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

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 genomes^a

Strain	Genotype				Predicted phenotype
Strain	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

^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

ISSN: 1471-2164