The Leptospirosis Research and Expertise Unit at the Institut Pasteur of New Caledonia has successfully isolated Leptospira strains from hospitalized patients over the past two decades. To date, molecular characterization of these isolates has relied primarily on lfb1-based genotyping, which uses sequence polymorphisms within a single genetic locus to discriminate among circulating strains.
To improve the resolution of Leptospira strain characterization and gain a more comprehensive understanding of the genetic diversity of strains responsible for human infections in New Caledonia, we aim to perform whole-genome sequencing (WGS) of a representative collection of clinical isolates recovered over the past 20 years. Genome-wide data will be used to establish a core-genome phylogeny and to assess its congruence with the phylogenetic structure currently inferred from lfb1 sequences.
This comparative approach will determine the extent to which the current lfb1-based genotyping scheme accurately reflects genome-wide relationships among circulating strains and will identify potential limitations in its discriminatory resolution. The results may therefore support the refinement of our molecular genotyping strategy, including the identification of additional genomic markers or approaches providing improved resolution for epidemiological surveillance of Leptospira strains circulating in New Caledonia.
In parallel, the unit has recently established the capacity to generate targeted Leptospira knockout mutants using CRISPR-Prime editing technology. Whole-genome sequencing will be performed on several recently generated mutant strains to confirm the presence and sequence accuracy of the intended genetic modifications and to screen for unintended genomic alterations that may have arisen during the genome-editing and strain-selection process.
