CV Science

Charlotte Michaux PhD, HDR, Inserm permanent researcher

Course and current status

Scientific summary

Antibiotic discovery is one of the greatest medical breakthroughs in history, however, these drugs show some limitations during infection. Indeed, even if antibiotics eradicate the majority of a genetically susceptible population during treatment, a subset of cells can survive in numerous clinical situations. Termed recalcitrant cells (also persisters or tolerant cells), these constitute a reservoir of bacteria that are thought to cause infection relapse if they regrow after antibiotic therapy is ceased. Moreover, these antibiotic survivors drive the evolution of antibiotic resistance, which will limit drastically treatment options in the near future. Awareness of the clinical importance of antibiotic recalcitrant cells has emerged over the last decade, leading to investigations of different determinants of antibiotic recalcitrance in various pathogens. However, very little is known about ESKAPE pathogens, especially Enterococcus faecium (Efm) and Enterobacter cloacae complex (Ecc). These ESKAPE members are nosocomial pathogens that represent a global threat to human health according to the World Health Organization (WHO) because of increasing antibiotic resistance and spread in hospital settings. These two species are the leading cause of hospital-acquired infections, impacting around 6 million patients each year in Europe and the USA, with a resulting 200,000 deaths and additional treatment costs of over ten billion dollars. Because antibiotic resistance feeds off recalcitrance, investigating the mechanisms governing this phenomenon in Efm and Ecc is a timely issue that should improve treatment by providing more targeted approaches. To take up this challenge, this proposal is articulated in three main work-packages (WPs). The first WP will provide insights into what triggers antibiotic recalcitrance. By screening different stresses relevant for infection (by CFU and Fluorescence Dilution), we will identify conditions that induce antibiotic recalcitrance. To understand how those conditions can trigger recalcitrance, we will investigate the hypothesis of a transcriptional switch induced by stress, and perform RNA-seq on bacterial populations stressed before (perturbome) and after (recalcitrome) antibiotic treatment to identify recalcitrance-associated signatures. These findings will be a stepping-stone in characterizing the genetic determinants of antibiotic recalcitrance. Actors of recalcitrance will then be identified by cutting-edge genetic screen approaches such as AB cycling or Tn-seq to generate a pool of primary targets and tackle antibiotic recalcitrance. In the second WP, we will investigate the origin of this antibiotic recalcitrance, notably by linking recalcitrance and relapse of infection using clinical isolates from patients suffering from recurrent infections caused by either Efm or Ecc. By comparing the Single Nucleotide Polymorphisms (SNPs) for different recurrent episodes experienced by the same patient, we will be able to assess the prevalence of relapse, thought to be caused by recalcitrant bacteria. Animal models will be used to identify the niches of recalcitrant bacteria during infection, and their transcriptomic analysis will reveal the gene expression signature leading to recalcitrance. The last WP will explore the link between recalcitrance and resistance in Efm and Ecc – the first being described in other species as the breeding ground of the latter. Mutations in recalcitrant bacteria leading to resistance as well as acquisition of antibiotic resistance genes through mobile genetic elements will be scrutinized both in vitro and in infection in the context of two last line antibiotics: vancomycin and imipemen. Altogether, this work will unravel the triggers and genetic determinants of recalcitrance, the niches of recalcitrance during infection leading to relapse, and their active role in promoting antibiotic resistance. We believe this proposal could ultimately provide ways to tackle recalcitrance and to apprehend the fight against antibiotic resistance by eradicating this recalcitrant population.