Project description
Gut microbiome: predictor of recurrent infections
Recurrent urinary tract infections affect many women over their lifetime and are often caused by bacteria residing in the gut. Therefore, the gut microbiome may serve as a predictor of recurrent infections as well as of antibiotic resistance. Funded by the European Research Council, the OUTSMART-infection project proposes to undertake phenotypic and genomic analysis of patient gut microbiomes. With the help of machine learning, researchers aim to develop an infectivity model that can be used to design treatment and avoid the emergence of resistance. Moreover, the project will test whether manipulation of the gut microbiome with specific antibiotics may prevent recurrent infections.
Objective
Antibiotics are a double-edged sword: they help clear the current infection, yet can also select for resistant pathogens, making future infections harder to treat. While treatment guidelines recognize this collateral damage, we currently lack strategies to predict how treatments affect future recurrence and resistance at the individual patient level. This problem is of particular importance in Urinary Tract Infections (UTIs); affecting the majority of women over their lifetime, UTIs can chronically recur despite antimicrobial treatment. Importantly, UTIs are often self-seeded by strains residing in the gut microbiome, suggesting that the gut microbiome may provide means to predict current and future infections and could possibly even be manipulated to minimize infections. Here, we propose an interdisciplinary approach combining high-throughput phenotyping and genomics of same-patient gut-microbiome and UTI samples with machine-learning analysis of clinical records, towards a look-ahead treatment strategy for recurrent infections. First, we will use whole-genome and meta-genome approaches to sensitively detect infecting strains within the patients microbiome and develop a gene-based model for the infectivity of strains and thereby for the likely infecting agent and resistance profile of infection. Second, we will use long-read sequencing to map genetic linkage among resistances in each patients microbiome, enabling the development of a reinforcement machine-learning model to assign treatments that minimize both the risk of treatment failure and of future resistance. Finally, quantifying in vivo and in vitro the impacts of antibiotic intake on microbiome composition, we will test the feasibility of prescribing antibiotics that manipulate the microbiome in favor of less infectious strains. Together, this unique research-to-clinic data-rich approach will establish the basic foundations for a microbiome-based paradigm of look-ahead treatment strategies.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences biological sciences genetics
- medical and health sciences basic medicine pharmacology and pharmacy pharmaceutical drugs antibiotics
- natural sciences biological sciences microbiology
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Keywords
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
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HORIZON.1.1 - European Research Council (ERC)
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Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
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Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
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Call for proposal
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Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
(opens in new window) ERC-2021-ADG
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32000 Haifa
Israel
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