TABLE 4

Quasimetagenomics detection and serotyping of S. Enteritidis on inoculated black pepper and lettuce samples

Sample and inoculum (CFU/g)CTOutput (Mb)aCoverage (%)bDepth ratiocN50dSerotypeSalmonella reads (%)eSalmonella abundance (%)f
Black pepper
    0.117.3019999.0620.63226,848Enteritidis97.5899.83
    118.7034399.1020.52117,116Enteritidis96.2899.27
    1018.7038599.1120.627,544Enteritidis96.2299.57
Lettuce
    0.119.7034598.768.2149,289Enteritidis38.3399.12
    116.2033299.0619.4070,588Enteritidis90.4999.91
    1015.5035499.0820.65175,495Enteritidis96.4999.93
  • 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.