Antimicrobial resistance phenotypes and genotype–phenotype concordance for the Gram-negative bacteria datasets using ECOFFs
| Antimicrobial . | E. coli (animal surveillance; DK) . | E. coli (animal surveillance; UK) . | E. coli (human and animal clinical and surveillance; DE) . | Salmonella sp. (human clinical, animal surveillance; USA) . | C. jejuni (animal surveillance; EU) . | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | |
| Ampicillin | 95 | 0 | 100 | 81 | 18 | 98.9 | 202 | 0 | 100 | 249 | 822 | 98.7 | – | – | – |
| Cefepime | 78 | 17 | 71.6 | – | – | – | 137 | 0 | 100 | – | – | – | – | – | – |
| Cefotaxime | 95 | 0 | 100 | 23 | 76 | 98.9 | 370 | 0 | 98.6 | – | – | – | – | – | – |
| Cefoxitin | 46 | 49 | 97.8 | – | – | – | – | – | – | 130 | 933 | 98.9 | – | – | – |
| Ceftazidime | 94 | 1 | 98.9 | – | – | – | 282 | 0 | 99.2 | – | – | – | – | – | – |
| Chloramphenicol | 8 | 87 | 100 | – | – | – | 63 | 67 | 73.1 | 41 | 1030 | 99.7 | – | – | – |
| Ciprofloxacin | 29 | 66 | 87.3 | 64 | 35 | 95.9 | 275 | 0 | 99.2 | 22 | 1049 | 97 | 134 | 105 | 99.1 |
| Colistin | 0 | 95 | 100 | 11 | 88 | 100 | – | – | – | – | – | – | – | – | – |
| Ertapenem | 1 | 94 | 98.9 | – | – | – | 60 | 70 | 54.6 | – | – | – | – | – | – |
| Erythromycin | – | – | – | – | – | – | – | – | – | – | – | – | 3 | 236 | 99.1 |
| Gentamicin | 15 | 80 | 100 | 34 | 65 | 100 | 129 | 258 | 97.6 | 126 | 945 | 98.9 | 0 | 239 | 100 |
| Imipenem | 0 | 95 | 100 | 0 | 98 | 100 | 2 | 192 | 100 | – | – | – | – | – | – |
| Meropenem | 0 | 95 | 100 | 0 | 99 | 100 | 2 | 0 | 100 | – | – | – | – | – | – |
| Nalidixic acid | 25 | 70 | 98.9 | 39 | 60 | 90.9 | 99 | 28 | 99.2 | 10 | 1061 | 99.4 | 131 | 108 | 97.9 |
| Streptomycin | – | – | – | – | – | – | – | – | – | – | – | – | 0 | 187 | 100 |
| Sulfamethoxazole | 61 | 34 | 98.9 | – | – | – | – | – | – | – | – | – | – | – | – |
| Tetracycline | 53 | 42 | 100 | 79 | 20 | 97.9 | 138 | 33 | 98.8 | 656 | 415 | 98.6 | 130 | 109 | 99.1 |
| Tigecycline | – | – | – | – | – | – | 5 | 147 | 96.7 | – | – | – | – | – | – |
| Trimethoprim | 29 | 66 | 100 | – | – | – | – | – | – | – | – | – | – | – | – |
| Antimicrobial . | E. coli (animal surveillance; DK) . | E. coli (animal surveillance; UK) . | E. coli (human and animal clinical and surveillance; DE) . | Salmonella sp. (human clinical, animal surveillance; USA) . | C. jejuni (animal surveillance; EU) . | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | |
| Ampicillin | 95 | 0 | 100 | 81 | 18 | 98.9 | 202 | 0 | 100 | 249 | 822 | 98.7 | – | – | – |
| Cefepime | 78 | 17 | 71.6 | – | – | – | 137 | 0 | 100 | – | – | – | – | – | – |
| Cefotaxime | 95 | 0 | 100 | 23 | 76 | 98.9 | 370 | 0 | 98.6 | – | – | – | – | – | – |
| Cefoxitin | 46 | 49 | 97.8 | – | – | – | – | – | – | 130 | 933 | 98.9 | – | – | – |
| Ceftazidime | 94 | 1 | 98.9 | – | – | – | 282 | 0 | 99.2 | – | – | – | – | – | – |
| Chloramphenicol | 8 | 87 | 100 | – | – | – | 63 | 67 | 73.1 | 41 | 1030 | 99.7 | – | – | – |
| Ciprofloxacin | 29 | 66 | 87.3 | 64 | 35 | 95.9 | 275 | 0 | 99.2 | 22 | 1049 | 97 | 134 | 105 | 99.1 |
| Colistin | 0 | 95 | 100 | 11 | 88 | 100 | – | – | – | – | – | – | – | – | – |
| Ertapenem | 1 | 94 | 98.9 | – | – | – | 60 | 70 | 54.6 | – | – | – | – | – | – |
| Erythromycin | – | – | – | – | – | – | – | – | – | – | – | – | 3 | 236 | 99.1 |
| Gentamicin | 15 | 80 | 100 | 34 | 65 | 100 | 129 | 258 | 97.6 | 126 | 945 | 98.9 | 0 | 239 | 100 |
| Imipenem | 0 | 95 | 100 | 0 | 98 | 100 | 2 | 192 | 100 | – | – | – | – | – | – |
| Meropenem | 0 | 95 | 100 | 0 | 99 | 100 | 2 | 0 | 100 | – | – | – | – | – | – |
| Nalidixic acid | 25 | 70 | 98.9 | 39 | 60 | 90.9 | 99 | 28 | 99.2 | 10 | 1061 | 99.4 | 131 | 108 | 97.9 |
| Streptomycin | – | – | – | – | – | – | – | – | – | – | – | – | 0 | 187 | 100 |
| Sulfamethoxazole | 61 | 34 | 98.9 | – | – | – | – | – | – | – | – | – | – | – | – |
| Tetracycline | 53 | 42 | 100 | 79 | 20 | 97.9 | 138 | 33 | 98.8 | 656 | 415 | 98.6 | 130 | 109 | 99.1 |
| Tigecycline | – | – | – | – | – | – | 5 | 147 | 96.7 | – | – | – | – | – | – |
| Trimethoprim | 29 | 66 | 100 | – | – | – | – | – | – | – | – | – | – | – | – |
DK, Denmark; DE, Germany.
Antimicrobial resistance phenotypes and genotype–phenotype concordance for the Gram-negative bacteria datasets using ECOFFs
| Antimicrobial . | E. coli (animal surveillance; DK) . | E. coli (animal surveillance; UK) . | E. coli (human and animal clinical and surveillance; DE) . | Salmonella sp. (human clinical, animal surveillance; USA) . | C. jejuni (animal surveillance; EU) . | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | |
| Ampicillin | 95 | 0 | 100 | 81 | 18 | 98.9 | 202 | 0 | 100 | 249 | 822 | 98.7 | – | – | – |
| Cefepime | 78 | 17 | 71.6 | – | – | – | 137 | 0 | 100 | – | – | – | – | – | – |
| Cefotaxime | 95 | 0 | 100 | 23 | 76 | 98.9 | 370 | 0 | 98.6 | – | – | – | – | – | – |
| Cefoxitin | 46 | 49 | 97.8 | – | – | – | – | – | – | 130 | 933 | 98.9 | – | – | – |
| Ceftazidime | 94 | 1 | 98.9 | – | – | – | 282 | 0 | 99.2 | – | – | – | – | – | – |
| Chloramphenicol | 8 | 87 | 100 | – | – | – | 63 | 67 | 73.1 | 41 | 1030 | 99.7 | – | – | – |
| Ciprofloxacin | 29 | 66 | 87.3 | 64 | 35 | 95.9 | 275 | 0 | 99.2 | 22 | 1049 | 97 | 134 | 105 | 99.1 |
| Colistin | 0 | 95 | 100 | 11 | 88 | 100 | – | – | – | – | – | – | – | – | – |
| Ertapenem | 1 | 94 | 98.9 | – | – | – | 60 | 70 | 54.6 | – | – | – | – | – | – |
| Erythromycin | – | – | – | – | – | – | – | – | – | – | – | – | 3 | 236 | 99.1 |
| Gentamicin | 15 | 80 | 100 | 34 | 65 | 100 | 129 | 258 | 97.6 | 126 | 945 | 98.9 | 0 | 239 | 100 |
| Imipenem | 0 | 95 | 100 | 0 | 98 | 100 | 2 | 192 | 100 | – | – | – | – | – | – |
| Meropenem | 0 | 95 | 100 | 0 | 99 | 100 | 2 | 0 | 100 | – | – | – | – | – | – |
| Nalidixic acid | 25 | 70 | 98.9 | 39 | 60 | 90.9 | 99 | 28 | 99.2 | 10 | 1061 | 99.4 | 131 | 108 | 97.9 |
| Streptomycin | – | – | – | – | – | – | – | – | – | – | – | – | 0 | 187 | 100 |
| Sulfamethoxazole | 61 | 34 | 98.9 | – | – | – | – | – | – | – | – | – | – | – | – |
| Tetracycline | 53 | 42 | 100 | 79 | 20 | 97.9 | 138 | 33 | 98.8 | 656 | 415 | 98.6 | 130 | 109 | 99.1 |
| Tigecycline | – | – | – | – | – | – | 5 | 147 | 96.7 | – | – | – | – | – | – |
| Trimethoprim | 29 | 66 | 100 | – | – | – | – | – | – | – | – | – | – | – | – |
| Antimicrobial . | E. coli (animal surveillance; DK) . | E. coli (animal surveillance; UK) . | E. coli (human and animal clinical and surveillance; DE) . | Salmonella sp. (human clinical, animal surveillance; USA) . | C. jejuni (animal surveillance; EU) . | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | nWT . | WT . | concordance (%) . | |
| Ampicillin | 95 | 0 | 100 | 81 | 18 | 98.9 | 202 | 0 | 100 | 249 | 822 | 98.7 | – | – | – |
| Cefepime | 78 | 17 | 71.6 | – | – | – | 137 | 0 | 100 | – | – | – | – | – | – |
| Cefotaxime | 95 | 0 | 100 | 23 | 76 | 98.9 | 370 | 0 | 98.6 | – | – | – | – | – | – |
| Cefoxitin | 46 | 49 | 97.8 | – | – | – | – | – | – | 130 | 933 | 98.9 | – | – | – |
| Ceftazidime | 94 | 1 | 98.9 | – | – | – | 282 | 0 | 99.2 | – | – | – | – | – | – |
| Chloramphenicol | 8 | 87 | 100 | – | – | – | 63 | 67 | 73.1 | 41 | 1030 | 99.7 | – | – | – |
| Ciprofloxacin | 29 | 66 | 87.3 | 64 | 35 | 95.9 | 275 | 0 | 99.2 | 22 | 1049 | 97 | 134 | 105 | 99.1 |
| Colistin | 0 | 95 | 100 | 11 | 88 | 100 | – | – | – | – | – | – | – | – | – |
| Ertapenem | 1 | 94 | 98.9 | – | – | – | 60 | 70 | 54.6 | – | – | – | – | – | – |
| Erythromycin | – | – | – | – | – | – | – | – | – | – | – | – | 3 | 236 | 99.1 |
| Gentamicin | 15 | 80 | 100 | 34 | 65 | 100 | 129 | 258 | 97.6 | 126 | 945 | 98.9 | 0 | 239 | 100 |
| Imipenem | 0 | 95 | 100 | 0 | 98 | 100 | 2 | 192 | 100 | – | – | – | – | – | – |
| Meropenem | 0 | 95 | 100 | 0 | 99 | 100 | 2 | 0 | 100 | – | – | – | – | – | – |
| Nalidixic acid | 25 | 70 | 98.9 | 39 | 60 | 90.9 | 99 | 28 | 99.2 | 10 | 1061 | 99.4 | 131 | 108 | 97.9 |
| Streptomycin | – | – | – | – | – | – | – | – | – | – | – | – | 0 | 187 | 100 |
| Sulfamethoxazole | 61 | 34 | 98.9 | – | – | – | – | – | – | – | – | – | – | – | – |
| Tetracycline | 53 | 42 | 100 | 79 | 20 | 97.9 | 138 | 33 | 98.8 | 656 | 415 | 98.6 | 130 | 109 | 99.1 |
| Tigecycline | – | – | – | – | – | – | 5 | 147 | 96.7 | – | – | – | – | – | – |
| Trimethoprim | 29 | 66 | 100 | – | – | – | – | – | – | – | – | – | – | – | – |
DK, Denmark; DE, Germany.
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