Evolutionary dynamics and differential mutation strategies of two avian pathogenic Escherichia coli lineages during experimental evolution

Experimental evolution offers a powerful framework to investigate bacterial adaptation dynamics. In this study, we performed long-term evolution experiments over an estimated 376 generations under glucose-limited conditions using 2 clinical avian pathogenic Escherichia coli (APEC) lineages with strain 729-021014-1-4 representing sequence type 95 (ST95-729-021014-1-4) and strain 729-141114-1-15 representing ST131 (ST131-729-141114-1-15). Whole-genome sequencing of isolates across eight time points revealed distinct adaptive trajectories. The ST95-729-021014-1-4 lineage exhibited a rapid adaptation strategy characterized by a relatively high mutation accumulation rate. Sequence-based analysis predicted the transcriptional upregulation of the anti-adaptor protein IraP via a promoter mutation and the translational optimization of metabolic genes via synonymous codon changes as primary drivers of its improved growth rate. Conversely, the ST131-729-141114-1-15 lineage displayed a conservative evolutionary pattern with a lower mutation rate and minor growth rate improvement, suggesting a pre-adapted state that relied on genomic maintenance rather than extensive regulatory remodelling. Its mutations were largely restricted to envelope-associated genes and synonymous variants with reduced translational efficiency. While both lineages maintained clonal stability, their differential mutation strategies highlight lineage-specific potentials for adaptation. These findings provide critical insights into how different APEC clinical isolates may persist and evolve during the typical production cycle of poultry, underscoring the diversity of evolutionary strategies.