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 genomes^a

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

^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