Sequence-Based Typing of Leptospira: Epidemiology in the Genomic Era

Leptospirosis is a zoonotic disease of global distribution, maintained in nature by chronic renal infection of carrier animals. Infected animals excrete the organisms in their urine and contaminate the environment. Human infection is acquired directly via exposure to the organism in tissues or body fluids, but most often occurs indirectly via exposure to the organisms in the environment. Thus human exposure usually occurs remotely from the reservoir or source animal. The incidence of leptospirosis is very strongly associated with rainfall. Excess rainfall events that cause massive flooding are associated with the potential for huge outbreaks, particularly in densely populated regions of the tropical world. In such situations it is difficult if not impossible to identify the reservoir(s) of the organisms that cause human cases. Historically, leptospires were classified into two species, Leptospira interrogans and L. biflexa, which comprised pathogenic and nonpathogenic strains, respectively. Within these two species, several hundred serovars were recognised [1]. Identification of isolates to serovar level is an essential step to understanding the epidemiology of the disease in both humans and animals in any geographic region. However, serovar identification remains a relatively blunt tool with which to investigate fine details of epidemiology. Genetic variation observed within the genus Leptospira [2,3] led to the replacement of the historical classification by one based on DNA relatedness [4,5]. In this system 14 species are currently recognised and at least another six species are in the process of being described. The development of a molecular classification provided the basis for understanding the genetically distinct subtypes of serovar Hardjo. Two genotypes of serovar Hardjo, with distinct biological characteristics and geographical distribution, named Hardjoprajitno and Hardjobovis [6–8] are classified within L. interrogans and L. borgpetersenii, respectively. Evidence of horizontal gene transfer within the genus, mediated by insertion sequences, is widespread [9–12]. A wide range of methods based upon restriction endonuclease digests, random amplification, or hybridization have been applied to typing of leptospiral isolates, with moderate success. The availability of increasing numbers of genome sequences has facilitated the application of sequence-based approaches that can yield much deeper information about relationships between strains [13–15].