Deng, Xiangyu and Shariat, Nikki and Driebe, Elizabeth M. and Roe, Chandler C. and Tolar, Beth and Trees, Eija and Keim, Paul and Zhang, Wei and Dudley, Edward G. and Fields, Patricia I. and Engelthaler, David M. (2015) Comparative analysis of subtyping methods against a whole-genome-sequencing standard for Salmonella enterica serotype Enteritidis. Journal of Clinical Microbiology, 53 (1). pp. 212-218. ISSN 1098-660X
|
Text
Deng_X_etal_2015_comparative_analysis_subtyping_methods.pdf Download (790kB) | Preview |
Abstract
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.
| Item Type: | Article |
|---|---|
| Publisher’s Statement: | Copyright © 2015, American Society for Microbiology. |
| ID number or DOI: | 10.1128/JCM.02332-14 |
| Keywords: | Salmonella enterica; foodborne pathogen; genome sequencing |
| Subjects: | Q Science > QR Microbiology |
| NAU Depositing Author Academic Status: | Faculty/Staff |
| Department/Unit: | College of Engineering, Forestry, and Natural Science > Biological Sciences |
| Date Deposited: | 29 Jan 2016 22:09 |
| URI: | http://openknowledge.nau.edu/id/eprint/829 |
Actions (login required)
 |
IR Staff Record View |
Downloads
Downloads per month over past year