Three different datasets were used for evaluation in the present study, comprising selected Salmonella Montevideo [17] (link), Staphylococcus aureus CC398 [5] , and Salmonella Typhimurium DT104 [18] (link) from previous studies.
For S. Montevideo 12 closely related outbreak strains where sequenced once by US Food and Drug Administration using Roche Genome sequencer FLX system, Illumina MiSeq and Life Technologies Ion Torrent and made publicly available (Table S1 ), although only the MiSeq data was used in the original study [16] (link). The raw data were downloaded from the Sequence Read Archive (SRA). For Staphylococcus aureus CC398, the completely sequenced and annotated strain SO385 (AM990992.1) as well as four additional strains were selected from a previously published study [5] and sequenced twice using both MiSeq and Ion Torrent. HiSeq was used in the original study for sequencing. All the strains except for the reference strain were chosen from the same clade, named IIa1i in the original study. The strains are not epidemiologically related but have all been isolated from Danish Pigs and are shown to be closely related in the original study. For S. Typhimurium DT104 the reference strain NCTC 13348 (HF937208.1) and an additional three isolates from the same outbreak [18] (link) were sequenced twice on both MiSeq and Ion Torrent.
Genomic DNA (gDNA) was purified from the isolates using the Easy-DNA extraction kit (Invitrogen) and DNA concentrations determined using the Qubit dsDNA BR Assay Kit (Invitrogen). The isolates were sequenced twice on the MiSeq platform (Illumina) and Ion Torrent PGM (Life Technologies).
For Ion Torrent the isolates were sequenced following the manufacturer’s protocols for 200 bp gDNA fragment library preparation (Ion Xpress Plus gDNA and Amplicon Library 96 Preparation), template preparation (Ion OneTouch System), and sequencing (Ion PGM 200 Sequencing kit) using the 316 chip. For MiSeq the isolates chromosomal DNA of the isolates was used to create genomic libraries using the Nextera XT DNA sample preparation kit (Illumina, cat. No. FC-131-1024) and sequenced using v2, 2×250 bp chemistry on the Illumina MiSeq platform (Illumina, Inc., San Diego, CA).
For S. Montevideo 12 closely related outbreak strains where sequenced once by US Food and Drug Administration using Roche Genome sequencer FLX system, Illumina MiSeq and Life Technologies Ion Torrent and made publicly available (
Genomic DNA (gDNA) was purified from the isolates using the Easy-DNA extraction kit (Invitrogen) and DNA concentrations determined using the Qubit dsDNA BR Assay Kit (Invitrogen). The isolates were sequenced twice on the MiSeq platform (Illumina) and Ion Torrent PGM (Life Technologies).
For Ion Torrent the isolates were sequenced following the manufacturer’s protocols for 200 bp gDNA fragment library preparation (Ion Xpress Plus gDNA and Amplicon Library 96 Preparation), template preparation (Ion OneTouch System), and sequencing (Ion PGM 200 Sequencing kit) using the 316 chip. For MiSeq the isolates chromosomal DNA of the isolates was used to create genomic libraries using the Nextera XT DNA sample preparation kit (Illumina, cat. No. FC-131-1024) and sequenced using v2, 2×250 bp chemistry on the Illumina MiSeq platform (Illumina, Inc., San Diego, CA).
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