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

doi:10.1099/mgen.0.000264

Volume 5, Issue 4

Other

Open Access

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

Alexander M. Wailan¹, Francesc Coll², Eva Heinz¹, Gerry Tonkin-Hill¹, Jukka Corander^1,3,4, Nicholas A. Feasey^5,6 and Nicholas R. Thomson^1,2
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Affiliations: ¹ 1Parasites and Microbes, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK ² 2London School of Hygiene & Tropical Medicine, Keppel St., London WC1E 7HT, UK ³ 3Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland ⁴ 4Department of Biostatistics, University of Oslo, Oslo, Norway ⁵ 5Liverpool School of Tropical Medicine, Pembroke Pl, Liverpool L3 5QA, UK ⁶ 6Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
*Correspondence: Eva Heinz [email protected]
Published: 28 March 2019 https://doi.org/10.1099/mgen.0.000264

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.

Received: 30/08/2018
Accepted: 14/03/2019
Published Online: 28/03/2019

Keyword(s): epidemiology , lineage definition , methicillin-resistant Staphylococcus aureus , phylogenetic tree , R and Salmonella Typhi

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

M Gen 5, e000264 (2019); https://doi.org/10.1099/mgen.0.000264

/content/journal/mgen/10.1099/mgen.0.000264

Volume 5, Issue 4

Other

Open Access

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

Abstract

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