TABLE 2.
Culture-based versus in silico E. coli detection
| Location | Sample ID | Detection method |
|||
|---|---|---|---|---|---|
| Culture baseda
|
In silicob
|
||||
| EcO157 | STEC | No. reads matching | % relative abundance | ||
| GABOSR | G130904 | − | − | 1,652 | 0.0062 |
| G140116 | − | + | 576 | 0.0019 | |
| G140128 | − | + | 406 | 0.0020 | |
| G140210 | − | + | 936 | 0.0032 | |
| G140224 | − | + | 644 | 0.0024 | |
| G140301 | − | + | 886 | 0.0026 | |
| G140319 | − | − | 866 | 0.0028 | |
| G140402 | − | + | 1,112 | 0.0030 | |
| G140415 | − | − | 711 | 0.0022 | |
| G140611 | − | − | 1,050 | 0.0029 | |
| TOWOSR | T130904 | − | − | 516 | 0.0022 |
| T130918 | − | + | 255 | 0.0011 | |
| T131023 | − | − | 606 | 0.0023 | |
| T131230 | − | + | 379 | 0.0013 | |
| T140116 | − | − | 505 | 0.0019 | |
| T140128 | − | + | 367 | 0.0016 | |
| T140210 | − | − | 607 | 0.0035 | |
| T140224 | + | − | 780 | 0.0026 | |
| T140319 | − | − | 459 | 0.0016 | |
| T140611 | − | − | 1,495 | 0.0037 | |
| Upstream GABOSR | GC1 | − | − | 411 | 0.0016 |
| GC2 | − | + | 419 | 0.0017 | |
| GC3 | − | − | 423 | 0.0015 | |
| Upstream TOWOSR | TC1 | − | + | 478 | 0.0016 |
| TC2 | − | − | 626 | 0.0017 | |
| West Salinas | WS1 | − | − | 958 | 0.0032 |
| WS2 | − | − | 601 | 0.0022 | |
Culture-based methods to detect E. coli in resuspended sediment/water samples included an enrichment culturing step followed by Shiga toxin (stx) PCR procedures to detect specific virulence genes and genotypes as described in Materials and Methods. Detection of E. coli O157 (EcO157) was determined using enzyme-linked immunosorbent assay (ELISA) serotyping and a sample was positive for STEC if PCR and/or ELISA data yielded a positive result.
In silico methods included a blastn search of metagenomic reads against an STEC reference genome with a 95% identity and 97% read coverage cutoff for a read match, which was then normalized by dividing by the total number of reads per metagenome. The two samples with highest relative abundance of reads matching the STEC reference genome are in boldface font.