TABLE 2

Quasimetagenomics sequencing of S. Enteritidis from raw chicken breast at different inoculation levels and after different culture enrichment durations

Sample prepnaInoculum (CFU/g)CTOutput (Mb)bCoverage (%)cDepth ratiodN50eSerotypeSalmonella reads (%)fSalmonella abundance (%)g
4-h enrichment
    RV4-IMS-MDA0.128.7648710.720.08NAhNA0.3818.37
    RV4-IMS-MDA122.6754621.610.12NAEnteritidis0.5931.49
    RV4-IMS-MDA1020.0848072.660.641,461Enteritidis3.1568.49
8-h enrichment
    RV8-IMS-MDA0.125.5259733.130.16NAEnteritidis0.7739.95
    RV8-IMS-MDA124.2160767.600.782,173Enteritidis3.8354.63
    RV8-IMS-MDA1019.6458399.048.23104,352Enteritidis39.899.46
12-h enrichment
    RV12-IMS-MDA0.119.7351592.924.4871,749Enteritidis21.6697.77
    RV12-IMS-MDA117.2560699.099.82156,488Enteritidis48.1499.35
    RV12-IMS-MDA1016.8378399.1011.46337,433Enteritidis54.7699.55
Negative controlNANA8330.020.00NANA0.150.15
  • a All results (except for the negative control) are reported as the averages from two replicates.

  • b Total output size (million bases) of raw reads per sample.

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

  • d 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.

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

  • f Percentage of Salmonella reads among all sequencing reads.

  • g Percentage of Salmonella reads among all bacterial reads.

  • h NA, no result was obtained. For serotyping, the result was recorded as NA unless both replicates were serotyped.