rPinecone

Define sub-lineages of a clonal expansion via a phylogenetic tree

Alexander M. Wailan, Francesc Coll, Eva Heinz, Gerry Tonkin-Hill, Jukka Corander, Nicholas A. Feasey, Nicholas R. Thomson

Tutkimustuotos: ArtikkelijulkaisuArtikkeliTieteellinenvertaisarvioitu

Kuvaus

The ability to distinguish different circulating pathogen clones from each other is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low-variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node. The utility of this software was demonstrated using both simulated outbreaks and real genomic data of two LV populations: a hospital outbreak of methicillin-resistant Staphylococcus aureus and endemic Salmonella Typhi from rural Cambodia. rPinecone identified the transmission branches of the hospital outbreak and geographically confined lineages in Cambodia. Sub-lineages identified by rPinecone in both analyses were phylogenetically robust. It is anticipated that rPinecone can be used to discriminate between lineages of bacteria from LV populations where other methods fail, enabling a deeper understanding of infectious disease epidemiology for public health purposes.
Alkuperäiskielienglanti
Artikkeli000264
LehtiMicrobial Genomics
Vuosikerta5
Numero4
Sivumäärä9
ISSN2057-5858
DOI - pysyväislinkit
TilaJulkaistu - huhtikuuta 2019
OKM-julkaisutyyppiA1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä, vertaisarvioitu

Tieteenalat

  • 111 Matematiikka
  • 318 Lääketieteen bioteknologia

Lainaa tätä

Wailan, A. M., Coll, F., Heinz, E., Tonkin-Hill, G., Corander, J., Feasey, N. A., & Thomson, N. R. (2019). rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree. Microbial Genomics, 5(4), [000264]. https://doi.org/10.1099/mgen.0.000264
Wailan, Alexander M. ; Coll, Francesc ; Heinz, Eva ; Tonkin-Hill, Gerry ; Corander, Jukka ; Feasey, Nicholas A. ; Thomson, Nicholas R. / rPinecone : Define sub-lineages of a clonal expansion via a phylogenetic tree. Julkaisussa: Microbial Genomics. 2019 ; Vuosikerta 5, Nro 4.
@article{ef591477f53b482c8fb941a2bfd88caa,
title = "rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree",
abstract = "The ability to distinguish different circulating pathogen clones from each other is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low-variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node. The utility of this software was demonstrated using both simulated outbreaks and real genomic data of two LV populations: a hospital outbreak of methicillin-resistant Staphylococcus aureus and endemic Salmonella Typhi from rural Cambodia. rPinecone identified the transmission branches of the hospital outbreak and geographically confined lineages in Cambodia. Sub-lineages identified by rPinecone in both analyses were phylogenetically robust. It is anticipated that rPinecone can be used to discriminate between lineages of bacteria from LV populations where other methods fail, enabling a deeper understanding of infectious disease epidemiology for public health purposes.",
keywords = "R, epidemiology, phylogenetic tree, lineage definition, methicillin-resistant Staphylococcus aureus, Salmonella Typhi, VERSION, PHAST, TOOL, 111 Mathematics, 318 Medical biotechnology",
author = "Wailan, {Alexander M.} and Francesc Coll and Eva Heinz and Gerry Tonkin-Hill and Jukka Corander and Feasey, {Nicholas A.} and Thomson, {Nicholas R.}",
year = "2019",
month = "4",
doi = "10.1099/mgen.0.000264",
language = "English",
volume = "5",
journal = "Microbial Genomics",
issn = "2057-5858",
publisher = "American Society for Microbiology",
number = "4",

}

Wailan, AM, Coll, F, Heinz, E, Tonkin-Hill, G, Corander, J, Feasey, NA & Thomson, NR 2019, 'rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree', Microbial Genomics, Vuosikerta 5, Nro 4, 000264. https://doi.org/10.1099/mgen.0.000264

rPinecone : Define sub-lineages of a clonal expansion via a phylogenetic tree. / Wailan, Alexander M.; Coll, Francesc; Heinz, Eva; Tonkin-Hill, Gerry; Corander, Jukka; Feasey, Nicholas A.; Thomson, Nicholas R.

julkaisussa: Microbial Genomics, Vuosikerta 5, Nro 4, 000264, 04.2019.

Tutkimustuotos: ArtikkelijulkaisuArtikkeliTieteellinenvertaisarvioitu

TY - JOUR

T1 - rPinecone

T2 - Define sub-lineages of a clonal expansion via a phylogenetic tree

AU - Wailan, Alexander M.

AU - Coll, Francesc

AU - Heinz, Eva

AU - Tonkin-Hill, Gerry

AU - Corander, Jukka

AU - Feasey, Nicholas A.

AU - Thomson, Nicholas R.

PY - 2019/4

Y1 - 2019/4

N2 - The ability to distinguish different circulating pathogen clones from each other is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low-variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node. The utility of this software was demonstrated using both simulated outbreaks and real genomic data of two LV populations: a hospital outbreak of methicillin-resistant Staphylococcus aureus and endemic Salmonella Typhi from rural Cambodia. rPinecone identified the transmission branches of the hospital outbreak and geographically confined lineages in Cambodia. Sub-lineages identified by rPinecone in both analyses were phylogenetically robust. It is anticipated that rPinecone can be used to discriminate between lineages of bacteria from LV populations where other methods fail, enabling a deeper understanding of infectious disease epidemiology for public health purposes.

AB - The ability to distinguish different circulating pathogen clones from each other is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low-variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node. The utility of this software was demonstrated using both simulated outbreaks and real genomic data of two LV populations: a hospital outbreak of methicillin-resistant Staphylococcus aureus and endemic Salmonella Typhi from rural Cambodia. rPinecone identified the transmission branches of the hospital outbreak and geographically confined lineages in Cambodia. Sub-lineages identified by rPinecone in both analyses were phylogenetically robust. It is anticipated that rPinecone can be used to discriminate between lineages of bacteria from LV populations where other methods fail, enabling a deeper understanding of infectious disease epidemiology for public health purposes.

KW - R

KW - epidemiology

KW - phylogenetic tree

KW - lineage definition

KW - methicillin-resistant Staphylococcus aureus

KW - Salmonella Typhi

KW - VERSION

KW - PHAST

KW - TOOL

KW - 111 Mathematics

KW - 318 Medical biotechnology

U2 - 10.1099/mgen.0.000264

DO - 10.1099/mgen.0.000264

M3 - Article

VL - 5

JO - Microbial Genomics

JF - Microbial Genomics

SN - 2057-5858

IS - 4

M1 - 000264

ER -