Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny

Abstract Although multilocus sequence typing (MLST) is highly discriminatory and useful for outbreak investigations and epidemiological surveillance, it has always been controversial whether clustering and phylogeny inferred from the MLST gene loci can represent the real phylogeny of bacterial strai...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Alan K. L. Tsang, Hwei Huih Lee, Siu-Ming Yiu, Susanna K. P. Lau, Patrick C. Y. Woo
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1aba6ee04ee84d78bd4d9a6d8d4e7d69
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:1aba6ee04ee84d78bd4d9a6d8d4e7d69
record_format	dspace
spelling	oai:doaj.org-article:1aba6ee04ee84d78bd4d9a6d8d4e7d692021-12-02T15:05:00ZFailure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny10.1038/s41598-017-04707-42045-2322https://doaj.org/article/1aba6ee04ee84d78bd4d9a6d8d4e7d692017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-04707-4https://doaj.org/toc/2045-2322Abstract Although multilocus sequence typing (MLST) is highly discriminatory and useful for outbreak investigations and epidemiological surveillance, it has always been controversial whether clustering and phylogeny inferred from the MLST gene loci can represent the real phylogeny of bacterial strains. In this study, we compare the phylogenetic trees constructed using three approaches, (1) concatenated blocks of homologous sequence shared between the bacterial genomes, (2) genome single-nucleotide polymorphisms (SNP) profile and (3) concatenated nucleotide sequences of gene loci in the corresponding MLST schemes, for 10 bacterial species with >30 complete genome sequences available. Major differences in strain clustering at more than one position were observed between the phylogeny inferred using genome/SNP data and MLST for all 10 bacterial species. Shimodaira-Hasegawa test revealed significant difference between the topologies of the genome and MLST trees for nine of the 10 bacterial species, and significant difference between the topologies of the SNP and MLST trees were present for all 10 bacterial species. Matching Clusters and R-F Clusters metrics showed that the distances between the genome/SNP and MLST trees were larger than those between the SNP and genome trees. Phylogeny inferred from MLST failed to represent genome phylogeny with the same bacterial species.Alan K. L. TsangHwei Huih LeeSiu-Ming YiuSusanna K. P. LauPatrick C. Y. WooNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Alan K. L. Tsang Hwei Huih Lee Siu-Ming Yiu Susanna K. P. Lau Patrick C. Y. Woo Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny
description	Abstract Although multilocus sequence typing (MLST) is highly discriminatory and useful for outbreak investigations and epidemiological surveillance, it has always been controversial whether clustering and phylogeny inferred from the MLST gene loci can represent the real phylogeny of bacterial strains. In this study, we compare the phylogenetic trees constructed using three approaches, (1) concatenated blocks of homologous sequence shared between the bacterial genomes, (2) genome single-nucleotide polymorphisms (SNP) profile and (3) concatenated nucleotide sequences of gene loci in the corresponding MLST schemes, for 10 bacterial species with >30 complete genome sequences available. Major differences in strain clustering at more than one position were observed between the phylogeny inferred using genome/SNP data and MLST for all 10 bacterial species. Shimodaira-Hasegawa test revealed significant difference between the topologies of the genome and MLST trees for nine of the 10 bacterial species, and significant difference between the topologies of the SNP and MLST trees were present for all 10 bacterial species. Matching Clusters and R-F Clusters metrics showed that the distances between the genome/SNP and MLST trees were larger than those between the SNP and genome trees. Phylogeny inferred from MLST failed to represent genome phylogeny with the same bacterial species.
format	article
author	Alan K. L. Tsang Hwei Huih Lee Siu-Ming Yiu Susanna K. P. Lau Patrick C. Y. Woo
author_facet	Alan K. L. Tsang Hwei Huih Lee Siu-Ming Yiu Susanna K. P. Lau Patrick C. Y. Woo
author_sort	Alan K. L. Tsang
title	Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny
title_short	Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny
title_full	Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny
title_fullStr	Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny
title_full_unstemmed	Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny
title_sort	failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/1aba6ee04ee84d78bd4d9a6d8d4e7d69
work_keys_str_mv	AT alankltsang failureofphylogenyinferredfrommultilocussequencetypingtorepresentbacterialphylogeny AT hweihuihlee failureofphylogenyinferredfrommultilocussequencetypingtorepresentbacterialphylogeny AT siumingyiu failureofphylogenyinferredfrommultilocussequencetypingtorepresentbacterialphylogeny AT susannakplau failureofphylogenyinferredfrommultilocussequencetypingtorepresentbacterialphylogeny AT patrickcywoo failureofphylogenyinferredfrommultilocussequencetypingtorepresentbacterialphylogeny
_version_	1718388940155650048

Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny

Ejemplares similares