Antimicrobial resistance phenotypes and genotype–phenotype concordance for the Gram-positive bacteria datasets using ECOFFs
| Antimicrobial . | E. faecium (human clinical; DE) . | E. faecium (human clinical; BE) . | E. faecalis (human clinical; DE) . | S. aureus (human clinical and surveillance; BE) . | S. aureus (human clinical and surveillance; DK) . | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | R . | S . | concordance (%) . | |
| Ampicillin | 50 | 0 | 100 | 55 | 1 | 100 | – | – | – | – | – | – | – | – | – |
| Cefoxitin | – | – | – | – | – | – | – | – | – | 63 | 0 | 100 | 99 | 1 | 100 |
| Chloramphenicol | 0 | 50 | 64 | – | – | – | – | – | – | – | – | – | – | – | – |
| Ciprofloxacin | 50 | 0 | 100 | 3 | 1 | 100 | – | – | – | 63 | 0 | 100 | – | – | – |
| Clindamycin | – | – | – | – | – | – | – | – | – | 31 | 32 | 96.8 | 36 | 64 | 97 |
| Erythromycin | 50 | 0 | 100 | – | – | – | 39 | 11 | 96 | 32 | 31 | 95.2 | 42 | 58 | 99 |
| Gentamicin | 13 | 0 | 100 | 6 | 2 | 75 | 31 | 4 | 97.1 | 63 | 0 | 100 | 13 | 86 | 93.9 |
| Linezolid | 2 | 48 | 92 | 2 | 33 | 94.2 | 16 | 34 | 96 | 0 | 63 | 100 | 2 | 98 | 99 |
| Tetracycline | 22 | 28 | 92 | – | – | – | 43 | 7 | 98 | 46 | 17 | 76.2 | 17 | 82 | 96.9 |
| Vancomycin | 40 | 10 | 100 | 53 | 3 | 96.4 | 16 | 34 | 98 | 0 | 63 | 100 | – | – | – |
| Antimicrobial . | E. faecium (human clinical; DE) . | E. faecium (human clinical; BE) . | E. faecalis (human clinical; DE) . | S. aureus (human clinical and surveillance; BE) . | S. aureus (human clinical and surveillance; DK) . | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | R . | S . | concordance (%) . | |
| Ampicillin | 50 | 0 | 100 | 55 | 1 | 100 | – | – | – | – | – | – | – | – | – |
| Cefoxitin | – | – | – | – | – | – | – | – | – | 63 | 0 | 100 | 99 | 1 | 100 |
| Chloramphenicol | 0 | 50 | 64 | – | – | – | – | – | – | – | – | – | – | – | – |
| Ciprofloxacin | 50 | 0 | 100 | 3 | 1 | 100 | – | – | – | 63 | 0 | 100 | – | – | – |
| Clindamycin | – | – | – | – | – | – | – | – | – | 31 | 32 | 96.8 | 36 | 64 | 97 |
| Erythromycin | 50 | 0 | 100 | – | – | – | 39 | 11 | 96 | 32 | 31 | 95.2 | 42 | 58 | 99 |
| Gentamicin | 13 | 0 | 100 | 6 | 2 | 75 | 31 | 4 | 97.1 | 63 | 0 | 100 | 13 | 86 | 93.9 |
| Linezolid | 2 | 48 | 92 | 2 | 33 | 94.2 | 16 | 34 | 96 | 0 | 63 | 100 | 2 | 98 | 99 |
| Tetracycline | 22 | 28 | 92 | – | – | – | 43 | 7 | 98 | 46 | 17 | 76.2 | 17 | 82 | 96.9 |
| Vancomycin | 40 | 10 | 100 | 53 | 3 | 96.4 | 16 | 34 | 98 | 0 | 63 | 100 | – | – | – |
For the S. aureus DK dataset only, R, resistant and S, susceptible interpretations according to EUCAST clinical breakpoints were available.
DK, Denmark; DE, Germany; BE, Belgium.
Antimicrobial resistance phenotypes and genotype–phenotype concordance for the Gram-positive bacteria datasets using ECOFFs
| Antimicrobial . | E. faecium (human clinical; DE) . | E. faecium (human clinical; BE) . | E. faecalis (human clinical; DE) . | S. aureus (human clinical and surveillance; BE) . | S. aureus (human clinical and surveillance; DK) . | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | R . | S . | concordance (%) . | |
| Ampicillin | 50 | 0 | 100 | 55 | 1 | 100 | – | – | – | – | – | – | – | – | – |
| Cefoxitin | – | – | – | – | – | – | – | – | – | 63 | 0 | 100 | 99 | 1 | 100 |
| Chloramphenicol | 0 | 50 | 64 | – | – | – | – | – | – | – | – | – | – | – | – |
| Ciprofloxacin | 50 | 0 | 100 | 3 | 1 | 100 | – | – | – | 63 | 0 | 100 | – | – | – |
| Clindamycin | – | – | – | – | – | – | – | – | – | 31 | 32 | 96.8 | 36 | 64 | 97 |
| Erythromycin | 50 | 0 | 100 | – | – | – | 39 | 11 | 96 | 32 | 31 | 95.2 | 42 | 58 | 99 |
| Gentamicin | 13 | 0 | 100 | 6 | 2 | 75 | 31 | 4 | 97.1 | 63 | 0 | 100 | 13 | 86 | 93.9 |
| Linezolid | 2 | 48 | 92 | 2 | 33 | 94.2 | 16 | 34 | 96 | 0 | 63 | 100 | 2 | 98 | 99 |
| Tetracycline | 22 | 28 | 92 | – | – | – | 43 | 7 | 98 | 46 | 17 | 76.2 | 17 | 82 | 96.9 |
| Vancomycin | 40 | 10 | 100 | 53 | 3 | 96.4 | 16 | 34 | 98 | 0 | 63 | 100 | – | – | – |
| Antimicrobial . | E. faecium (human clinical; DE) . | E. faecium (human clinical; BE) . | E. faecalis (human clinical; DE) . | S. aureus (human clinical and surveillance; BE) . | S. aureus (human clinical and surveillance; DK) . | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | R . | S . | concordance (%) . | |
| Ampicillin | 50 | 0 | 100 | 55 | 1 | 100 | – | – | – | – | – | – | – | – | – |
| Cefoxitin | – | – | – | – | – | – | – | – | – | 63 | 0 | 100 | 99 | 1 | 100 |
| Chloramphenicol | 0 | 50 | 64 | – | – | – | – | – | – | – | – | – | – | – | – |
| Ciprofloxacin | 50 | 0 | 100 | 3 | 1 | 100 | – | – | – | 63 | 0 | 100 | – | – | – |
| Clindamycin | – | – | – | – | – | – | – | – | – | 31 | 32 | 96.8 | 36 | 64 | 97 |
| Erythromycin | 50 | 0 | 100 | – | – | – | 39 | 11 | 96 | 32 | 31 | 95.2 | 42 | 58 | 99 |
| Gentamicin | 13 | 0 | 100 | 6 | 2 | 75 | 31 | 4 | 97.1 | 63 | 0 | 100 | 13 | 86 | 93.9 |
| Linezolid | 2 | 48 | 92 | 2 | 33 | 94.2 | 16 | 34 | 96 | 0 | 63 | 100 | 2 | 98 | 99 |
| Tetracycline | 22 | 28 | 92 | – | – | – | 43 | 7 | 98 | 46 | 17 | 76.2 | 17 | 82 | 96.9 |
| Vancomycin | 40 | 10 | 100 | 53 | 3 | 96.4 | 16 | 34 | 98 | 0 | 63 | 100 | – | – | – |
For the S. aureus DK dataset only, R, resistant and S, susceptible interpretations according to EUCAST clinical breakpoints were available.
DK, Denmark; DE, Germany; BE, Belgium.
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