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Patterns of genome evolution that have accompanied host adaptation in Salmonella

Langridge, Gemma C.; Fookes, Maria; Connor, Thomas R.; Feltwell, Theresa; Feasey, Nicholas; Parsons, Bryony N.; Seth-Smith, Helena M.B.; Barquist, Lars; Stedman, Anna; Humphrey, Tom; Wigley, Paul; Peters, Sarah E.; Maskell, Duncan J.; Corander, Jukka; Chabalgoity, Jose A.; Barrow, Paul; Parkhill, Julian; Dougan, Gordon; Thomson, Nicholas R.


Gemma C. Langridge

Maria Fookes

Thomas R. Connor

Theresa Feltwell

Nicholas Feasey

Bryony N. Parsons

Helena M.B. Seth-Smith

Lars Barquist

Anna Stedman

Tom Humphrey

Paul Wigley

Sarah E. Peters

Duncan J. Maskell

Jukka Corander

Jose A. Chabalgoity

Paul Barrow

Julian Parkhill

Gordon Dougan

Nicholas R. Thomson


Many bacterial pathogens are specialized, infecting one or few hosts, and this is often associated with more acute disease presentation. Specific genomes show markers of this specialization, which often reflect a balance between gene acquisition and functional gene loss. Within Salmonella enterica subspecies enterica, a single lineage exists that includes human and animal pathogens adapted to cause infection in different hosts, including S. enterica serovar Enteritidis (multiple hosts), S. Gallinarum (birds), and S. Dublin (cattle). This provides an excellent evolutionary context in which differences between these pathogen genomes can be related to host range. Genome sequences were obtained from ∼60 isolates selected to represent the known diversity of this lineage. Examination and comparison of the clades within the phylogeny of this lineage revealed signs of host restriction as well as evolutionary events that mark a path to host generalism. We have identified the nature and order of events for both evolutionary trajectories. The impact of functional gene loss was predicted based upon position within metabolic pathways and confirmed with phenotyping assays. The structure of S. Enteritidis is more complex than previously known, as a second clade of S. Enteritidis was revealed that is distinct from those commonly seen to cause disease in humans or animals, and that is more closely related to S. Gallinarum. Isolates from this second clade were tested in a chick model of infection and exhibited a reduced colonization phenotype, which we postulate represents an intermediate stage in pathogen–host adaptation.


Langridge, G. C., Fookes, M., Connor, T. R., Feltwell, T., Feasey, N., Parsons, B. N., …Thomson, N. R. (2015). Patterns of genome evolution that have accompanied host adaptation in Salmonella. Proceedings of the National Academy of Sciences, 112(3), 863-868.

Journal Article Type Article
Acceptance Date Nov 26, 2014
Online Publication Date Dec 22, 2014
Publication Date Jan 20, 2015
Deposit Date Oct 19, 2017
Publicly Available Date Nov 17, 2020
Journal Proceedings of the National Academy of Sciences
Print ISSN 0027-8424
Electronic ISSN 1091-6490
Publisher National Academy of Sciences
Peer Reviewed Peer Reviewed
Volume 112
Issue 3
Pages 863-868
Public URL
Publisher URL
PMID 00034804
Additional Information Freely available online through the PNAS open access option.


Patterns of genome evolution (901 Kb)

Copyright Statement
Freely available online through the PNAS open access option.

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