Opportunistic pathogens

The TFM will be included into the objectives of the Project which summary is included below. Depending on the availability and skills of the candidate, the TFM will address either experimental evolution towards resistance or global regulation of antibiotic resistance.

Infectious disease have been historically the main cause of human death. Because of this, the use of antibiotics for treating infections is likely the therapeutic advance, which has contribute the most to decrease human mortality, hence allowing that life expectancy has been doubled in the last 60 years. Nevertheless, as stated by the WHO, infectious diseases still remain as major causes for morbidity and mortality all around the world. This is not just a problem for poor countries. In the developed word, infections are a common life-threatening complication, mainly at hospitals, for patients with underlying diseases as cystic fibrosis of AIDS and in elderly population. A problem associated to antibiotic usage is the acquisition of resistance by bacterial pathogens. Historically, this situation was solved by introducing novel antibiotics into the market. Nevertheless, the amount of novel antibiotics at the pipeline is decreasing. Under this situation antibiotic resistance is a global problem and there are concerns on the possibility of a return to a pre-antibiotic era, with few options for fighting infectious diseases. In this context, predicting the mechanisms that allow bacteria to resist the action of antibiotics, even before these resistances emerge is critical. This prediction may allow implementing novel strategies for fighting infections. In addition, may serve to predict the mechanisms of resistance to novel antibiotics still at their first stages of development, which could help the pharmaceutical industry to choose the best compounds for future stages of development. The aim of the current project is the standardization of the methods required for such a predictive analysis of antibiotic resistance. Within the project, we will analyze three clinically relevant bacterial species: P. aeruginosa, S. maltophilia y K. pneumoniae. In the study we will include antibiotics currently in use, but also other on their first stages of development, which will be supplied by the associated partners, which have shown an interest on our project. The studies will include the analysis of the susceptibility to antibiotics of mutants obtained from transposon-tagged libraries as well as experimental evolution assays in the presence of different concentrations of antibiotics, followed by whole genome sequencing. This will allow to define the intrinsic resistome of the studied pathogens as well as to track the most relevant mutations leading to resistance. The fixation of a mechanism of resistance largely depends on the associated fitness costs. Because of this, we will analyze the fitness costs of a selected set of mutants both by classical co-culture approaches and by using minimal models of virulence.

A second aspect the will be addressed in the project consists on the analysis of the role that global regulators of the bacterial physiology, namely Crc and RNase G, have on the modulation of the bacterial susceptibility to antibiotics. To that goal, we will make use of transcriptomics and proteomics tools to get a global picture of such regulation. Our group is pioneer in these studies, which major goal is understanding the integration of antibiotic resistance into basic physiological bacterial networks. This, more global, understanding of resistance may allow the implementation of novel strategies for fighting antibiotic resistance.