Universidad Peruana Cayetano Heredia

Comparison of Whole Genome Sequencing versus Standard Molecular Diagnostics for Species Identification in the Leishmania Viannia Subgenus.

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dc.contributor.author Lau, Rachel
dc.contributor.author Mukkala, Avinash N.
dc.contributor.author Kariyawasam, Ruwandi
dc.contributor.author Clarke, Shareese
dc.contributor.author Valencia, Braulio M.
dc.contributor.author Llanos Cuentas, Elmer Alejandro
dc.contributor.author Boggild, Andrea K.
dc.date.accessioned 2021-10-04T23:00:56Z
dc.date.available 2021-10-04T23:00:56Z
dc.date.issued 2021
dc.identifier.uri https://hdl.handle.net/20.500.12866/9800
dc.description.abstract The prognosis and treatment of New World tegumentary leishmaniasis is dependent on the infecting species, yet such species identification in the Leishmania Viannia subgenus poses a diagnostic challenge. Currently, speciation relies on standard molecular techniques such as restriction fragment length polymorphism (RFLP) analysis, and Sanger sequencing (SS). Whole-genome sequencing (WGS) is a robust and increasingly cost-efficient tool that may improve Leishmania species identification. We evaluated WGS versus standard RFLP-SS for species identification in three reference and five clinical strains of Leishmania Viannia spp. Internal transcribed spacer1 (its1), cysteine proteinase b (cpb), and heat shock protein 70 (hsp70) polymerase chain reaction-restriction fragment length polymorphism (RFLP) was performed, followed by SS of the its2, cpb, hsp70, and mannose phosphate isomerase (mpi) loci. After de novo assembly, sequences were mapped, and homology compared with both reference strains and reference genomes on National Center for Biotechnology Information. All American Type Culture Collection strains were confirmed to be single-species of L. V. braziliensis, L. V. guyanensis, or L. V. panamensis by WGS. Conversely, RFLP-SS was able to definitively identify one of three isolates to the species level. Clinical samples were identified as either single-species (N = 3), mixed (N = 1), or hybrid (N = 1) infections by WGS, while standard molecular diagnosis required multi-target composite analysis for identification due to loci-dependent results by RFLP-SS. We have corroborated the utility of WGS as a diagnostic tool to speciate members of the L. Viannia subgenus and to discriminate between mixed and hybrid infections. WGS is a potentially useful complement to multistaged RFLP-SS for species identification in Leishmania infections en_US
dc.language.iso eng
dc.publisher American Journal of Tropical Medicine and Hygiene
dc.relation.ispartofseries American Journal of Tropical Medicine and Hygiene (ASTMH Journal)
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject Genome Sequencing en_US
dc.subject Standard Molecular Diagnostics en_US
dc.subject Species Identification en_US
dc.subject Leishmania Viannia en_US
dc.title Comparison of Whole Genome Sequencing versus Standard Molecular Diagnostics for Species Identification in the Leishmania Viannia Subgenus. en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.4269/ajtmh.21-0273
dc.relation.issn 1476-1645


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