Table 3. Virulence of the Flye assemblies obtained with the WIMP E. coli extracted reads.
| Samplea | WIMP E. coli Reads | Serotypeb | stx type | eae type | Contig No. (genome and plasmid)c | Percent EDL933_2 Genome Assembled |
|---|---|---|---|---|---|---|
| Water | 10,806 | O9 | - | - | 31 | - |
| Water+Ecoli1 | 1,659,463 | O157:H7 | 1a | gamma-1 | 44 (1+) | 100% |
| Water+Ecoli2 | 432,649 | O157:H7 | 1a | gamma-1 | 40 (1+) | 100% |
| Water+Ecoli3 | 73,783 | O157:H7/ O9 | 1a | gamma-1 | 41 (8+) | 100% |
| Water+Ecoli4d | 17,203 | O157:H7/ O9 | 1a | gamma-1 | 92 (63+) | 85% |
| Water+Ecoli5 | 10,086 | O9 | - | - | 28 | - |
| Water+Ecoli6e | 8,515 | O9 | - | - | 24 | - |
aCFU/ml levels of EDL933_2 inoculation can be found in Table 2.
bin 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/).
cIn 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.
dfragmented genome assembly limit.
eE. coli O157 detection limit (4 reads matching O157 by BLAST classification).