Molecular analysis of clonally related Salmonella Typhi recovered from epidemiologically unrelated cases of typhoid fever, Brazil.

•This study brings up new information regarding the strengths and drawbacks of WGS using different analytic approaches compared to the traditional typing method, PFGE, for retrospectively typing cluster cases of S. Typhi isolated in São Paulo, Brazil.•Although any exposure factor could be associated with the cases in this study, a common unidentified source probably exists since different laboratorial tests and analysis of WGS identify a common pattern among the contemporary S. Typhi strains recovered from patients with typhoid fever.•In our study, WGS based typing, using ND, SNP analysis and wgMLST, was able to compete with PFGE for outbreak clustering. The performance of the three selected WGS based typing methods was validated based on the clusters of S. Typhi strains.