Genomic Analysis of Colombian Leishmania panamensis strains with different level of virulence

Daniel Alfonso Urrea,Jean-Claude Dujardin,Janny Alexander Villa,Omar Triana-Chavez,Hideo Imamura,Natalia Muñoz,Juanita Gil,Jorge Duitama,Juan F ÁLzate,José R Ramirez-Pineda

doi:10.1038/s41598-018-35778-6

Abstract

The establishment of Leishmania infection in mammalian hosts and the subsequent manifestation of clinical symptoms require internalization into macrophages, immune evasion and parasite survival and replication. Although many of the genes involved in these processes have been described, the genetic and genomic variability associated to differences in virulence is largely unknown. Here we present the genomic variation of four Leishmania (Viannia) panamensis strains exhibiting different levels of virulence in BALB/c mice and its application to predict novel genes related to virulence. De novo DNA sequencing and assembly of the most virulent strain allowed comparative genomics analysis with sequenced L. (Viannia) panamensis and L. (Viannia) braziliensis strains, and showed important variations at intra and interspecific levels. Moreover, the mutation detection and a CNV search revealed both base and structural genomic variation within the species. Interestingly, we found differences in the copy number and protein diversity of some genes previously related to virulence. Several machine-learning approaches were applied to combine previous knowledge with features derived from genomic variation and predict a curated set of 66 novel genes related to virulence. These genes can be prioritized for validation experiments and could potentially become promising drug and immune targets for the development of novel prophylactic and therapeutic interventions.

Highlights

Leishmaniasis is a group of neglected tropical diseases caused by parasites belonging to the Leishmania genus, affecting around 14 million people worldwide and with 350 million people at risk of infection
To investigate the mechanisms that mediate virulence in the American cutaneous leishmaniasis (ACL) caused by L. panamensis, we report here the genome of the virulent UA946 strain, and the genomic variability between this and another three L. panamensis strains exhibiting different levels of virulence in BALB/c mice
All BALB/c mice infected with UA946 develop lesions that progressed to large ulcers within 8 weeks, whiles mice infected with UA140 develop no lesion or a mild disease (Fig. 1A–E)

Summary

Introduction

Leishmaniasis is a group of neglected tropical diseases caused by parasites belonging to the Leishmania genus, affecting around 14 million people worldwide and with 350 million people at risk of infection. Genome comparison between Leishmania donovani and L. major allowed to identify genes involved in virulence and tissue tropism after infections in animal models[4,5]. These genes have been experimentally associated to processes necessary to establish infection and response to different pressures or stress, the variability of these genes among and within Leishmania species is largely unknown. A wide spectrum of clinical manifestations caused by this group of parasites has been reported in humans[1,10] and animal models[11] This variation is attributed to variability in the host immune response and in parasite virulence[12,13,14,15,16]. Our results suggest that differences in dosage of some genes involved in virulence and allelic diversity through single nucleotide mutations may be determinant in the level of virulence of these strains in the murine model

Methods

Results

Conclusion