Skip to main content

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

From: Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing

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
  1. aNo antimicrobial resistance genes (ARGs) were detected in E. coli O26:H11 CFSAN027343, E. coli O26:H11 CFSAN027350, E. cancerogenus CFSAN086183, S. Bareilly CFSAN000189, C. sakazakii CFSAN068773, or L. monocytogenes CFSAN008100, as predicted based on their hybrid assemblies using MaSuRCA, SPAdes, and Unicycler