We are planning to genotype the infecting Leptospira strain(s) directly from the biological samples of leptospirosis patients thus overcoming the time-consuming cultivation steps (more than 4 weeks of incubation are usually required). We will apply Targeted genome capture using L. interrogans oligonucleotide probes to enrich specific Leptospira nucleic acids in clinical samples isolated from patients having leptospirosis. Direct sequencing of Leptospira genomes from clinical material will enable the identification of the infecting strain by a core-genome MLST scheme that we recently described. Using this approach we should also be able to investigate the genomic evolution of the pathogen during the course of infection.
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