TABLE 3

Quasimetagenomics detection and serotyping of Salmonella in unspiked raw chicken parts

Sample prepnMPN/gCTOutput (Mb)aCoverage (%)bDepth ratiocN50dSerotypeSalmonella reads (%)eSalmonella abundance (%)f
Sample A
    RV8-IMS-MDA4323.3022713.310.41665Enteritidis1.749.87
    RV12-IMS-MDA4317.6024861.000.88731Enteritidis4.088.31
Sample B
    RV24-IMS-MDA<322.2024589.251.742,121Typhimurium8.269.79
Sample C
    RV24-IMS-MDA<325.2428912.530.312,169NAg1.352.41
  • a Total output size (million bases) of raw reads per sample.

  • b Percentage of S. Enteritidis reference genome (NCBI reference sequence NC_011294.1) that was mapped by sequencing reads.

  • c Average depth of sequencing was calculated as the ratio between the total size of Salmonella sequences per 100 million bases of sequencing data and the size of the S. Enteritidis reference genome.

  • d N50 was calculated from de novo assemblies of sequencing reads classified as Salmonella.

  • e Percentage of Salmonella reads among all sequencing reads.

  • f Percentage of Salmonella reads among all bacterial reads.

  • g No result was obtained, but was determined as serotype Heidelberg by WGS.