Table 5 Genotypes and predicted phenotypes of antimicrobial resistance (AMR) of bacterial strains with real Illumina short reads and Oxford Nanopore long reads, as predicted based on their MaSuRCA, SPAdes, and Unicycler assemblies and compared to their corresponding reference genomesa
Strain | Genotype | Predicted phenotype | ||||||
|---|---|---|---|---|---|---|---|---|
MaSuRCA | SPAdes | Unicycler | Reference | MaSuRCA | SPAdes | Unicycler | Reference | |
Klebsiella variicola CFSAN086180 | blaLEN16 | blaLEN16 | blaLEN16 | blaLEN16 | Ampicillin | Ampicillin | Ampicillin | Ampicillin |
Klebsiella pneumonia CFSAN086181 | blaSHV-11 fosA6 oqxA oqxB | blaSHV-11 fosA6 oqxA oqxB | blaSHV-11 fosA6 oqxA oqxB | blaSHV-11 fosA6 oqxA oqxB | Ampicillin Fosfomycin Chloramphenicol | Ampicillin Fosfomycin Chloramphenicol | Ampicillin Fosfomycin Chloramphenicol | Ampicillin Fosfomycin Chloramphenicol |
Citrobacter braakii CFSAN086182 | blaCMY-83 | blaCMY-83 | blaCMY-83 | blaCMY-83 | Ampicillin Amoxicillin/clavulanic acid Cefoxitin Ceftriaxone | Ampicillin Amoxicillin/clavulanic acid Cefoxitin Ceftriaxone | Ampicillin Amoxicillin/clavulanic acid Cefoxitin Ceftriaxone | Ampicillin Amoxicillin/clavulanic acid Cefoxitin Ceftriaxone |
Staphylococcus aureus CFSAN007894 | msr(A) tet(K) | blaZ | blaZ | blaZ | Erythromycin Azithromycin Tetracycline | Ampicillin | Ampicillin | Ampicillin |
Campylobacter jejuni CFSAN032806 | aph(2″)-Ig aph(3′)-III blaOXA-61 tet(O) | aph(2″)-Ig aph(3′)-III blaOXA-61 tet(O) | aph(2″)-Ig aph(3′)-III blaOXA-61 tet(O) | aph(2″)-Ig aph(3′)-III blaOXA-61 tet(O) | Kanamycin Ampicillin Tetracycline | Kanamycin Ampicillin Tetracycline | Kanamycin Ampicillin Tetracycline | Kanamycin Ampicillin Tetracycline |
Campylobacter coli CFSAN032805 | aph(2″)-Ig aph(3′)-III blaOXA-61 tet(O) | aph(2″)-Ig aph(3′)-III blaOXA-61 tet(O) | aph(2″)-Ig aph(3′)-III blaOXA-61 tet(O) | aph(2″)-Ig aph(3′)-III blaOXA-61 tet(O) | Kanamycin Ampicillin Tetracycline | Kanamycin Ampicillin Tetracycline | Kanamycin Ampicillin Tetracycline | Kanamycin Ampicillin Tetracycline |