Figure 2 | Scientific Reports

Figure 2

From: A preliminary study of the use of MinION sequencing to specifically detect Shiga toxin-producing Escherichia coli in culture swipes containing multiple serovars of this species

Figure 2

Suggested protocol for clinical diagnostics of STEC with minION sequencing of DNA extracted from culture swipes. Real-time integrated basecalling allows for direct upload of sequence reads to the Epi2me cloud service and WIMP workflow. The suggested procedure results in identification of STEC serotype in less than 24 h. For further characterization of the STEC genome, FASTQ files can be assembled and online tools such as VirulenceFinder will identify virulence factors. If a near complete genome can be assembled and stx is detected in it, the presence of STEC is confirmed. If de novo assembly results in multiple smaller contigs, indicative of multiple E. coli, stx may still be identified as described. However, sequence typing and detailed characterization of the STEC isolate will be difficult.

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