Antibiotic persistence is a phenomenon observed when genetically-susceptible cells survive long-term exposure to antibiotics. These so called ‘persister cells’ or ‘persisters’ are an intrinsic component of bacterial populations and stem from phenotypic heterogeneity induced by factors such as noise in gene expression, asymmetry in cell division or uneven distribution of nutrients in the environment. Persistence to antibiotics is a growing concern for public health globally as it increases treatment duration and can contribute to treatment failure, especially in immunocompromised individuals. Furthermore, there is a growing array of evidence that persistence is a ‘stepping-stone’ for the development of genetic antimicrobial resistance (AMR).
Currently, in clinical settings, routine laboratory screening of pathogenic isolates does not determine neither the presence nor the frequency of persister cells. Furthermore, the majority of research undertaken on antibiotic persistence has been done on lab-adapted bacterial strains. In the study presented here, we aimed to characterise antibiotic persisters in a panel of clinical UTI E. coli isolates collected from hospitals in the United Kingdom and Australia. We demonstrate that the gold-standard assay conditions can be misleading since they are not representative of the in vivo environment. We also show that a nutrient-limited, low pH environment not only induces higher levels of antibiotic persistence to meropenem and colistin, but also results in rapid development colistin resistance. Finally, we aim to assess biofilm-formation capabilities of these clinical isolates and investigate how this growth state responds to antibiotic exposure.