Sample ID | Bacteria reported by culture and metagenomics | Culture-reported resistance | CMg predicted resistance | Relevant genes identified | Genotype/phenotype match? | CMg-based treatment recommendationa |
---|---|---|---|---|---|---|
S1 | K. aerogenes | No | – | – | Y | Meropenem |
S10 | K. pneumoniae | No | – | – | Y | Co-amoxiclav |
S11 | K. pneumoniae | No | – | – | Y | Co-amoxiclav |
S20 | S. aureus | Erythromycin | Erythromycin | erm | Y | Co-amoxiclav |
S21 | E. cloacae | No | No | – | Y | Meropenem |
S31 | K. pneumoniae | ESBL Co-trimoxazole | ESBL Co-trimoxazole | blaTEM, blaSHV blaCTX-M, sul | Y Y | Meropenem |
S34 | K. pneumoniae | No | ESBL | blaTEM, blaSHV | N | Meropenemb |
S35 | A. baumannii | ESBL | – |  | N | Meropenem |
S36 | S. aureus | Erythromycin Trimethoprim | Erythromycin Trimethoprim | erm dfrG | Y | Co-amoxiclav |
S37 | P. mirabilis | No | Amoxicillin Trimethoprim | blaOXA dfrA | N N | Meropenem |
M. morganni | Co-trimoxazole Fosfomycin Nitrofurantoin | Co-trimoxazole – – | dfrA | Y N N | ||
S39 | C. koseri | Amoxicillin | Amoxicillin | blaCKO | Y | Co-amoxiclav |
S44 | S. marcescens | No | – | – | Y | Meropenem |
S49 | K. pneumoniae | ESBL | ESBL | blaTEM | Y | Meropenem |
S51 | S. aureus | Erythromycin | Erythromycin | erm | Y | Co-amoxiclav |
C. koseri | Amoxicillin | Amoxicillin | blaCKO | Y | ||
S52 | K. aerogenes | Gentamicin | – | – | N | Meropenem |
S56 | P. mirabilis | Amoxicillin Co-trimoxazole | Amoxicillin – | blaTEM – | Y N | Co-amoxiclav |
S59 | K. pneumoniae | ESBL Co-trimoxazole | ESBL Co-trimoxazole | blaTEM, blaSHV, sul | Y Y | Meropenem |
S61 | P. mirabilis | No | – | – | Y | Co-amoxiclav |
K. pneumoniae | No | – | – | Y | ||
S62 | K. aerogenes | ESBL | – | – | N | Meropenem |
S63 | K. pneumoniae | ESBL | ESBL | blaSHV | Y | Meropenem |