217 closed Salmonella reference genomes using PacBio sequencing

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Whole Genome Sequencing (WGS) is crucial for food safety pathogen surveillance.
• Existing public databases often lack comprehensive genomic data due to reliance on short-read sequencing, limiting insights into repetitive regions, structural variations, and mobile genetic elements.
• Accurate genomic information is vital for tracking antimicrobial resistance (AMR) and virulence genes.

Purpose of the Study:

• To improve the accuracy and completeness of genomic data in public databases for foodborne pathogens.
• To provide high-quality, closed-circular Salmonella enterica genomes generated by PacBio long-read sequencing.
• To enrich the NCBI Pathogen Detection (PD) database and GenBank with diverse Salmonella genomes.

Main Methods:

• Utilized PacBio long-read sequencing technology to generate 217 closed circular Salmonella enterica genomes.
• Sequenced genomes from 78 distinct Salmonella serovars, representing unique strains or SNP clusters.
• Contributed the generated high-quality genome data to the NCBI PD database and GenBank.

Main Results:

• Successfully generated and contributed 217 complete, closed-circular Salmonella enterica genomes.
• The dataset includes genomes from 78 different Salmonella serovars, significantly increasing genomic diversity in public databases.
• The PacBio long-read data provides enhanced resolution for repetitive regions, structural variations, and mobile genetic elements compared to short-read data.

Conclusions:

• The addition of PacBio-generated complete genomes significantly enhances the accuracy and utility of public genomic databases for food safety applications.
• This dataset enables more precise analysis of Salmonella genomes, facilitating better understanding of AMR and virulence gene distribution.
• Complete reference genomes are essential for robust pathogen detection, investigation, and control strategies in food safety.