Real-Time WGS-based Typing of VTEC Isolates for Surveillance and Outbreak Detection

Objectives: Fast and accurate typing of foodborne pathogens is essential for effective surveillance and the ability to detect and prevent outbreaks. Current routine typing is based on a variety of different typing techniques, making the complete typing procedure laborious, time-consuming and expensive. With whole-genome sequencing (WGS) becoming continuously cheaper and more available, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to evaluate WGS-based typing, in a real-time setup, for routine typing and surveillance of verocytotoxin-producing E.coli (VTEC) infections.
Methods: As part of the routine surveillance in Denmark, suspected VTEC isolates are sent to Statens Serum Institut (SSI) for phenotypic and molecular characterisation by a range of methods. During 7 weeks in the fall 2012, the isolates were simultaneously subjected to WGS using the IonTorrent PGM benchtop sequencing technology. WGS-based typing was carried out using web-based tools, developed by the Center for Genomic Epidemiology (www.genomicepidemiology.org), for determination of MLST types, virulence genes and phylogenetic relationship between the isolates. The WGS-based typing was compared to the routine typing and surveillance, with regard to typing results, time consumption and price.
Results: In total, 47 suspected VTEC isolates were typed during the 7 weeks, both by the routine procedures and in parallel by the WGS-approach, and during the period of the study a small outbreak occurred. For all isolates, apart from one resulting in poor sequence output, the WGS-based typing led to detection of the same virulence gene variants as the routine typing, and was also able to detect many other possible virulence features, and in most instances produce a useful typing result faster than routine typing. Also, the WGS-approach was able to correctly detect, according to the routine typing, the isolates belonging to the outbreak.
Conclusion: The real-time WGS-based typing was able to produce typing results comparable to the routine typing, at least as fast as the routine typing. Thus, the benchtop WGS-based typing approach is a reasonable alternative to conventional typing strategies, and could be applicable to typing and surveillance of other pathogens.