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Table 3 Comparison of CMg-identified genotypic resistance with phenotypic culture results and the impact on guideline-recommended beta-lactam antibiotic treatment

From: Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units

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
  1. aRecommended antibiotics are those defined in the Guy’s and St Thomas’ Guideline for empiric and targeted first-line treatment for ITU-acquired ventilator-associated pneumonia (VAP). Piperacillin-tazobactam is the first line empiric choice with recommendation to change therapy based on culture results and discussion with microbiology and infectious diseases. Meropenem is used for ESBL-Enterobacterales and E. cloacae, K. aerogenes (formally E. aerogenes), M. morganii and S. marcescens that have inducible β-lactam resistance. Co-amoxiclav is recommended for susceptible organisms
  2. bDetection of ESBL by metagenomics for K. pneumoniae in this sample was not confirmed by culture