Protocol for high-throughput isolation of bacterial intracellular nonreplicating persisters v1

Failure of antibiotics to clear a bacterial infection is arguably one of the most severe threat to global health. Bacteria ability to withstand drug treatment partly relies on the formation of a subpopulation of persisters. Persisters are rare nonreplicating individuals, transiently refractory to antibiotic treatment and responsible for non-resolving bacterial infection and relapse. Studying persisters is challenging as it is a reversible physiological state occurring in a small fraction of the pathogen population hidden in a complex environment. Persisters have been primarily analyzed in broth, hardly reflecting the conditions prevailing within a host. In addition, indirect read-outs used to detect the persisters, a posteriori, limited a comprehensive understanding of the persisters peculiar physiology during the infection. Here, we describe a high-throughput method to track, and collect the bacterial persisters generated during the infection of phagocytic cells, with single-cell resolution. Persisters are detected based on the bacterial division rate measured for each individual bacterium using the Timer fluorescent growth rate reporter and subsequently recover using fluorescence-activated cell sorting (FACS). We will illustrate this method with Legionella pneumophila, a facultative intracellular pathogen and the agent of the Legionnaires’ disease for which persistence to antibiotics and relapsing infections are clinically documented. Isolated persisters can be analyzed biochemically and functionally, yielding fundamental new insights into the molecular and cellular processes underlying persistence, and into the peculiar physiology of the persisters within the host. This method is adaptable to other microbial pathogens and alternative infection models.