Seeing Bacterial Persistence Through Different Experimental Lenses: How Methodology Shapes Biological Interpretation

Bacterial persister cells are a rare subpopulation that survives antibiotic treatment without acquiring heritable resistance. Despite decades of research, concepts of bacterial persistence have evolved alongside experimental methods, yet the mechanisms underlying persistence remain debated, and different approaches often lead to seemingly conflicting conclusions. In this Review, we argue that these discrepancies arise not only from the heterogeneity of persister cells but also from differences in experimental methodology and biological context. We present persistence as a dynamic continuum extending from the physiological state preceding antibiotic exposure, through survival during treatment, recovery after antibiotic removal, and clonal expansion. We examine how experimental approaches—including CFU assays, population-based analyses, fluorescence microscopy, microfluidics, enrichment strategies, and cell sorting—interrogate different stages of this continuum, thereby addressing distinct biological questions rather than providing equivalent views of persistence. We further discuss how experimental context shapes the populations available for analysis and influences the interpretation of persistence phenotypes. Seemingly conflicting observations often arise from different experimental frameworks, each revealing a distinct aspect of bacterial persistence. Combining approaches that interrogate different stages of the continuum can strengthen persister identification and mechanistic interpretation. Recognizing these complementary perspectives is essential for accurately interpreting persistence and integrating findings across studies.