Development of Phylodynamic Methods for Bacterial Pathogens

Danielle J Ingle; Benjamin P Howden; Sebastian Duchene

doi:10.1016/j.tim.2021.02.008

Development of Phylodynamic Methods for Bacterial Pathogens

Trends Microbiol. 2021 Sep;29(9):788-797. doi: 10.1016/j.tim.2021.02.008. Epub 2021 Mar 15.

Authors

Danielle J Ingle¹, Benjamin P Howden², Sebastian Duchene³

Affiliations

¹ Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
² Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
³ Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia. Electronic address: sebastian.duchene@unimelb.edu.au.

PMID: 33736902
DOI: 10.1016/j.tim.2021.02.008

Abstract

Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases. To date, the field has centered on viruses. Bacterial pathogens are seldom analyzed under such phylodynamic frameworks, due to their complex genome evolution and, until recently, a paucity of whole-genome sequence data sets with rich associated metadata. We posit that the increasing availability of bacterial genomes and epidemiological data means that the field is now ripe to lay the foundations for applying phylodynamics to bacterial pathogens. The development of new methods that integrate more complex genomic and ecological data will help to inform public heath surveillance and control strategies for bacterial pathogens that represent serious threats to human health.

Keywords: bacteria; pathogens; phylodynamics.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Animals
Bacteria / classification
Bacteria / genetics*
Bacteria / isolation & purification
Bacterial Infections / epidemiology
Bacterial Infections / microbiology*
Evolution, Molecular
Genome, Bacterial
Genomics / methods*
Genomics / trends
Humans
Phylogeny