Whole-genome sequencing of Argentinean isolates of Leptospira: SNPs analysis for epidemiological purposes

VANINA VARNI; KARINA CAIMI; ARIEL NAGEL; PAULA RUYBAL; BIBIANA BRIHUEGA; ARIEL AMADIO

Semaranga

Congreso; 9th International Leptospirosis Society Scientific Meeting; 2015

International Leptospirosis Society

Leptospirosis, caused by more than 250 different serotypes of the genus Leptospira, is one of the most common and widespread zoonotic disease worldwide. Infection is primarily spread through contact with water contaminated by urine of infected carrier animals. Leptospirosis is clearly an emerging and reemerging infectious disease. In recent years the whole-genome sequencing has become a technology increasingly used for diagnosis and molecular epidemiology of various pathogens due to the fast data generation and the decrease of the costs involved. Our group has focused on the development of molecular markers based on the sequencing of gene regions (MLST). These studies led to the identification of the major genotypes of Leptospira circulating in Argentina, both in cattle and humans. However, these markers have a low resolution when investigating outbreaks with one predominant serogroup or genotype. The generation of genomic sequences of predominant serogroups in Argentina, Pomona and Canicola was performed, in order to compare them with other genomes previously sequenced. The aim was to identify SNPs that enable discrimination, with the perspective of developing a high resolution typing tool.ObjectiveIdentification of SNPs in Argentinean genomes from predominant serogroups that enable an accurate discrimination among closely related strains.MethodsAmong the Argentinean strains previously studied by MLST, we selected two isolates for whole genome sequencing using the Illumina "MySeq technology. Those belonged to Leptospira interrogans, serogroups Pomona and Canicola respectively. Additionally we selected and downloaded 8 L. interrogans sv. Pomona genomes from public databases, isolated in different countries. The alignment of the 10 total genomes with a reference genome (L. interrogans sv. Cophenageni, strain Fiocruz L1-130) allowed the identification of polymorphic positions. The SNPs obtained were used to perform a phylogenetic analysis in order to explore the genetic differences among the strains.ResultsA panel of 47,182 SNPs between the reference genome and the 9 Pomona were identified, 67% of them located in coding regions. The phylogenetic analyses enabled the differentiation of strains that were previously indistinguishable by their genotype or serogroup. The clustering of isolates was related to their geographic origins.ConclusionsThe comparison of local Leptospira genomes with worldwide genomes allowed the identification of SNPs, both within a serogroup as among serogroups. The SNPs analysis arises as a promising perspective for local epidemiology of Leptospira, leading to the discrimination of isolates that could not be achieved by traditional molecular markers. The further selection of a reduced set of SNPs, when validated in a larger set of strains, may lead to the development of a tool for high-resolution typing of this pathogen.