1. Group Name
Ecoli2
Marie Anne Chattaway
Saskia Kuipers
Tone Johansen
Sanne Hansen
Klara De Rauw

2. Isolates Sample name Country Collection date ec11-4623 France ec
c227-11
Germany ec
2011 ec
2004

3. Result of species identification (KmerFinder)
Strain
Species acc. to Grad et al 2012
Predicted species
Closest matching strain
Template coverage ec
E.coli
E.coli O104:H2, 2011/3493
99.84% ec
99.63%
c227-11
99.53% ec
Poor Data ec
E.coli O104:H2, 2009EL
97.56%
Red strains were not sequenced in the paper, ID was performed phenotypically.

4. Representative KmerFinder result

5. Result of Multilocus Sequence Typing (MLST)
Strain
ST acc. to Grad et al 2012
Predicted ST ec
ST678 ec
c227-11 ec
Poor data ec
Red strains were not sequenced in the paper, MLST was performed by PCR/Sanger sequencing.

6. Representative Multilocus Sequence Typing result

7. Result of serotyping ec11-4623 ec11-5537 c227-11 ec11-3798 ec04-8351
Strain
Serotype acc. to Grad et al 2012
Predicted serotype ec
O104:H4 ec
c227-11 ec
Poor data ec
Red strains were not sequenced in the paper, Serotyping done by PCR

8. Representative serotyping result

9. Result of antibiotics resistance analysis
Isolate
Ampicillin (blaZ, blaTem-1B)
Third-generation cephalosporins (blaCTX-M-15)
Streptomycin (strA, strB, aadA)
Nalidixic acid (chromosomal mutations)
Tetracycline (tetC, tetM, tetR, tetS, tetA) ec
blaTEM1B
CTX-M-15
STR A, STRB
unknown
TET(A) ec
c227-11 ec
Poor data ec
susceptible
Isolate
Cotri-moxazole (dfr)
Carbape-nems (blaNDM)
Ciprofloxacin (chromosomal mutations)
Chloram-phenicol (cat)
Kanamycin (aph(3’)-II/aph(3’)-III)
Gentamicin (aac(6')-aph(2'')) ec
dfrA7, Sul1, Sul2
susceptible
unknown ec
c227-11 ec
Poor data ec

10. How does it compare to the results presented in Grad et al 2012?
Results matched for the plasmid encoded genes.
We were unable to predict genes encoding resistance for Nalidixic acid and ciprofloxacin as these are chromosomally encoded and res finder only contains plasmid genes or acquired genes so cannot detected mutated genes.

11. Virulence factors Isolate stx2 (stx2a variant) aggR pic stx1 eae hlyA
astA
papG
dsbD ec X ec
c227-11 ec
Poor data ec
Indicate with , e.g., a “X”, if the gene was present or not
Which pathovar does the outbreak isolates seem to belong to?
STEC/EAEC hybrid strain

12. Result of plasmid analysis
Isolate
IncFII
IncFIB
IncI1
IncP
IncQ1
IncB/O/K/Z ec
NODE 1.7
NODE 1.6
NODE 1.3 ec
NODE 1.5
NODE 1.4
NODE 1.2
c227-11
NODE 1.10 ec
POOR DATA ec
NODE 1.7
For each strain write which node the replicon was found on. If not found, leave the cell empty.
Which plasmid is the blaCTX-M-15 gene on? INCI1
Which plasmid are the aggR gene on? INCFII, INCFIB – FORM THE PAA PLASMID

13. Distance matrix made by NDtree and tree made with neighbour-joining
escherichia_coli_c227-11
3412
525
624
escherichia_coli_ec
3297
3366
escherichia_coli_ec
387
escherichia_coli_ec

14. Distance matrix made by CSIPhylogeny
and tree made with neighbour-joining