Table 2. Virulence genes assessment of the Flye assemblies obtained with all reads.
| Sample | Innoculation Level (CFU/ml)e | Serotypea | stx type | eae type | Contig No. (genome and plasmid)b | Percent EDL933_2 Genome Assembled |
|---|---|---|---|---|---|---|
| Water | 0 | O9 | - | - | 677 | - |
| Water+Ecoli1 | 7.3 x 108 | O157:H7 | 1a | gamma-1 | 555 (3+) | 100% |
| Water+Ecoli2 | 7.3 x 107 | O157:H7 | 1a | gamma-1 | 627 (4+) | 100% |
| Water+Ecoli3 | 7.3 x 106 | O157:H7/ O9 | 1a | gamma-1 | 753 (35+) | 100% |
| Water+Ecoli4c | 7.3 x 105 | O157:H7/ O9 | 1a | gamma-1 | 780 (80+) | 85% |
| Water+Ecoli5 | 7.3 x 104 | O9 | - | - | 640 | - |
| Water+Ecoli6d | 7.3 x 103 | O9 | - | - | 644 | - |
| Water+Ecoli7 | 7.3 x 102 | O9 | - | - | 526 | - |
ain silico serotype using genes defined by the Center for Genomic Epidemiology at the technical University of Denmark (DTU) (https://cge.cbs.dtu.dk/services/SerotypeFinder/).
bIn parenthesis, the number of contigs that contain the entire chromosome, a plus sign (+) indicates the presence of a contig that matched the EDL933_2 circular plasmid.
cfragmented genome assembly limit.
dE. coli O157 detection limit (4 reads matching O157 by BLAST classification).
eLevel of E. coli O157 inoculated (combination of 1 ml of enriched water and 1 ml of the E. coli O157 dilution).