Table 1 Comparison of conventional methods and Sanger sequencing for the detection of individual DPs
Bacteria | Culture | Sequencing | Sensitivity | Specificity | PPV | NPV | Accuracy | |
|---|---|---|---|---|---|---|---|---|
+ | − | |||||||
Vibrio | + | 23 | 0 | 0.575 | 1.000 | 1.000 | 0.971 | 0.972 |
− | 17 | 573 | ||||||
S. typhimurium | + | 17 | 0 | 0.415 | 1.000 | 1.000 | 0.960 | 0.961 |
− | 24 | 572 | ||||||
S. enteritis | + | 2 | 0 | 0.333 | 1.000 | 1.000 | 0.993 | 0.993 |
− | 4 | 607 | ||||||
Shigella | + | 3 | 0 | 0.333 | 1.000 | 1.000 | 0.990 | 0.990 |
− | 6 | 604 | ||||||
C. difficile | + | 6 | 0 | 0.214 | 1.000 | 1.000 | 0.964 | 0.964 |
− | 22 | 585 | ||||||
C. jejuni | + | 12 | 0 | 0.267 | 1.000 | 1.000 | 0.946 | 0.947 |
− | 33 | 578 | ||||||
Y. enterocolitica | + | 0 | 0 | 0.000 | 1.000 | – | 0.998 | 0.998 |
− | 1 | 612 | ||||||
EPEC | + | 49 | 0 | 0.325 | 1.000 | 1.000 | 0.819 | 0.834 |
− | 102 | 462 | ||||||
ETEC | + | 11 | 0 | 0.379 | 1.000 | 1.000 | 0.970 | 0.971 |
− | 18 | 584 | ||||||
EAEC | + | 8 | 0 | 0.296 | 1.000 | 1.000 | 0.969 | 0.969 |
− | 19 | 586 | ||||||
EIEC | + | 2 | 0 | 0.250 | 1.000 | 1.000 | 0.990 | 0.990 |
− | 6 | 605 | ||||||
EHEC | + | 0 | 0 | 0.000 | 1.000 | – | 0.993 | 0.993 |
− | 4 | 609 | ||||||
E. coli O157 | + | 1 | 0 | 0.167 | 1.000 | 1.000 | 0.992 | 0.992 |
− | 5 | 607 | ||||||
Viruses | Singleplex real-time PCR | |||||||
Norovirus | + | 31 | 2 | 1.000 | 0.997 | 0.939 | 1.000 | 0.997 |
− | 0 | 580 | ||||||
Rotavirus | + | 55 | 3 | 1.000 | 0.995 | 0.948 | 1.000 | 0.995 |
− | 0 | 555 | ||||||
Adenovirus | + | 8 | 1 | 1.000 | 0.998 | 0.888 | 1.000 | 0.995 |
− | 0 | 604 | ||||||
Astrovirus | + | 4 | 0 | 1.000 | 1.000 | 1.000 | 1.000 | 0.997 |
− | 0 | 609 | ||||||