Background: Escherichia coli O104:H4, a new pathotype Enteroaggregative Hemorrhagic Escherichia coli (EAHEC), was the cause of a 2011 severe outbreak affecting European countries especially Germany. The effects of Rifampicin and Gentamicin were evaluated to determine potential treatment modes for the novel strain Escherichia coli O104:H4, and to assess the SOS response and its effect on Stx2 toxin release. Methods: Pulsed field gel electrophoresis (PFGE) was carried out on the new E. coli O104:H4 pathotype and two pre-outbreak E. coli O104:H4 CDC isolates.Relative expression of stx2 gene and recA gene (SOS response inducer) were assessed using RT-qPCR in the novel E.coli O104:H4 samples treated with different regimens of Rifampicin and Gentamicin. Subsequently, Reverse passive latex agglutination (RPLA) was used to determine the Stx-II titers. LexA levels (SOS response repressor) in E. coli O104:H4 were assessed by western blot. The efficacy of treatment with antimicrobial agents was determined in BALB/c mice. Results: PFGE analysis demonstrated slight genomic differences between the new pathotype and one pre-outbreak isolate, denoting that these 2 isolates could be related. Expression of stx2 gene was 1.41 and 1.75 fold higher in the new pathotype in comparison to the 2 pre-outbreak strains respectively. Moreover expression of stx2 gene in the new pathotype, was substantially decreased with different combinations of MICs and MBCs of the antibiotics. RPLA data were in accordance with the RT-qPC. Gentamicin at both sub MIC levels resulted in high expression of recA gene and lack of expression of Lex A protein, indicating that the SOS response was activated. Rifampicin resulted in low transcript levels of rec A gene at both sub MIC levels, indicating that the SOS response was not activated. In vivo, the highest survival rate in BALB/c mice was observed in the group receiving MBC gentamicin. Conclusion: The Germany outbreak strain could have originated from a 2009 E. coli O104:H4 strain. Unlike Shiga toxin producing strains of E. coli, the outbreak strain E. coli O104:H4 seems to be positively affected by antimicrobial agents. This provides a promising ground for treatment of E. coli O104:H4 and encourages more research to further verify these findings.