Selective whole-genome amplification of Leishmania braziliensis from patient biopsies

In Brazil, Leishmania braziliensis is the main causative agent of the neglected tropical disease, cutaneous leishmaniasis (CL). CL caused by L. braziliensis can present 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. Finally, we show that parasite genome sequencing data generated by SWGA of skin biopsies collected from patients in Corte de Pedra, Bahia, Brazil, exhibit substantial genetic diversity and can be integrated with published whole genome data from parasite isolates to identify variants associated with high treatment failure rates observed in Northeast Brazil.