Table 2 Overview of MinION sequencing data and results from bioinformatic analysis.

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

 

Experiment 1

Experiment 2

Experiment 3

E. coli strains in each experiment (relative abundance)

STEC O145:H28 (~ 10%) + STEC-LST O145:H28 (~ 90%)

STEC O145:H28 (~ 10%)

STEC-LST O145:H28 ~ 7%)

EPEC O21 (~ 23%)

EAEC O104:H4 (~ 29%)

ExPEC O6:H31 (~ 29%)

STEC O145:H28 (~ 2%)

STEC-LST O145:H28 (~ 21%)

EPEC O21 (~ 12%)

EAEC O104:H4 (~ 37%)

ExPEC O6:H31 (~ 27%)

Data output minION

2.5 gB

2.3gB

2.3 gB

# of reads minION

417 000

379 000

386 920

Serotypes identified by WIMP*

O145:H28

O145:H28, O104:H4

O145:H28, O104:H4,

# of contigs after assembly CANU

3 (5,4 Mb, 141 kb, 142 kb)

135

160

PathogenFinder

Input organism predicted as human pathogen

Input organism predicted as human pathogen

Input organism predicted as human pathogen

Serogroups identified by SerotypeFinder

O145, H28

O6, H28, H4, H31

O21, H28, H4

Virulence genes identified by VirulenceFinder

STEC: stx2A, stx2B, astA, iha, ehxA, chu, cib, cif, etpD, gad, iuc, iutA, neuC, tccP, terC, traT

EPEC/STEC: Eae, tir, efa1, espA/B/F/, nleA/B/C

STEC: stx2A, stx2B, astA, iha, ehxA, chu, cib, cif, etpD, gad, iuc, iutA, tccP, terC, traT

EPEC/STEC: Eae, tir, efa1, espA/B/F/, nleA/B/C

EAEC: aap, aar, aatA, aagA, aagB/C/D/R, aaiC, pic, capU, sepA, sigA, mcmA, safD, safe, sfaF, vat

ExPEC: cnf1, usp, clbB, kpsMII, kpsE, fyuA, irp2, papA/C, hra, iss

STEC: astA, iha, ehxA, chu, cib, cif, etpD, gad, iuc, iutA, tccP, terC, traT

EPEC/STEC: Eae, tir, efa1, espA/B/F/, nleA/B/C

EAEC: aaiC, pic, capU, sepA, mchB/C/F, mcmA, safD, safe, sfaF, vat

ExPEC: cnf1, usp, clbB, kpsE, fyuA, irp2, papA/C, hra, iss

MLSTFinder

ST6130

No ST

No ST

Plasmid Finder

RM13516 (IncFIB)

None

None

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