title: The impact of host metapopulation structure on the population genetics of colonizing bacteria.
abstract: Many key bacterial pathogens are frequently carried asymptomatically, and the emergence and spread of these opportunistic pathogens can be driven, or mitigated, via demographic changes within the host population. These inter-host transmission dynamics combine with basic evolutionary parameters such as rates of mutation and recombination, population size and selection, to shape the genetic diversity within bacterial populations. Whilst many studies have focused on how molecular processes underpin bacterial population structure, the impact of host migration and the connectivity of the local populations has received far less attention. A stochastic neutral model incorporating heightened local transmission has been previously shown to fit closely with genetic data for several bacterial species. However, this model did not incorporate transmission limiting population stratification, nor the possibility of migration of strains between subpopulations, which we address here by presenting an extended model. We study the consequences of migration in terms of shared genetic variation and show by simulation that the previously used summary statistic, the allelic mismatch distribution, can be insensitive to even large changes in microepidemic and migration rates. Using likelihood-free inference with genotype network topological summaries we fit a simpler model to commensal and hospital samples from the common nosocomial pathogens Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis and Enterococcus faecium. Only the hospital data for E. faecium display clearly marked deviations from the model predictions which may be attributable to its adaptation to the hospital environment.
authors.affiliation: Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
authors.forename: Elina
authors.initials: E
authors.lastname: Numminen
authors.affiliation: Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland; Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Finland.
authors.forename: Michael
authors.initials: M
authors.lastname: Gutmann
authors.affiliation: Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Shubin
authors.affiliation: Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Finland.
authors.forename: Pekka
authors.initials: P
authors.lastname: Marttinen
authors.affiliation: College of Medicine, Swansea University, Institute of Life Science, Swansea, UK.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Méric
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Willem
authors.initials: W
authors.lastname: van Schaik
authors.affiliation: Department of Microbiology, Ramón y Cajal University Hospital, Madrid, Spain.
authors.forename: Teresa M
authors.initials: TM
authors.lastname: Coque
authors.affiliation: Department of Microbiology, Ramón y Cajal University Hospital, Madrid, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: Baquero
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Rob J L
authors.initials: RJ
authors.lastname: Willems
authors.affiliation: College of Medicine, Swansea University, Institute of Life Science, Swansea, UK.
authors.forename: Samuel K
authors.initials: SK
authors.lastname: Sheppard
authors.affiliation: Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Feil
authors.affiliation: Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA, USA.
authors.forename: William P
authors.initials: WP
authors.lastname: Hanage
authors.affiliation: Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
authors.forename: Jukka
authors.initials: J
authors.lastname: Corander
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000254:growth & development*; D005828:Genetics, Population; D008957:Models, Genetic
keywords: Bacterial evolution; Genetic structure; Migration; Population dynamics