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Volume 20, Number 9—September 2014
Research

Genomic Epidemiology of Salmonella enterica Serotype Enteritidis based on Population Structure of Prevalent Lineages

Xiangyu DengComments to Author , Prerak T. Desai, Henk C. den Bakker, Matthew Mikoleit, Beth Tolar, Eija Trees, Rene S. Hendriksen, Jonathan G. Frye, Steffen Porwollik, Bart C. Weimer, Martin Wiedmann, George M. Weinstock, Patricia I. Fields1, and Michael McClelland1
Author affiliations: University of Georgia, Griffin, Georgia, USA (X. Deng); University of California Irvine, Irvine, California, USA (P.T. Desai, S. Porwollik, M. McClelland); Cornell University, Ithaca, New York, USA (H.C. den Bakker, M. Wiedmann); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (M. Mikoleit, B. Tolar, E. Trees, P.I. Fields); Technical University of Denmark, Lyngby, Denmark (R.S. Hendriksen); US Department of Agriculture, Athens, Georgia, USA (J.G. Frye); University of California Davis, Davis, California, USA (B.C. Weimer); Washington University School of Medicine, St. Louis, Missouri, USA (G.M. Weinstock)

Main Article

Table

Dating of nodes in the maximum-likelihood tree of Salmonella enterica serotype Enteritidis using BEAST and strict and relaxed mutation rates*

Node, cluster Median MRCA (95% CI)
Relaxed clock
 Strict clock, constant population size
Constant population size GMRF
MRCA, node N01 1549 (1351–1704) 1896 (1858–1933) 1520 (1455–1576)
MRCA II, III, IV, V 1709 (1608–1788) NA 1680 (1636–1716)
MRCA II 1831 (1760–1897) 1937 (1903–1966) 1824 (1799–1846)
MRCA III 1941 (1919–1957) 1950 (1933–1962) 1934 (1924–1944)
MRCA V 1888 (1858–1911) 1917 (1900–1936) 1883 (1869–1897)
Expansion 1, Pacific 1968 (1958–1976) 1975 (1964–1982) 1964 (1958–1970)
Expansion 2 1928 (1916–1937) 1934 (1926–1943) 1926 (1919–1933)
Expansion 3, poultry
 1969 (1956–1981)
 1984 (1974–1995)
 1970 (1964–1976)
*BEAST (16). MRCA, most recent common ancestor; GMRF, Gaussian Markov random field; NA, not available.

Main Article

1These authors contributed equally to this article.

Page created: August 13, 2014
Page updated: August 13, 2014
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