Phylogenetic methods for genome surveillance of microbial pathogens

Grant number: DE190100805 | Funding period: 2019 - 2022

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Abstract

This project aims to develop phylogenetic approaches to harness the potential evolution of bacterial and virus pathogens data and to improve early detection of infectious outbreaks. Genome surveillance programs consist in routine sequencing of particular organisms to track their evolution over time. Such programs currently exist for important bacterial and virus pathogens. This project expects to develop computational methods to improve our understanding of pathogen outbreak emergence and infectious spread using genome data. This project will expand our knowledge base and research capability in the evolution and epidemiology of infectious agents, and aid in the prevention and control strateg..

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Related publications (8)

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Development of Phylodynamic Methods for Bacterial Pathogens

Danielle J Ingle, Benjamin P Howden, Sebastian Duchene

2021-09-01

Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases..

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Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia

Danielle J Ingle, Rebecca L Ambrose, Sarah L Baines, Sebastian Duchene, Anders Goncalves da Silva, Darren YJ Lee, Miriam Jones, Mary Valcanis, George Taiaroa, Susan A Ballard, Martyn D Kirk, Benjamin P Howden, Jaclyn S Pearson, Deborah A Williamson

2021-08-09

Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emer..

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Infectious disease phylodynamics with occurrence data

Leo A Featherstone, Francesca Di Giallonardo, Edward C Holmes, Timothy G Vaughan, Sebastian Duchene

2021-05-27

Phylodynamic models use pathogen genome sequence data to infer epidemiological dynamics. With the increasing genomic surveillance ..

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The Impacts of Low Diversity Sequence Data on Phylodynamic Inference during an Emerging Epidemic

Anthony Lam, Sebastian Duchene

2021-01-01

Phylodynamic inference is a pivotal tool in understanding transmission dynamics of viral outbreaks. These analyses are strongly gu..

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Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

Sebastian Duchene, Philippe Lemey, Tanja Stadler, Simon YW Ho, David A Duchene, Vijaykrishna Dhanasekaran, Guy Baele

2020-11-01

Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimati..

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The Recovery, Interpretation and Use of Ancient Pathogen Genomes

Sebastian Duchene, Simon YW Ho, Ann G Carmichael, Edward C Holmes, Hendrik Poinar

2020-10-05

The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biolog..

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Temporal signal and the phylodynamic threshold of SARS-CoV-2

Sebastian Duchene, Leo Featherstone, Melina Haritopoulou-Sinanidou, Andrew Rambaut, Philippe Lemey, Guy Baele

2020-07-01

The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publi..

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Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference

David A Duchene, K Jun Tong, Charles SP Foster, Sebastian Duchene, Robert Lanfear, Simon YW Ho

2020-04-01

Evolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees ..

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