EP4637795A1 - Faecalibacterium prausnitzii strain cncm i-4573 for the treatment and prevention of clostridioides difficile infection - Google Patents

Faecalibacterium prausnitzii strain cncm i-4573 for the treatment and prevention of clostridioides difficile infection

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Publication number
EP4637795A1
EP4637795A1 EP23836836.9A EP23836836A EP4637795A1 EP 4637795 A1 EP4637795 A1 EP 4637795A1 EP 23836836 A EP23836836 A EP 23836836A EP 4637795 A1 EP4637795 A1 EP 4637795A1
Authority
EP
European Patent Office
Prior art keywords
bacterial strain
culture supernatant
individual
composition
cncm
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP23836836.9A
Other languages
German (de)
French (fr)
Inventor
Philippe Langella
Séverine PECHINE
Camille CAMPIDELLI
Jean-Marc CHATEL
Harry SOKOL
Claire JANOIR
Benjamin HADIDA
Pauline RUFFIE
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Exeliom Biosciences
Assistance Publique Hopitaux de Paris APHP
Sorbonne Universite
Institut des Sciences et Industries du Vivant et de lEnvironnement AgroParisTech
Universite Paris Saclay
Institut National de Recherche pour lAgriculture lAlimentation et lEnvironnement
Original Assignee
Exeliom Biosciences
Assistance Publique Hopitaux de Paris APHP
Sorbonne Universite
Institut des Sciences et Industries du Vivant et de lEnvironnement AgroParisTech
Universite Paris Saclay
Institut National de Recherche pour lAgriculture lAlimentation et lEnvironnement
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Exeliom Biosciences, Assistance Publique Hopitaux de Paris APHP, Sorbonne Universite, Institut des Sciences et Industries du Vivant et de lEnvironnement AgroParisTech, Universite Paris Saclay, Institut National de Recherche pour lAgriculture lAlimentation et lEnvironnement filed Critical Exeliom Biosciences
Publication of EP4637795A1 publication Critical patent/EP4637795A1/en
Pending legal-status Critical Current

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Classifications

    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
    • A61K35/741—Probiotics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K2035/11—Medicinal preparations comprising living procariotic cells
    • A61K2035/115—Probiotics

Definitions

  • the present invention relates to a Faecalibacterium prausnitzii strain for use thereof in the treatment and prevention of a Clostridioides difficile infection in an individual.
  • Clostridioides difficile (also referred to as C. difficile, and formerly known as Clostridium difficile') is an anaerobic, spore-forming, toxin- producing, gram-positive bacterium that is transmitted among humans via the fecal-oral route.
  • C. difficile emerged as a major, globally-distributed enteric pathogen.
  • C. difficile is responsible for 15-25% of cases of antibiotic-associated bacterial diarrhoea and is considered the leading cause of healthcare-associated diarrhoea in adults. After a first episode, the risk of first recurrence is high and problematic (about 20%) and it increases further after a first recurrence reaching up to 60%. The symptoms associated with this infection can range from simple diarrhoea to pseudomembranous colitis.
  • C. difficile is accordingly classified as one of the top three urgent antibiotic resistance threats by the Centers for Disease Control and Prevention (CDC), and CDI has become the most common cause of antibiotic-associated diarrhea and gastroenteritis- associated death in developed countries.
  • CDC Centers for Disease Control and Prevention
  • CDI the standard treatment for CDI is antibiotics, with vancomycin or fidaxomicin being the most commonly prescribed compounds. Metronidazole is only used if vancomycin or fidaxomicin are not available. Fecal microbiota transplant (FMT) has only been used as a last resort following multiple recurrences. Probiotics have also been used as a preventive treatment with mixed results while vaccines are not yet available. Within healthcare facilities, preventive measures include judicious use of antibiotics and infection control practices. Use of monoclonal antibodies has also been studied with the aim of improving host resistance to CDI, however this approach has yielded mixed results.
  • FMT Fecal microbiota transplant
  • the objective of the present invention is to provide novel substances, in particular probiotics, and compositions for the treatment and/or prevention of a Clostridioides difficile infection in an individual.
  • the terms “prevent”, “prevention” and “preventing” denote the reduction to a lesser degree of the risk or of the probability of occurrence of a given phenomenon, that is to say, in the present invention, a C. difficile infection, and in particular the development of symptoms following infection by C. difficile.
  • the terms “prevent”, “prevention” and “preventing” denote the reduction to a lesser degree of the risk or of the probability of a first episode of C.
  • the target population may in particular correspond to any patient for whom an antibiotic treatment and/or a treatment comprising administration of Proton pump inhibitors (PPI) is prescribed, and in particular any patient for whom an antibiotic treatment is prescribed.
  • PPI Proton pump inhibitors
  • Recurrence of CDI is defined as recurrence of diarrhea with a positive test for C. difficile toxin within 8 weeks of completion of effective anti-C. difficile therapy.
  • treating include alleviation of the symptoms associated with a specific disorder or condition and/or elimination of said symptoms as well as the complete disappearance of the considered disorder or condition.
  • the present invention is based on the discovery, by the present inventors, of the ability of the Faecalibacterium prausnitzii strain deposited with the CNCM under accession number CNCM 1-4573 to prevent and/or treat a Clostridioides difficile infection in an individual.
  • a specific strain of Faecalibacterium prausnitzii (F. prausnitzii) deposited with the CNCM on January 21, 2012, under accession number CNCM 1-4573 by Institut National de la Recherche Agronomique (INRA) has the unexpected capacity to treat and prevent, in vivo, the infection of an individual by C. difficile, and in particular the unexpected capacity to delay intestinal colonisation by C. difficile of said individual, to rapidly eliminate C. difficile from the intestine, and to reduce symptoms following infection by C. difficile or even to prevent the appearance of any symptom following infection by C. difficile.
  • F. prausnitzii Faecalibacterium prausnitzii
  • the present invention relates to a bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573, and/or a culture supernatant thereof, for use in the treatment and/or prevention of a Clostridioides difficile infection in an individual.
  • This strain identified by the inventors is therefore a probiotic strain which may be used for the applications indicated herein.
  • An individual according to the invention may be selected from the group consisting of human beings; Suidae, in particular pigs, more particularly piglets; Bovinae, in particular cattle, more particularly bulls, and more particularly steers; Canidae, in particular dogs; Equidae, in particular horses; and Phasianidae, in particular poultry, more particularly chickens; preferably a mammal, and more particularly a human being (J. Scott Weese; Journal of Veterinary Diagnostic Investigation 2020, Vol. 32(2) 213-221).
  • the bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573 may be administered to the said individual in a live, inactive and/or dead form, preferably in a live or inactive form, more particularly in a live form.
  • a live bacterial form means a bacterial strain which is cultivable and/or metabolically active, in particular cultivable and metabolically active.
  • An inactive form of a bacterial strain according to the invention may for example be a lyophilisate, prepared using method of the art well known by the skilled artisan.
  • the Clostridioides difficile infection may occur after the use of at least one antibiotic medication and/or at least one Proton pump inhibitors (PPI) medication by the individual.
  • PPI Proton pump inhibitors
  • the bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573, and/or the culture supernatant thereof, may be administered simultaneously and/or separately, in particular simultaneously, with the at least one antibiotic medication and/or at least one PPI medication.
  • the bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573, and/or the culture supernatant thereof may be administered simultaneously with and/or after the at least one antibiotic medication and/or the at least one PPI medication.
  • the bacterial strain for use thereof, and/or the culture supernatant thereof, according to the invention may be included in a composition comprising a physiologically acceptable medium, preferably in an oral or rectal composition, and more particularly preferably in a pharmaceutical product.
  • physiologically acceptable medium is intended to denote a medium which is compatible with the body of the individual to whom said composition must be administered. It is, for example, a non-toxic solvent such as water. In particular, said medium is compatible with oral administration.
  • a composition of the invention is preferably for oral or rectal administration, in particular for oral administration.
  • a composition of the invention for oral administration may be chosen from the group consisting of a food product, a beverage, a pharmaceutical product, a nutraceutical, a food additive, a food supplement and a milk product and is, in particular, in the form of a pharmaceutical product.
  • a composition for use according to the invention may be suitable for the administration of a daily dose representing from 10 4 to 10 15 total cell count (TCC), more preferably from 10 8 to 10 13 TCC of the F. prausnitzii strain of the invention as a medicament, for example as a daily dose representing 10 13 TCC of the bacterial strain according to the invention.
  • TCC total cell count
  • Figure 1 illustrates the evaluation of weight loss in mice treated or not with F. prausnitzii 1-4573 according to the invention. Mice were weighed to monitor the development of clinical signs after infection with C. difficile. Two groups of mice are tested: mice treated with PBS- Glycerol 16% (vehicle); mice treated with F. prausnitzii strain I- 4573.
  • Abscissa Days (from DO to D20, DO being the day the mice, previously treated with antibiotics, are fed with C. difficile R20291). Ordinate: Weight of the mice (% compared to their weight at DO).
  • FIG. 2 illustrates survival of mice treated with PBS- Glycerol 16% (vehicle) or treated with F. prausnitzii strain 1-4573 of 7 days
  • Abscissa Days (from DO to D7). Ordinate: Probability of survival (between 0 and 1).
  • Figure 3 illustrates the colonization of mice (10 mice per group) by C. difficile R20291 over time (from DO to D20 - DO being the day the mice, previously treated with antibiotics, are fed with C. difficile R20291). Abscissa (arrow), from left to right: DO, D2, D3, D4, D5, D6, D8, DIO, D14 and D20. Ordinate: % of mice with detectable C. difficile in feces.
  • the present inventors have carried out thorough studies in order to identify the capacity of a specific strain of Faecalibacterium prausnitzii to treat and/or prevent Clostridioides difficile (C. difficile) infection in an individual.
  • the inventors have determined, unexpectedly, that the F. prausnitzii strain 1-4573 has the capacity to not only delay intestinal colonisation by C. difficile, but to also rapidly eliminate C. difficile from the intestine, and to significantly reduce symptoms following infection by C. difficile, in particular to prevent the appearance of any symptom following infection by C. difficile, in an individual.
  • F. prausnitzii is a major member of the phylum Firmicutes and is part of the commensal bacteria that are the most abundant in the microbiota of the healthy human large intestine.
  • F. prausnitzii is an extremely oxygen- sensitive (EOS) bacterium which is therefore difficult to culture, even under anaerobic conditions (Duncan et al. 2002, Int. J. Syst. Evol. Microbiol. 52(Pt 6): 2141-6 and Lopez-Siles et al. Appl. Environ Microbiol. January 2012; 78 (2):420-8).
  • EOS extremely oxygen- sensitive
  • F. prausnitzii is in particular known to be one of the most abundant butyrate-producing bacteria in the human digestive tract, the butyrate short-chain fatty acid being very important in intestinal physiology, systemic functions and beneficial effects on human health (Macfarlane and Macfarlane (2011), J. Clin. Gastroenterol. 45 Suppl: S 120-7).
  • a suitable daily dose of a bacterial strain according to the invention may be from 10 7 to 10 14 colony-forming units (cfu) of the F. prausnitzii strain of the invention as a medicament.
  • Daily dosages may also range from 10 4 to 10 15 total cell count (TCC), more preferably from 10 8 to 10 13 TCC of the F. prausnitzii strain of the invention as a medicament, for example as a daily dose equivalent to 10 13 TCC.
  • TCC total cell count
  • the F. prausnitzii strain specifically implemented in the present invention is the bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573.
  • a Faecalibacterium prausnitzii strain of the invention is for use in the treatment and/or prevention of a Clostridioides difficile infection in an individual.
  • a Faecalibacterium prausnitzii bacterial strain deposited to the CNCM under the accession number 1-4573 for use according to the invention may be in an isolated form.
  • isolated form it is meant in a form isolated from any fecal material, or intestinal sampling.
  • a bacterial strain of the invention is preferably not administered to a patient in the form of a Fecal Microbiota Transplant (FMT).
  • FMT Fecal Microbiota Transplant
  • An individual according to the invention may be selected from the group consisting of human beings; Suidae. in particular pigs, more particularly piglets; Bovinae. in particular cattle, more particularly bulls, and more particularly steers; Canidae. in particular dogs; Equidae, in particular horses; and Phasianidae, in particular poultry, more particularly chickens.
  • an individual according to the invention is a mammal, in particular a human being.
  • the strain of the invention is a probiotic, the activity of which is located in the intestines.
  • a probiotic bacterium according to the invention denotes a bacterium which, when it is ingested live in sufficient amounts, may exert beneficial effects on an individual’s health.
  • the bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573 may be administered to an individual in need thereof in a live, inactive and/or dead form, and is preferably administered in a live form in the intestines.
  • the bacterial strain of the invention may be administered to the digestive tract of an individual to be treated in various ways, namely orally or rectally.
  • a bacterium according to the invention is preferably administered orally.
  • the bacterial strain of the invention is included in a composition comprising a physiologically acceptable medium.
  • a composition is preferably for oral or rectal, in particular oral, administration, and in particular in the form of a pharmaceutical product.
  • the present invention also relates to a composition for use according to the invention, the composition comprising, in a physiologically acceptable medium, at least the Faecalibacterium prausnitzii bacterial strain 1-4573 of the invention.
  • a composition for use according to the invention is intended for the digestive tract, in particular the intestines.
  • composition for use according to the invention may be chosen from an oral or rectal composition.
  • a composition of the invention is preferably an oral or rectal composition, more preferably an oral composition.
  • a composition for use of the invention being an oral composition is intended for oral administration to an individual.
  • composition for use of the invention being a rectal composition is intended for rectal administration to an individual.
  • An oral composition may be in the form of a suspension, a tablet, a pill, a capsule, a granule or a powder.
  • a composition for use according to the invention for oral administration may be chosen from the group consisting of a food product, a beverage, a pharmaceutical product, a nutraceutical, a food additive, a food supplement or a milk product and is, in particular, a pharmaceutical product.
  • a composition for use according to the invention is a pharmaceutical product.
  • a pharmaceutical product for oral administration may be present in capsules, gel capsules, soft capsules, tablets, sugar-coated tablets, pills, pastes, lozenges, gums, oral solutions or emulsions, a syrup or a gel.
  • a pharmaceutical product according to the invention for oral administration may be in a capsule, in particular in a capsule under the form of a lyophilisate, preferably together with pharmaceutically acceptable excipients.
  • a composition for use according to the invention intended for oral administration, may be provided with a gastric -juice-resistant coating, in order to ensure that the bacterial strain of the invention included in said composition can pass through the damaged stomach. The release of the bacterial strain may thus take place for the first time in the upper intestinal tract.
  • a pharmaceutical product for oral use according to the invention may also comprise a sweetener, a stabilizer, an antioxidant, an additive, a flavoring agent and/or a dye.
  • the formulation thereof is carried out by means of the usual methods for producing sugar-coated tablets, gel capsules, gels, controlled-release hydrogels, emulsions, tablets or capsules.
  • a composition for use containing the bacterial strain of the invention may be administered intrarectally.
  • a rectal administration may in particular be carried out in the form of a suppository, an enema or a foam, in particular an enema.
  • a composition for use according to the invention may also be in the form of a nutritional composition.
  • a nutritional composition for use according to the invention may be in the form of a yogurt, a cereal bar, breakfast cereals, a dessert, a frozen food, a soup, a pet food, a liquid suspension, a powder, a tablet, a gum or a candy.
  • composition for use of the invention may be suitable for the administration of a daily dose representing from 10 7 to 10 14 colony-forming units (cfu) of the strain according to the invention as a medicament, preferably a daily dose equivalent to 10 11 cfu.
  • composition for use according to the invention may be administered to an individual requiring it, at a single daily dose of 1 g containing the 1-4573 bacterial strain of the invention in an amount equivalent to a dose of between 10 7 and 10 14 cfu, preferably 10 11 cfu.
  • a composition for use according to the invention may be administered to an individual requiring it, at a single daily dose of 0.2 g containing the I- 4573 bacterial strain of the invention in an amount equivalent to an amount of between 10 7 and 10 14 cfu, preferably 10 11 cfu.
  • daily dosages may also range from 10 4 to 10 15 total cell count (TCC), more preferably from 10 8 to 10 13 TCC of the F. prausnitzii strain of the invention as a medicament, for example as a daily dose equivalent to 10 13 TCC.
  • a composition for use according to the invention may be administered to an individual requiring it from 1 to 10 times a day, each dose containing the 1-4573 bacterial strain of the invention in an amount of for example between 5.10 8 and 5.10 11 TCC, so that the total daily dose of the 1-4573 bacterial strain of the invention administered to the individual is as indicated above.
  • a composition for use according to the invention may be administered to an individual for 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 10 days, 14 days, 15 days, 3 weeks, 1 month or for more than 1 month.
  • the same daily amount of the F. prausnitzii strain of the invention can be administered every day or the daily amount can vary along the treatment period.
  • the daily dosage of the F. prausnitzii strain of the invention may be higher during the first days of the treatment and then gradually decrease.
  • a composition according to the invention may also comprise at least one among: antioxidants, fish oils, DHA, EPA, vitamins, minerals, phytonutrients, a protein, a lipid, probiotics, and combinations thereof.
  • An individual according to the invention may accordingly be: an individual which will start or has already started an antibiotic treatment; and/or an individual which is finishing or has just finished an antibiotic treatment; and/or an individual which will start or has already started a Proton pump inhibitors (PPI) treatment; and/or an individual which is finishing or has just finished a Proton pump inhibitors (PPI) treatment; and/or an individual who has been treated for an episode of C. difficile infection, for example a first episode of C. difficile infection, for example with vancomycine and/or fidaxomicine; and/or an individual with a first episode of C. difficile infection or with a recurrent C. difficile infection.
  • PPI Proton pump inhibitors
  • Clostridioides difficile infection to be treated and/or prevented according to the invention may in particular occur after the use of at least one antibiotic and/or PPI medication by the considered individual. Accordingly, an individual according to the invention may in particular be an individual which will start or has already started an antibiotic and/or PPI treatment or with a dysbiosis.
  • a bacterial strain for use according to the invention, a culture supernatant thereof, or a composition comprising it, may accordingly be administered simultaneously and/or separately, in particular simultaneously, with at least one antibiotic medication (antibiotic) of the antibiotic treatment and/or with at least one and/or PPI medication, such as for example separately during the same day, or even separately with at least one, or even more, days between the administration of the bacterial strain and the administration of the antibiotic/PPI medication.
  • at least one antibiotic medication (antibiotic) of the antibiotic treatment and/or with at least one and/or PPI medication, such as for example separately during the same day, or even separately with at least one, or even more, days between the administration of the bacterial strain and the administration of the antibiotic/PPI medication.
  • the bacterial strain for use according to the invention or culture supernatant thereof and the at least one antibiotic and/or PPI are administered to the individual in the same composition.
  • the bacterial strain for use according to the invention or culture supernatant thereof and the at least one antibiotic and/or PPI are administered in separate compositions.
  • compositions can be administered to the individual simultaneously or separately through the same route of through different routes.
  • the bacterial strain for use according to the invention, culture supernatant thereof, or composition comprising it can be administered at the same moment or up to the same day or couple of days as the antibiotic and/or PPI.
  • the bacterial strain for use according to the invention, culture supernatant thereof, or composition comprising it can be administered with at least several days, for example at least three days of difference.
  • a bacterial strain for use according to the invention, a culture supernatant thereof, or a composition comprising it may be administered simultaneously and separately with at least one antibiotic medication (antibiotic) of the antibiotic treatment and/or with at least one and/or PPI medication, such as for example the bacterial strain for use according to the invention, the culture supernatant thereof or the composition comprising it according to the invention may be administered simultaneously as the administration of the antibiotic/PPI medication and also after the end of the antibiotic and/or PPI treatment.
  • the dosage and frequency of administration of a bacterial strain for use according to the invention or culture supernatant thereof may be adapted depending on the host response.
  • the frequency of administration of a bacterial strain for use according to the invention, culture supernatant or composition comprising it may be a daily administration for 5 to 15 consecutive days.
  • the administration can alternatively be every 2, 3, 4, 5, 6 or 7 days for a period of up to several months.
  • the frequency of administration of a bacterial strain for use according to the invention, culture supernatant or composition comprising it may be a daily administration all along the treatment of the individual, in particular all along the antibiotic and/or PPI treatment, and the administration of bacterial strain for use according to the invention, culture supernatant or composition comprising it :
  • - may be started one or several days before the start of the above-mentioned treatment, in particular antibiotic and/or PPI treatment; and/or
  • - may end one or several days after the end of the above-mentioned treatment, in particular antibiotic and/or PPI treatment.
  • An antibiotic medication, or antibiotic, and/or PPI medication relevant according to the invention can be any medication which alters, inhibits the growth of or destroys microorganisms of the gut microbiota.
  • such antibiotic can for example be selected from the group consisting of Penicillins, Tetracyclines, Cephalosporins, Quinolones, Lincomycins, Macrolides, Sulfonamides, Glycopeptides, Aminoglycosides, Carbapenems and mixtures thereof, and in particular selected from the group consisting of amoxicillin, doxycycline, cephalexin, ciprofloxacin, clindamycin, metronidazole, azithromycin, sulfamethoxazole and trimethoprim, clavulanate, ofloxacin, levofloxacin and mixtures thereof.
  • Antibiotic can for example be selected from the group consisting of amoxicillin, doxycycline, cephalexin, ciprofloxacin, clindamycin, metronidazole, azithromycin, sulfamethoxazole and trimethoprim, clavulanate, levofloxacin, vancomycin, fidaxomicin, metronidazole, kanamycin, gentamycin, colistin, clindamycin and mixtures thereof.
  • such PPI can for example be selected from the group consisting of Omeprazole, lansoprazole, pantoprazole, rabeprazole, esomeprazole and dexlansoprazole.
  • the present invention also relates to the use of:
  • composition comprising, in a physiologically acceptable medium, the bacterial strain or culture supernatant thereof, for treating and/or preventing a Clostridioides difficile infection in an individual.
  • the present invention also relates to a method for treating and/or preventing a Clostridioides difficile infection in an individual, comprising administering to the said individual:
  • the present invention also relates to the use of:
  • composition comprising, in a physiologically acceptable medium, the bacterial strain or culture supernatant thereof, for the manufacture of a medicament for treating and/or preventing a Clostridioides difficile infection in an individual.
  • the F. prausnitzii strain according to the invention deposited with the CNCM under the accession number CNCM 1-4573, was tested for its capacity to modulate, in vitro and in vivo, C. difficile intestinal colonization, in particular in mice presenting an induced dysbiosis.
  • mice Twenty 6-week-old conventional C57 Black 6 (C57BL/6) female mice were identified and caged with sterile food and water in isolators to protect them from the external environment. The mice are divided into 2 groups:
  • mice are treated with PBS- Glycerol 16% (Vehicle);
  • mice were given a cocktail of antibiotics in the drinking water consisting of Kanamycin 0.4 mg/mL, Gentamycin 0.035 mg/mL, Colistin 0.0567 mg/mL, Metronidazole 0.215 mg/mL and Vancomycin 0.045 mg/mL.
  • IP intraperitoneal
  • mice On DO, all mice were infected by gastric gavage with 500 pL of C. difficile strain R20291 (DSM 27147) at a concentration of 2 x 10 5 CFU/mL.
  • pre-cultures were performed the day before with C. difficile strain R20291 (DSM 27147) and the following morning, a Gram stain was performed to verify the purity of the suspension and the culture was diluted with 27 mL of BHI with 3 mL of pre-culture. After approximately 7 hours of anaerobic culture, the suspension was enumerated and adjusted to 2xl0 5 bacteria/mL in 50 mL of regenerated 1 X PBS. Following infection with C. difficile, mice are then weighed daily for 8 days from infection and then at D10, D14 and D20.
  • mice In order to monitor intestinal colonisation by C. difficile, the faeces of the mice were collected at DI, D2, D3, D5, D8, D12, D14 and D20 and resuspended in PBS to obtain a final concentration of 10 mg/mL.
  • the suspensions are then diluted to 10’ 1 , 10' 2 and 10' 3 and spread on BHI agar + 3% blood + C. difficile selective supplement (Biomerieux®) and incubated for 48 hours at 37 °C under anaerobic conditions.
  • the suspension non-diluted is also spread in the same conditions.
  • mice All mice were given a cocktail of antibiotics to induce dysbiosis and allow better implantation of C. difficile R20291 (DSM 27147) in the gut. Mice were fed every day of the experiment (D-6 to D14) with F. prausnitzii CNCM 1-4573 or PBS-Glycerol 16% (Vehicle). After infection with the toxigenic C. difficile strain R20291 (DSM 27147), clinical scores (loss of weight and activity, diarrhoea, mortality) were evaluated, colonisation was monitored by counting the bacteria in the faeces.
  • mice in the corresponding control group PBS - vehicle
  • a loss of weight from D2 onwards then a return to their normal weight at D6 postinfection, a loss of activity and diarrhoea were observed.
  • the survival of the animals after challenge was monitored.
  • following infection with C. difficile 2 mice died in the PBS-Glycerol 16% group (control - vehicle) and 1 mouse treated with F. prausnitzii CNCM 1-4573 died 5 days after infection.
  • mice in the F. prausnitzii strain of the invention group were well colonised although they did not appear to develop symptoms. There was a delay in colonisation compared to the control group (vehicle group) and a more rapid elimination of C. difficile (from D6, compared to D14 for the control group). At DIO, the mice were still colonised by C. difficile, 4 out of 4 mice treated with PBS-Glycerol 16% (vehicle control group), 1 out of 6 mice for the group treated with the F. prausnitzii strain of the invention.
  • a treatment based on the administration of the F. prausnitzii strain of the invention unexpectedly demonstrated the ability to provide a protection from a C. difficile infection.
  • the mice did not develop clinical signs (stable weight, normal faeces and activity) despite all being colonized. The colonization was delayed and a faster elimination of C. difficile was surprisingly observed.

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Abstract

The present invention relates to a bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM I- 4573, and/or a culture supernatant thereof, for use in the treatment and/or prevention of a Clostridioides difficile infection in an individual.

Description

FAECALIBACTERIUMPRAUSNITZII STRAIN CNCM 1-4573 FOR THE TREATMENT AND PREVENTION OF CLOSTRIDIOIDES DIFFICILE INFECTION
Field of the invention
The present invention relates to a Faecalibacterium prausnitzii strain for use thereof in the treatment and prevention of a Clostridioides difficile infection in an individual.
Prior art
Clostridioides difficile (also referred to as C. difficile, and formerly known as Clostridium difficile') is an anaerobic, spore-forming, toxin- producing, gram-positive bacterium that is transmitted among humans via the fecal-oral route. Elderly, immunocompromised individuals whose gut microbiota have been disrupted by antibiotic therapy have the greatest risk of contracting this highly-contagious, life-threatening, and potentially-fatal diarrheal disease. After highly -virulent strains began appearing during the early 2000s, C. difficile emerged as a major, globally-distributed enteric pathogen.
Generally, C. difficile is regarded as a nosocomial pathogen, being hospital- acquired, even though C. difficile infections can also occur also outside hospitals.
However, the disease is now appearing more frequently in individuals once considered to be at low risk. These cases tend to occur in younger individuals. Recent antibiotic exposure is an important risk factor in this population, but use of gastric acid suppressants and co-morbidities such as inflammatory bowel disease, chronic kidney disease, immunodeficiency disease, malignant lesions and solid organ transplants have also been associated with C. difficile (CDI). In some rare cases, the infection can even spontaneously appear in otherwise healthy individuals in the absence of antibiotic exposure.
C. difficile is responsible for 15-25% of cases of antibiotic-associated bacterial diarrhoea and is considered the leading cause of healthcare-associated diarrhoea in adults. After a first episode, the risk of first recurrence is high and problematic (about 20%) and it increases further after a first recurrence reaching up to 60%. The symptoms associated with this infection can range from simple diarrhoea to pseudomembranous colitis.
C. difficile is accordingly classified as one of the top three urgent antibiotic resistance threats by the Centers for Disease Control and Prevention (CDC), and CDI has become the most common cause of antibiotic-associated diarrhea and gastroenteritis- associated death in developed countries.
Currently, the standard treatment for CDI is antibiotics, with vancomycin or fidaxomicin being the most commonly prescribed compounds. Metronidazole is only used if vancomycin or fidaxomicin are not available. Fecal microbiota transplant (FMT) has only been used as a last resort following multiple recurrences. Probiotics have also been used as a preventive treatment with mixed results while vaccines are not yet available. Within healthcare facilities, preventive measures include judicious use of antibiotics and infection control practices. Use of monoclonal antibodies has also been studied with the aim of improving host resistance to CDI, however this approach has yielded mixed results.
There is a need for novel substances, in particular probiotics, or compositions comprising them, for the treatment and/or prevention of an infection by C. difficile.
There is in particular a need for novel substances, in particular probiotics, or compositions comprising them, able to decrease the risk of C. difficile infection following a gut microbiota perturbation with antibiotics and/or Proton pump inhibitors (PPI).
There is in particular a need for novel substances, in particular probiotics, or compositions comprising them, able to decrease the risk of C. difficile infection recurrence after a given episode.
There is in particular a need for novel substances, in particular probiotics, or compositions comprising them, able to delay intestinal colonisation by C. difficile.
There is also a need for novel substances, in particular probiotics, or compositions comprising them, allowing reduced, or even the absence of, symptoms following infection by C. difficile.
There is also a need for novel substances, in particular probiotics, or compositions comprising them, allowing limiting intestinal colonization by the bacteria, a faster elimination of C. difficile from the intestine and advantageously then a reduced or even the absence of symptoms following infection.
Summary of the invention
The objective of the present invention is to provide novel substances, in particular probiotics, and compositions for the treatment and/or prevention of a Clostridioides difficile infection in an individual. In the context of the present invention, the terms “prevent”, “prevention” and “preventing” denote the reduction to a lesser degree of the risk or of the probability of occurrence of a given phenomenon, that is to say, in the present invention, a C. difficile infection, and in particular the development of symptoms following infection by C. difficile. In particular, the terms “prevent”, “prevention” and “preventing” denote the reduction to a lesser degree of the risk or of the probability of a first episode of C. difficile infection (CD I) and/or the reduction to a lesser degree of the risk or of the probability of recurrence of C. difficile infection in an individual. For the prevention of the first episode, the target population may in particular correspond to any patient for whom an antibiotic treatment and/or a treatment comprising administration of Proton pump inhibitors (PPI) is prescribed, and in particular any patient for whom an antibiotic treatment is prescribed.
Recurrence of CDI is defined as recurrence of diarrhea with a positive test for C. difficile toxin within 8 weeks of completion of effective anti-C. difficile therapy.
As used herein, the terms “treating”, “treat” or “treatment” include alleviation of the symptoms associated with a specific disorder or condition and/or elimination of said symptoms as well as the complete disappearance of the considered disorder or condition.
The present invention is based on the discovery, by the present inventors, of the ability of the Faecalibacterium prausnitzii strain deposited with the CNCM under accession number CNCM 1-4573 to prevent and/or treat a Clostridioides difficile infection in an individual.
According to the experimental results of the inventors, a specific strain of Faecalibacterium prausnitzii (F. prausnitzii) deposited with the CNCM on January 21, 2012, under accession number CNCM 1-4573 by Institut National de la Recherche Agronomique (INRA) has the unexpected capacity to treat and prevent, in vivo, the infection of an individual by C. difficile, and in particular the unexpected capacity to delay intestinal colonisation by C. difficile of said individual, to rapidly eliminate C. difficile from the intestine, and to reduce symptoms following infection by C. difficile or even to prevent the appearance of any symptom following infection by C. difficile.
According to a first subject, the present invention relates to a bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573, and/or a culture supernatant thereof, for use in the treatment and/or prevention of a Clostridioides difficile infection in an individual. This strain identified by the inventors is therefore a probiotic strain which may be used for the applications indicated herein.
An individual according to the invention may be selected from the group consisting of human beings; Suidae, in particular pigs, more particularly piglets; Bovinae, in particular cattle, more particularly bulls, and more particularly steers; Canidae, in particular dogs; Equidae, in particular horses; and Phasianidae, in particular poultry, more particularly chickens; preferably a mammal, and more particularly a human being (J. Scott Weese; Journal of Veterinary Diagnostic Investigation 2020, Vol. 32(2) 213-221).
The bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573 may be administered to the said individual in a live, inactive and/or dead form, preferably in a live or inactive form, more particularly in a live form.
A live bacterial form means a bacterial strain which is cultivable and/or metabolically active, in particular cultivable and metabolically active.
An inactive form of a bacterial strain according to the invention may for example be a lyophilisate, prepared using method of the art well known by the skilled artisan.
According to an embodiment, the Clostridioides difficile infection may occur after the use of at least one antibiotic medication and/or at least one Proton pump inhibitors (PPI) medication by the individual. The bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573, and/or the culture supernatant thereof, may be administered simultaneously and/or separately, in particular simultaneously, with the at least one antibiotic medication and/or at least one PPI medication. The bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573, and/or the culture supernatant thereof, may be administered simultaneously with and/or after the at least one antibiotic medication and/or the at least one PPI medication.
The bacterial strain for use thereof, and/or the culture supernatant thereof, according to the invention may be included in a composition comprising a physiologically acceptable medium, preferably in an oral or rectal composition, and more particularly preferably in a pharmaceutical product. The term “physiologically acceptable medium” is intended to denote a medium which is compatible with the body of the individual to whom said composition must be administered. It is, for example, a non-toxic solvent such as water. In particular, said medium is compatible with oral administration.
A composition of the invention is preferably for oral or rectal administration, in particular for oral administration.
A composition of the invention for oral administration may be chosen from the group consisting of a food product, a beverage, a pharmaceutical product, a nutraceutical, a food additive, a food supplement and a milk product and is, in particular, in the form of a pharmaceutical product.
A composition for use according to the invention may be suitable for the administration of a daily dose representing from 104 to 1015 total cell count (TCC), more preferably from 108 to 1013 TCC of the F. prausnitzii strain of the invention as a medicament, for example as a daily dose representing 1013 TCC of the bacterial strain according to the invention.
Figures’ legends
Figure 1 illustrates the evaluation of weight loss in mice treated or not with F. prausnitzii 1-4573 according to the invention. Mice were weighed to monitor the development of clinical signs after infection with C. difficile. Two groups of mice are tested: mice treated with PBS- Glycerol 16% (vehicle); mice treated with F. prausnitzii strain I- 4573.
Abscissa: Days (from DO to D20, DO being the day the mice, previously treated with antibiotics, are fed with C. difficile R20291). Ordinate: Weight of the mice (% compared to their weight at DO).
Figure 2 illustrates survival of mice treated with PBS- Glycerol 16% (vehicle) or treated with F. prausnitzii strain 1-4573 of 7 days
Abscissa: Days (from DO to D7). Ordinate: Probability of survival (between 0 and 1).
Figure 3 illustrates the colonization of mice (10 mice per group) by C. difficile R20291 over time (from DO to D20 - DO being the day the mice, previously treated with antibiotics, are fed with C. difficile R20291). Abscissa (arrow), from left to right: DO, D2, D3, D4, D5, D6, D8, DIO, D14 and D20. Ordinate: % of mice with detectable C. difficile in feces.
Detailed description of the invention
The present inventors have carried out thorough studies in order to identify the capacity of a specific strain of Faecalibacterium prausnitzii to treat and/or prevent Clostridioides difficile (C. difficile) infection in an individual.
Indeed, the inventors have determined, unexpectedly, that the F. prausnitzii strain 1-4573 has the capacity to not only delay intestinal colonisation by C. difficile, but to also rapidly eliminate C. difficile from the intestine, and to significantly reduce symptoms following infection by C. difficile, in particular to prevent the appearance of any symptom following infection by C. difficile, in an individual.
Faecalibacterium prausnitzii strain of the invention
F. prausnitzii is a major member of the phylum Firmicutes and is part of the commensal bacteria that are the most abundant in the microbiota of the healthy human large intestine.
F. prausnitzii is an extremely oxygen- sensitive (EOS) bacterium which is therefore difficult to culture, even under anaerobic conditions (Duncan et al. 2002, Int. J. Syst. Evol. Microbiol. 52(Pt 6): 2141-6 and Lopez-Siles et al. Appl. Environ Microbiol. January 2012; 78 (2):420-8). F. prausnitzii is in particular known to be one of the most abundant butyrate-producing bacteria in the human digestive tract, the butyrate short-chain fatty acid being very important in intestinal physiology, systemic functions and beneficial effects on human health (Macfarlane and Macfarlane (2011), J. Clin. Gastroenterol. 45 Suppl: S 120-7).
A suitable daily dose of a bacterial strain according to the invention may be from 107 to 1014 colony-forming units (cfu) of the F. prausnitzii strain of the invention as a medicament.
Daily dosages may also range from 104 to 1015 total cell count (TCC), more preferably from 108 to 1013 TCC of the F. prausnitzii strain of the invention as a medicament, for example as a daily dose equivalent to 1013 TCC. The F. prausnitzii strain specifically implemented in the present invention is the bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573.
As previously mentioned, a Faecalibacterium prausnitzii strain of the invention, and/or a culture supernatant thereof, is for use in the treatment and/or prevention of a Clostridioides difficile infection in an individual.
A Faecalibacterium prausnitzii bacterial strain deposited to the CNCM under the accession number 1-4573 for use according to the invention may be in an isolated form. By “isolated form” according to the invention, it is meant in a form isolated from any fecal material, or intestinal sampling. Accordingly, a bacterial strain of the invention is preferably not administered to a patient in the form of a Fecal Microbiota Transplant (FMT). Methods for isolating a bacteria from the gut microbiota are well known to the man skilled in the art, such as for example illustrated in Foditsch et al. (PLoS One. 2014; 9(12): el 16465).
An individual according to the invention may be selected from the group consisting of human beings; Suidae. in particular pigs, more particularly piglets; Bovinae. in particular cattle, more particularly bulls, and more particularly steers; Canidae. in particular dogs; Equidae, in particular horses; and Phasianidae, in particular poultry, more particularly chickens. In particular, an individual according to the invention is a mammal, in particular a human being.
The strain of the invention is a probiotic, the activity of which is located in the intestines. A probiotic bacterium according to the invention denotes a bacterium which, when it is ingested live in sufficient amounts, may exert beneficial effects on an individual’s health.
Consequently, the bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573 may be administered to an individual in need thereof in a live, inactive and/or dead form, and is preferably administered in a live form in the intestines.
The bacterial strain of the invention may be administered to the digestive tract of an individual to be treated in various ways, namely orally or rectally. A bacterium according to the invention is preferably administered orally.
According to one preferred embodiment, the bacterial strain of the invention is included in a composition comprising a physiologically acceptable medium. Such a composition is preferably for oral or rectal, in particular oral, administration, and in particular in the form of a pharmaceutical product.
Compositions
The present invention also relates to a composition for use according to the invention, the composition comprising, in a physiologically acceptable medium, at least the Faecalibacterium prausnitzii bacterial strain 1-4573 of the invention.
A composition for use according to the invention is intended for the digestive tract, in particular the intestines.
Consequently, a composition for use according to the invention may be chosen from an oral or rectal composition. A composition of the invention is preferably an oral or rectal composition, more preferably an oral composition.
A composition for use of the invention being an oral composition is intended for oral administration to an individual.
A composition for use of the invention being a rectal composition is intended for rectal administration to an individual.
An oral composition may be in the form of a suspension, a tablet, a pill, a capsule, a granule or a powder.
A composition for use according to the invention for oral administration may be chosen from the group consisting of a food product, a beverage, a pharmaceutical product, a nutraceutical, a food additive, a food supplement or a milk product and is, in particular, a pharmaceutical product.
According to one preferred embodiment, a composition for use according to the invention is a pharmaceutical product.
A pharmaceutical product for oral administration may be present in capsules, gel capsules, soft capsules, tablets, sugar-coated tablets, pills, pastes, lozenges, gums, oral solutions or emulsions, a syrup or a gel.
For example, a pharmaceutical product according to the invention for oral administration may be in a capsule, in particular in a capsule under the form of a lyophilisate, preferably together with pharmaceutically acceptable excipients.
Advantageously, a composition for use according to the invention, intended for oral administration, may be provided with a gastric -juice-resistant coating, in order to ensure that the bacterial strain of the invention included in said composition can pass through the damaged stomach. The release of the bacterial strain may thus take place for the first time in the upper intestinal tract.
A pharmaceutical product for oral use according to the invention may also comprise a sweetener, a stabilizer, an antioxidant, an additive, a flavoring agent and/or a dye.
The formulation thereof is carried out by means of the usual methods for producing sugar-coated tablets, gel capsules, gels, controlled-release hydrogels, emulsions, tablets or capsules.
A composition for use containing the bacterial strain of the invention may be administered intrarectally.
A rectal administration may in particular be carried out in the form of a suppository, an enema or a foam, in particular an enema.
A composition for use according to the invention may also be in the form of a nutritional composition.
A nutritional composition for use according to the invention may be in the form of a yogurt, a cereal bar, breakfast cereals, a dessert, a frozen food, a soup, a pet food, a liquid suspension, a powder, a tablet, a gum or a candy.
In particular, a composition for use of the invention may be suitable for the administration of a daily dose representing from 107 to 1014 colony-forming units (cfu) of the strain according to the invention as a medicament, preferably a daily dose equivalent to 1011 cfu.
For example, a composition for use according to the invention may be administered to an individual requiring it, at a single daily dose of 1 g containing the 1-4573 bacterial strain of the invention in an amount equivalent to a dose of between 107 and 1014 cfu, preferably 1011 cfu.
In another example, a composition for use according to the invention may be administered to an individual requiring it, at a single daily dose of 0.2 g containing the I- 4573 bacterial strain of the invention in an amount equivalent to an amount of between 107 and 1014 cfu, preferably 1011 cfu. As previously mentioned, daily dosages may also range from 104 to 1015 total cell count (TCC), more preferably from 108 to 1013 TCC of the F. prausnitzii strain of the invention as a medicament, for example as a daily dose equivalent to 1013 TCC.
A composition for use according to the invention may be administered to an individual requiring it from 1 to 10 times a day, each dose containing the 1-4573 bacterial strain of the invention in an amount of for example between 5.108 and 5.1011 TCC, so that the total daily dose of the 1-4573 bacterial strain of the invention administered to the individual is as indicated above.
In particular, a composition for use according to the invention may be administered to an individual for 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 10 days, 14 days, 15 days, 3 weeks, 1 month or for more than 1 month. When a composition for use according to the invention is administered for more than 1 day, the same daily amount of the F. prausnitzii strain of the invention can be administered every day or the daily amount can vary along the treatment period. In particular, the daily dosage of the F. prausnitzii strain of the invention may be higher during the first days of the treatment and then gradually decrease.
A composition according to the invention may also comprise at least one among: antioxidants, fish oils, DHA, EPA, vitamins, minerals, phytonutrients, a protein, a lipid, probiotics, and combinations thereof.
An individual according to the invention may accordingly be: an individual which will start or has already started an antibiotic treatment; and/or an individual which is finishing or has just finished an antibiotic treatment; and/or an individual which will start or has already started a Proton pump inhibitors (PPI) treatment; and/or an individual which is finishing or has just finished a Proton pump inhibitors (PPI) treatment; and/or an individual who has been treated for an episode of C. difficile infection, for example a first episode of C. difficile infection, for example with vancomycine and/or fidaxomicine; and/or an individual with a first episode of C. difficile infection or with a recurrent C. difficile infection.
The Clostridioides difficile infection to be treated and/or prevented according to the invention may in particular occur after the use of at least one antibiotic and/or PPI medication by the considered individual. Accordingly, an individual according to the invention may in particular be an individual which will start or has already started an antibiotic and/or PPI treatment or with a dysbiosis.
A bacterial strain for use according to the invention, a culture supernatant thereof, or a composition comprising it, may accordingly be administered simultaneously and/or separately, in particular simultaneously, with at least one antibiotic medication (antibiotic) of the antibiotic treatment and/or with at least one and/or PPI medication, such as for example separately during the same day, or even separately with at least one, or even more, days between the administration of the bacterial strain and the administration of the antibiotic/PPI medication.
In a particular embodiment, the bacterial strain for use according to the invention or culture supernatant thereof and the at least one antibiotic and/or PPI are administered to the individual in the same composition.
In a particular embodiment, the bacterial strain for use according to the invention or culture supernatant thereof and the at least one antibiotic and/or PPI are administered in separate compositions.
When the bacterial strain for use according to the invention or culture supernatant thereof and the at least one antibiotic and/or PPI are administered in separate compositions, the compositions can be administered to the individual simultaneously or separately through the same route of through different routes.
By simultaneously, it is understood that the bacterial strain for use according to the invention, culture supernatant thereof, or composition comprising it, can be administered at the same moment or up to the same day or couple of days as the antibiotic and/or PPI. By separately, it is understood that the bacterial strain for use according to the invention, culture supernatant thereof, or composition comprising it, can be administered with at least several days, for example at least three days of difference.
A bacterial strain for use according to the invention, a culture supernatant thereof, or a composition comprising it, may be administered simultaneously and separately with at least one antibiotic medication (antibiotic) of the antibiotic treatment and/or with at least one and/or PPI medication, such as for example the bacterial strain for use according to the invention, the culture supernatant thereof or the composition comprising it according to the invention may be administered simultaneously as the administration of the antibiotic/PPI medication and also after the end of the antibiotic and/or PPI treatment.
The dosage and frequency of administration of a bacterial strain for use according to the invention or culture supernatant thereof may be adapted depending on the host response.
For illustrative purposes only, the frequency of administration of a bacterial strain for use according to the invention, culture supernatant or composition comprising it, may be a daily administration for 5 to 15 consecutive days. The administration can alternatively be every 2, 3, 4, 5, 6 or 7 days for a period of up to several months.
In case of an individual which will start or has already started a treatment as mentioned above, and in particular an antibiotic and/or PPI treatment, the frequency of administration of a bacterial strain for use according to the invention, culture supernatant or composition comprising it, may be a daily administration all along the treatment of the individual, in particular all along the antibiotic and/or PPI treatment, and the administration of bacterial strain for use according to the invention, culture supernatant or composition comprising it :
- may be started one or several days before the start of the above-mentioned treatment, in particular antibiotic and/or PPI treatment; and/or
- may end one or several days after the end of the above-mentioned treatment, in particular antibiotic and/or PPI treatment.
As is known in the art, adjustments for protein degradation, systemic versus localized delivery, as well as the age, body weight, general health, sex, diet, time of administration, drug interaction and the severity of the condition may be necessary, and is easily determined with routine experimentation by those skilled in the art. An antibiotic medication, or antibiotic, and/or PPI medication relevant according to the invention can be any medication which alters, inhibits the growth of or destroys microorganisms of the gut microbiota.
In a non-limiting way, such antibiotic can for example be selected from the group consisting of Penicillins, Tetracyclines, Cephalosporins, Quinolones, Lincomycins, Macrolides, Sulfonamides, Glycopeptides, Aminoglycosides, Carbapenems and mixtures thereof, and in particular selected from the group consisting of amoxicillin, doxycycline, cephalexin, ciprofloxacin, clindamycin, metronidazole, azithromycin, sulfamethoxazole and trimethoprim, clavulanate, ofloxacin, levofloxacin and mixtures thereof.
Antibiotic can for example be selected from the group consisting of amoxicillin, doxycycline, cephalexin, ciprofloxacin, clindamycin, metronidazole, azithromycin, sulfamethoxazole and trimethoprim, clavulanate, levofloxacin, vancomycin, fidaxomicin, metronidazole, kanamycin, gentamycin, colistin, clindamycin and mixtures thereof.
In a non-limiting way, such PPI can for example be selected from the group consisting of Omeprazole, lansoprazole, pantoprazole, rabeprazole, esomeprazole and dexlansoprazole.
The present invention also relates to the use of:
- a bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573; and/or
- a culture supernatant thereof; and/or
- a composition comprising, in a physiologically acceptable medium, the bacterial strain or culture supernatant thereof, for treating and/or preventing a Clostridioides difficile infection in an individual.
The present invention also relates to a method for treating and/or preventing a Clostridioides difficile infection in an individual, comprising administering to the said individual:
- a bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573; and/or
- a culture supernatant thereof; and/or - a composition comprising, in a physiologically acceptable medium, the bacterial strain or culture supernatant thereof.
The present invention also relates to the use of:
- a bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573; and/or
- a culture supernatant thereof; and/or
- a composition comprising, in a physiologically acceptable medium, the bacterial strain or culture supernatant thereof, for the manufacture of a medicament for treating and/or preventing a Clostridioides difficile infection in an individual.
The invention is described below in greater details by means of the following examples which are given solely by way of illustration.
All the references to percentages are percentages by weight unless otherwise indicated.
EXAMPLES
The F. prausnitzii strain according to the invention, deposited with the CNCM under the accession number CNCM 1-4573, was tested for its capacity to modulate, in vitro and in vivo, C. difficile intestinal colonization, in particular in mice presenting an induced dysbiosis.
Twenty 6-week-old conventional C57 Black 6 (C57BL/6) female mice were identified and caged with sterile food and water in isolators to protect them from the external environment. The mice are divided into 2 groups:
-10 mice are treated with PBS- Glycerol 16% (Vehicle); and
-10 mice treated with F. prausnitzii strain CNCM 1-4573.
In order to create an intestinal dysbiosis, 6 days prior to infection (D-6) and for 3 days (D-6 to D-3), all the mice were given a cocktail of antibiotics in the drinking water consisting of Kanamycin 0.4 mg/mL, Gentamycin 0.035 mg/mL, Colistin 0.0567 mg/mL, Metronidazole 0.215 mg/mL and Vancomycin 0.045 mg/mL. On D-l, all mice were given a single 200 pL intraperitoneal (IP) dose of clindamycin 50 mg/kg. From D-6 to D+14, for each group, mice are fed once daily with 200 pL of the strain corresponding to their group. On DO, all mice were infected by gastric gavage with 500 pL of C. difficile strain R20291 (DSM 27147) at a concentration of 2 x 105 CFU/mL. For this purpose, pre-cultures were performed the day before with C. difficile strain R20291 (DSM 27147) and the following morning, a Gram stain was performed to verify the purity of the suspension and the culture was diluted with 27 mL of BHI with 3 mL of pre-culture. After approximately 7 hours of anaerobic culture, the suspension was enumerated and adjusted to 2xl05 bacteria/mL in 50 mL of regenerated 1 X PBS. Following infection with C. difficile, mice are then weighed daily for 8 days from infection and then at D10, D14 and D20.
In order to monitor intestinal colonisation by C. difficile, the faeces of the mice were collected at DI, D2, D3, D5, D8, D12, D14 and D20 and resuspended in PBS to obtain a final concentration of 10 mg/mL. The suspensions are then diluted to 10’1, 10'2 and 10'3 and spread on BHI agar + 3% blood + C. difficile selective supplement (Biomerieux®) and incubated for 48 hours at 37 °C under anaerobic conditions. The suspension non-diluted is also spread in the same conditions.
Results
All mice were given a cocktail of antibiotics to induce dysbiosis and allow better implantation of C. difficile R20291 (DSM 27147) in the gut. Mice were fed every day of the experiment (D-6 to D14) with F. prausnitzii CNCM 1-4573 or PBS-Glycerol 16% (Vehicle). After infection with the toxigenic C. difficile strain R20291 (DSM 27147), clinical scores (loss of weight and activity, diarrhoea, mortality) were evaluated, colonisation was monitored by counting the bacteria in the faeces.
1) Clinical evaluation
Regarding the evaluation of clinical scores (Figure 1), no weight loss, loss of activity or diarrhoea was observed in the mice treated with the F. prausnitzii strain of the invention.
On the other hand, for the mice in the corresponding control group (PBS - vehicle), a loss of weight from D2 onwards, then a return to their normal weight at D6 postinfection, a loss of activity and diarrhoea were observed. The survival of the animals after challenge was monitored. As shown in Figure 2, following infection with C. difficile, 2 mice died in the PBS-Glycerol 16% group (control - vehicle) and 1 mouse treated with F. prausnitzii CNCM 1-4573 died 5 days after infection.
2) Monitoring of colonisation
With regard to monitoring the colonisation of mice by C. difficile (Figure 3), all mice were colonised by C. difficile at D4.
The mice in the F. prausnitzii strain of the invention group were well colonised although they did not appear to develop symptoms. There was a delay in colonisation compared to the control group (vehicle group) and a more rapid elimination of C. difficile (from D6, compared to D14 for the control group). At DIO, the mice were still colonised by C. difficile, 4 out of 4 mice treated with PBS-Glycerol 16% (vehicle control group), 1 out of 6 mice for the group treated with the F. prausnitzii strain of the invention.
A treatment based on the administration of the F. prausnitzii strain of the invention unexpectedly demonstrated the ability to provide a protection from a C. difficile infection. The mice did not develop clinical signs (stable weight, normal faeces and activity) despite all being colonized. The colonization was delayed and a faster elimination of C. difficile was surprisingly observed.
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Claims

1. A bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573, and/or a culture supernatant thereof, for use in the treatment and/or prevention of a Clostridioides difficile infection in an individual.
2. The bacterial strain, and/or culture supernatant thereof, for use thereof as claimed in claim 1, characterized in that the individual is selected from the group consisting of human beings; Suidae, in particular pigs, more particularly piglets; Bovinae, in particular cattle, more particularly bulls, and more particularly steers; Canidae, in particular dogs; Equidae, in particular horses; and Phasianidae, in particular poultry, more particularly chickens.
3. The bacterial strain, and/or culture supernatant thereof, for use thereof as claimed in claim 1 or 2, characterized in that the individual is a mammal and is more particularly a human being.
4. The bacterial strain, and/or culture supernatant thereof, for use thereof as claimed in any one of claims 1 to 3, characterized in that the bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM I- 4573 is administered to the said individual in a live, inactive and/or dead form, preferably in a live or inactive form, more particularly in a live form.
5. The bacterial strain, and/or culture supernatant thereof, for use thereof as claimed in any one of claims 1 to 4, characterized in that the Clostridioides difficile infection occurs after the use of at least one antibiotic medication and/or at least one Proton pump inhibitors (PPI) medication by the individual.
6. The bacterial strain, and/or culture supernatant thereof, for use thereof as claimed in any one of claims 1 to 5, characterized in that the bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM I- 4573, and/or the culture supernatant thereof, is administered simultaneously with and/or after the at least one antibiotic medication and/or the at least one PPI medication.
7. The bacterial strain, and/or culture supernatant thereof, for use thereof as claimed in any one of claims 1 to 6, wherein the bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM I- 4573 is included in a composition comprising a physiologically acceptable medium.
8. The bacterial strain, and/or culture supernatant thereof, for use thereof as claimed in claim 7, characterized in that the bacterial strain of the species Faecalibacterium prausnitzii deposited with the CNCM under accession number CNCM 1-4573 is included in an oral or rectal composition, in particular in an oral composition.
9. The bacterial strain, and/or culture supernatant thereof, for use thereof as claimed in claim 7 or 8, characterized in that the bacterial strain is included in a pharmaceutical product.
10. The bacterial strain, and/or culture supernatant thereof, for use thereof as claimed in any one of claims 7 to 9, characterized in that the composition is suitable for the administration of a daily dose representing from 104 to 1015 total cell count (TCC) of the bacterial strain as a medicament, preferably in the form of a daily dose representing from 108 to 1013 TCC, more particular representing 1013 TCC.
EP23836836.9A 2022-12-20 2023-12-20 Faecalibacterium prausnitzii strain cncm i-4573 for the treatment and prevention of clostridioides difficile infection Pending EP4637795A1 (en)

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EP22306952.7A EP4389134A1 (en) 2022-12-20 2022-12-20 Faecalibacterium prausnitzii strain cncm i-4573 for the treatment and prevention of clostridioides difficile infection
PCT/EP2023/087147 WO2024133596A1 (en) 2022-12-20 2023-12-20 Faecalibacterium prausnitzii strain cncm i-4573 for the treatment and prevention of clostridioides difficile infection

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EP23836836.9A Pending EP4637795A1 (en) 2022-12-20 2023-12-20 Faecalibacterium prausnitzii strain cncm i-4573 for the treatment and prevention of clostridioides difficile infection

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KR (1) KR20250161519A (en)
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AU (1) AU2023413727A1 (en)
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US11013783B2 (en) * 2012-12-26 2021-05-25 Institut National De Recherche Pour L'agriculture, L'alimentation Et L'environnement Anti-inflammatory peptides and methods for treating inflammatory diseases
US20190381115A1 (en) * 2014-11-13 2019-12-19 Institut National De La Recherche Agronomique (Inra) Faecalibacterium prausnitzii strains for treating and preventing gastrointestinal pain
FR3046934B1 (en) * 2016-01-25 2018-01-26 Institut National De La Recherche Agronomique (Inra) FAECALIBACTERIUM PRAUSNITZII STRAIN CNCM I-4573 FOR THE TREATMENT AND PREVENTION OF GASTROINTESTINAL INFLAMMATION
EP3838276A1 (en) * 2019-12-17 2021-06-23 Exeliom Biosciences Association of faecalibacterium prausnitzii strain cncm i-4573 with pentasa® for the treatment and prevention of gastrointestinal inflammation

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JP2025542179A (en) 2025-12-25
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KR20250161519A (en) 2025-11-17
WO2024133596A1 (en) 2024-06-27
IL321512A (en) 2025-08-01

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