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

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...

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Autores principales: Pilling, Olivia A., Reis-Cunha, João L., Grace, Cooper A., Berry, Alexander S. F., Mitchell, Matthew W., Yu, Jane A., Malekshahi, Clara R., Krespan, Elise, Go, Christina K., Lombana, Cláudia, Song, Yun S., Amorim, Camila F., Lago, Alexsandro S., Carvalho, Lucas P., Carvalho, Edgar M., Brisson, Dustin, Scott, Phillip, Jeffares, Daniel C., Beiting, Daniel P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10063166/
https://www.ncbi.nlm.nih.gov/pubmed/36940219
http://dx.doi.org/10.1371/journal.ppat.1011230
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author Pilling, Olivia A.
Reis-Cunha, João L.
Grace, Cooper A.
Berry, Alexander S. F.
Mitchell, Matthew W.
Yu, Jane A.
Malekshahi, Clara R.
Krespan, Elise
Go, Christina K.
Lombana, Cláudia
Song, Yun S.
Amorim, Camila F.
Lago, Alexsandro S.
Carvalho, Lucas P.
Carvalho, Edgar M.
Brisson, Dustin
Scott, Phillip
Jeffares, Daniel C.
Beiting, Daniel P.
author_facet Pilling, Olivia A.
Reis-Cunha, João L.
Grace, Cooper A.
Berry, Alexander S. F.
Mitchell, Matthew W.
Yu, Jane A.
Malekshahi, Clara R.
Krespan, Elise
Go, Christina K.
Lombana, Cláudia
Song, Yun S.
Amorim, Camila F.
Lago, Alexsandro S.
Carvalho, Lucas P.
Carvalho, Edgar M.
Brisson, Dustin
Scott, Phillip
Jeffares, Daniel C.
Beiting, Daniel P.
author_sort Pilling, Olivia A.
collection PubMed
description 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.
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spelling pubmed-100631662023-03-31 Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies Pilling, Olivia A. Reis-Cunha, João L. Grace, Cooper A. Berry, Alexander S. F. Mitchell, Matthew W. Yu, Jane A. Malekshahi, Clara R. Krespan, Elise Go, Christina K. Lombana, Cláudia Song, Yun S. Amorim, Camila F. Lago, Alexsandro S. Carvalho, Lucas P. Carvalho, Edgar M. Brisson, Dustin Scott, Phillip Jeffares, Daniel C. Beiting, Daniel P. PLoS Pathog Research Article 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. Public Library of Science 2023-03-20 /pmc/articles/PMC10063166/ /pubmed/36940219 http://dx.doi.org/10.1371/journal.ppat.1011230 Text en © 2023 Pilling et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Pilling, Olivia A.
Reis-Cunha, João L.
Grace, Cooper A.
Berry, Alexander S. F.
Mitchell, Matthew W.
Yu, Jane A.
Malekshahi, Clara R.
Krespan, Elise
Go, Christina K.
Lombana, Cláudia
Song, Yun S.
Amorim, Camila F.
Lago, Alexsandro S.
Carvalho, Lucas P.
Carvalho, Edgar M.
Brisson, Dustin
Scott, Phillip
Jeffares, Daniel C.
Beiting, Daniel P.
Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies
title Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies
title_full Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies
title_fullStr Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies
title_full_unstemmed Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies
title_short Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies
title_sort selective whole-genome amplification reveals population genetics of leishmania braziliensis directly from patient skin biopsies
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10063166/
https://www.ncbi.nlm.nih.gov/pubmed/36940219
http://dx.doi.org/10.1371/journal.ppat.1011230
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