Polynucleotides for the amplification and detection of

1. A composition comprising a set of primers selected from the group consisting of:

i. a primer set comprising a forward outer primer comprising SEQ ID NO: 87, a backward outer primer comprising SEQ ID NO: 82, a forward inner primer comprising SEQ ID NO: 94, a backward inner primer comprising SEQ ID NO: 84, a forward loop primer comprising SEQ ID NO: 76, and a backward loop primer comprising SEQ ID NO: 86;

ii. a primer set comprising a forward outer primer comprising SEQ ID NO: 87, a backward outer primer comprising SEQ ID NO: 82, a forward inner primer comprising SEQ ID NO: 94, and a backward inner primer comprising SEQ ID NO: 84; and

iii. a primer set comprising a forward inner primer comprising SEQ ID NO: 94 and a backward inner primer comprising SEQ ID NO: 84.

2. The composition of claim 1 , further comprising a probe.

3. The composition of claim 2 , wherein the probe is a labeled polynucleotide.

4. The composition of claim 3 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of nucleotides 5-34 of SEQ ID NO: 97, nucleotides 5-31 of SEQ ID NO: 98, nucleotides 3-31 of SEQ ID NO: 99, nucleotides 5-30 of SEQ ID NO: 100, nucleotides 6-29 of SEQ ID NO: 101, nucleotides 5-26 of SEQ ID NO: 103, nucleotides 4-27 of SEQ ID NO: 104, nucleotides 7-30 of SEQ ID NO: 105, nucleotides 5-27 of SEQ ID NO: 106, nucleotides 6-29 of SEQ ID NO: 107, nucleotides 6-29 of SEQ ID NO: 108, nucleotides 6-29 of SEQ ID NO: 109, nucleotides 6-30 of SEQ ID NO: 110, nucleotides 8-31 of SEQ ID NO: 111, nucleotides 6-29 of SEQ ID NO: 112, nucleotides 8-31 of SEQ ID NO: 113, nucleotides 5-29 of SEQ ID NO: 114, nucleotides 5-29 of SEQ ID NO: 115, nucleotides 4-28 of SEQ ID NO: 116, nucleotides 5-30 of SEQ ID NO: 117, nucleotides 8-28 of SEQ ID NO: 118, nucleotides 8-30 of SEQ ID NO: 119, nucleotides 8-29 of SEQ ID NO: 120, nucleotides 4-33 of SEQ ID NO: 121, nucleotides 7-34 of SEQ ID NO: 122, nucleotides 9-34 of SEQ ID NO: 123, nucleotides 8-34 of SEQ ID NO: 124, nucleotides 6-28 of SEQ ID NO: 125, nucleotides 7-28 of SEQ ID NO: 126, nucleotides 3-27 of SEQ ID NO: 127, nucleotides 7-32 of SEQ ID NO: 128, nucleotides 4-27 of SEQ ID NO: 129, and nucleotides 6-27 of SEQ ID NO: 130.

5. The composition of claim 2 , wherein the probe is a molecular beacon comprising a fluorophore, a quencher, and a polynucleotide.

6. The composition of claim 5 , wherein the molecular beacon comprises a sequence selected from the group consisting of nucleotides 5-34 of SEQ ID NO: 97, nucleotides 5-31 of SEQ ID NO: 98, nucleotides 3-31 of SEQ ID NO: 99, nucleotides 5-30 of SEQ ID NO: 100, nucleotides 6-29 of SEQ ID NO: 101, nucleotides 5-26 of SEQ ID NO: 103, nucleotides 4-27 of SEQ ID NO: 104, nucleotides 7-30 of SEQ ID NO: 105, nucleotides 5-27 of SEQ ID NO: 106, nucleotides 6-29 of SEQ ID NO: 107, nucleotides 6-29 of SEQ ID NO: 108, nucleotides 6-29 of SEQ ID NO: 109, nucleotides 6-30 of SEQ ID NO: 110, nucleotides 8-31 of SEQ ID NO: 111, nucleotides 6-29 of SEQ ID NO: 112, nucleotides 8-31 of SEQ ID NO: 113, nucleotides 5-29 of SEQ ID NO: 114, nucleotides 5-29 of SEQ ID NO: 115, nucleotides 4-28 of SEQ ID NO: 116, nucleotides 5-30 of SEQ ID NO: 117, nucleotides 8-28 of SEQ ID NO: 118, nucleotides 8-30 of SEQ ID NO: 119, nucleotides 8-29 of SEQ ID NO: 120, nucleotides 4-33 of SEQ ID NO: 121, nucleotides 7-34 of SEQ ID NO: 122, nucleotides 9-34 of SEQ ID NO: 123, nucleotides 8-34 of SEQ ID NO: 124, nucleotides 6-28 of SEQ ID NO: 125, nucleotides 7-28 of SEQ ID NO: 126, nucleotides 3-27 of SEQ ID NO: 127, nucleotides 7-32 of SEQ ID NO: 128, nucleotides 4-27 of SEQ ID NO: 129, and nucleotides 6-27 of SEQ ID NO: 130.

7. The composition of claim 6 , wherein the molecular beacon comprises a sequence selected from the group consisting of SEQ ID NOs: 97-101 and 103-130.

8. The composition of claim 7 , wherein the polynucleotide sequence consists of SEQ ID NO: 115.

9. A kit comprising a composition according to claim 1 .

10. The kit of claim 9 , further comprising a strand displacement polymerase.

11. The kit of claim 9 , further comprising a molecular beacon comprising a fluorophore, a quencher, and a polynucleotide, wherein the polynucleotide consists of a sequence selected from the group consisting of SEQ ID NOs: 97-101 and 103-130.

12. The kit of claim 11 , wherein the polynucleotide consists of SEQ ID NO: 115.

13. The composition of claim 1 , wherein the set of primers is selected from the group consisting of:

i. a primer set consisting of a forward outer primer consisting essentially of SEQ ID NO: 87, a backward outer primer consisting essentially of SEQ ID NO: 82, a forward inner primer consisting essentially of SEQ ID NO: 94, a backward inner primer consisting essentially of SEQ ID NO: 84, a forward loop primer consisting essentially of SEQ ID NO: 76, and a backward loop primer consisting essentially of SEQ ID NO: 86;

ii. a primer set consisting of a forward outer primer consisting essentially of SEQ ID NO: 87, a backward outer primer consisting essentially of SEQ ID NO: 82, a forward inner primer consisting essentially of SEQ ID NO: 94, and a backward inner primer consisting essentially of SEQ ID NO: 84; and

iii. a primer set consisting of a forward inner primer consisting essentially of SEQ ID NO: 94 and a backward inner primer consisting essentially of SEQ ID NO: 84.

14. A method of detecting Chlamydia trachomatis in a test sample, the method comprising:

(a) extracting nucleic acid from the test sample;

(b) amplifying a target sequence by reacting the nucleic acid extracted in step (a) with a reaction mixture comprising a strand displacement DNA polymerase and a sequence-specific primer set, wherein said sequence-specific primer set is selected from the group consisting of:

(i) a primer set comprising a forward outer primer comprising SEQ ID NO: 87, a backward outer primer comprising SEQ ID NO: 82, a forward inner primer comprising SEQ ID NO: 94, a backward inner primer comprising SEQ ID NO: 84, a forward loop primer comprising SEQ ID NO: 76, and a backward loop primer comprising SEQ ID NO: 86;

(ii) a primer set comprising a forward outer primer comprising SEQ ID NO: 87, a backward outer primer comprising SEQ ID NO: 82, a forward inner primer comprising SEQ ID NO: 94, and a backward inner primer comprising SEQ ID NO: 84; and

(iii) a primer set comprising a forward inner primer comprising SEQ ID NO: 94 and a backward inner primer comprising SEQ ID NO: 84; and

(c) detecting the presence or absence of an amplified product of step (b); wherein the presence of said amplification product is indicative of the presence of Chlamydia trachomatis in the test sample.

15. The method of claim 14 , wherein the amplification in step (b) of the target sequence is performed at between about 60° C. and about 67° C. for less than fifteen minutes.

16. The method of claim 15 , wherein the amplification step is performed for less than ten minutes.

17. The method of claim 14 , wherein the reaction mixture further comprises a reverse transcriptase.

18. The method of claim 14 , wherein detecting the presence or absence of the amplification product comprises hybridizing the amplified product with a probe comprising a polynucleotide attached to a label.

19. The method of claim 18 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of nucleotides 5-34 of SEQ ID NO: 97, nucleotides 5-31 of SEQ ID NO: 98, nucleotides 3-31 of SEQ ID NO: 99, nucleotides 5-30 of SEQ ID NO: 100, nucleotides 6-29 of SEQ ID NO: 101, nucleotides 5-26 of SEQ ID NO: 103, nucleotides 4-27 of SEQ ID NO: 104, nucleotides 7-30 of SEQ ID NO: 105, nucleotides 5-27 of SEQ ID NO: 106, nucleotides 6-29 of SEQ ID NO: 107, nucleotides 6-29 of SEQ ID NO: 108, nucleotides 6-29 of SEQ ID NO: 109, nucleotides 6-30 of SEQ ID NO: 110, nucleotides 8-31 of SEQ ID NO: 111, nucleotides 6-29 of SEQ ID NO: 112, nucleotides 8-31 of SEQ ID NO: 113, nucleotides 5-29 of SEQ ID NO: 114, nucleotides 5-29 of SEQ ID NO: 115, nucleotides 4-28 of SEQ ID NO: 116, nucleotides 5-30 of SEQ ID NO: 117, nucleotides 8-28 of SEQ ID NO: 118, nucleotides 8-30 of SEQ ID NO:119, nucleotides 8-29 of SEQ ID NO: 120, nucleotides 4-33 of SEQ ID NO: 121, nucleotides 7-34 of SEQ ID NO: 122, nucleotides 9-34 of SEQ ID NO: 123, nucleotides 8-34 of SEQ ID NO: 124, nucleotides 6-28 of SEQ ID NO: 125, nucleotides 7-28 of SEQ ID NO: 126, nucleotides 3-27 of SEQ ID NO: 127, nucleotides 7-32 of SEQ ID NO: 128, nucleotides 4-27 of SEQ ID NO: 129, and nucleotides 6-27 of SEQ ID NO: 130.

20. The method of claim 19 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of SEQ ID NOs: 97-101 and 103-130.

21. The method of claim 20 , wherein the sequence of the labeled polynucleotide is SEQ ID NO: 115.

22. The method of claim 14 , wherein Chlamydia trachomatis is present in the test sample at a concentration of <100 IFU/mL.

23. The method of claim 22 , wherein Chlamydia trachomatis is present in the test sample at a concentration of <5 IFU/ml and the amplification step is performed for less than 15 minutes.

24. The method of claim 22 , wherein Chlamydia trachomatis is present in the test sample at a concentration of <10 IFU/ml and the amplification step is performed for less than six minutes.

25. A method of detecting Chlamydia trachomatis in a test sample, the method comprising:

(a) extracting nucleic acid from the test sample;

(b) amplifying a target sequence by reacting the nucleic acid extracted in step (a) for less than ten minutes with a reaction mixture comprising a strand displacement DNA polymerase and a sequence-specific LAMP primer set comprising a forward outer primer comprising SEQ ID NO: 87, a backward outer primer comprising SEQ ID NO: 82, a forward inner primer comprising SEQ ID NO: 94, a backward inner primer comprising SEQ ID NO: 84, a forward loop primer comprising SEQ ID NO: 76, and a backward loop primer comprising SEQ ID NO: 86; and

(c) detecting the presence or absence of an amplified product of step (b); wherein the presence of said amplification product is indicative of the presence of Chlamydia trachomatis in the test sample.

26. The method of claim 25 , wherein detecting the presence or absence of the amplification product comprises hybridizing the amplified product with a molecular beacon comprising a polynucleotide sequence selected from the group consisting of nucleotides 5-34 of SEQ ID NO: 97, nucleotides 5-31 of SEQ ID NO: 98, nucleotides 3-31 of SEQ ID NO: 99, nucleotides 5-30 of SEQ ID NO: 100, nucleotides 6-29 of SEQ ID NO: 101, nucleotides 5-26 of SEQ ID NO: 103, nucleotides 4-27 of SEQ ID NO: 104, nucleotides 7-30 of SEQ ID NO: 105, nucleotides 5-27 of SEQ ID NO: 106, nucleotides 6-29 of SEQ ID NO: 107, nucleotides 6-29 of SEQ ID NO: 108, nucleotides 6-29 of SEQ ID NO: 109, nucleotides 6-30 of SEQ ID NO: 110, nucleotides 8-31 of SEQ ID NO: 111, nucleotides 6-29 of SEQ ID NO: 112, nucleotides 8-31 of SEQ ID NO: 113, nucleotides 5-29 of SEQ ID NO: 114, nucleotides 5-29 of SEQ ID NO: 115, nucleotides 4-28 of SEQ ID NO: 116, nucleotides 5-30 of SEQ ID NO: 117, nucleotides 8-28 of SEQ ID NO: 118, nucleotides 8-30 of SEQ ID NO: 119, nucleotides 8-29 of SEQ ID NO: 120, nucleotides 4-33 of SEQ ID NO: 121, nucleotides 7-34 of SEQ ID NO: 122, nucleotides 9-34 of SEQ ID NO: 123, nucleotides 8-34 of SEQ ID NO: 124, nucleotides 6-28 of SEQ ID NO: 125, nucleotides 7-28 of SEQ ID NO: 126, nucleotides 3-27 of SEQ ID NO: 127, nucleotides 7-32 of SEQ ID NO: 128, nucleotides 4-27 of SEQ ID NO: 129, and nucleotides 6-27 of SEQ ID NO: 130.

27. The method of claim 25 , wherein detecting the presence or absence of the amplification product comprises hybridizing the amplified product with a molecular beacon comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOs: 97-101 and 103-130.