US 12,077,827 B2
Methods for predicting the risk of developing pulmonary colonization/infection by Pseudomonas aeruginosa
Geneviève Hery-Arnaud, Brest (FR); Jérôme Mounier, Plouzané (FR); Marlène Keravec, Plouzané (FR); Stanislas Mondot, Jouy-en-Josas (FR); Patricia Lepage, Jouy-en-Josas (FR); and Charles-Antoine Guilloux, Brest (FR)
Assigned to INSERM (INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE), Paris (FR); UNIVERSITE DE BRETAGNE OCCIDENTALE, Brest (FR); ETABLISSEMENT FRANCAIS DU SANG (EFS), La Plaine Saint Denis (FR); CENTRE HOSPITALIER REGIONAL ET UNIVERSITAIRE DE BREST, Brest (FR); and INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'EVIRONNEMENT, Paris (FR)
Appl. No. 16/651,426
Filed by INSERM (INSTITUT NATIONAL DE LA SANTÉ ET DE LA RECHERCHE MÉDICALE), Paris (FR); UNIVERSITÉ DE BRETAGNE OCCIDENTALE, Brest (FR); ETABLISSEMENT FRANCAIS DU SANG (EFS), La Plaine Saint Denis (FR); CENTRE HOSPITALIER REGIONSL ET UNIVERSITAIRE DE BREST, Brest (FR); and INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'ENVIRONNEMENT, Paris (FR)
PCT Filed Sep. 28, 2018, PCT No. PCT/EP2018/076442
§ 371(c)(1), (2) Date Mar. 27, 2020,
PCT Pub. No. WO2019/063783, PCT Pub. Date Apr. 4, 2019.
Claims priority of application No. 17306297 (EP), filed on Sep. 29, 2017; and application No. 17306717 (EP), filed on Dec. 7, 2017.
Prior Publication US 2020/0283829 A1, Sep. 10, 2020
Int. Cl. C12Q 1/68 (2018.01); A61K 35/741 (2015.01); C07K 16/12 (2006.01); C12Q 1/689 (2018.01); A61K 35/00 (2006.01); A61K 45/06 (2006.01)
CPC C12Q 1/689 (2013.01) [A61K 35/741 (2013.01); C07K 16/1214 (2013.01); A61K 2035/115 (2013.01); A61K 45/06 (2013.01); C12Q 2600/118 (2013.01); G01N 2800/12 (2013.01); G01N 2800/50 (2013.01)] 4 Claims
 
1. A method for treating pulmonary colonization or infection by Pseudomonas aeruginosa in a subject suffering from cystic fibrosis (CF) comprising:
Measuring, using 16S rRNA deep-sequencing, the relative abundance of all Porphyromonas genus bacteria in a biological sample obtained from said subject, wherein the biological sample is bronchoalveolar lavage (BAL) or sputum or protected specimen brushing from bronchoscopic sampling or pharyngeal swabs, the relative abundance of Porphyromonas genus bacteria being the percent composition of Porphyromonas genus bacteria relative to the total number of bacteria genus in said biological sample;
determining that the measured relative abundance of Porphyromonas genus bacteria is less than 5.33% and thus that the biological sample has a low relative abundance of Porphyromonas genus bacteria as compared to a corresponding biological sample obtained from an uninfected subject which is indicative of a high risk of developing pulmonary colonization/infection by Pseudomonas aeruginosa; and then
administering to the subject a therapeutically effective amount of P. aeruginosa specific antibiotics.