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Related Concept Videos

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Related Experiment Video

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Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples
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Salmonella serotype determination utilizing high-throughput genome sequencing data.

Shaokang Zhang1, Yanlong Yin2, Marcus B Jones3

  • 1Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, Georgia, USA.

Journal of Clinical Microbiology
|March 13, 2015
PubMed
Summary
This summary is machine-generated.

SeqSero is a new tool that uses whole-genome sequencing (WGS) to accurately determine Salmonella serotypes. This WGS-based method supports global surveillance of this common foodborne pathogen.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Salmonella serotyping is crucial for global foodborne pathogen surveillance.
  • Whole-genome sequencing (WGS) is revolutionizing public health microbiology.
  • Current methods for Salmonella serotyping can be time-consuming.

Purpose of the Study:

  • To develop and evaluate a novel web-based tool, SeqSero, for determining Salmonella serotypes using WGS data.
  • To enable rapid and accurate serotype determination from high-throughput sequencing data.
  • To support the integration of WGS into Salmonella surveillance networks.

Main Methods:

  • SeqSero utilizes curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles).
  • The tool analyzes both raw sequencing reads and genome assemblies.
  • Performance was validated using isolates with known serotypes, large public datasets, and metagenomic samples.

Main Results:

  • SeqSero accurately determined serotypes for a wide range of Salmonella serotypes (>2,300).
  • The tool demonstrated high performance on diverse datasets, including raw reads and assembled genomes.
  • Successful serotype determination was achieved from fecal metagenomes.

Conclusions:

  • SeqSero provides a rapid and accurate WGS-based method for Salmonella serotyping.
  • The tool can maintain the utility of traditional serotyping within modern WGS-based subtyping platforms.
  • SeqSero facilitates enhanced surveillance and characterization of Salmonella.