Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies

Abstract

In Brazil, Leishmania braziliensis is the main causative agent of the neglected tropical disease, cutaneous leishmaniasis (CL). CL presents on a spectrum of disease severity with a high rate of treatment failure. Yet the parasite factors that contribute to disease presentation and treatment outcome are not well understood, in part because successfully isolating and culturing parasites from patient lesions remains a major technical challenge. Here we describe the development of selective whole genome amplification (SWGA) for Leishmania and show that this method enables culture-independent analysis of parasite genomes obtained directly from primary patient skin samples, allowing us to circumvent artifacts associated with adaptation to culture. We show that SWGA can be applied to multiple Leishmania species residing in different host species, suggesting that this method is broadly useful in both experimental infection models and clinical studies. SWGA carried out directly on skin biopsies collected from patients in Corte de Pedra, Bahia, Brazil, showed extensive genomic diversity. Finally, as a proof-of-concept, we demonstrated that SWGA data can be integrated with published whole genome data from cultured parasite isolates to identify variants unique to specific geographic regions in Brazil where treatment failure rates are known to be high. SWGA provides a relatively simple method to generate Leishmania genomes directly from patient samples, unlocking the potential to link parasite genetics with host clinical phenotypes.

A novel hybridization capture method for direct whole genome sequencing of clinical specimens to inform Legionnaires’ disease investigations

“…Additionally, a selective whole genome amplification (SWGA) for Treponema pallidum has shown robust direct WGS of specimens containing very low pathogen load, which has been challenging until now ( 21 ). In a similar study focused on cutaneous leishmaniasis, for which there is a technical challenge of isolating and culturing parasites from patient lesions, SWGA provided a relatively simple method to generate Leishmania genomes directly from patient specimens, unlocking the potential to link parasite genetics with host clinical phenotypes ( 22 ). In another study, a new strategy to identify mixed infections and minority variants in Mycobacterium tuberculosis by WGS is described.…”