TABLE 1

Effect of IMS and MDA on selective concentration of Salmonella

Sample prepnaCTOutput (Mb)bCoverage (%)cDepth ratiodN50eSerotypeSalmonella reads (%)fSalmonella abundance (%)g
RV12-MDAh20.1272596.261.015106Enteritidis4.7496.37
RV12-IMS-MDAh17.2560699.099.82156488Enteritidis48.1499.35
RV4-IMS-MDAh22.6754621.610.12N/AEnteritidis0.5931.49
RV8-IMS-MDAh24.2160767.600.782173Enteritidis3.8354.63
RV0NAi1400.270.00NANA0.020.05
RV4NA3070.370.00NANA0.010.03
RV8NA1700.420.01NANA0.030.18
RV12h25.5516211.040.10576NA0.491.22
RV24h14.125498.873.6034048Enteritidis16.7418.00
  • a All samples were inoculated with S. Enteritidis at ∼1 CFU/g; RV12, enrichment in RV broth for 12 h; RV12-IMS-MDA, IMS-MDA treatment after 12 h of RV broth enrichment.

  • 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 Average of two replicate samples.

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