Method for labeling specifically living microorganisms comprising the use of modified monosaccharide compounds

1. A method for labeling specifically living microorganisms in a sample comprising microorganisms, wherein said method comprises the steps of:

a) incubating said microorganisms of said sample with at least one modified monosaccharide compound comprising a first reactive group Ra, which is capable to chemically react with a second reactive group, so that a residue bearing said first reactive group is incorporated into said living microorganisms, and

b) contacting said residue incorporated into said microorganism with a labeling molecule comprising said second reactive group, for generating the chemical reaction of said first reactive group of said residue incorporated into said living microorganism with said second reactive group of said labeling molecule, resulting in a covalent link,

wherein said modified monosaccharide compound has the following formula (I′), or a salt thereof:

X is O, and

R1 and R2 are independently H, OH, or NH 2 , wherein the OH and NH2 are each being substituted or not by a protecting group selected from the group consisting of alkyl, hydroxyalkyl, acyl, formyl and imidoyl groups, and

R3 is an alkyl chain of C 1 to C 4 , each carbon being substituted or not by OH or NH 2 , wherein the OH or NH 2 being substituted or not by a protecting group selected from the group consisting of alkyl, hydroxyalkyl, acyl, formyl and imidoyl groups,

R3 group being substituted by said first reactive group Ra, and

wherein the first reactive group Ra is selected from the group consisting of an azido group, a group bearing an azido, an alkyne group, and a group bearing an alkyne, and said second reactive group is selected from the group consisting of an alkyne group, a group bearing an alkyne, an azido group, and a group bearing an azido, wherein said first reactive group is capable of reacting with said second reactive group via an azide alkyne cycloaddition.

2. The method according to claim 1 , wherein said modified monosaccharide compound is a stereoisomer having the formula (I) or a salt thereof

3. The method according to claim 1 , wherein:

R1 and R2 are OH, which is substituted or not by said protecting group, and

R3 is —CH 3 , —CH 2 OH, or —CH 2 NH 2 , which is substituted by said first reactive group Ra.

4. The method according to claim 1 , wherein said modified monosaccharide compound is a compound having the following stereoisomer formula (Ia), or a salt thereof:

5. The method according to claim 1 , wherein Ra is —N 3 or —C≡CH.

6. The method according to claim 1 , wherein said microorganism is selected from the group consisting of:

Prokaryotic microorganisms, and

Unicellular eukaryotic microorganisms.

7. The method according to claim 6 , for labeling one or more microorganisms selected from the group consisting of the following species microorganisms:

a) bacteria: Acinetobacter baumannii, Bacillus cereus, Bacillus cereus, Bacillus cereus paris, Bacillus subtilis, Cronobacter sakazakii, Enterococcus durans, Enterococcus faecalis, Escherichia coli, Klebsiella pneumophila, Legionella pneumophila, Listeria monocytogenes, Micrococcus luteus, Neisseria gonorrhoeae, Neisseria meningitides, Proteus mirabilis, Providencia stuartii, Pseudomonas fluorescens Migula, Pseudomonas fluorescens Paris, Salmonella typhimurium, Serratia marcescens, Staphylococcus aureus, Staphylococcus aureus aureus, Staphylococcus epidermis, Staphylococcus saprophyticus, Stenotrophomonas maltophilia, Streptococcus agalactiae, Vibrio cholera,

b) fungi: Aspergillus niger, Candida albicans, Fusarium and Geotrichum candidum , and

c) amoebas: Acanthamoebae castellanii.

8. The method according to claim 1 , comprising the further step of:

c) detecting living microorganism in detecting whether said microorganism comprise said labeling molecule bound to said living microorganism and/or immobilizing said living microorganism bearing said labeling molecule onto a solid substrate, wherein said labeling molecule is a molecule comprising a detectable substance or capable to react or to be bound to a detectable substance or said labeling molecule is a first molecule bearing said second reactive group, said first molecule being capable to react or to be bound to a second molecule and/or to a solid substrate.

9. The method according to claim 8 , wherein said labeling molecule is a detectable molecule comprising a detectable substance, wherein in step c), detecting living microorganism comprises detecting whether said microorganism comprise said detectable molecule bound to said microorganism.

10. The method according to claim 8 , wherein said labeling molecule is a first ligand or first binding protein bearing said second reactive group and in step c) said living microorganism coupled to said first ligand or first binding protein is detected and/or immobilized by contacting said first ligand or first binding protein with a second ligand or second binding protein reacting or binding specifically to said first ligand or first binding protein.

11. A kit for carrying out the method of claim 1 , which comprises:

said modified monosaccharide compound of formula (I),

said labeling molecule comprising said second reactive group capable of reacting with said first reactive group, and

optionally, reactants for generating the reaction of said first reactive group with said second reactive group of said labeling molecule.

12. The kit according to claim 11 , which further comprises:

said detectable molecule or said second molecule bearing a detectable substance comprising a fluorochrome or luminescent molecule or an enzyme, and/or

a solid substrate bearing said second molecule capable of specifically reacting or binding with said labeling molecule.

13. The kit according to claim 12 , which further comprises a culture or incubation medium allowing the growth of said microorganism.