Table 1.
The hybrid, MinION, and MiSeq assemblies of Salmonella isolates.
Fig 1.
Bioinformatic workflow of the hybrid, MinION, and MiSeq assemblies.
Fig 2.
Circular chromosome map of S. Indiana isolate 43 (SI43H) based on its hybrid assembly.
Table 2.
Antimicrobial resistance (AMR) phenotypes of S. Indiana isolates, and their corresponding AMR genotypes, as predicted based on their hybrid, MinION, and MiSeq assemblies.
Table 3.
Antimicrobial resistance (AMR) phenotypes of S. Typhimurium isolates, and their corresponding AMR genotypes, as predicted based on their hybrid, MinION, and MiSeq assemblies.
Table 4.
Antimicrobial resistance (AMR) phenotypes of S. Enteritidis isolates, and their corresponding AMR genotypes, as predicted based on their hybrid, MinION, and MiSeq assemblies.
Table 5.
Numbers of false positives and false negatives of antimicrobial resistance (AMR) genotypes of Salmonella isolates for each antibiotic, as predicted based on their hybrid, MinION, and MiSeq assemblies.
Table 6.
Numbers of virulence genes and Salmonella pathogenicity islands (SPIs) of Salmonella isolates, as predicted based on their hybrid, MinION, and MiSeq assemblies.
Fig 3.
Whole-genome phylogenetic trees of Salmonella isolates based on their hybrid (H), MinION (N), and MiSeq (M) assemblies.
Fig 4.
Pan-genome compositions (a), and core-genome phylogenetic trees compared to matrices with the presence and absence of core and accessory genes (b) of Salmonella isolates based on their hybrid (A), MinION (B), and MiSeq (C) assemblies.