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Volume 20, Number 8—August 2014
Research

Rapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis

Henk C. den Bakker, Marc W. Allard, Dianna Bopp, Eric W. Brown, John Fontana, Zamin Iqbal, Aristea Kinney, Ronald Limberger, Kimberlee A. Musser, Matthew Shudt, Errol Strain, Martin Wiedmann, and William J. WolfgangComments to Author 
Author affiliations: Cornell University, Ithaca, New York, USA (H. den Bakker, M. Wiedmann); US Food and Drug Administration, College Park, Maryland, USA (M.W. Allard, E.W. Brown, E. Strain); New York State Department of Health/Wadsworth Center, Albany, New York, USA (D. Bopp, R. Limberger, M. Shudt, K.A. Musser, W.J. Wolfgang); Connecticut Department of Public Health, Rocky Hill, Connecticut, USA (J. Fontana, A. Kinney); Wellcome Trust Centre for Human Genetics, Oxford, UK (Z. Iqbal)

Main Article

Figure 2

Maximum-likelihood tree of population structure of Salmonella enterica serovar Enteritidis isolates obtained in New York and neighboring states, USA. The tree was inferred by using a general time-reversible model with a gamma distribution, which was inferred to be the best fit model by the maximum-likelihood method implemented in MEGA 5.1 (22). Values on branches are bootstrap values based on 150 bootstrap replicates. Pulsed-field gel electrophoresis (PFGE) types are indicated on branches. Label

Figure 2. Figure 2. Maximum-likelihood tree of population structure of Salmonella enterica serovar Enteritidis isolates obtained in New York and neighboring states, USA. The tree was inferred by using a general time-reversible model with a gamma distribution, which was inferred to be the best fit model by the maximum-likelihood method implemented in MEGA 5.1 (22). Values on branches are bootstrap values based on 150 bootstrap replicates. Pulsed-field gel electrophoresis (PFGE) types are indicated on branches. Labels of isolates are colored according to their New York State Department of Health Wadsworth Laboratories multilocus variable-number tandem-repeat subtype designation. Green, MLVA subtype B; red, MLVA subtype W; orange, MLVA subtype AE; blue, MLVA subtype CR; black, MLVA subtype data missing and isolates from Allard et al. (11) . Rectangles indicate well-supported clusters of at least 3 isolates; letters within the rectangles correspond to the cluster designation in the Table. LTCF, long-term care facility. Scale bar indicates single-nucleotide polymorphisms per site.

Main Article

Page created: July 18, 2014
Page updated: July 18, 2014
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