Inferring social network structure from bacterial sequence data

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Pluciński, Mateusz M ^a,b   Starfield, Richard ^a   Almeida, Rodrigo P P ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL PARAMETERS; ARTICLE; BACTERIAL GENETICS; BACTERIAL TRANSMISSION; BACTERIUM ISOLATE; COMMENSAL; COMMUNITY STRUCTURE; CORRELATION ANALYSIS; DNA SEQUENCE; EPIDEMIC; GENETIC DISTANCE; MOLECULAR DYNAMICS; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PATHOGENESIS; SEQUENCE DATABASE; SOCIAL NETWORK; STRUCTURE ANALYSIS;

BACTERIA (MICROORGANISMS);

EID: 79960943229     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0022685     Document Type: Article

References (20)

1. Lewis F, Hughes G, Rambaut A, Poźniak A, Leigh Brown A, (2008) Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med 5: e50.
2. Harris S, Feil E, Holden M, Quail M, Nickerson E, et al. (2010) Evolution of MRSA during hospital transmission and intercontinental spread. Science 327: 469.
3. Real L, Henderson J, Biek R, Snaman J, Jack T, et al. (2005) Unifying the spatial population dynamics and molecular evolution of epidemic rabies virus. Proc Natl Acad Sci USA 102: 12107.
4. Cottam E, Thébaud G, Wadsworth J, Gloster J, Mansley L, et al. (2008) Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus. Proc R Soc London, Ser B 275: 887.
5. Spada E, Sagliocca L, Sourdis J, Garbuglia A, Poggi V, et al. (2004) Use of the minimum spanning tree model for molecular epidemiological investigation of a nosocomial outbreak of hepatitis C virus infection. J of Clin Microbiol 42: 4230.
6. Gardy JL, Johnston JC, Sui SJH, Cook VJ, Shah L, et al. (2011) Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. NEJM 364: 730-739.
7. Jeger M, Pautasso M, Holdenrieder O, Shaw M, (2007) Modelling disease spread and control in networks: implications for plant sciences. New Phytol 174: 279-297.
8. Buckee C, Gupta S, (2010) A Network Approach to Understanding Pathogen Population Structure. Infectious Disease Informatics pp. 167-185.
9. Buckee C, Koelle K, Mustard M, Gupta S, (2004) The effects of host contact network structure on pathogen diversity and strain structure. Proc Natl Acad Sci USA 101: 10839.
10. Maiden M, Bygraves J, Feil E, Morelli G, Russell J, et al. (1998) Multilocus sequence typing: a portable approach to the identi_cation of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95: 3140.
11. Fraser C, Hanage W, Spratt B, (2005) Neutral microepidemic evolution of bacterial pathogens. Proc Natl Acad Sci USA 102: 1968.
12. Buckee C, Jolley K, Recker M, Penman B, Kriz P, et al. (2008) Role of selection in the emergence of lineages and the evolution of virulence in Neisseria meningitidis. Proc Natl Acad Sci USA 105: 15082.
13. Watts D, Strogatz S, (1998) Collective dynamics of small-world networks. Nature 393: 440-442.
14. Turnbaugh P, Ley R, Hamady M, Fraser-Liggett C, Knight R, et al. (2007) The human microbiome project. Nature 449: 804-810.
15. Fierer N, Lauber C, Zhou N, McDonald D, Costello E, et al. (2010) Forensic identification using skin bacterial communities. Proc Natl Acad Sci USA 107: 6477.
16. Beaumont M, Zhang W, Balding D, (2002) Approximate Bayesian computation in population genetics. Genetics 162: 2025.
17. Marjoram P, Molitor J, Plagnol V, Tavaré S, (2003) Markov Chain Monte Carlo without likelihoods. Proc Natl Acad Sci USA 100: 15324.
18. Day N, Moore C, Enright M, Berendt A, Smith J, et al. (2001) A link between virulence and ecological abundance in natural populations of Staphylococcus aureus. Science 292: 114.
19. Jolley K, Kalmusova J, Feil E, Gupta S, Musilek M, et al. (2000) Carried meningococci in the Czech Republic: a diverse recombining population. J Clin Microbiol 38: 4492.
20. Hanage W, Auranen K, Syrjanen R, Herva E, Makela P, et al. (2004) Ability of pneumococcal serotypes and clones to cause acute otitis media: implications for the prevention of otitis media by conjugate vaccines. Infect Immun 72: 76.