US2021301325A1PendingUtilityA1
Polynucleotides for the amplification and detection of chlamydia trachomatis

Assignee: TALIS BIOMEDICAL CORPPriority: May 9, 2018Filed: May 9, 2019Published: Sep 30, 2021
Est. expiryMay 9, 2038(~11.8 yrs left)· nominal 20-yr term from priority
Inventors:Daniel Capule Andrea Dedent Matt Lee Shuyuan Ma Hédia Maamar Dana Kelly Vanatta
C12Q 1/689C12Q 2600/166C12Q 2600/16C12Q 2600/112C12Q 2521/107C12Q 2600/118C12Q 2563/107C12Q 1/682C12Q 2531/101C12Q 1/6844C12Q 2565/101
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References
Claims
Abstract

The invention provides methods and compositions for the detection of Chlamydia trachomatis in a test sample. Its presence or absence in the sample is determined by nucleic acid based testing methods using primers and/or probes and or molecular beacons that bind to the 23S ribosomal genes or gene transcripts.
Claims

exact text as granted — not AI-modified
We claim: 
     
         1 . A composition comprising a set of polynucleotides selected from the group consisting of Set-20, Set-24, Set-47, Set-51, Set-74 and Set-78. 
     
     
         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 molecular beacon comprising a fluorophore, a quencher, and a polynucleotide, wherein the 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. 
     
     
         10 . The molecular beacon of  claim 9 , wherein the polynucleotide comprises a sequence selected from the group consisting of SEQ ID NOs: 97-101 and 103-130. 
     
     
         11 . The composition of  claim 10 , wherein the polynucleotide sequence consists of SEQ ID NO: 115. 
     
     
         12 . The molecular beacon of  claim 9 , wherein the fluorophore is FAM and the quencher is BHQ1. 
     
     
         13 . 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 Set-20, Set-24, Set-47, Set-51, Set-74, and Set-78; 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.   
     
     
         14 . The method of  claim 13 , 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. 
     
     
         15 . The method of  claim 14 , wherein the amplification step is performed for less than ten minutes. 
     
     
         16 . The method of  claim 13 , wherein the reaction mixture further comprises a reverse transcriptase. 
     
     
         17 . The method of  claim 13 , 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. 
     
     
         18 . The method of  claim 17 , 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. 
     
     
         19 . The method of  claim 18 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of SEQ ID NOs: 97-101 and 103-130. 
     
     
         20 . The method of  claim 19 , wherein the sequence of the labeled polynucleotide is SEQ ID NO: 115. 
     
     
         21 . The method of  claim 13 , wherein  Chlamydia trachomatis  is present in the test sample at a concentration of ≤100 IFU/mL. 
     
     
         22 . The method of  claim 21 , 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. 
     
     
         23 . The method of  claim 21 , 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. 
     
     
         24 . A kit comprising a composition according to  claim 1 . 
     
     
         25 . The kit of  claim 24 , further comprising a strand displacement polymerase. 
     
     
         26 . The kit of  claim 24 , 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. 
     
     
         27 . The kit of  claim 26 , wherein the polynucleotide consists of SEQ ID NO: 115. 
     
     
         28 . 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 selected from the group consisting of Set-20 and Set-24; 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.   
     
     
         29 . The method of  claim 28 , 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. 
     
     
         30 . The method of  claim 28 , 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. 
     
     
         31 . A composition comprising a set of polynucleotides selected from the group consisting of Set-1 through Set-81. 
     
     
         32 . The composition of  claim 31 , further comprising a probe. 
     
     
         33 . The composition of  claim 32 , wherein the probe comprises a label. 
     
     
         34 . The composition of  claim 33 , wherein the probe is a labeled polynucleotide. 
     
     
         35 . The composition of  claim 34 , 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 6-30 of SEQ ID NO: 102, 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, and 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, nucleotides 6-27 of SEQ ID NO: 130, and nucleotides 8-29 of SEQ ID NO: 131. 
     
     
         36 . The composition of  claim 34 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of SEQ ID NOs: 97 through 131. 
     
     
         37 . The composition of  claim 34 , wherein the label is a fluorophore. 
     
     
         38 . The composition of  claim 37 , wherein the fluorophore is covalently attached to a terminus of the polynucleotide. 
     
     
         39 . The composition of  claim 31 , further comprising a labeled polynucleotide comprising a sequence selected from the group consisting of 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 6-29 of SEQ ID NO: 107, nucleotides 6-29 of SEQ ID NO: 108, nucleotides 6-29 of SEQ ID NO: 109, nucleotides 8-31 of SEQ ID NO: 111, 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 9-34 of SEQ ID NO: 123, nucleotides 8-34 of SEQ ID NO: 124, nucleotides 7-32 of SEQ ID NO: 128, and nucleotides 4-27 of SEQ ID NO: 129, and wherein the set of polynucleotides is selected from the group consisting of Set-12, Sets 14-27, Set-39, Sets 41-54, Set-66, and Sets 68-81.   
     
     
         40 . The composition of  claim 39 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 128, and SEQ ID NO: 129. 
     
     
         41 . The composition of  claim 40 , wherein the sequence of the labeled polynucleotide is SEQ ID NO: 115, and the set of polynucleotides is selected from the group consisting of Set-20, Set-24, Set-47, Set-51, Set-74 and Set-78. 
     
     
         42 . The composition of  claim 41 , wherein the set of polynucleotides is Set-20 or Set-24. 
     
     
         43 . The composition of  claim 31 , further comprising a labeled polynucleotide comprising 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 5-27 of SEQ ID NO: 106, nucleotides 6-30 of SEQ ID NO: 110, nucleotides 6-29 of SEQ ID NO: 112, nucleotides 8-29 of SEQ ID NO: 120, nucleotides 4-33 of SEQ ID NO: 121, and nucleotides 7-34 of SEQ ID NO: 122, and wherein the set of polynucleotides is selected from the group consisting of Sets 12-27, Sets 39-54, and Sets 66-81. 
     
     
         44 . The composition of  claim 43 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 112, SEQ ID NO: 120, SEQ ID NO: 121, and SEQ ID NO: 122. 
     
     
         45 . The composition of  claim 31 , further comprising a labeled polynucleotide comprising a sequence selected from the group consisting of nucleotides 6-28 of SEQ ID NO: 125 and nucleotides 7-28 of SEQ ID NO: 126, and wherein the set of polynucleotides is selected from the group consisting of Set-12, Sets 14-18, Set-20, Set-24, Set-27, Set-39, Sets 41-45, Set-47, Set-51, Set-54, Set-66, Sets 68-72, Set 74, Set-78, and Set-81. 
     
     
         46 . The composition of  claim 45 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 125 and SEQ ID NO: 126. 
     
     
         47 . The composition of  claim 31 , further comprising a labeled polynucleotide comprising a sequence selected from the group consisting of nucleotides 8-31 of SEQ ID NO: 113 and nucleotides 3-27 of SEQ ID NO: 127, and wherein the set of polynucleotides is selected from the group consisting of Sets 14-27, Sets 41-54, and Sets 68-81. 
     
     
         48 . The composition of  claim 47 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 113 and SEQ ID NO: 127. 
     
     
         49 . The composition of  claim 31 , further comprising a labeled polynucleotide comprising nucleotides 6-27 of SEQ ID NO: 130, and wherein the set of polynucleotides is selected from the group consisting of Sets 12-20, Sets 22-27, Sets 39-47, Sets 49-54, Sets 66-74, and Sets 76-81. 
     
     
         50 . The composition of  claim 49 , wherein the labeled polynucleotide comprises SEQ ID NO: 130. 
     
     
         51 . The composition of  claim 31 , further comprising a labeled polynucleotide comprising a sequence selected from the group consisting of nucleotides 6-30 of SEQ ID NO: 102 and nucleotides 8-29 of SEQ ID NO: 131, and wherein the set of polynucleotides is selected from the group consisting of Set-13, Set-40 and Set-67. 
     
     
         52 . The composition of  claim 51 , wherein the polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 102 and SEQ ID NO: 131. 
     
     
         53 . The composition of  claim 52 , wherein the probe is a molecular beacon comprising a fluorophore, a quencher, and a polynucleotide. 
     
     
         54 . The composition of  claim 53 , 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 6-30 of SEQ ID NO: 102, 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. 
     
     
         55 . The composition of  claim 54 , wherein the molecular beacon comprises a sequence selected from the group consisting of SEQ ID NO: 97 through SEQ ID NO: 130. 
     
     
         56 . The composition of  claim 55 , wherein the polynucleotide sequence consists of SEQ ID NO: 115. 
     
     
         57 . A molecular beacon comprising a fluorophore, a quencher, and a polynucleotide, wherein the 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 6-30 of SEQ ID NO: 102, 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, and nucleotides 8-29 of SEQ ID NO: 120. 
     
     
         58 . The molecular beacon of  claim 57 , wherein the polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 99 through SEQ ID NO: 120. 
     
     
         59 . The molecular beacon of  claim 58 , wherein the polynucleotide consists of a sequence selected from the group consisting of SEQ ID NO: 99 through SEQ ID NO: 120. 
     
     
         60 . The molecular beacon of  claim 57 , wherein the fluorophore is FAM and the quencher is BHQ1. 
     
     
         61 . The molecular beacon of  claim 57 , wherein the fluorophore is ATTO 565 or Alexa 594 and the quencher is BHQ1 or BHQ2. 
     
     
         62 . 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 Set-1 through Set-81; 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.   
     
     
         63 . The method of  claim 62 , wherein the amplification in step (b) of the target sequence is performed at between about 60° C. and about 67° C. for less than 30 minutes. 
     
     
         64 . The method of  claim 63 , wherein the amplification step is performed for less than fifteen minutes. 
     
     
         65 . The method of  claim 64 , wherein the amplification step is performed for less than ten minutes. 
     
     
         66 . The method of  claim 65 , wherein the amplification step is performed for less than six minutes. 
     
     
         67 . The method of  claim 62 , wherein the reaction mixture further comprises a reverse transcriptase. 
     
     
         68 . The method of  claim 62 , 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. 
     
     
         69 . The method of  claim 68 , wherein the label is a fluorophore. 
     
     
         70 . The method of  claim 69 , wherein the fluorophore is covalently attached to a terminus of the polynucleotide. 
     
     
         71 . The method of  claim 68 , 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 6-30 of SEQ ID NO: 102, 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, nucleotides 6-27 of SEQ ID NO: 130, and nucleotides 8-29 of SEQ ID NO: 131. 
     
     
         72 . The method of  claim 71 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of SEQ ID NOs: 97 through 130. 
     
     
         73 . The method of  claim 68 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of 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 6-29 of SEQ ID NO: 107, nucleotides 6-29 of SEQ ID NO: 108, nucleotides 6-29 of SEQ ID NO: 109, nucleotides 8-31 of SEQ ID NO: 111, 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 9-34 of SEQ ID NO: 123, nucleotides 8-34 of SEQ ID NO: 124, nucleotides 7-32 of SEQ ID NO: 128, and nucleotides 4-27 of SEQ ID NO: 129, and wherein the sequence-specific primer set is selected from the group consisting of Set-12, Sets 14-27, Set-39, Sets 41-54, Set-66, and Sets 68-81. 
     
     
         74 . The method of  claim 73 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 128, and SEQ ID NO: 129 
     
     
         75 . The method of  claim 74 , wherein the sequence of the labeled polynucleotide is SEQ ID NO: 115, and the sequence-specific primer set is selected from the group consisting of Set-20, Set-24, Set-47, Set-51, Set-74 and Set-78. 
     
     
         76 . The method of  claim 75 , wherein the sequence-specific primer set is Set-20 or Set-24. 
     
     
         77 . The method of  claim 68 , 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 5-27 of SEQ ID NO: 106, nucleotides 6-30 of SEQ ID NO: 110, nucleotides 6-29 of SEQ ID NO: 112, nucleotides 8-29 of SEQ ID NO: 120, nucleotides 4-33 of SEQ ID NO: 121, and nucleotides 7-34 of SEQ ID NO: 122, and wherein the sequence-specific primer set is selected from the group consisting of Sets 12-27, Sets 39-54, and Sets 66-81. 
     
     
         78 . The method of  claim 77 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 112, SEQ ID NO: 120, SEQ ID NO: 121, and SEQ ID NO: 122 
     
     
         79 . The method of  claim 68 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of nucleotides 6-28 of SEQ ID NO: 125 and nucleotides 7-28 of SEQ ID NO: 126, and wherein the sequence-specific primer set is selected from the group consisting of Set-12, Sets 14-18, Set-20, Set-24, Set-27, Set-39, Sets 41-45, Set-47, Set-51, Set-54, Set-66, Sets 68-72, Set 74, Set-78, and Set-81. 
     
     
         80 . The method of  claim 79 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 125 and SEQ ID NO: 126. 
     
     
         81 . The method of  claim 68 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of nucleotides 8-31 of SEQ ID NO: 113 and nucleotides 3-27 of SEQ ID NO: 127, and wherein the sequence-specific primer set is selected from the group consisting of Sets 14-27, Sets 41-54, and Sets 68-81. 
     
     
         82 . The method of  claim 81 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 113 and SEQ ID NO: 127. 
     
     
         83 . The method of  claim 68 , wherein the labeled polynucleotide comprises nucleotides 6-27 of SEQ ID NO: 130, and wherein the sequence-specific primer set is selected from the group consisting of Sets 12-20, Sets 22-27, Sets 39-47, Sets 49-54, Sets 66-74, and Sets 76-81. 
     
     
         84 . The method of  claim 83 , wherein the labeled polynucleotide comprises SEQ ID NO: 130. 
     
     
         85 . The method of  claim 68 , wherein the labeled polynucleotide comprises a sequence selected from the group consisting of nucleotides 6-30 of SEQ ID NO: 102 and nucleotides 8-29 of SEQ ID NO: 131, and wherein sequence-specific primer set is selected from the group consisting of Set-13, Set-40 and Set-67. 
     
     
         86 . The method of  claim 85 , wherein the polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 102 and SEQ ID NO: 131. 
     
     
         87 . The method of  claim 62 , wherein  Chlamydia trachomatis  is present in the test sample at a concentration of ≤100 IFU/mL. 
     
     
         88 . The method of  claim 87 , wherein  Chlamydia trachomatis  is present in the test sample at a concentration of ≤50 IFU/mL. 
     
     
         89 . The method of  claim 88 , wherein  Chlamydia trachomatis  is present in the test sample at a concentration of ≤5 IFU/mL. 
     
     
         90 . The method of  claim 89 , wherein  Chlamydia trachomatis  is present in the test sample at a concentration of ≤2 IFU/mL. 
     
     
         91 . The method of  claim 87 , 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. 
     
     
         92 . The method of  claim 87 , 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. 
     
     
         93 . A kit comprising a composition according to  claim 31 . 
     
     
         94 . The kit of  claim 93 , further comprising a strand displacement polymerase. 
     
     
         95 . The kit of  claim 94 , further comprising a molecular beacon comprising a fluorophore, a quencher, and a polynucleotide, wherein the 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 6-30 of SEQ ID NO: 102, 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, nucleotides 6-27 of SEQ ID NO: 130, and nucleotides 8-29 of SEQ ID NO: 131. 
     
     
         96 . The kit of  claim 95 , wherein the polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 97 through SEQ ID NO: 131. 
     
     
         97 . The kit of  claim 96 , wherein the polynucleotide consists of a sequence selected from the group consisting of SEQ ID NO: 97 through SEQ ID NO: 131. 
     
     
         98 . The kit of  claim 97 , wherein the polynucleotide consists of SEQ ID NO: 115 and the set of polynucleotides is Set-20 or Set-24. 
     
     
         99 . 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; 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.   
     
     
         100 . The method of  claim 99 , wherein  Chlamydia trachomatis  is present in the test sample at a concentration of ≤100 IFU/mL. 
     
     
         101 . The method of  claim 100 , wherein  Chlamydia trachomatis  is present in the test sample at a concentration of ≤10 IFU/mL. 
     
     
         102 . The method of  claim 99 , wherein the amplifying step comprises 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 Set-1 through Set-81. 
     
     
         103 . The method of  claim 102 , 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 NO: 97 through SEQ ID NO: 131. 
     
     
         104 . The method of  claim 102 , 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 NO: 99 through SEQ ID NO: 120.
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