NEW YORK (GenomeWeb) – By sequencing isolates from sites around the world, researchers from Canada, France, and elsewhere have identified dozens of previously unappreciated Leptospira species.
"The implication of several new potentially infectious Leptospira species for human and animal health remains to be determined, but our data also provide new insights into the emergence of virulence in the pathogenic species," co-senior and corresponding author Mathieu Picardeau, a researcher at the Pasteur Institute, and his co-authors wrote in a paper about the study published yesterday in PLOS Neglected Tropical Diseases.
Picardeau and his colleagues focused on 90 isolates from water or soil samples collected at 18 sites in Japan, Malaysia, New Caledonia, mainland France, Mayotte, and Algeria over nearly a decade. Their subsequent phylogenetic analyses highlighted 30 new Leptospira species falling into two clades and four clades — a classification scheme that differs from prior attempts to organize the species into clusters based on their suspected virulence.
"Our results reveal that the genus Leptospira now contains 64 named species, including species from a new subclade that is sister to the one that contains the traditional saprophytic species," the authors explained, noting that their proposed classification system would replace a classification scheme based on sometimes-uncharacterized Leptospira virulence levels.
The team noted that an enhanced appreciation for Leptospira pan-genomes and evolutionary trajectories may have repercussions in the public health setting by helping to distinguish strains or species most prone to causing leptospirosis infections in animals, including the zoonotic infections that can jump to humans via contaminated environmental sites.
Using Illumina instruments, the investigators sequenced and assembled genomes for Leptospira isolates collected between 2008 and 2017, comparing genomes covered to at least 50-fold average coverage to one another and to dozens of published Leptospira genomes.
"[W]e have isolated new strains from diverse geographical origins and have undertaken a large genomic study in order to dust off the Leptospira genus to draw a better picture of its diversity and to propose new standards on its classification and nomenclature to replace the current one that is complex and obsolete," the authors wrote.
The newly sequenced genomes ranged from just over 3.7 million to almost 5 million bases, the team noted. Across all 124 new and available genomes, the investigators' phylogenetic analyses and pairwise comparisons pointed to the presence of 34 known Leptospira species and another 30 species that were not reported — or were purportedly misclassified as other species — in the past.
Along with two broad clades that roughly coincided with pathogenic or saprophytic forms of Leptospira, the authors outlined four proposed sub-clades and a nomenclature they designed to "limit the assumption of virulence" in yet-to-be-characterized strains. Based on their subsequent analyses, they cautioned that 16S ribosomal RNA gene sequence data does not offer a refined look at Leptospira phylogeny, since several species share the same 16S sequences.
The team also began digging into phenotypes for the new strains, as well as the genomic features and evolutionary trajectory that may lead to virulent forms of Leptospira, in the hopes of identifying and thwarting costly and dangerous leptospirosis infections in livestock, wild animals, and humans.
Moreover, the authors suggested that the current findings may have implications for public health and diagnostic tools, hinting that they "should be updated to take into account the new species described in the present study in order to evaluate their association with infection of both animals and humans and their role in clinical disease."