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Table 4 Genotypes and predicted phenotypes of antimicrobial resistance (AMR) of bacterial strains with simulated Illumina short reads and either mediocre-quality or low-quality 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
Pseudomonas aeruginosa PAO1 aph(3′)-IIb
blaOXA-50
blaPAO
catB7
fosA
aph(3′)-IIb
blaOXA-50
blaPAO
catB7
fosA
aph(3′)-IIb
blaOXA-50
blaPAO
catB7
fosA
aph(3′)-IIb
blaOXA-50
blaPAO
catB7
fosA
Kanamycin
Ampicillin
Amoxicillin/clavulanic acid
Cefoxitin
Ceftriaxone
Chloramphenicol
Fosfomycin
Kanamycin
Ampicillin
Amoxicillin/clavulanic acid
Cefoxitin
Ceftriaxone
Chloramphenicol
Fosfomycin
Kanamycin
Ampicillin
Amoxicillin/clavulanic acid
Cefoxitin
Ceftriaxone
Chloramphenicol
Fosfomycin
Kanamycin
Ampicillin
Amoxicillin/clavulanic acid
Cefoxitin
Ceftriaxone
Chloramphenicol
Fosfomycin
Bacillus anthracis Ames Ancestor fosB2 fosB2 fosB2 fosB2 Fosfomycin Fosfomycin Fosfomycin Fosfomycin
Klebsiella variicola DSM 15968 blaLEN17 blaLEN17 blaLEN17 blaLEN17 Ampicillin Ampicillin Ampicillin Ampicillin
Listeria monocytogenes EGD-e fosX fosX fosX fosX Fosfomycin Fosfomycin Fosfomycin Fosfomycin
Campylobacter jejuni NCTC 11168 blaOXA-61 blaOXA-61 blaOXA-61 blaOXA-61 Ampicillin Ampicillin Ampicillin Ampicillin
  1. aNo antimicrobial resistance genes (ARGs) were detected in E. coli O157:H7 Sakai, S. Typhimurium LT2, C. sakazakii ATCC 29544, or S. aureus NCTC 8325 as predicted based on their hybrid assemblies using MaSuRCA, SPAdes, and Unicycler