lunes, 17 de noviembre de 2014

Comparative analysis of subtyping methods against a whole genome se... - PubMed - NCBI

Comparative analysis of subtyping methods against a whole genome se... - PubMed - NCBI



 2014 Nov 5. pii: JCM.02332-14. [Epub ahead of print]

Comparative analysis of subtyping methods against a whole genome sequencing standard in Salmonella enterica serotype Enteritidis.

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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