Modèle pré-clinique de décolonisation de klebsiella pneumoniae résistantes aux antibiotiques par des bactériophages // Preclinical model of decolonisation of multi resistant klebsiella pneumoniae by bacteriophages

Rationale : Antimicrobials resistance (AMR) is a major threat to human and animal health, and accounted for up to 4.5 millions deaths worldwide in 2019 (Antimicrobial Resistance Collaborators, 2022). Klebsiella pneumoniae (KP) is a central hub in the acquisition and transmission of antibiotics resistance and is the 3rd cause of deaths associated to AMR in the world with about 650 000 deaths. A major risk of developing an infection by KP lies in the carriage of the strain in the microbiota. Developing new non antibiotics strategies to limit or eradicate multi-resistant KP carriage without globally perturbing the microbiota is thus needed to limit its health impact. Bacteriophages, viruses specific to bacteria, represent one such strategy. Despite the low number and the disparity of results reported in the literature in in vivo models of multi-resistant bacteria decolonisation by bacteriophages (due to the diversity of experimental conditions and the poor characterization of bacteriophages), this strategy has already been successfully used in clinics (Corbellino et al. 2020). Thus the use of these viruses constitutes an innovative strategy to decolonize patients from intestinal carriage of multi-resistant KP. Moreover, the underlying mechanisms pertaining to efficient decolonisation by bacteriophages remain unclear.
Objectives: This project aims to (i) select and characterize appropriate phages and multi-resistant KP strains, (ii) set-up a preclinical murine colonisation model by multi-resistant KP, (iii) assess the performances in decolonisation of several bacteriophages used alone or in cocktail, and (iv) better understand phage bacteria interactions within the microbiota. The proof of concept of the usefulness of our preclinical model will be built by using clinically relevant multi-resistant KP strains.

Methodology: New bacteriophages targeting relevant multi-resistant KP clinical strains will first be isolated, identified and characterized (sequence, burst size, stability, efficiency of plating, ...). These bacteriophages will rapidly be screened in a recently described Galleria mellonella larvae colonisation model (Mirza et al. 2024) to identify promising decolonizing bacteriophages. Their activity will be further assessed in a mouse gut colonisation model in several ways: i) bacteria and phage numeration from stools, ii) macroscopic and microscopic visualisation and quantification of bacteria and phages tissue-, mucus- and luminal- associated, at various portions of the gut using fluorescent bacteria and antibodies generated against the phages, iii) evaluation of the emergence of phage-resistant bacteria and characterisation of their resistance mechanisms, iv) characterisation of the dynamics of the microbiota (bacteria and virus) during colonisation and treatment by bacteriophage.

Expected results and perspectives: This work will provide proof of principle and detailed analysis of gut decolonization by bacteriophages. This knowledge will provide knowledge supporting translation into clinics. Moreover, this murine model will allow further investigation of the mechanisms leading to KP infections subsequent to colonisation.
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Rationale : Antimicrobials resistance (AMR) is a major threat to human and animal health, and accounted for up to 4.5 millions deaths worldwide in 2019 (Antimicrobial Resistance Collaborators, 2022). Klebsiella pneumoniae (KP) is a central hub in the acquisition and transmission of antibiotics resistance and is the 3rd cause of deaths associated to AMR in the world with about 650 000 deaths. A major risk of developing an infection by KP lies in the carriage of the strain in the microbiota. Developing new non antibiotics strategies to limit or eradicate multi-resistant KP carriage without globally perturbing the microbiota is thus needed to limit its health impact. Bacteriophages, viruses specific to bacteria, represent one such strategy. Despite the low number and the disparity of results reported in the literature in in vivo models of multi-resistant bacteria decolonisation by bacteriophages (due to the diversity of experimental conditions and the poor characterization of bacteriophages), this strategy has already been successfully used in clinics (Corbellino et al. 2020). Thus the use of these viruses constitutes an innovative strategy to decolonize patients from intestinal carriage of multi-resistant KP. Moreover, the underlying mechanisms pertaining to efficient decolonisation by bacteriophages remain unclear.
Objectives: This project aims to (i) select and characterize appropriate phages and multi-resistant KP strains, (ii) set-up a preclinical murine colonisation model by multi-resistant KP, (iii) assess the performances in decolonisation of several bacteriophages used alone or in cocktail, and (iv) better understand phage bacteria interactions within the microbiota. The proof of concept of the usefulness of our preclinical model will be built by using clinically relevant multi-resistant KP strains.

Methodology: New bacteriophages targeting relevant multi-resistant KP clinical strains will first be isolated, identified and characterized (sequence, burst size, stability, efficiency of plating, ...). These bacteriophages will rapidly be screened in a recently described Galleria mellonella larvae colonisation model (Mirza et al. 2024) to identify promising decolonizing bacteriophages. Their activity will be further assessed in a mouse gut colonisation model in several ways: i) bacteria and phage numeration from stools, ii) macroscopic and microscopic visualisation and quantification of bacteria and phages tissue-, mucus- and luminal- associated, at various portions of the gut using fluorescent bacteria and antibodies generated against the phages, iii) evaluation of the emergence of phage-resistant bacteria and characterisation of their resistance mechanisms, iv) characterisation of the dynamics of the microbiota (bacteria and virus) during colonisation and treatment by bacteriophage.

Expected results and perspectives: This work will provide proof of principle and detailed analysis of gut decolonization by bacteriophages. This knowledge will provide knowledge supporting translation into clinics. Moreover, this murine model will allow further investigation of the mechanisms leading to KP infections subsequent to colonisation.
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Début de la thèse : 01/10/2025

Public funding alone (i.e. government, region, European, international organization research grant)

Concours pour un contrat doctoral

Sorbonne Université SIM (Sciences, Ingénierie, Médecine)

515 Complexité du vivant

M2 degree with skills in bacteriology, knowledge with phages will be a plus. Experience with work in L2/A2 environment. Experience with animal experimentation is a plus. WIllingness to work with mice is necessary. English read, written and spoken essential, level B2 minimum, Capacity to work autonomously and independently in a team environment Enthusiasm, flexibility, capacity to interact with academic and industrial partners
M2 degree with skills in bacteriology, knowledge with phages will be a plus. Experience with work in L2/A2 environment. Experience with animal experimentation is a plus. WIllingness to work with mice is necessary. English read, written and spoken essential, level B2 minimum, Capacity to work autonomously and independently in a team environment Enthusiasm, flexibility, capacity to interact with academic and industrial partners