Comparative analysis of subtyping methods against a whole-genome-sequencing standard for Salmonella enterica serotype Enteritidis.
A retrospective investigation was performed to evaluate whole-genome sequencing as a benchmark for comparing molecular subtyping methods for Salmonella enterica serotype Enteritidis and survey the population structure of commonly encountered S. enterica serotype Enteritidis outbreak isolates in the United States. A total of 52 S. enterica serotype Enteritidis isolates representing 16 major outbreaks and three sporadic cases collected between 2001 and 2012 were sequenced and subjected to subtyping by four different methods: (i) whole-genome single-nucleotide-polymorphism typing (WGST), (ii) multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA), (iii) clustered regularly interspaced short palindromic repeats combined with multi-virulence-locus sequence typing (CRISPR-MVLST), and (iv) pulsed-field gel electrophoresis (PFGE). WGST resolved all outbreak clusters and provided useful robust phylogenetic inference results with high epidemiological correlation. While both MLVA and CRISPR-MVLST yielded higher discriminatory power than PFGE, MLVA outperformed the other methods in delineating outbreak clusters whereas CRISPR-MVLST showed the potential to trace major lineages and ecological origins of S. enterica serotype Enteritidis. Our results suggested that whole-genome sequencing makes a viable platform for the evaluation and benchmarking of molecular subtyping methods.
Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, Georgia, USA xdeng@uga.edu.
Xiangyu
X
Deng
Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA.
Nikki
N
Shariat
Translational Genomics Research Institute, Flagstaff, Arizona, USA.
Elizabeth M
EM
Driebe
Translational Genomics Research Institute, Flagstaff, Arizona, USA.
Chandler C
CC
Roe
Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Beth
B
Tolar
Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Eija
E
Trees
Translational Genomics Research Institute, Flagstaff, Arizona, USA Northern Arizona University, Flagstaff, Arizona, USA.
Paul
P
Keim
Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, Illinois, USA.
Wei
W
Zhang
Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA Center for Molecular Immunology and Infectious Diseases, The Pennsylvania State University, University Park, Pennsylvania, USA.
Edward G
EG
Dudley
Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Patricia I
PI
Fields
Translational Genomics Research Institute, Flagstaff, Arizona, USA.
David M
DM
Engelthaler
D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D004196:Disease Outbreaks; D016521:Electrophoresis, Gel, Pulsed-Field; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D018895:Microsatellite Repeats; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D012480:Salmonella Infections / Q000453:epidemiology* / Q000382:microbiology*; D012477:Salmonella enteritidis / Q000145:classification* / Q000235:genetics*; D065288:Serogroup