Thyme and cinnamon essential oils inhibit multidrug resistant Escherichia coli and Klebsiella pneumoniae and alter virulence transcripts

The increasing incidence of multidrug-resistant (MDR) Gram-negative pathogens, particularly Escherichia coli and Klebsiella pneumoniae, continues to narrow effective treatment options and motivates evaluation of alternative antimicrobial strategies. Here, 33 essential oils (EOs) were screened against six MDR clinical isolates, identifying thyme and cinnamon oils as the most active. Both oils produced large inhibition zones (up to 26 mm) and low minimum inhibitory concentrations (MICs), with cinnamon oil showing a uniform MIC of 0.0488% (v/v) across all strains. For transcriptional analysis, cultures were exposed to cinnamon oil at 0.0244% (v/v) (0.5×MIC). Because this exposure corresponds to a near-MIC/inhibitory condition, observed decreases in virulence-gene transcript levels should be interpreted as inhibitory/stress-associated transcriptional responses rather than definitive sub-MIC anti-virulence effects. GC–MS profiling indicated enrichment of carvacrol (23.4%) and thymol (3.58%) in thyme oil, while cinnamon oil was dominated by cinnamaldehyde (45.8%) and eugenol (10.89%). Cinnamon also showed slightly higher antioxidant capacity than thyme (DPPH RSA 70.57% vs. 67%). Finally, molecular docking (HADDOCK/AutoDock Vina) was used as supportive in-silico screening to explore plausible ligand–target interaction hypotheses. Collectively, thyme and cinnamon EOs demonstrated antibacterial activity and were associated with reduced virulence-gene transcript abundance under near-MIC exposure, supporting further validation using verified sub-MIC conditions and growth controls.