Persisters represent a subpopulation of nonreplicating individuals transiently refractory to antibiotic treatment. Here we describe a high-throughput single-cell method to track and collect the persisters formed within phagocytes. Cells are infected with bacteria expressing the Timer fluorescent growth rate reporter, and nonreplicating individuals are recovered using fluorescence-activated cell sorting (FACS).
During the colonization of the host, the pathogen encounters highly heterogeneous host micro-environments [1], elaborate a complex interplay with the component of the immune systems [2] and/or develops microbial communities with high degree of phenotypic specialization [3] which produce, within the micrometer ranges, a multitude of genetically identical individuals with alternative physiologies [4]. Bacterial variability is further increased as clonal bacteria constantly develop functionally distinct subpopulations [5]. This reversible and regulated phenomenon termed phenotypic heterogeneity is of major clinical importance as it implies the formation of persisters [6]. Persisters are preestablished or stress induced individuals that transiently evade the bactericidal activity of antibiotics by entering a rare and peculiar physiological state at the cost of abrogation of bacterial division, and finally resume growth on the onset of the treatment termination [7]. The emergence of persisters has been documented for major bacterial pathogens including Staphylococcus aureus, Mycobacterium tuberculosis, Escherichia coli, Salmonella enterica, Pseudomonas spp., Listeria monocytogenes and Legionella pneumophila [4,6,8–16]. Traditionally, the presence of bacterial persisters has been revealed by the “biphasic killing” phenomenon of bacterial cultures exposed to bactericidal antibiotics [17]. However, such population-averaging methods, performed a posteriori, are poorly suited to comprehensively and dynamically analyze a phenomenon where reversible cell-to-cell variations plays a key role. The development of high-throughput fluorescence-based single-cell technologies has rendered important breakthroughs reachable. Notably, the microfluidic device called mother machine has been incredibly useful to directly monitor the formation of persisters and the underlying regulatory mechanisms using a combination of genetic and environmental manipulations [6]. Persisters have been mostly studied using non-infectious model organisms cultivated in broth, hardly reflecting the conditions prevailing within a host. Deciphering the biology of the persisters during the infection has remained technically challenging as the persisters represent a rare and unstable subpopulation of the pathogen, that is generated within complex environments.
The ubiquitous environmental Gram-negative bacterium Legionella pneumophila is a waterborne human pathogen responsible for a life-threatening pneumonia termed Legionnaires’ disease (LD) [18], the inventoried cases of which have doubled since 2013 [19]. LD is fatal for 5-15% of the patients (up to 50% among the elderly), even when promptly diagnosed and treated [20]. A nation-wide retrospective study describing those cases of slowly or non-resolving LD proposed that recalcitrance to antibiotic treatments or relapsing infections were the expression of bacterial persistence [21]. L. pneumophila survives its ingestion by a diverse array of protozoan predators, as well as lung alveolar macrophages, and establishes a replicative membrane-bound compartment termed the Legionella-containing vacuole (LCV) [22,23]. LCV formation requires the Icm/Dot type IV secretion system (T4SS) and involves approximately 300 different so-called « effector » proteins, which are translocated into host cells [24,25] to hijack numerous host cell functions. The amoebozoa Acanthamoeba castellanii has proved a reliable, easy-to-use and cost effective model organism to investigate the molecular interactions of L. pneumophila with its host cell, and at large, the pathogenic potential and process of many other human opportunistic pathogens [26].
The plasmid based Timer growth rate reporter [4] is a powerful technology to track the nonreplicating persisters produced during an infection. Timer is a stable fluorescent protein that slowly maturates from a green to a red fluorescent protein. As a consequence, in growing bacteria, constitutively producing Timer, green fluorescent Timer dominates over red fluorescent Timer, which is diluted by cell division before maturation, and the individual bacteria show a high [500 nm (green)/600 nm (red)] fluorescence (color) ratio (i.e. “green” fluorescence). By contrast, growth-arrested bacteria accumulate both green and red fluorescent Timer, and the individual bacteria show a low green/red color ratio (i.e., “red” fluorescence).
Here, coupling the protozoan model of infection, the innovative Timer fluorescent growth rate reporter and high-throughput single-cell technologies, we are defining a pipeline to track and collect the persisters produced by L. pneumophila with an unprecedented resolution. Isolated persisters can be analyzed biochemically and functionally. To date, using this methodology, we demonstrated that L. pneumophila persisters are a preestablished subpopulation of nongrowers and the expression of a regulated pathogen strategy which is applied to evolutionarily distant host cells (i.e., protists and macrophages) [15,16]. Near in situ biochemical characterization of the intracellular L. pneumophila persisters unveiled a unique physiology and, remarkably, a specific virulence program in order to survive the combined action of the host defenses and the antibiotics, hence, breaking the dogma that persisters are dormant bacteria [15]. Of note, this approach can be applied to the study nonreplicating persisters produced by other pathogens during the infection or within complex microbial communities.
Research at the CIRI is supported by the Inserm, CNRS, University Lyon 1, and ENS Lyon. N.P. was the recipient of an SNF Ambizione fellowship (PZ00P3_161492, PZ00P3_185529). The research in the laboratory of N.P. is supported by a CIRI seed fund and the ANR. The funders had no role in study design, decision to publish, or preparation of the manuscript.
The authors have nothing to disclose.
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