Abstract:
Through staphylococcal enterotoxin (SE) production, Staphylococcus aureus is a
common cause of food poisoning. Detection of staphylococcal food poisoning (SFP)
is mostly performed using immunoassays, which, however, only detect five of 27
SEs described to date. Polymerase chain reactions are, therefore, frequently used
in complement to identify a bigger arsenal of SE at the gene level (se) but are
labor-intensive. Complete se profiling of isolates from different sources, i.e., food and
human cases, is, however, important to provide an indication of their potential link
within foodborne outbreak investigation. In addition to complete se gene profiling,
relatedness between isolates is determined with more certainty using pulsed-field gel
electrophoresis, Staphylococcus protein A gene typing and other methods, but these
are shown to lack resolution. We evaluated how whole genome sequencing (WGS) can
offer a solution to these shortcomings. By WGS analysis of a selection of S. aureus
isolates, including some belonging to a confirmed foodborne outbreak, its added value
as the ultimate multiplexing method was demonstrated. In contrast to PCR-based
se gene detection for which primers are sometimes shown to be non-specific, WGS
enabled complete se gene profiling with high performance, provided that a database
containing reference sequences for all se genes was constructed and employed. The
custom compiled database and applied parameters were made publicly available in
an online user-friendly interface. As an all-in-one approach with high resolution, WGS
additionally allowed inferring correct isolate relationships. The different DNA extraction
kits that were tested affected neither se gene profiling nor relatedness determination,
which is interesting for data sharing during SFP outbreak investigation. Although confirming the production of enterotoxins remains important for SFP investigation, we
delivered a proof-of-concept that WGS is a valid alternative and/or complementary tool
for outbreak investigation.
