Patent Application
20190284617
The present invention relates to the fields of molecular biology and nucleic acid chemistry. The invention provides methods and reagents for detecting pathogens, such as Chlamydia trachomatis and accordingly, also relates to the fields of medical diagnostics and prognostics. In particular, the invention relates to polynucleotides and methods for amplifying and detecting Chlamydia trachomatis.
There is an urgent need for the development of a rapid, affordable, sample-in answer-out point of care (POC) diagnostic platform for sexually transmitted infections (STIs). The World Health Organization (WHO) estimates that more than 499 million new cases of curable STIs, namely those due to Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), Trichomonas vaginalis (TV) and Syphilis occur every year worldwide in men and women aged 15-49 years, causing significant morbidity and mortality. Untreated gonococcal and chlamydial infections in women in sub-Saharan Africa have been implicated as the cause of up to 85% of infertility among women seeking infertility intervention.
C. trachomatis is responsible for the most common STD in the US. Chlamydia can cause urethritis in men and pelvic inflammatory disease, ectopic pregnancy and infertility in women.
Asymptomatic infections are common both in men and women which warrants screenings to prevent the spread of the disease (as recommended by the CDC).
The present invention encompasses, in some embodiments, a composition comprising a set of polynucleotides selected from the group consisting of Set-1 through Set-58. In some embodiments, the composition further comprises a probe. In some embodiments, the probe comprises a label. In some embodiments, the probe is a labeled polynucleotide.
In some embodiments, the probe is a labeled polynucleotide having a sequence selected from the group consisting of SEQ ID NO: 49, SEQ ID NO: 50, and SEQ ID NO: 51 and the set of polynucleotides is selected from the group consisting of Set-5, Set-15, Set-24, and Set-32. In some embodiments, the probe is a labeled polynucleotide having a sequence selected from the group consisting of SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, and SEQ ID NO: 54 and the set of polynucleotides is selected from the group consisting of Set-1, Set-2, Set-3, Set-4, Set-10, Set-11, Set-12, Set-13, Set-14, Set-20, Set-21, Set-22, Set-23, Set-29, Set-30, Set-31, Set-39, Set-40, Set-41, Set-43,47, Set-48, Set-49, Set-50, Set-54, Set-55, Set-56, and Set-57. In some embodiments, the probe is a labeled polynucleotide having a sequence selected from the group consisting of SEQ ID NO: 55 and SEQ ID NO: 56 and the set of polynucleotides is selected from the group consisting of Set-3, Set-4, Set-5, Set-6, Set-13, Set-14, Set-15, Set-16, Set-22, Set-23, Set-24, Set-25, Set-30, Set-31, Set-32, Set-33, Set-39, Set-40, Set-47, Set-48, Set-54, and Set-55. In some embodiments, the probe is a labeled polynucleotide having a sequence SEQ ID NO: 57 and the set of polynucleotides is selected from the group consisting of Set-1, Set-2, Set-3, Set-4, Set-10, Set-11, Set-12, Set-13, Set-14, Set-20, Set-21, Set-22, Set-23, Set-29, Set-30, Set-31, Set-39, Set-41, Set-43, Set-47, Set-49, Set-50, Set-54, Set-56, and Set-57. In some embodiments, the probe is a labeled polynucleotide having a sequence selected from the group consisting of SEQ ID NO: 58 and SEQ ID NO: 59and the set of polynucleotides is selected from the group consisting of Set-7, Set-8, Set-9, Set-17, Set-18, Set-19, Set-26, Set-27, Set-28, Set-34, Set-35, and Set-36. In some embodiments, the probe is a labeled polynucleotide having a sequence selected from the group consisting of SEQ ID NO: 106, SEQ ID NO: 107, and SEQ ID NO: 108 and the set of polynucleotides is selected from the group consisting of Set-37, Set-45, and Set-52. In some embodiments, the probe is a labeled polynucleotide having a sequence SEQ ID NO: 109and the set of polynucleotides is selected from the group consisting of Set-38, Set-46, and Set-53. In some embodiments, the probe is a labeled polynucleotide having a sequence SEQ ID NO: 110 and the set of polynucleotides is selected from the group consisting of Set-1, Set-2, Set-3, Set-4, Set-5, Set-6, Set-10, Set-11, Set-12, Set-13, Set-14, Set-15, Set-16, Set-20, Set-21, Set-22, Set-23, Set-24, Set-25, Set-29, Set-30, Set-31, Set-32, Set-33, Set-40, Set-43, Set-39, Set-41, Set-47, Set-48, Set-49, Set-50, Set-54, Set-55, Set-56, and Set-57. In some embodiments, the probe is a labeled polynucleotide having a sequence selected from the group consisting of SEQ ID NO: 111, SEQ ID NO: 114, and SEQ ID NO: 115, and the set of polynucleotides is selected from the group consisting of Set-1, Set-2, Set-3, Set-4, Set-10, Set-11, Set-12, Set-13, Set-14, Set-20, Set-21, Set-22, Set-23, Set-29, Set-30, Set-31, Set-40, Set-43, Set-39, Set-41, Set-47, Set-48, Set-49, Set-50, Set-54, Set-55, Set-56, and Set-57. In some embodiments, the probe is a labeled polynucleotide having a sequence SEQ ID NO: 112 and the set of polynucleotides is selected from the group consisting of Set-1, Set-3, Set-4, Set-10, Set-11, Set-13, Set-14, Set-20, Set-22, Set-23, Set-30, Set-31, Set-39, Set-41, Set-43, Set-47, Set-49, Set-50, Set-54, Set-56, and Set-57. In some embodiments, the probe is a labeled polynucleotide having a sequence SEQ ID NO: 113 and the set of polynucleotides is selected from the group consisting of Set-44, Set-51, and Set-58. In some embodiments, the probe is a labeled polynucleotide having a sequence SEQ ID NO: 116 and the set of polynucleotides is selected from the group consisting of Set-1, Set-2, Set-3, Set-4, Set-10, Set-11, Set-12, Set-13, Set-14, Set-20, Set-21, Set-22, Set-23, Set-29, Set-30, Set-31, Set-39, Set-41, Set-43, Set-47, Set-49, Set-50, Set-54, Set-56, and Set-57. In some embodiments, the probe is a labeled polynucleotide having a sequence SEQ ID NO: 117 and the set of polynucleotides is selected from the group consisting of Set-1, Set-2, Set-3, Set-4, Set-5, Set-6, Set-10, Set-11, Set-12, Set-13, Set-14, Set-15, Set-16, Set-20, Set-21, Set-22, Set-23, Set-24, Set-25, Set-29, Set-30, Set-31, Set-32, Set-33, Set-39, Set-40, Set-41, Set-47, Set-48, Set-49, Set-54, Set-55, and Set-56.
In some embodiments, the label is a fluorophore. In some embodiments, the fluorophore is covalently attached to a terminus of the polynucleotide. In some embodiments, the probe is a molecular beacon comprising a quencher. In some embodiments, the fluorophore is FAM and the quencher is BHQ1. In other embodiments, the fluorophore is ATTO 565 or Alexa 594 and the quencher is BHQ1 or BHQ2.
Also provided herein is a molecular beacon comprising a fluorophore, a quencher, and a polynucleotide, wherein the polynucleotide is selected from the group consisting of: SEQ ID NO: 49 through SEQ ID NO: 59 and SEQ ID NO: 106 through SEQ ID NO: 117. In some embodiments, the fluorophore is FAM and the quencher is BHQ1. In other embodiments, the fluorophore is ATTO 565 or Alexa 594 and the quencher is BHQ1 or BHQ2.
Also provided herein is 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-36; 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.
In some embodiments of the method, 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. In some embodiments of the method, the amplification step is performed for less than 15 minutes. In some embodiments of the method, the amplification step is performed for less than nine minutes.
In some embodiments of the method, detecting the presence or absence of the amplification product comprises hybridizing the amplified product with a probe comprising a polynucleotide attached to a label.
In some embodiments of the method, the polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 49, SEQ ID NO: 50, and SEQ ID NO: 51 and the set of polynucleotides is selected from the group consisting of Set-5, Set-15, Set-24, and Set-32. In some embodiments of the method, the polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, and SEQ ID NO: 54 and the set of polynucleotides is selected from the group consisting of Set-1, Set-2, Set-3, Set-4, Set-10, Set-11, Set-12, Set-13, Set-14, Set-20, Set-21, Set-22, Set-23, Set-29, Set-30, Set-31, Set-39, Set-40, Set-41, Set-43,47, Set-48, Set-49, Set-50, Set-54, Set-55, Set-56, and Set-57. In some embodiments of the method, the polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 55 and SEQ ID NO: 56 and the set of polynucleotides is selected from the group consisting of Set-3, Set-4, Set-5, Set-6, Set-13, Set-14, Set-15, Set-16, Set-22, Set-23, Set-24, Set-25, Set-30, Set-31, Set-32, Set-33, Set-39, Set-40, Set-47, Set-48, Set-54, and Set-55. In some embodiments of the method, the polynucleotide comprises a sequence SEQ ID NO: 57 and the set of polynucleotides is selected from the group consisting of Set-1, Set-2, Set-3, Set-4, Set-10, Set-11, Set-12, Set-13, Set-14, Set-20, Set-21, Set-22, Set-23, Set-29, Set-30, Set-31, Set-39, Set-41, Set-43, Set-47, Set-49, Set-50, Set-54, Set-56, and Set-57. In some embodiments of the method, the polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 58 and SEQ ID NO: 59 and the set of polynucleotides is selected from the group consisting of Set-7, Set-8, Set-9, Set-17, Set-18, Set-19, Set-26, Set-27, Set-28, Set-34, Set-35, and Set-36. In some embodiments of the method, the polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 106, SEQ ID NO: 107, and SEQ ID NO: 108 and the set of polynucleotides is selected from the group consisting of Set-37, Set-45, and Set-52. In some embodiments of the method, the polynucleotide comprises a sequence SEQ ID NO: 109and the set of polynucleotides is selected from the group consisting of Set-38, Set-46, and Set-53. In some embodiments of the method, the polynucleotide comprises a sequence SEQ ID NO: 110 and the set of polynucleotides is selected from the group consisting of Set-1, Set-2, Set-3, Set-4, Set-5, Set-6, Set-10, Set-11, Set-12, Set-13, Set-14, Set-15, Set-16, Set-20, Set-21, Set-22, Set-23, Set-24, Set-25, Set-29, Set-30, Set-31, Set-32, Set-33, Set-40, Set-43, Set-39, Set-41, Set-47, Set-48, Set-49, Set-50, Set-54, Set-55, Set-56, and Set-57. In some embodiments of the method, the polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO: 111, SEQ ID NO: 114, and SEQ ID NO: 115, and the set of polynucleotides is selected from the group consisting of Set-1, Set-2, Set-3, Set-4, Set-10, Set-11, Set-12, Set-13, Set-14, Set-20, Set-21, Set-22, Set-23, Set-29, Set-30, Set-31, Set-40, Set-43, Set-39, Set-41, Set-47, Set-48, Set-49, Set-50, Set-54, Set-55, Set-56, and Set-57. In some embodiments of the method, the polynucleotide comprises a sequence SEQ ID NO: 112 and the set of polynucleotides is selected from the group consisting of Set-1, Set-3, Set-4, Set-10, Set-11, Set-13, Set-14, Set-20, Set-22, Set-23, Set-30, Set-31, Set-39, Set-41, Set-43, Set-47, Set-49, Set-50, Set-54, Set-56, and Set-57. In some embodiments of the method, the polynucleotide comprises a sequence SEQ ID NO: 113 and the set of polynucleotides is selected from the group consisting of Set-44, Set-51, and Set-58. In some embodiments of the method, the polynucleotide comprises a sequence SEQ ID NO: 116 and the set of polynucleotides is selected from the group consisting of Set-1, Set-2, Set-3, Set-4, Set-10, Set-11, Set-12, Set-13, Set-14, Set-20, Set-21, Set-22, Set-23, Set-29, Set-30, Set-31, Set-39, Set-41, Set-43, Set-47, Set-49, Set-50, Set-54, Set-56, and Set-57. In some embodiments of the method, the polynucleotide comprises a sequence SEQ ID NO: 117 and the set of polynucleotides is selected from the group consisting of Set-1, Set-2, Set-3, Set-4, Set-5, Set-6, Set-10, Set-11, Set-12, Set-13, Set-14, Set-15, Set-16, Set-20, Set-21, Set-22, Set-23, Set-24, Set-25, Set-29, Set-30, Set-31, Set-32, Set-33, Set-39, Set-40, Set-41, Set-47, Set-48, Set-49, Set-54, Set-55, and Set-56.
In some embodiments of the method, the probe is a molecular beacon. In some embodiments of the method, the reaction mixture further comprises a reverse transcriptase.
In some embodiments of the method, Chlamydia trachomatis is present in the test sample at a concentration of ≤100 IFU/mL. In some embodiments of the method, Chlamydia trachomatis is present in the test sample at a concentration of ≤50 IFU/mL. In some embodiments of the method, Chlamydia trachomatis is present in the test sample at a concentration of ≤5 IFU/mL.
In some embodiments of the method, Chlamydia trachomatis is present in the test sample at a concentration of ≤2 IFU/ml and the amplification step is performed for less than 15 minutes.
Also provided herein is a kit comprising the composition of claim 1 and amplification reagents. In some embodiments of the kit, the amplification reagents comprise a strand displacement polymerase.
Also provided herein, in some embodiments, is 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 twenty 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.
In some embodiments of the method, the nucleic acid is reacted with the reaction mixture for less than fifteen minutes.
In some embodiments of the method, the target sequence is located in the 16S ribosomal subunit of Chlamydia trachomatis. In some embodiments of the method, the target sequence is located in the 23S ribosomal subunit of Chlamydia trachomatis.
In some embodiments of the method, the LAMP primer set consists of a forward inner primer (FIP), a backward inner primer (BIP), a forward loop primer (LF) and a backward loop primer (LB). In some embodiments of the method, the LAMP primer set consists of a forward inner primer (FIP), a backward inner primer (BIP), a forward outer primer (F3) and a backward outer primer (B3). In some embodiments of the method, the LAMP primer set consists of a forward inner primer (FIP), a backward inner primer (BIP), a forward outer primer (F3), a backward outer primer (B3), a forward loop primer (LF) and a backward loop primer (LB).
In some embodiments of the method, Chlamydia trachomatis is present in the test sample at a concentration of ≤100 IFU/mL. In some embodiments of the method, Chlamydia trachomatis is present in the test sample at a concentration of ≤50 IFU/mL. In some embodiments of the method, Chlamydia trachomatis is present in the test sample at a concentration of ≤5 IFU/mL.
In some embodiments of the method, the test sample comprises one or more other microorganisms in addition to Chlamydia trachomatis, and wherein the target sequence from Chlamydia trachomatis is preferentially amplified over a polynucleotide sequence from the one or more other microorganisms.
In some embodiments, the invention provides a nucleic acid sequence at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to SEQ ID NOs 1-59 and methods of using those nucleic acid sequences to detect Chlamydia trachomatis in a test sample.
Detecting low concentrations of species (down to a few molecules or microorganisms in a sample) is a challenge in medicine. The present invention relates to the selective detection of Chlamydia trachomatis. In particular, based on new detection strategies utilizing nucleic acid amplification, particularly RT-LAMP, and molecular beacon detection, Chlamydia infections can be diagnosed using the methods and reagents described herein. Using RNA (either ribosomal RNA (rRNA) or messenger RNA) as the target regions provides multiple copies of the target per C. trachomatis genome. Accordingly, this facilitates the detection of C. trachomatis in samples utilizing the approaches described herein relative to techniques that target genomic DNA, even when present in multiple copies per genome. In addition, the molecular beacon detection reagents described herein provide additional specificity, failing to bind, in most cases, to off target amplified DNA, thereby minimizing the occurrence of, e.g., false positives. This specificity is illustrated in, inter alia, Example 4 provided below. Many other features of the invention are also described herein.
As used herein, “nucleic acid” includes both DNA and RNA, including DNA and RNA containing non-standard nucleotides. A “nucleic acid” contains at least one polynucleotide (a “nucleic acid strand”). A “nucleic acid” may be single-stranded or double-stranded. The term “nucleic acid” refers to nucleotides and nucleosides which make up, for example, deoxyribonucleic acid (DNA) macromolecules and ribonucleic acid (RNA) macromolecules. Nucleic acids may be identified by the base attached to the sugar (e.g., deoxyribose or ribose).
As used herein, a “polynucleotide” refers to a polymeric chain containing two or more nucleotides, which contain deoxyribonucleotides, ribonucleotides, and/or their analog, such as those containing modified backbones (e.g. peptide nucleic acids (PNAs) or phosphorothioates) or modified bases. “Polynucleotides” includes primers, oligonucleotides, nucleic acid strands, etc. A polynucleotide may contain standard or non-standard nucleotides. Thus the term includes mRNA, tRNA, rRNA, ribozymes, DNA, cDNA, recombinant nucleic acids, branched nucleic acids, plasmids, vectors, probes, primers, etc. Typically, a polynucleotide contains a 5′ phosphate at one terminus (“5′ terminus”) and a 3′ hydroxyl group at the other terminus (“3′ terminus”) of the chain. The most 5′ nucleotide of a polynucleotide may be referred to herein as the “5′ terminal nucleotide” of the polynucleotide. The most 3′ nucleotide of a polynucleotide may be referred to herein as the “3′ terminal nucleotide” of the polynucleotide. Where nucleic acid of the invention takes the form of RNA, it may or may not have a 5′ cap.
LAMP is a nucleic acid amplification method that relies on auto-cycle strand-displacement DNA synthesis performed by Bst DNA polymerase, or other strand displacement polymerases. The amplified products are stem-loop structures with several repeated sequences of the target, and have multiple loops. The principal merit of this method is that denaturation of the DNA template is not required, and thus the LAMP reaction can be conducted under isothermal conditions (ranging from 60 to 67° C.). LAMP requires only one enzyme and four types of primers that recognize six distinct hybridization sites in the target sequence. The reaction can be accelerated by the addition of two additional primers. The method produces a large amount of amplified product, resulting in easier detection, such as detection by visual judgment of the turbidity or fluorescence of the reaction mixture.
In brief, the reaction is initiated by annealing and extension of a pair of ‘loop-forming’ primers (forward and backward inner primers, FIP and BIP, respectively), followed by annealing and extension of a pair of flanking primers (F3 and B3). Extension of these primers results in strand-displacement of the loop-forming elements, which fold up to form terminal hairpin-loop structures. Once these key structures have appeared, the amplification process becomes self-sustaining, and proceeds at constant temperature in a continuous and exponential manner (rather than a cyclic manner, like PCR) until all of the nucleotides (dATP, dTTP, dCTP & dGTP) in the reaction mixture have been incorporated into the amplified DNA. Optionally, an additional pair of primers can be included to accelerate the reaction. These primers, termed Loop primers, hybridize to non-inner primer bound terminal loops of the inner primer dumbbell shaped products.
The term “primer” as used herein refers to an oligonucleotide, which is capable of acting as a point of initiation of synthesis when placed under conditions in which synthesis of primer extension product which is complementary to a nucleic acid strand (template) is induced, i.e., in the presence of nucleotides and an agent for polymerization, such as DNA polymerase, and at a suitable temperature and pH.
LAMP allows amplification of target DNA sequences with higher sensitivity and specificity than PCR, often with reaction times of below 30 minutes, which is equivalent to the fastest real-time PCR tests. The target sequence which is amplified is typically 200-300 base-pairs (bp) in length, and the reaction relies upon recognition of between 120 bp and 160 bp of this sequence by several primers simultaneously during the amplification process. This high level of stringency makes the amplification highly specific, such that the appearance of amplified DNA in a reaction occurs only if the entire target sequence was initially present.
Applications for LAMP have been further extended to include detection of RNA molecules by addition of Reverse Transcriptase enzyme (RT). By including RNA detection, the types of targets for which LAMP can be applied are also expanded and add the ability to additionally target RNA based viruses, important regulatory non-coding RNA (sRNA, miRNA), and RNA molecules that have been associated with particular disease or physiological states. The ability to detect RNA also has the potential to increase assay sensitivity, for instance in choosing highly expressed, stable, and/or abundant messenger RNA (mRNA) or ribosomal RNA (rRNA) targets. This preliminary phase of amplification involves the reverse transcription of RNA molecules to complementary DNA (cDNA). The cDNA then serves as template for the strand displacing DNA polymerase. Use of a thermostable RT enzyme (i.e., NEB RTx) enables the reaction to be completed at a single temperature and in a one step, single mix reaction.
A “target sequence,” as used herein, means a nucleic acid sequence of Chlamydia trachomatis, or complement thereof, that is amplified, detected, or both amplified and detected using one or more of the polynucleotides herein provided. Additionally, while the term target sequence sometimes refers to a double stranded nucleic acid sequence, those skilled in the art will recognize that the target sequence can also be single stranded, e.g., RNA. A target sequence may be selected that is more or less specific for a particular organism. For example, the target sequence may be specific to an entire genus, to more than one genus, to a species or subspecies, serogroup, auxotype, serotype, strain, isolate or other subset of organisms.
The speed, specificity and sensitivity of the primers/probe compositions and method described herein result from several aspects. Exemplary primers for use in the compositions and methods according to the present invention include:
Detection of the LAMP amplified products can be achieved via a variety of methods. In a preferred embodiment, detection of product is conducted by adding a fluorescently-labeled probe to the primer mix. The term used herein “probe” refers to a single-stranded nucleic acid molecule comprising a portion or portions that are complementary, or substantially complementary, to a target sequence. In certain implementations, the fluorescently-labeled probe is a molecular beacon.
As used herein, “molecular beacon” refers to a single stranded hairpin-shaped oligonucleotide probe designed to report the presence of specific nucleic acids in a solution. A molecular beacon consists of four components; a stem, hairpin loop, end labelled fluorophore and opposite end-labelled quencher (Tyagi et al., (1998) Nature Biotechnology 16:49-53). When the hairpin-like beacon is not bound to a target, the fluorophore and quencher lie close together and fluorescence is suppressed. In the presence of a complementary target nucleotide sequence, the stem of the beacon opens to hybridize to the target. This separates the fluorophore and quencher, allowing the fluorophore to fluoresce. Alternatively, molecular beacons also include fluorophores that emit in the proximity of an end-labelled donor. “Wavelength-shifting Molecular Beacons” incorporate an additional harvester fluorophore enabling the fluorophore to emit more strongly. Current reviews of molecular beacons include Wang et al., 2009, Angew Chem Int Ed Engl, 48(5):856-870; Cissell et al., 2009, Anal Bioanal Chem 393(1):125-35; Li et al., 2008, Biochem Biophys Res Comm 373(4):457-61; and Cady, 2009, Methods Mol Biol 554:367-79.
The term “label” as used herein means a molecule or moiety having a property or characteristic which is capable of detection and, optionally, of quantitation. A label can be directly detectable, as with, for example (and without limitation), radioisotopes, fluorophores, chemiluminophores, enzymes, colloidal particles, fluorescent microparticles and the like; or a label may be indirectly detectable, as with, for example, specific binding members. It will be understood that directly detectable labels may require additional components such as, for example, substrates, triggering reagents, quenching moieties, light, and the like to enable detection and/or quantitation of the label. When indirectly detectable labels are used, they are typically used in combination with a “conjugate”. A conjugate is typically a specific binding member that has been attached or coupled to a directly detectable label. Coupling chemistries for synthesizing a conjugate are well known in the art and can include, for example, any chemical means and/or physical means that does not destroy the specific binding property of the specific binding member or the detectable property of the label. As used herein, “specific binding member” means a member of a binding pair, i.e., two different molecules where one of the molecules through, for example, chemical or physical means specifically binds to the other molecule. In addition to antigen and antibody specific binding pairs, other specific binding pairs include, but are not intended to be limited to, avidin and biotin; haptens and antibodies specific for haptens; complementary nucleotide sequences; enzyme cofactors or substrates and enzymes; and the like.
The molecular beacon can be composed of nucleic acid only such as DNA or RNA, or it can be composed of a peptide nucleic acid (PNA) conjugate. The fluorophore can be any fluorescent organic dye or a single quantum dot. The quenching moiety desirably quenches the luminescence of the fluorophore. Any suitable quenching moiety that quenches the luminescence of the fluorophore can be used. A fluorophore can be any fluorescent marker/dye known in the art. Examples of suitable fluorescent markers include, but are not limited to, Fam, Hex, Tet, Joe, Rox, Tamra, Max, Edans, Cy dyes such as Cy5, Fluorescein, Coumarin, Eosine, Rhodamine, Bodipy, Alexa, Cascade Blue, Yakima Yellow, Lucifer Yellow, Texas Red, and the family of ATTO dyes. A quencher can be any quencher known in the art. Examples of quenchers include, but are not limited to, Dabcyl, Dark Quencher, Eclipse Dark Quencher, ElleQuencher, Tamra, BHQ and QSY (all of them are Trade-Marks). The skilled person would know which combinations of dye/quencher are suitable when designing a probe. In an exemplary embodiment, fluorescein (FAM) is used in conjunction with Blackhole Quencher™ (BHQ™) (Novato, Calif.). Binding of the molecular beacon to amplified product can then be directly, visually assessed. Alternatively, the fluorescence level can be measured by spectroscopy in order to improve sensitivity.
A variety of commercial suppliers produce standard and custom molecular beacons, including Abingdon Health (UK; www.abingdonhealth.com), Attostar (US, MN; www.attostar.com), Biolegio (NLD; www.biolegio.com), Biomers.net (DEU; www.biomers.net), Biosearch Technologies (US, CA; www.biosearchtech.com), Eurogentec (BEL; www.eurogentec.com), Gene Link (US, NY; www.genelink.com) Integrated DNA Technologies (US, IA; www.idtdna.com), Isogen Life Science (NLD; www.isogen-lifescience.com), Midland Certified Reagent (US, TX; www.oligos.com), Eurofins (DEU; www.eurofinsgenomics.eu), Sigma-Aldrich (US, TX; www.sigmaaldrich.com), Thermo Scientific (US, MA; www.thermoscientific.com), TIB MOLBIOL (DEU; www.tib-molbiol.de), TriLink Bio Technologies (US, CA; www.trilinkbiotech.com). A variety of kits, which utilize molecular beacons are also commercially available, such as the Sentinel™ Molecular Beacon Allelic Discrimination Kits from Stratagene (La Jolla, Calif.) and various kits from Eurogentec SA (Belgium, eurogentec.com) and Isogen Bioscience BV (The Netherlands, isogen.com).
The oligonucleotide probes and primers of the invention are optionally prepared using essentially any technique known in the art. In certain embodiments, for example, the oligonucleotide probes and primers described herein are synthesized chemically using essentially any nucleic acid synthesis method, including, e.g., according to the solid phase phosphoramidite triester method described by Beaucage and Caruthers (1981), Tetrahedron Setts. 22(20):1859-1862, which is incorporated by reference, or another synthesis technique known in the art, e.g., using an automated synthesizer, as described in Needham-VanDevanter et al. (1984) Nucleic Acids Res. 12:6159-6168, which is incorporated by reference. A wide variety of equipment is commercially available for automated oligonucleotide synthesis. Multi-nucleotide synthesis approaches (e.g., tri-nucleotide synthesis, etc.) are also optionally utilized. Moreover, the primer nucleic acids described herein optionally include various modifications. To further illustrate, primers are also optionally modified to improve the specificity of amplification reactions as described in, e.g., U.S. Pat. No. 6,001,611, issued Dec. 14, 1999, which is incorporated by reference. Primers and probes can also be synthesized with various other modifications as described herein or as otherwise known in the art.
In addition, essentially any nucleic acid (and virtually any labeled nucleic acid, whether standard or non-standard) can be custom or standard ordered from any of a variety of commercial sources, such as Integrated DNA Technologies, the Midland Certified Reagent Company, Eurofins, Biosearch Technologies, Sigma Aldrich and many others.
Test samples are generally derived or isolated from subjects, typically mammalian subjects, more typically human subjects, suspected of having a Chlamydia infection. Exemplary samples or specimens include blood, plasma, serum, urine, synovial fluid, seminal fluid, seminal plasma, prostatic fluid, vaginal fluid, cervical fluid, uterine fluid, cervical scrapings, amniotic fluid, anal scrapings, mucus, sputum, tissue, and the like. Essentially any technique for acquiring these samples is optionally utilized including, e.g., scraping, venipuncture, swabbing, biopsy, or other techniques known in the art.
The term “test sample” as used herein, means a sample taken from an organism or biological fluid that is suspected of containing or potentially contains a target sequence. The test sample can be taken from any biological source, such as for example, tissue, blood, saliva, sputa, mucus, sweat, urine, urethral swabs, cervical swabs, vaginal swabs, urogenital or anal swabs, conjunctival swabs, ocular lens fluid, cerebral spinal fluid, milk, ascites fluid, synovial fluid, peritoneal fluid, amniotic fluid, fermentation broths, cell cultures, chemical reaction mixtures and the like. The test sample can be used (i) directly as obtained from the source or (ii) following a pre-treatment to modify the character of the sample. Thus, the test sample can be pre-treated prior to use by, for example, preparing plasma or serum from blood, disrupting cells or viral particles, preparing liquids from solid materials, diluting viscous fluids, filtering liquids, distilling liquids, concentrating liquids, inactivating interfering components, adding reagents, purifying nucleic acids, and the like.
Advantageously, the invention enables reliable rapid detection of Chlamydia trachomatis in a clinical sample, such as a urine sample.
To further illustrate, prior to analyzing the target nucleic acids described herein, those nucleic acids may be purified or isolated from samples that typically include complex mixtures of different components. Cells in collected samples are typically lysed to release the cell contents. For example, C. trachomatis and other cells in the particular sample can be lysed by contacting them with various enzymes, chemicals, and/or lysed by other approaches known in the art, which degrade, e.g., bacterial cell walls. In some embodiments, nucleic acids are analyzed directly in the cell lysate. In other embodiments, nucleic acids are further purified or extracted from cell lysates prior to detection. Essentially any nucleic acid extraction methods can be used to purify nucleic acids in the samples utilized in the methods of the present invention. Exemplary techniques that can be used to purifying nucleic acids include, e.g., affinity chromatography, hybridization to probes immobilized on solid supports, liquid-liquid extraction (e.g., phenol-chloroform extraction, etc.), precipitation (e.g., using ethanol, etc.), extraction with filter paper, extraction with micelle-forming reagents (e.g., cetyl-trimethyl-ammonium-bromide, etc.), binding to immobilized intercalating dyes (e.g., ethidium bromide, acridine, etc.), adsorption to silica gel or diatomic earths, adsorption to magnetic glass particles or organo silane particles under chaotropic conditions, and/or the like. Sample processing is also described in, e.g., U.S. Pat. Nos. 5,155,018, 6,383,393, and 5,234,809, which are each incorporated by reference.
A test sample may optionally have been treated and/or purified according to any technique known by the skilled person, to improve the amplification efficiency and/or qualitative accuracy and/or quantitative accuracy. The sample may thus exclusively, or essentially, consist of nucleic acid(s), whether obtained by purification, isolation, or by chemical synthesis. Means are available to the skilled person, who would like to isolate or purify nucleic acids, such as DNA, from a test sample, for example to isolate or purify DNA from cervical scrapes (e.g., QIAamp-DNA Mini-Kit; Qiagen, Hilden, Germany).
Considering the constitutive and high level of expression of the ribosomal genes in bacterial cells, these genes were chosen as targets for the amplification assay, specifically the 16S and 23S genes.
16S and 23S gene sequences for multiple serovars of C. trachomatis, closely related species such as Chlamydophila pneumoniae and Chlamydia psittaci, and for other species commonly found in the urine or vaginal fluid were retrieved from the NCBI database. Sequences were aligned using Clustal omega (Sievers, et al. 2011. Molecular Systems Biology 7:539) and regions with unique specific bases to C. trachomatis species were identified. Loop mediated amplification primers were designed using LAMP designer (Premier Biosoft). For added specificity, molecular beacons or probes targeting the amplified products were designed manually or using Beacon designer (Premier Biosoft). Designed primer sets and beacons were further analyzed for specificity using BLAST against the human genome and the NCBI nucleotide database. Various primer sets and probes were designed and screened for reaction speed.
The inventive primer sets are summarized in Table 2, which include, at a minimum, a forward inner primer (FIP) and backward inner primer (BIP). Additionally, the primer sets typically also include at least two additional primers selected from the forward outer primer (F3), backward outer primer (B3), forward loop primer (LF) and backward loop primer (LB).
A negative urine matrix was spiked with titred C. trachomatis (serially diluted in PBS, Zeptometrix CN#0801775) at two different concentrations (103 IFU/mL and 10 IFU/mL). Nucleic acids were extracted using standard extraction methods and the sample was amplified using LAMP primers (SEQ ID NOs: 1-6). YoPro™ dye (Life Technologies; green fluorescent carbocyanine nucleic acid stain) was used for the detection of the amplified product. In this example a 25 μl reaction contained 1× Isothermal Amplification Buffer (New England Biolabs) supplemented with 4.8 mM or 6 mM MgCl2, 1.4 mM or 1.6 mM dNTP, 200 nM YO-PRO-1 dye (Life Technologies), primers (2 μM of F3 and B3, when present; 1.6 μM of FIP and BIP; 8 μM of LF and LB, when present), 8 or 12 Units of Bst2 polymerase (New England Biolabs), 7.5 Units RTx Warmstart (reverse transcriptase; New England Biolabs), and the extracted nucleic acid (as template) or water (as no template control). The reactions were incubated at 63° or 65° C. and kinetics were monitored using a Roche real-time Lightcycler96 (Roche).
This example shows that using this set of primers and the loop mediated amplification method, fast amplification kinetics are achieved. Results are summarized in Table 3, in which the Time to Positive (Tp) was calculated by the instrument. Results are classified by the time to position: A having Tp in less or equal to 8 minutes, B having Tp between 8 minutes and 12 minutes (inclusive), and C having Tp greater than 12 minutes.
Amplification reactions containing some of the above primers sets and the intercalating dye resulted in the detection of an amplification product when using water or negative urine extraction or the DNA of closely related specie such as C. pneumoniae or C. psittaci as templates at frequencies ranging between 0% to 75% of the time (Table 4), within variable intervals of our cut off window for the assay time. Results are classified by the time to position: A having Tp in less or equal to 8 minutes, B having Tp between 8 minutes and 12 minutes (inclusive), C having Tp greater than 12 minutes, and D having no amplification detected.
C. pneumoniae
C. psittaci
For added specificity molecular beacons were designed along these primers sets to make sure only signal from the C. trachomatis target is detected (sequences listed in table 5). Each molecular beacon probe was designed with 5′ fluorophore/3′ quencher modifications (6-Carboxyfluorescein (FAM) and Black Hole Quencher 1 (BHQ1)) included to provide target-specific fluorescent detection.
A negative urine matrix was spiked with titred C. trachomatis (serially diluted in PBS, Zeptometrix CN#0801775) at two different concentrations (103 IFU/mL and 10 IFU/mL). Nucleic acids were extracted using standard extraction methods and the sample was amplified using a LAMP primer set (Sets described in Table 2, SEQ ID NOs) and one of the molecular beacons (table 4) was used for the detection of the amplified product. In this example a 25 μl reaction contained 1× Isothermal Amplification Buffer or Thermopol DF buffer (New England Biolabs) supplemented with 4.8 mM or 6 mM MgCl2, 1.4 mM or 1.6 mM dNTP, 200 nM molecular beacon (Sigma-Aldrich), primers (0.2 μM of F3 and B3, if present; 1.6 μM or 2 μM of FIP and BIP; 8 μM of LF and LB, if present), 8 or 12 Units of Bst2 polymerase (New England Biolabs), 7.5 Units RTx Warmstart (reverse transcriptase; New England Biolabs), and the extracted nucleic acid (as template) or water (as no template control). The reactions were incubated at 63° C. or 65° C. and kinetics were monitored using a Roche real-time Lightcycler96 (Roche). The time to positive for each primer-probe combination is reported in Table 6. Results are classified by the time to positive (Tp) from reaction initiation as follows: “A” indicates a Tp of less than or equal to 10 minutes, “B” indicates a Tp of between 10 minutes and 15 minutes (inclusive), and “C” indicates a Tp of greater than 15 minutes. “NT” indicates that this combination was not tested.
Chlamydia trachomatis gDNA (ATCC CN#VR-885D) was diluted using TE buffer at two different concentrations (105 genome copies/μl and 103 genome copies/μl). The sample was amplified using a LAMP primer set (Sets described in Table 2, SEQ ID NOs) and one of the molecular beacons (Table 5) was used for the detection of the amplified product. In this example a 25 μl reaction contained 1× Isothermal Amplification Buffer or Thermopol DF buffer (New England Biolabs) supplemented with 4.8 mM or 6 mM MgCl2, 1.4 mM or 1.6 mM dNTP, 200 nM molecular beacon(Sigma-Aldrich), primers (0.2 μM of F3 and B3, if present; 1.6 μM or 2 μM of FIP and BIP; 0.8 μM of LF and LB, if present), 8 or 12 Units of Bst2 polymerase (New England Biolabs), 7.5 Units RTx Warmstart (reverse transcriptase; New England Biolabs), and the gDNA dilutions (as template) or water (as no template control). The reactions were incubated at 63° C. or 65° C. and kinetics were monitored using a Roche real-time Lightcycler96 (Roche). The time to positive for each primer-probe combination is reported in Table 7. Results are classified by the time to positive: A having Tp in less or equal to 10 minutes, B having Tp between 10 minutes and 15 minutes (inclusive), C having Tp greater that 15 minutes. NT indicates that this combination was not tested.
Use of Molecular Beacons for detection resulted in a slight increase in reaction Tp, however the significant enhancement in assay specificity provided a reasonable tradeoff, no amplification was observed in the negative urine extract or water sample or DNA from a close related species within the testing period of 45 min.
A negative urine matrix was spiked with titred C. trachomatis or with organisms commonly associated with urine infections at high loads (e.g., E. coli, C. albicans, S. aureus, P. mirabilis), sexually transmitted infections (e.g., Neisseria gonorrhoeae) or species closely related to C. trachomatis (C. pneumonia or C. psittaci). Bacterial stocks were serially diluted in PBS before addition to the urine matrix at the desired concentration. Corresponding extracted nucleic acids or DNAs of the test species were used as templates in RT-LAMP reactions containing the LAMP primers (set-1) and the molecular beacon probe MB2. Reaction conditions are equivalent to those described above in Example 3. The designed primers and probe resulted in no amplification after 45 minutes with the non-C. trachomatis species tested.
This example shows that the designed CT23S assay and its reaction formulation is highly specific and does not cross react with sequences of organisms commonly found in urine and vaginal clinical samples.
A negative urine matrix was spiked with titred C. trachomatis at various concentrations (104 IFU/mL to 1 IFU/mL). Bacterial stock was serially diluted in PBS before addition to the urine matrix at the desired concentration. Extracted samples were amplified using LAMP primers (Table 2) and the molecular beacon probe (Table 5). Reaction conditions were equivalent to those described above in Example 3. Amplification signal was obtained with concentrations as low as 0.05 IFU/reaction (see Table 8). Results are classified by the time to positive (Tp) from reaction initiation as follows: “A” indicates a Tp of less than or equal to 10 minutes, “B” indicates a Tp of between 10 minutes and 15 minutes (inclusive), and “C” indicates a Tp of greater than 15 minutes. “NT” indicates that this combination was not tested.
A negative urine matrix was spiked with titred C. trachomatis at various concentrations (10 IFU/mL, 4 IFU/mL, 2 IFU/mL). Similarly, swabs (BD BBL culture Swab EZ Collection and Transport System single swab Fisher Cat# 220144) were infused with C. trachomatis diluted to the same concentrations as used in the urine. Bacterial stock was serially diluted in PBS before addition to the urine matrix or infused to the swab at the desired concentration. For each experiment (for each bacterial serial dilution), one nucleic acid extraction was performed from C. trachomatis in urine or on a swab at 10 IFU/mL, 10 extractions from samples at 4 IFU/mL, 10 extractions from samples at 2 IFU/mL and one extraction from negative urine or swab matrix. The experiment was repeated 3 times on different days by different operators. One tenth of each extracted sample was amplified using the LAMP primers (Set-1) and the molecular beacon probe MB2 listed in Table 5. In this example the 25 μl reaction contained the Isothermal buffer 1× (New England Biolabs) supplemented with 4.8 mM MgCl2, 1.6 mM dNTP, 200 nM of molecular beacon (Sigma Aldrich), primers (0.2 μM of F3 and B3; 2 μM of FIP and BIP; 0.8 μM of LF and LB), 12 Units of Bst2 polymerase (New England Biolabs), 7.5 Units RTx Warmstart (New England Biolabs), and nucleic acid template or water (as no template control). The reactions were incubated at 63° C. and kinetics were monitored using the Roche real-time Lightcycler96 (Roche). Two RT-LAMP reactions were run per extraction. Reactions were scored positive if their Cq were below 15 cycles. The frequency detection of C. trachomatis in urine or swab was calculated based on the number of positive reactions divided by the total number of reactions (Table 9). All reactions originating from samples at 10 IFU/mL were positives, those originating from negative swab or urine samples were negative. The limit of detection for this assay is estimated to be around 4 IFU/mL for both urine and swab samples. Bacterial load is the concentration in the starting material (urine or swab) 0.5 mL is used for the extractions. Detection was determined to be positive if Tp was less than 15 minutes.
To assess the contribution of each primer set to the RTLAMP reaction, we also investigated use of just the inner primers or the inner primers plus the loop primers and compared those reactions to the complete 6 primer RTLAMP reaction, using a Molecular Beacon for detection. Table 10 provides an example using an assay comprised of various subsets of Set-1 and MB1. Interestingly and noteworthy, the reaction still proceeds when the F3/B3 primers (Set-10) are excluded. The absence of F3/B3 appears to have an impact on sensitivity, specifically consistency at low concentrations (Table 10, indicated IFU is per mL of sample, 0.5 mL are used for the extraction, 5 uL of which was used per RTLAMP reaction). The reaction does proceed if only the inner primers are included (Set-11) with substantial delays in the onset of reaction at the highest concentration tested and the sensitivity being poor. Results are classified by the time to positive (Tp) from reaction initiation as follows: “A” indicates a Tp of less than or equal to 10 minutes, “B” indicates a Tp of between 10 minutes and 15 minutes (inclusive), and “C” indicates a Tp of greater than 15 minutes. “ND” indicates that no amplification was detected.
This application claims the benefit of U.S. Provisional Patent Application No. 62/420,488, filed 10 Nov. 2016, the contents of which are incorporated herein by reference.
This invention was made with government support under contract number HR0011-11-2-0006 awarded by the Department of Defense. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2017/061402 | 11/13/2017 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62420488 | Nov 2016 | US |
