Toxin-antitoxin (TA) systems are modules that are associated with some physiological processes of bacteria, such as the formation of persistent cells, biofilm formation, protection against bacteriophages and responses to stressful environments. In these modules, the toxin is related to the inhibition of physiological processes and the antitoxin provides protection to the cell against the toxin. In the genome of a hybrid pathogenic E. coli strain (atypical enteropathogenic E. coli and extraintestinal E. coli strain - BA1250) were found eight type II TA systems, and some of them with more than one copy. Only TA systems CcdB-CcdA, YhaV-PrlF, MazF-MazE, YoeB-YefM and PasI-PasT were present in one copy. Therefore by transcription analysis under stress conditions such as nutritional, oxidative, osmotic, acid and in antibiotic presence (ciprofloxacin and ampicillin) were analyzed either at log or stationary phase of BA1250 strain. We observed significant changes in the expression levels of the CcdB-CcdA, YhaV-PrlF, YoeB-YefM and PasT-PasI systems in the presence of nutritional stress at stationary phase. It’s worth mentioning that CcdB-CcdA and YoeB-YefM were the most affected systems at the log phase in the presence of antibiotics and nutritional stress. On the contrary, the MazF-MazE system none changes in the expression levels was observed. These data indicate that these four TA systems are related to the bacterial stress response, ongoing experiments will elucidate how these mechanisms may be involved with the pathogenicity of this hybrid strain.