WHO Collaborating Centre for Reference and Research on Escherichia and Klebsiella
Department of Microbiology & Infection Control
Statens Serum Institut
Artillerivej 5, DK-2300 København S, Danmark
Whole genome sequencing (WGS) for typing of E. coli
Accurate and rapid typing of pathogens is essential for effective surveillance and outbreak detection. During the fall of 2012 a real-time evaluation of WGS for routine typing and surveillance of Shiga toxin-producing E. coli (STEC) was tested in Denmark. All suspected STEC isolates were concurrently subjected to WGS. Real-time bioinformatic analysis was performed using web-tools (www.genomicepidemiology.org) for species determination, MLST typing, determination of phylogenetic relationship, and a specific VirulenceFinder for detection of E. coli virulence genes was developed.
In total, 46 suspected STEC isolates were characterized in parallel with conventional typing methods. VirulenceFinder proved successful in detecting virulence genes included in routine typing, and also detected additional virulence genes. VirulenceFinder has since been improved to include the assignment of all stx subtypes and a novel SerotypeFinder predicting the O and H antigens is being developed.
Conventional serotyping of Escherichia coli is a delicate procedure that is laborious, time-consuming and expensive. The current serotyping scheme comprises 188 O groups designated O1-O188 and 53 H-antigens, designated H1-H56, with the exception of O groups O31, O47, O67, O72, O94 and O122, and H types H13, H22 and H50, which have been withdrawn from the scheme. A database including the O-antigen processing genes wzx (O-antigen flippase) and wzy (O-antigen polymerase), and the alternative ABC transporter pathway genes wzm (translocation) and wzt (ATP-binding component) plus the flagellin genes, fliC, flkA, fllA, flmA and flnA was constructed. The database was evaluated on 682 E. coli genomes, 108 of which were sequenced for this study, where both the whole genome and the serotype were available. In total, 601 and 509 isolates were included for O -and H-typing, respectively. Evaluation of the SerotypeFinder proved successful in detecting the O-antigen genes, wzx, wzy, wzm and wzt, and the flagellin genes, fliC, flkA, fllA, flmA and flnA, employed for WGS-based O –and H-typing, respectively. Overall, the SerotypeFinder predicted serotypes consistent with conventional serotyping.
Efforts are currently focusing on expanding the VirulenceFinder tools to include more pathotypes such as enteroaggregative E. coli (EAEC) and extraintestinal E. coli (ExPEC) associated genes. In combination with other available WGS-typing tools, E. coli sero- and virulence typing can now be performed solely from WGS-data, providing faster and cheaper typing than current routine procedures, making WGS-typing a superior alternative to conventional typing strategies.