Comparative analysis of subtyping methods against a whole genome se... - PubMed - NCBI
Comparative analysis of subtyping methods against a whole genome sequencing standard in Salmonella enterica serotype Enteritidis.
Deng X1,
Shariat N2,
Driebe EM3,
Roe CC3,
Tolar B4,
Trees E4,
Keim P5,
Zhang W6,
Dudley EG7,
Fields PI4,
Engelthaler DM3.
Abstract
A retrospective investigation was performed to evaluate whole genome sequencing as a benchmark for comparing molecular subtyping methods for Salmonella enterica serotype Enteritidis (SE) and survey the population structure of commonly encountered SE outbreak isolates in the United States. A total of 52 SE isolates representing 16 major outbreaks and three sporadic cases between 2001 and 2012 were sequenced and subjected to subtyping by four different methods: 1) whole genome single nucleotide polymorphism typing (WGST), 2) multiple loci VNTR (variable-number tandem repeat) analysis (MLVA), 3) clustered regularly interspaced short palindromic repeats combined with multi-virulence-locus sequence typing (CRISPR-MVLST) and 4) pulsed-field gel electrophoresis (PFGE). WGST resolved all outbreak clusters and provided useful robust phylogenetic inference with high epidemiological correlation. While both MLVA and CRISPR-MVLST yielded higher discriminatory power than PFGE, MLVA outperformed in delineating outbreak clusters whereas CRISPR-MVLST showed the potential to trace major lineages and ecological origins of SE. Our results suggested that whole genome sequencing makes a viable platform for the evaluation and benchmarking molecular subtyping methods. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
- PMID:
- 25378576
- [PubMed - as supplied by publisher]
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