Group Name MRSA 1 Group member name Raluca

Group Name MRSA 1 Group member name Raluca Datcu Group member name Mihaela Oprea Group member name Oana Barbu Group member name Anita Forslund Group member name Cathrine Fladeby Group member name Mona Holberg Workshop on Whole Genome Sequencing and Analysis, 27 -29 Mar. 2016

Isolates Sample name ERR 070039 -P 11 ERR 108054 -P 15 ERR 128707 -P 26 ERR 128718 -HW ERR 070041 -notoutbreak Subtype Notes ST 2371 From Patient 11 ST 2371 From Patient 15 ST 2371 From Patient 26 From Health Care Worker - misses the erm. C ST 2371 plasmid ST 1 Not part of the outbreak

Result of species identification (Kmer. Finder) Strain ERR 070039 -P 11 ERR 108054 -P 15 ERR 128707 -P 26 ERR 128718 -HW ERR 070041 -notoutbreak Species acc. Predicted to Harris et al species 2013 S. aureus subsp. aureus S. aureus subsp. aureus Closest matching strain Template coverage HO 50960412 97. 46 HO 50960412 97. 44 HO 50960412 97. 46 MSSA 476 98. 59

Representative Kmer. Finder result

Result of Multilocus Sequence Typing (MLST) Strain ERR 070039 -P 11 ERR 108054 -P 15 ERR 128707 -P 26 ERR 128718 -HW ERR 070041 -notoutbreak ST acc. to Harris Predicted ST et al 2014 ST-2371 ST-2371 ST-1

Representative Multilocus Sequence Typing result

Result of antibiotics resistance analysis Cefoxitin/M Ciproethicillin floxacin (Mec. A) (chromosomal mutation) Erythromycin (Erm(A), Erm(B), Erm(C)) Fusidic acid Gentamicin Mupirocin (chromo(aac(6’)(chromosomal aph(2'')) somal mutation) Rifampicin (chromosomal mutation) Tetracycline (tet. C, tet. M, tet. R, tet. S Vancomycin (Chromosomal mutations or the van. A or van. B gene cluster. ) Neomycin (aad. D, aac(6')aph(2'')) P 11 Res Unknown Sus Res P 15 Res Unknown Sus Unknown Res Unknown Sus Res P 26 Res Unknown Sus Res HW Res Unknown Sus Unknown Res Unknown Sus Res non-out Res -break Unknown Res Unknown Sus Sus Isolate How is the agreement with the results presented in Harris et al 2013? Good agreement, but for the HW isolate our DNA did not contained erm genes, and Harris identified both susceptible and resistant colonies to erythromycin

Result of plasmid analysis Isolate rep 10 rep. US 12 rep 20 rep 5 rep 16 rep 7 ERR 070039 P 11 ERR 108054 P 15 ERR 128707 P 26 ERR 128718 HW ERR 070041 not-outbreak NODE 1 NODE 25 NODE 37 37 - - - NODE 15 - - NODE 9 NODE 5 NODE 80 - - - NODE 37 NODE 142 - - NODE 1 - - NODE 2 NODE 8 For each strain write which node the replicon was found on. If not found, leave the cell empty. Which plasmid is the erm. C gene on? - PLASMID rep 10

Distance matrix made by NDtree and tree made with neighbour-joining

Tree made with neighbour-joining

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

Tree made with neighbour-joining