Salmonella Enterica Whole And Core Genome MLST Schemas And Profiles For 4,589 Genomes

Mirko Rossi from the University of Helsinki provides a reference dataset of 4,589 Salmonella enterica genome assemblies. The collection includes 4,307 public genomes downloaded in April 2017 and 282 additional genomes assembled for the INNUENDO project. It features curated whole-genome and core-genome MLST schemas of 8,558 and 3,255 loci respectively, along with corresponding allelic profiles.

Use Cases

• Developing bacterial subtyping schemes based on the provided whole-genome and core-genome MLST schemas.
• Comparative genomic analysis of Salmonella Enteritidis and Typhimurium serovars based on the 1,465 and 2,442 genomes respectively.
• Tracing the epidemiology of specific strains using metadata fields like year, country, and host of isolation.
• Validating new genomic analysis pipelines against a standardized, curated reference dataset.

Strengths

• Includes 4,589 genome assemblies, with specific counts for key serovars like S. Enteritidis (1,465) and S. Typhimurium (2,442).
• Provides two curated MLST schemas: a whole-genome schema with 8,558 loci and a core-genome schema with 3,255 loci.
• Metadata includes specific fields such as source, host, isolation year and country, serotype, and sequence type.

Limitations

• The primary public genome data snapshot is from April 2017, which may not reflect recent genomic diversity.
• Column-level documentation for the metadata and profile files is absent; field semantics must be inferred after download.
• Data may reflect geographic bias, with a noted focus on European serovars and a specific Italian surveillance study.

Provenance

Source

Public repositories including EnteroBase, NCBI, and EMBL-EBI, with additional genomes from the INNUENDO project (PRJEB27020).

Collection Method

Genome assemblies were downloaded and processed; schemas were curated using the chewBBACA software suite.

Time Range

Isolation years for the specific Italian surveillance subset are 2012-2014; public genome access date was April 2017.

Geography

Includes genomes from various countries, with a noted collection from different Italian regions and a focus on serovars frequently isolated in Europe.