April 2014 and largely phased out conventional serotyping of Salmonella isolates since April 2015. It now employs Multi Locus Sequence Typing (MLST) to correlate isolates with traditional serotypes and then uses whole genome sequencing (WGS) to compare each isolate with an appropriate reference genome.
The aim is to identify individual nucleotide differences (single nucleotide polymorphisms or SNPs) and use them to identify clusters of related isolates. These clusters can then be investigated further by generating phylogenetic trees to study genome variation and ancestral relationships.
PHE says that WGS has been especially useful for detecting outbreaks of genetically monomorphic clones such as Salmonella Enteritidis, helping to exclude unrelated cases and trace a common source. The technique is also facilitating detection of smaller and geographically scattered clusters.
For anyone interested in these techniques, PHE has set up an online e-learning module on the topic here.