Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.

Autores
Diosque, Patricio; Tomasini, Nicolás; Lauthier, Juan José; Messenger, Louisa Alexandra; Monje Rumi, Maria Mercedes; Ragone, Paula Gabriela; Alberti D'Amato, Anahi Maiten; Perez Brandan, Cecilia Maria; Barnabe, Christian; Tibayrenc, Michel; Lewis, Michael David; Llewellyn, Martin Stephen; Miles, Michael Alexander; Yeo, Matthew
Año de publicación
2014
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Trypanosoma cruzi, the aetiological agent of Chagas disease possess extensive genetic diversity. This has led to the development of a plethora of molecular typing methods for the identification of both the known major genetic lineages and for more fine scale characterization of different multilocus genotypes within these major lineages. Whole genome sequencing applied to large sample sizes is not currently viable and multilocus enzyme electrophoresis, the previous gold standard for T. cruzi typing, is laborious and time consuming. In the present work, we present an optimized Multilocus Sequence Typing (MLST) scheme, based on the combined analysis of two recently proposed MLST approaches. Here,thirteen concatenated gene fragments were applied to a panel of T. cruzi reference strains encompassing all known genetic lineages. Concatenation of 13 fragments allowed assignment of all strains to the predicted Discrete Typing Units (DTUs), or near-clades, with the exception of one strain that was an outlier for TcV, due to apparent loss of heterozygosity in one fragment. Monophyly for all DTUs, along with robust bootstrap support, was restored when this fragment was subsequently excluded from the analysis. All possible combinations of loci were assessed against predefined criteria with the objective of selecting the most appropriate combination of between two and twelve fragments, for an optimized MLST scheme. The optimum combination consisted of 7 loci and discriminated between all reference strains in the panel, with the majority supported by robust bootstrap values. Additionally, a reduced panel of just 4 gene fragments displayed high bootstrap values for DTU assignment and discriminated 21 out of 25 genotypes. We propose that the seven-fragment MLST scheme could be used as a gold standard for T. cruzi typing, against which other typing approaches, particularly single locus approaches or systematic PCR assays based on amplicon size, could be compared.
Fil: Diosque, Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Tomasini, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Lauthier, Juan José. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Messenger, Louisa Alexandra. London School of Hygiene and Tropical Medicine; Reino Unido
Fil: Monje Rumi, Maria Mercedes. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Ragone, Paula Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Alberti D'Amato, Anahi Maiten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Perez Brandan, Cecilia Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Barnabe, Christian. Institut de Recherche pour le Développement. Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle; Francia
Fil: Tibayrenc, Michel. Institut de Recherche our le Développement. Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle; Francia
Fil: Lewis, Michael David. London School of Hygiene and Tropical Medicine; Reino Unido
Fil: Llewellyn, Martin Stephen. London School of Hygiene and Tropical Medicine; Reino Unido
Fil: Miles, Michael Alexander. London School of Hygiene and Tropical Medicine; Reino Unido
Fil: Yeo, Matthew. London School of Hygiene and Tropical Medicine; Reino Unido
Materia
MULTILOCUS SEQUENCE TYPING
TRYPANOSOMA CRUZI
SCHEME OF OPTIMIZATION
GENETIC DIVERSITY
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/7087
Acceder
id CONICETDig_b2f43c27d31db927b3f8a4ba34af122f
oai_identifier_str oai:ri.conicet.gov.ar:11336/7087
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.Diosque, PatricioTomasini, NicolásLauthier, Juan JoséMessenger, Louisa AlexandraMonje Rumi, Maria MercedesRagone, Paula GabrielaAlberti D'Amato, Anahi MaitenPerez Brandan, Cecilia MariaBarnabe, ChristianTibayrenc, MichelLewis, Michael DavidLlewellyn, Martin StephenMiles, Michael AlexanderYeo, MatthewMULTILOCUS SEQUENCE TYPINGTRYPANOSOMA CRUZISCHEME OF OPTIMIZATIONGENETIC DIVERSITYhttps://purl.org/becyt/ford/3.3https://purl.org/becyt/ford/3Trypanosoma cruzi, the aetiological agent of Chagas disease possess extensive genetic diversity. This has led to the development of a plethora of molecular typing methods for the identification of both the known major genetic lineages and for more fine scale characterization of different multilocus genotypes within these major lineages. Whole genome sequencing applied to large sample sizes is not currently viable and multilocus enzyme electrophoresis, the previous gold standard for T. cruzi typing, is laborious and time consuming. In the present work, we present an optimized Multilocus Sequence Typing (MLST) scheme, based on the combined analysis of two recently proposed MLST approaches. Here,thirteen concatenated gene fragments were applied to a panel of T. cruzi reference strains encompassing all known genetic lineages. Concatenation of 13 fragments allowed assignment of all strains to the predicted Discrete Typing Units (DTUs), or near-clades, with the exception of one strain that was an outlier for TcV, due to apparent loss of heterozygosity in one fragment. Monophyly for all DTUs, along with robust bootstrap support, was restored when this fragment was subsequently excluded from the analysis. All possible combinations of loci were assessed against predefined criteria with the objective of selecting the most appropriate combination of between two and twelve fragments, for an optimized MLST scheme. The optimum combination consisted of 7 loci and discriminated between all reference strains in the panel, with the majority supported by robust bootstrap values. Additionally, a reduced panel of just 4 gene fragments displayed high bootstrap values for DTU assignment and discriminated 21 out of 25 genotypes. We propose that the seven-fragment MLST scheme could be used as a gold standard for T. cruzi typing, against which other typing approaches, particularly single locus approaches or systematic PCR assays based on amplicon size, could be compared.Fil: Diosque, Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; ArgentinaFil: Tomasini, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; ArgentinaFil: Lauthier, Juan José. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; ArgentinaFil: Messenger, Louisa Alexandra. London School of Hygiene and Tropical Medicine; Reino UnidoFil: Monje Rumi, Maria Mercedes. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; ArgentinaFil: Ragone, Paula Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; ArgentinaFil: Alberti D'Amato, Anahi Maiten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; ArgentinaFil: Perez Brandan, Cecilia Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; ArgentinaFil: Barnabe, Christian. Institut de Recherche pour le Développement. Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle; FranciaFil: Tibayrenc, Michel. Institut de Recherche our le Développement. Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle; FranciaFil: Lewis, Michael David. London School of Hygiene and Tropical Medicine; Reino UnidoFil: Llewellyn, Martin Stephen. London School of Hygiene and Tropical Medicine; Reino UnidoFil: Miles, Michael Alexander. London School of Hygiene and Tropical Medicine; Reino UnidoFil: Yeo, Matthew. London School of Hygiene and Tropical Medicine; Reino UnidoPublic Library Of Science2014-08-28info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/7087Diosque, Patricio; Tomasini, Nicolás; Lauthier, Juan José; Messenger, Louisa Alexandra; Monje Rumi, Maria Mercedes; et al.; Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.; Public Library Of Science; Neglected Tropical Diseases; 8; 8; 28-8-2014; e31171935-2735enginfo:eu-repo/semantics/altIdentifier/doi/info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pntd.0003117info:eu-repo/semantics/altIdentifier/url/http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003117info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:25:11Zoai:ri.conicet.gov.ar:11336/7087instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 14:25:11.291CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.
title Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.
spellingShingle Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.
Diosque, Patricio
MULTILOCUS SEQUENCE TYPING
TRYPANOSOMA CRUZI
SCHEME OF OPTIMIZATION
GENETIC DIVERSITY
title_short Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.
title_full Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.
title_fullStr Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.
title_full_unstemmed Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.
title_sort Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.
dc.creator.none.fl_str_mv Diosque, Patricio
Tomasini, Nicolás
Lauthier, Juan José
Messenger, Louisa Alexandra
Monje Rumi, Maria Mercedes
Ragone, Paula Gabriela
Alberti D'Amato, Anahi Maiten
Perez Brandan, Cecilia Maria
Barnabe, Christian
Tibayrenc, Michel
Lewis, Michael David
Llewellyn, Martin Stephen
Miles, Michael Alexander
Yeo, Matthew
author Diosque, Patricio
author_facet Diosque, Patricio
Tomasini, Nicolás
Lauthier, Juan José
Messenger, Louisa Alexandra
Monje Rumi, Maria Mercedes
Ragone, Paula Gabriela
Alberti D'Amato, Anahi Maiten
Perez Brandan, Cecilia Maria
Barnabe, Christian
Tibayrenc, Michel
Lewis, Michael David
Llewellyn, Martin Stephen
Miles, Michael Alexander
Yeo, Matthew
author_role author
author2 Tomasini, Nicolás
Lauthier, Juan José
Messenger, Louisa Alexandra
Monje Rumi, Maria Mercedes
Ragone, Paula Gabriela
Alberti D'Amato, Anahi Maiten
Perez Brandan, Cecilia Maria
Barnabe, Christian
Tibayrenc, Michel
Lewis, Michael David
Llewellyn, Martin Stephen
Miles, Michael Alexander
Yeo, Matthew
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv MULTILOCUS SEQUENCE TYPING
TRYPANOSOMA CRUZI
SCHEME OF OPTIMIZATION
GENETIC DIVERSITY
topic MULTILOCUS SEQUENCE TYPING
TRYPANOSOMA CRUZI
SCHEME OF OPTIMIZATION
GENETIC DIVERSITY
purl_subject.fl_str_mv https://purl.org/becyt/ford/3.3
https://purl.org/becyt/ford/3
dc.description.none.fl_txt_mv Trypanosoma cruzi, the aetiological agent of Chagas disease possess extensive genetic diversity. This has led to the development of a plethora of molecular typing methods for the identification of both the known major genetic lineages and for more fine scale characterization of different multilocus genotypes within these major lineages. Whole genome sequencing applied to large sample sizes is not currently viable and multilocus enzyme electrophoresis, the previous gold standard for T. cruzi typing, is laborious and time consuming. In the present work, we present an optimized Multilocus Sequence Typing (MLST) scheme, based on the combined analysis of two recently proposed MLST approaches. Here,thirteen concatenated gene fragments were applied to a panel of T. cruzi reference strains encompassing all known genetic lineages. Concatenation of 13 fragments allowed assignment of all strains to the predicted Discrete Typing Units (DTUs), or near-clades, with the exception of one strain that was an outlier for TcV, due to apparent loss of heterozygosity in one fragment. Monophyly for all DTUs, along with robust bootstrap support, was restored when this fragment was subsequently excluded from the analysis. All possible combinations of loci were assessed against predefined criteria with the objective of selecting the most appropriate combination of between two and twelve fragments, for an optimized MLST scheme. The optimum combination consisted of 7 loci and discriminated between all reference strains in the panel, with the majority supported by robust bootstrap values. Additionally, a reduced panel of just 4 gene fragments displayed high bootstrap values for DTU assignment and discriminated 21 out of 25 genotypes. We propose that the seven-fragment MLST scheme could be used as a gold standard for T. cruzi typing, against which other typing approaches, particularly single locus approaches or systematic PCR assays based on amplicon size, could be compared.
Fil: Diosque, Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Tomasini, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Lauthier, Juan José. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Messenger, Louisa Alexandra. London School of Hygiene and Tropical Medicine; Reino Unido
Fil: Monje Rumi, Maria Mercedes. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Ragone, Paula Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Alberti D'Amato, Anahi Maiten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Perez Brandan, Cecilia Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina. Universidad Nacional de Salta; Argentina
Fil: Barnabe, Christian. Institut de Recherche pour le Développement. Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle; Francia
Fil: Tibayrenc, Michel. Institut de Recherche our le Développement. Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle; Francia
Fil: Lewis, Michael David. London School of Hygiene and Tropical Medicine; Reino Unido
Fil: Llewellyn, Martin Stephen. London School of Hygiene and Tropical Medicine; Reino Unido
Fil: Miles, Michael Alexander. London School of Hygiene and Tropical Medicine; Reino Unido
Fil: Yeo, Matthew. London School of Hygiene and Tropical Medicine; Reino Unido
description Trypanosoma cruzi, the aetiological agent of Chagas disease possess extensive genetic diversity. This has led to the development of a plethora of molecular typing methods for the identification of both the known major genetic lineages and for more fine scale characterization of different multilocus genotypes within these major lineages. Whole genome sequencing applied to large sample sizes is not currently viable and multilocus enzyme electrophoresis, the previous gold standard for T. cruzi typing, is laborious and time consuming. In the present work, we present an optimized Multilocus Sequence Typing (MLST) scheme, based on the combined analysis of two recently proposed MLST approaches. Here,thirteen concatenated gene fragments were applied to a panel of T. cruzi reference strains encompassing all known genetic lineages. Concatenation of 13 fragments allowed assignment of all strains to the predicted Discrete Typing Units (DTUs), or near-clades, with the exception of one strain that was an outlier for TcV, due to apparent loss of heterozygosity in one fragment. Monophyly for all DTUs, along with robust bootstrap support, was restored when this fragment was subsequently excluded from the analysis. All possible combinations of loci were assessed against predefined criteria with the objective of selecting the most appropriate combination of between two and twelve fragments, for an optimized MLST scheme. The optimum combination consisted of 7 loci and discriminated between all reference strains in the panel, with the majority supported by robust bootstrap values. Additionally, a reduced panel of just 4 gene fragments displayed high bootstrap values for DTU assignment and discriminated 21 out of 25 genotypes. We propose that the seven-fragment MLST scheme could be used as a gold standard for T. cruzi typing, against which other typing approaches, particularly single locus approaches or systematic PCR assays based on amplicon size, could be compared.
publishDate 2014
dc.date.none.fl_str_mv 2014-08-28
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/7087
Diosque, Patricio; Tomasini, Nicolás; Lauthier, Juan José; Messenger, Louisa Alexandra; Monje Rumi, Maria Mercedes; et al.; Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.; Public Library Of Science; Neglected Tropical Diseases; 8; 8; 28-8-2014; e3117
1935-2735
url http://hdl.handle.net/11336/7087
identifier_str_mv Diosque, Patricio; Tomasini, Nicolás; Lauthier, Juan José; Messenger, Louisa Alexandra; Monje Rumi, Maria Mercedes; et al.; Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi.; Public Library Of Science; Neglected Tropical Diseases; 8; 8; 28-8-2014; e3117
1935-2735
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/
info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pntd.0003117
info:eu-repo/semantics/altIdentifier/url/http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003117
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Public Library Of Science
publisher.none.fl_str_mv Public Library Of Science
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1846082682478395392
score 13.216834

Publicaciones similares