An integrated approach to tackle the interplay among adaptation, stressful conditions and antimicrobial resistance of challenging pathogens

Rapidly emerging resistant bacteria threaten the extraordinary health benefits that have been achieved with antibiotics. This crisis is global, reflecting the worldwide overuse of these drugs and the lack of development of new antibiotic agents by pharmaceutical companies to address this challenge.
Antibiotic-resistant infections place a substantial health and economic burden on the Italian health care system and population as reported in the annual EARS-Net report (EARSNet ECDC https://ecdc.europa.eu/en/antimicrobial-resistance/surveillance-and-dise...). The European Center for Disease Prevention and Control (ECDC) in Stockholm, after an institutional visit to Italy as part of the program to support Member States against the serious phenomenon of AMR, reiterated the need in Italy for a strong coordination between institutions and the areas affected by the phenomenon, at all levels, to tackle the problem. In response to this strong request, the Ministry of Health, in collaboration with multiple institutions, scientific societies and experts, has developed the first National Antimicrobial-Resistance Plan (PNCAR) 2017-2020.
Understanding the scientific basis of antimicrobial resistance/tolerance is essential in combatting this public health threat. This understanding should cover the knowledge of resistance mechanisms (including mechanistic aspects), new knowledge into the genome and resistome structure of resistant bacteria, but also the adaptive phenomena that can emerge as a consequence of antibiotic concentration gradients, as well as growth in stressful condition and contact with inhibitory concentrations of drugs, which can easily occur in human patients. Adaptive resistance has been correlated with the appearance and stability of MDR, although the underlined biological processes are not well understood. Population structure of bacteria, mutation rates, gene acquisition and expression, efflux pump, biofilm formation and dormancy were all reported as possible explanations. Furthermore, in some study models, high-level expression of resistance or integron-mediated acquisition of antibiotic resistance involves the stringent response, induced upon starvation.
This research proposal gathers together 6 research units (RUs), located in the South of Italy, with expertise in antimicrobial resistance, microbial pathogenesis, structural biology, host-parasite interaction, and development of animal models of disease, with the final goal of acquiring new information on: i) genome and resistome; ii) molecular mechanisms of action and resistance; and iii) adaptive mechanisms under stress conditions in different challenging pathogens.
The project is structured in three WGs: in WG1 three RUs will contribute to the genome and resistome comparative analysis of two important nosocomial pathogens (A.baumannii and K.pneumoniae, above all the new ST101 clone) with the aim, in the former, of contributing to our knowledge on the organization of the genomic structure and homogenization of the typing scheme, and, in the latter, of understanding genome variability and the ability to acquire an MDR phenotype and become an epidemic clone in Italy; WP2 gathers together RUs with the aim of studying resistance mechanisms in different models i.e. Acinetobacter, Klebsiella and H.pylori, by using conventional and molecular approaches in different stressful states and biofilm, as well as in the presence of sub-inhibitory concentrations of drugs and disinfectants; WP3, is the most complex package. The RUs involved will try to identify traits in the intersection among stringent response, virulome, resistome and dormancy in different microbial models included in the research project (A.baumanni, pathogenic Neisseriae, H.pylori and Mycoplasma). In vitro and in vivo experiments will be performed to address the role of the stringent response in all these adaptive responses during infection.
The three WPS comprise different RUs, in which all scientists will interact with each other. A number of experimental approaches will be used, including omics technologies (genome and transcriptome), genetic and molecular biology techniques (construction of knock-out mutants, gene silencing), and cellular and animal infection models.
Expected outputs can be identified in: i) genome and resistome insights of challenging pathogens; ii) mechanism of resistance influenced by secondary traits, slow-growing and stressful conditions; iii) involvement of a stringent response, in different experimental conditions, confering advantages to these pathogens. The aim of all this is to find possible targets for disarming pathogens instead of inhibiting or killing them.
We think that coordinated efforts to renew studies on different models and in the complex regulation of different systems, also covering secondary bacterial traits correlated with resistance acquisition and stabilization, are needed. Taking steps now, to manage the crisis, is a must.