Protocol detail

Whole-Genome Sequencing of STEC Strains

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DNA extracted from the two Swedish STEC strains was analyzed using the Ion Torrent S5 XL platform (Thermo Fisher Scientific, Waltham, Massachusetts, USA) as previously described [11 (link)]. The sequencing reads were de novo assembled with Spades (v3.13.1) [12 (link)] in “careful mode” to correct mismatches. The Danish strain was sequenced using an Illumina Nextseq (Illumina, San Diego, CA, USA) as previously described [13 (link)]. The sequencing reads were de novo assembled with SKESA (version 2.3.0) with default settings [14 (link)].

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Bai X., Scheutz F., Dahlgren H.M., Hedenström I, & Jernberg C. (2021). Characterization of Clinical Escherichia coli Strains Producing a Novel Shiga Toxin 2 Subtype in Sweden and Denmark. Microorganisms, 9(11), 2374.

Publication 2021

Ion Torrent S5 XL Nextseq

Stec Strain

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Variable analysis

independent variables

Sequencing platform used: Ion Torrent S5 XL (for the two Swedish STEC strains) and Illumina Nextseq (for the Danish strain)

dependent variables

DNA sequencing and de novo assembly of the genomes from the two Swedish STEC strains and the Danish strain

control variables

The sequencing and assembly methods used for the Swedish and Danish strains were previously described in the referenced publications [11, 13].

controls

No positive or negative controls were explicitly mentioned in the provided information.

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