Environmental stress shapes persistence-like phenotypes and genomic changes in Escherichia coli and Morganella morganii: an exploratory study

Introduction Enterobacterales, including E. coli and M. morganii , employ adaptive mechanisms to withstand environmental and host-related stressors, including extreme temperatures, osmotic pressure changes, acidic conditions, and antibiotic pressures. Survival in these conditions can consequently enhance their antibiotic tolerance and persistence. Bacterial persistence contributes to chronic infections and antibiotic treatment failure. This exploratory study investigates the impact of stress conditions (pH, temperature, osmotic, and antibiotic stress) on persistence and genomic adaptations in E. coli and M. morganii . Methods Clinical and environmental M. morganii and E. coli strains from Ghanaian tertiary hospitals were exposed to extreme temperatures (cold ~4 °C, and heat ~45 °C), extreme pH (pH 3, pH 9, pH 10), and hyperosmolarity (1.71M NaCl). Growth kinetics were monitored by OD600 and CFU determinations, and persister-like cell formation was assessed using time-kill assays at 2 × MIC antibiotic conditions. Genomic changes associated with stress recovery including both adaptive mutations and enrichment of pre-existing variants were captured using comparative whole genome sequencing (WGS) of stress-recovered isolates to parental strains. Results Strains exhibited variation in growth kinetics under different stress conditions compared to controls. Temperature, pH, and osmotic stress each affected bacterial growth to varying degrees. Heat stress in particular promoted increased persister-like cell formation in E. coli (with strain-specific differences) and, to a lesser extent, in M. morganii upon exposure to meropenem as observed in the isolates examined in this study. WGS analysis revealed that all four studied strains harbored virulence and resistance genes, with missense mutations detected in stress-recovered variants. Most of the mutated genes encode proteins that may play key roles in metabolic processes, transport functions and transcriptional regulations. Discussion This exploratory study suggests that environmental stress drives both phenotypic and genotypic changes, and that these enhance subsequent survival upon challenge with antibiotics. These adaptive responses may contribute to antibiotic tolerance and chronic infection, emphasizing the need for therapeutic strategies targeting stress response pathways.