Genetic Affinities within a Large Global Collection of Pathogenic Leptospira: Implications for Strain Identification and Molecular Epidemiology.

Leptospirosis is an important zoonosis with widespread human health implications. The non-availability of accurate
identification methods for the individualization of different Leptospira for outbreak investigations poses bountiful problems
in the disease control arena. We harnessed fluorescent amplified fragment length polymorphism analysis (FAFLP) for
Leptospira and investigated its utility in establishing genetic relationships among 271 isolates in the context of species level
assignments of our global collection of isolates and strains obtained from a diverse array of hosts. In addition, this method
was compared to an in-house multilocus sequence typing (MLST) method based on polymorphisms in three housekeeping
genes, the rrs locus and two envelope proteins. Phylogenetic relationships were deduced based on bifurcating Neighborjoining
trees as well as median joining network analyses integrating both the FAFLP data and MLST based haplotypes. The
phylogenetic relationships were also reproduced through Bayesian analysis of the multilocus sequence polymorphisms. We
found FAFLP to be an important method for outbreak investigation and for clustering of isolates based on their
geographical descent rather than by genome species types. The FAFLP method was, however, not able to convey much
taxonomical utility sufficient to replace the highly tedious serotyping procedures in vogue. MLST, on the other hand, was
found to be highly robust and efficient in identifying ancestral relationships and segregating the outbreak associated strains
or otherwise according to their genome species status and, therefore, could unambiguously be applied for investigating
phylogenetics of Leptospira in the context of taxonomy as well as gene flow. For instance, MLST was more efficient, as
compared to FAFLP method, in clustering strains from the Andaman island of India, with their counterparts from mainland
India and Sri Lanka, implying that such strains share genetic relationships and that leptospiral strains might be frequently
circulating between the islands and the mainland.