Deep clustering of bacterial tree images
File(s)
Published version
Author(s)
Hayati, Maryam
Chindelevitch, Leonid
Aanensen, David
Colijn, Caroline
Type
Journal Article
Abstract
The field of genomic epidemiology is rapidly growing as many jurisdictions begin to deploy whole-genome sequencing (WGS) in their national or regional pathogen surveillance programmes. WGS data offer a rich view of the shared ancestry of a set of taxa, typically visualized with phylogenetic trees illustrating the clusters or subtypes present in a group of taxa, their relatedness and the extent of diversification within and between them. When methicillin-resistant Staphylococcus aureus (MRSA) arose and disseminated widely, phylogenetic trees of MRSA-containing types of S. aureus had a distinctive ‘comet’ shape, with a ‘comet head’ of recently adapted drug-resistant isolates in the context of a ‘comet tail’ that was predominantly drug-sensitive. Placing an S. aureus isolate in the context of such a ‘comet’ helped public health laboratories interpret local data within the broader setting of S. aureus evolution. In this work, we ask what other tree shapes, analogous to the MRSA comet, are present in bacterial WGS datasets. We extract trees from large bacterial genomic datasets, visualize them as images and cluster the images. We find nine major groups of tree images, including the ‘comets’, star-like phylogenies, ‘barbell’ phylogenies and other shapes, and comment on the evolutionary and epidemiological stories these shapes might illustrate.
This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
Date Issued
2022-10-10
Date Acceptance
2022-05-17
Citation
Philosophical Transactions of the Royal Society B: Biological Sciences, 2022, 377 (1861)
ISSN
0962-8436
Publisher
The Royal Society
Journal / Book Title
Philosophical Transactions of the Royal Society B: Biological Sciences
Volume
377
Issue
1861
Copyright Statement
© 2022 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
License URL
Identifier
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000843974900011&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=a2bf6146997ec60c407a63945d4e92bb
Subjects
Biology
clustering
deep learning
image processing
Life Sciences & Biomedicine
Life Sciences & Biomedicine - Other Topics
phylogenetics
RESISTANT STAPHYLOCOCCUS-AUREUS
Science & Technology
TRANSMISSION
Publication Status
Published
Coverage Spatial
England
Article Number
20210231
Date Publish Online
2022-08-22