Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent.

摘要: Whole genome sequencing (WGS) is increasingly used for molecular diagnosis and epidemiology of infectious diseases. Current Leishmania genomic studies rely on DNA extracted from cultured parasites, which might introduce sampling biological biases into the subsequent analyses. Up to now, direct analysis in clinical samples hampered by high levels human large variation parasite load samples. Here, we present a method, based target enrichment donovani with Agilent SureSelect technology, that allows genomes directly We validated our protocol set artificially mixed samples, followed 63 (bone marrow or spleen aspirates) visceral leishmaniasis patients Nepal. were able identify genotypes using diagnostic SNPs almost all these (97%) access comprehensive genome-wide information most (83%). This allowed us perform phylogenomic analysis, assess chromosome copy number variants (CNVs). Pairwise comparisons between derived vitro promastigotes showed lower aneuploidy amastigotes as well differences, suggesting polyclonal infections patients. Altogether results underline need host