The genus Leptospira includes 35 Leptospira species, including L. mayottensis (see below), and more than 300 serovars have been described. Little is known about the circulating etiological agents of leptospirosis in most of the regions of the world. Detailed characterization of Leptospira isolates is important for understanding the epidemiology of leptospirosis (Leptospira serovars are usually associated with a restricted number of animal reservoirs). Local Leptospira isolates can serve as antigens for the serodiagnosis of leptospirosis. The diverse distributions of Leptospira serovars and genotypes may have implications for vaccine design and efficacy.
We developped a Multilocus variable number tandem repeat (VNTR) analysis (MLVA) for the DNA fingerprinting of the pathogenic species L. interrogans, L. kirschneri, L. borgpetersenii, and L. santarosai. Molecular and serological analysis also allowed to investigate leptospirosis outbreaks among participants of a canyoning in Martinique and a triathlon on Réunion Island. Serological investigations was also performed among patients during a plague outbreak in Democratic Republic of the Congo, and in patients negative for dengue, Japanese encephalitis and Chikungunya viruses in rural Cambodian communities. These studies suggest that the burden of leptospirosis in these in these countries, where very little is known about leptospirosis, is high. We characterized the molecular features of leptospires isolated from >300 leptospirosis patients in the French West Indies (Carribean sea) and Mayotte (a French department located in the Comoros archipelago, Indian Ocean). Typing of leptospiral isolates suggested the existence of previously undescribed serovars/genotypes, including a new pathogenic Leptospira species called Leptospira mayottensis. Molecular typing directly on kidneys extracts also allowed to describe Leptospira prevalence, species and strains in rodent populations in Southeast Asia and Niger. Our findings show that Leptospira strains are not only circulating in wetlands as is commonly accepted but also in arid regions (Niger) or dry habitats (non-floodable lands in Southeast Asia).
To advance our understanding of the biodiversity of Leptospira strains at the global level, we evaluated the performance of whole-genome sequencing (WGS) as a new genotyping tool. We propose a set of 545 highly conserved loci as a core genome MLST (cgMLST) genotyping scheme targeting the entire Leptospira genus, including non-pathogenic strains. Phylogenetic analysis showed that cgMLST defines species, clades, subclades, clonal groups and strains, with high precision. New Leptospira species were identified from the environment. The cgMLST scheme also enables the efficient identification of serogroups and closely related serovars. cgMLST analysis demonstrated congruence with current MLST schemes, but with much improved resolution and with wider applicability, as non-pathogenic lineages were not typeable by classical MLST. In conclusion, the proposed cgMLST scheme allows high-resolution genotyping of Leptospira isolates across the phylogenetic breadth of the genus. The unified nomenclature of cgMLST genotypes, available publicly at http://bigsdb.pasteur.fr/leptospira, should enable global harmonization of Leptospira genotyping, strain emergence follow-up and novel collaborative studies of the epidemiology and evolution of this emerging pathogen.