Methods of reducing or preventing clostridioides difficile colonization
Embodiments of the present disclosure relate to a method of preventing and/or reducing C. difficile colonization of a surface. In certain embodiments, the aptamer can be used to kill and/or deactivate a C. difficile spore. In certain embodiments, the aptamer can be used to increase the sporicidal activity of a sporicidal agent. Embodiments of the present disclosure relate to the use of aptamers which specifically bind to C. difficile surface proteins, for example proteins located on the surface of a C. difficile spore.
1 . A method for killing or inactivating Clostridioides difficile ( C. difficile ) spores, comprising contacting the spores with an agent selected from the group consisting of a sporicidal agent and a sporostatic agent; and an aptamer capable of specifically binding to C. difficile , wherein the aptamer includes a nucleic acid sequence having at least 95% sequence identity with any one of the nucleic acid sequences as set forth in any of SEQ ID NOs: 1 to 14, 23 to 39, or 43 to 55.
2 . A method for enhancing a sporicidal effect against C. difficile of a sporicidal agent, the method comprising contacting C. difficile spores with an aptamer capable of specifically binding to C. difficile spores and an agent selected from the group consisting of a sporicidal agent and a sporostatic agent, wherein the aptamer includes a nucleic acid sequence having at least 95% sequence identity with any one of the nucleic acid sequences as set forth in any of SEQ ID NOs: 1 to 14, 23 to 39, or 43 to 55.
3 . The method according to claim 1 or claim 2 , wherein the agent is a sporicidal agent.
4 . The method according to claim 1 or claim 2 , comprising locating the aptamer and the sporicidal agent at a location suspected of comprising C. difficile spores.
5 . The method according to claim 4 , wherein the location comprises a surface and the method comprises contacting the surface with the sporicidal agent prior to, at essentially the same time, or subsequent to contacting the surface with the aptamer.
6 . The method according to claim 5 , which comprises:
contacting the surface with the aptamers for a predetermined period of time configured to enable the aptamer to bind to the C. difficile spore to form aptamer-spore complex, and
contacting the surface comprising the aptamer-spore complex with the sporicidal agent.
7 . The method according to claim 5 , further comprising contacting the surface with a GH neutralizer.
8 . The method according to claim 5 , comprising submerging the C. difficile spores with a composition comprising the aptamer and/or submerging the spores in the sporicidal agent.
9 . The method according to claim 5 , wherein the method comprises spraying the C. difficile spores with a composition comprising the aptamer and/or spraying the C. difficile spores with the sporicidal agent.
10 . The method according to claim 5 wherein the method comprises applying a composition comprising the aptamer by means of a cloth and/or applying the sporicidal agent by means of a cloth and/or a wipe.
11 . The method according to claim 1 or claim 2 , wherein the method is performed at a temperature of about 5° C., 10° C., 15° C., 20° C., 25° C., 30° C., 35° C., 40° C., 45° C., 50° C., 55° C., 60° C., 65° C., 70° C., 75° C., 80° C. or 90° C.
12 . The method according to claim 1 or claim 2 , wherein a C. difficile spore comprises a coat surface protein or an exosporium layer protein.
13 . The method according to claim 12 , wherein the C. difficile protein comprises CdeC, CdeM, CotA, CotE or CotE Chitinase.
14 . The method according to claim 13 , wherein the C. difficile protein is a CdeC protein having an amino acid sequence as set forth in SEQ. ID. NO. 18.
15 . The method according to claim 13 , wherein the C. difficile protein is a CdeM protein having an amino acid sequence as set forth in SEQ. ID. NO. 19.
16 . The method according to claim 13 , wherein the C. difficile protein is a CotA protein having an amino acid sequence as set forth in SEQ. ID. NO. 15.
17 . The method according to claim 13 , wherein the C. difficile protein is a CotE protein having an amino acid sequence as set forth in SEQ. ID. NO. 16.
18 . The method according to claim 13 , wherein the C. difficile protein is a CotE Chitinase protein having an amino acid sequence as set forth in SEQ. ID. NO. 17.
19 . The method according to claim 1 , wherein the aptamer comprises or consists of:
(a) a nucleic acid sequence selected from any one of the nucleic acid sequences as set forth in any of SEQ ID NOs: 1 to 14, 23 to 39, or 43 to 55; or
(b) a nucleic acid sequence having at least 95%, sequence identity with SEQ ID NO: 1, 5 and 6.
20 . The method according to claim 12 , wherein the aptamer is a single stranded DNA aptamer.
21 . The method according to claim 12 , wherein the aptamer is selected from:
a) an aptamer which specifically binds to a CdeC;
b) an aptamer which specifically binds to CdeM,
c) an aptamer which specifically binds to CotA,
d) an aptamer which specifically binds to CotE;
e) an aptamer which specifically binds to CotE Chitinase; and
f) a combination of any of (a) to (e).
22 . The method according to claim 4 , comprising contacting the location with a plurality of aptamers, wherein each aptamer is capable of specifically binding to a C. difficile spore, wherein the plurality of aptamers comprises at least two aptamers capable of specifically binding to the same epitope of a C. difficile spore and/or at least two aptamers each aptamer capable of specifically binding to a different epitope of a C. difficile spore.
23 . The method according to claim 22 , wherein the plurality of aptamers comprises at least two aptamers selected from the group consisting of an aptamer comprising, consisting essentially of, or consisting of:
(a) a nucleic acid sequence selected from any one of the nucleic acid sequences as set forth in any of SEQ ID NOs: 1 to 14, 23 to 39, or 43 to 55;
(b) a nucleic acid sequence having at least 95% sequence identity with any one of the nucleic acid sequences as set forth in any of SEQ ID NOs: 1 to 14, 23 to 39, or 43 to 55;
or
(c) a combination of (a) to (b).
24 . The method according to claim 22 , wherein the plurality of aptamers comprises at least two aptamers selected from the group consisting of:
a) an aptamer which specifically binds to a CdeC;
b) an aptamer which specifically binds to CdeM,
c) an aptamer which specifically binds to CotA,
d) an aptamer which specifically binds to CotE;
e) an aptamer which specifically binds to CotE Chitinase; and
f) a combination of any of (a) to (e).
25 . The method according to claim 22 , wherein the plurality of aptamers comprises:
an aptamer comprising, consisting essentially of, or consisting of a nucleic acid sequence as set forth in SEQ. ID. NO. 1;
an aptamer comprising, consisting essentially of, or consisting of a nucleic acid sequence as set forth in SEQ. ID. NO. 5; and
an aptamer comprising, consisting essentially of, or consisting of a nucleic acid sequence as set forth in SEQ. ID. NO. 6.
26 . The method according to claim 1 or claim 2 , wherein the method comprises determining the presence, absence and/or concentration of C. difficile at a location prior to contacting the location with the sporicidal agent and/or sporostatic agent, wherein the step of determining comprises contacting the location with an aptamer and a detection molecule for a time sufficient for an aptamer-spore complex to form.
27 . The method according to claim 26 , wherein the aptamer comprises a detectable label.
28 . The method according to claim 27 , wherein the detectable label is selected from a fluorophore, a nanoparticle, a quantum dot, an enzyme, a radioactive isotope a biotin, a desthiobiotin, a thiol group, an amine group, an azide, an aminoallyl group, a digoxigenin, an antibody, a catalyst, a colloidal metallic particle, a colloidal non-metallic particle, an organic polymer, a latex particle, a nanofiber, a nanotube, a dendrimer, a protein, and a liposome.
29 . The method according to claim 1 or claim 2 , wherein the agent is a sporicidal solution comprising chlorhexidine gluconate and optionally isopropyl alcohol.
30 . The method according to claim 1 or claim 2 , wherein the agent is a sporicidal agent which comprises peracetic acid and/or peracetic acid generating agent.
31 . The method according to claim 30 , wherein the sporicidal agent is a peracetic acid generating agent, and wherein the method further comprises wetting a wipe comprising sodium percarbonate with an aqueous solution prior to contacting a location suspected of comprising C. difficile spores.
32 . The method according to claim 1 or claim 2 , wherein the agent is a sporicidal solution comprising hydrogen peroxide and optionally a silver stabilised hydrogen peroxide.
33 . The method according to claim 1 or claim 2 , wherein the agent is a sporicidal solution comprising chlorhexidine gluconate and 70% isopropyl alcohol complex.
34 . The method according to claim 1 or claim 2 , comprising locating a combination of sporicidal and/or sporostatic agents.
35 . The method according to claim 34 , wherein the combination comprises peracetic acid and hydrogen peroxide.