# Patent

## Title
Assay for mycobacterium avium/intracellulare nucleic acid

## Abstract

Disclosed is a method for determining the presence of Mycobacterium avium complex nucleic acids in a biological sample. In particular, the mig gene of M. avium and the DT1 gene of M. intracellulare are detected, preferably following amplification. In addition, the method distinguishes between species of M. avium and M. intracellulare. Also described are oligonucleotides that can be used as primers to amplify target genes such as mig and DT1 genes and as probes as well as kits containing the oligonucleotides.

## Background
FIELD OF THE INVENTION
The present invention relates to methods and nucleotide sequences for detecting nucleic acids in a sample from Mycobacterium avium (M. avium) and Mycobacterium intracellulare (M. intracellulare).
BACKGROUND OF THE INVENTION
Mycobacterium avium complex (MAC) disease emerged early in the epidemic of AIDS as one of the common opportunistic infections afflicting human immunodeficiency virus-infected patients. M. avium was well known to mycobacteriologists decades before AIDS and known to cause disease, albeit uncommon, in humans and animals. The interaction of MAC with the immune system is complex, and putative MAC virulence factors appear to have a direct effect on the components of cellular immunity, including the regulation of cytokine expression and function. (C. B. Inderlied, et al., Clin Microbiol Rev 6:266-310, 1993).
The genus Mycobacterium contains approximately 50 species. The best known and widest spread diseases caused by mycobacteria are leprosy, caused by M. leprae, and tuberculosis caused by M. tuberculosis. Most other mycobacteria normally occur only as environmental saprophytes. However, saprophytic mycobacterial species also cause opportunist diseases, which happens often, but not exclusively, in individuals suffering from suppressed immune systems, such as AIDS patients or individuals undergoing immuno-suppression therapy. The opportunist strains comprise the slow-growing species M. avium, and the closely related M. intracellulare and M. scrofulaceum (often together referred to as the MAIS complex), M. kansai, M. marinum and M. ulcerans, and the fast-growing species M. chelonae and M. fortuitum. Although quite rare in the Western world for several decades, the occurrence of opportunist mycobacterial diseases and tuberculosis has shown a significant increase with the incidence of AIDS.
M. avium and M. intracellulare are two species that together, form the MAC. Because of poor phenotypic differences, conventional culture and biochemical tests give little information to separate these two closely related and nearly indistinguishable species. Therefore the two are commonly referred to as MAC. These opportunistic pathogens are found in water, dust, soil and bird droppings which can enter the body through ingestion of food or water or inhalation through the lungs. Most people usually have small numbers of these bacteria growing in their gut or lungs, but do not have any symptoms. A weakened immune system allows the bacteria to attack the lining of the gut and multiply. From there, infection can disseminate by entering into the blood and spreading through the body. The symptoms of MAC can include weight loss, fevers, chills, night sweats, swollen glands, abdominal pains, diarrhea and overall weakness.
A rapid diagnosis of MAC infection has important clinical and therapeutic implications because of the heightened susceptibility in AIDS patients. Also, MAC infection is not confined and disseminates to a wide variety of organs. A sensitive clinical diagnosis to distinguish between M. avium, M. intracellulare and other mycobacterial species allows for more precise knowledge of which MAC components are involved in clinical infections and could give better insight into the relevance that these species have as human pathogens. The prognosis of pulmonary diseases may be worse when they are associated with M. avium than when they are associated with M. intracellulare. (S. Yamori, et al., Chest 102:89-90, 1992). Consequently, differential diagnosis of MAC infections or infections caused by other mycobacteria is important for patient management, antimicrobial treatment, and epidemiology. (J. Kulski, et al., Journal of Clinical Microbiology 34: 1985-91, 1996).
Earlier efforts aimed at differentiating among strains of MAC on a nucleic acid level largely failed due to remarkable internal heterogeneity of organisms within the complex suggesting that MAC probably contains several unknown taxonomic groups. (M. C. Menendez, et al., J Clinical Microbiology 39:4241-46, 2001). Wide genetic diversity existing among the members of MAC complicate species-specific identification. (T. Koivula, et al., Microbes and Infection 6:1320-25, 2004).
Polymerase chain reaction (PCR) has been widely utilized to improve sensitivity of standard hybridization methods. Hybridization assays using self-quenching fluorescence probes with or without internal controls for detection of nucleic acid amplification products are known in the art, for example, U.S. Pat. Nos. 6,258,569; 6,030,787; 5,952,202; 5,876,930; 5,866,336; 5,736,333; 5,723,591; 5,691,146; and 5,538,848.
U.S. Pat. No. 6,136,529 describes a method which uses PCR targeting of the 16S rRNA to distinguish MAC organisms from other mycobacteria in test samples. Bruijnesteijn van Coppenraet, et al., J. Clin. Microbiol. 42(6): 2644-50, 2004 report the detection of M. avium using Real-time PCR (Taqman® systems). Other methods for detecting mycobacterial nucleic acids that have been reported include Menendez et al., “Characterization of a Mycobacterium intracellulare Variant Strain by Molecular Techniques” J. Clin. Microbiol. 39:4241-46, 2001 and Koivula et al., “Genetic diversity in clinical isolates of Mycobacterium avium complex from Guinea-Bissau, West Africa” Microbes and Infection 6:1320-25, 2004.
SUMMARY OF THE INVENTION
Provided herein are methods and sequences for detecting MAC nucleic acids, M. avium and M. intracellulare in a sample. This method is accomplished through assaying a nucleic acid-containing sample for two different gene sequences, one sequence is characteristic of M. avium and the other is primarily characteristic of M. intracellulare. 
Generally it is preferred that detection of the first gene is indicative of the presence of M. avium nucleic acids whereas detection of the second gene is indicative of M. intracellulare, M. avium serovar 2, or M. avium serovar 3 nucleic acids. The two gene sequences detected are preferably from different genes.
In one approach, the sample is assayed for the presence or absence of target sequences from the two different genes by amplification and detection of the resulting amplification products. In a preferred embodiment, amplification of target nucleic acids is accomplished by polymerase chain reaction (PCR).
Amplification of the two genes can be performed simultaneously in a single reaction vessel. In this case, the probes may be distinguishably labeled. Alternatively, the assay could be performed in parallel in separate reaction vessels. In such later case, the probes could have the same label.
In a preferred embodiment, the gene sequence that is characteristic of M. avium is from the macrophage-induced gene (mig), while the gene sequence that is characteristic of M. intracellulare, M. avium serovar 2, or M. avium serovar 3 is from the DT1 gene. If the sample is positive for both mig and DT1, then M. avium of either serovar 2 or 3 is present in the sample, but not M. intracellulare. In another preferred embodiment, the gene sequence that is characteristic of M. avium is from the insertion sequence transposase gene (IS1245). The IS1245 gene may also be found in M. paratuberculosis, however, M. paratuberculosis is generally only found in cattle. Therefore, IS1245 is a suitable gene for detecting the presence of M. avium in human samples. Preferably, the genes targeted for detection are not the 16S rRNA gene.
In one approach, the present invention provides a method of detecting if a sample contains nucleic acid from Mycobacterium avium (M. avium) or Mycobacterium intracellulare (M. intracellulare), the method including detecting a first target nucleic acid sequence specific for M. avium and detecting a second target nucleic acid sequence specific for M. intracellulare where the first and second target nucleic acid sequences are from different genes. In one embodiment, each target nucleic acid sequence is amplified and then detected.
In a further embodiment, the amplified regions are detected by hybridizing to an oligonucleotide probe having the sequence set forth in SEQ ID NO:3, SEQ ID NO:9 or SEQ ID NO:9 in the presence of an enzyme that cleaves the probe when the probe hybridizes to the target nucleic acid. The probe is preferably conjugated to a detectable label that generates an increased detectable signal upon cleavage. The method further involves detecting a signal from the detectable label, where an increased signal from the detectable label indicates the presence of nucleic acids in the sample. Additional exemplary probes hybridize to a region of the mig sequence (SEQ ID NO:10) between about nucleotides 517 to 536, 524 to 543, 545 to 564, 557 to 576, 595 to 615 and 614 to 633. Additional exemplary probes hybridize to a region of the IS1245 sequence (SEQ ID NO:11) between about nucleotides 502 to 521, 512 to 530, 527 to 550, 551 to 570, 564 to 582, 581 to 600 and 668 to 691. Additional exemplary probes hybridize to a region of the DT1 sequence (SEQ ID NO:12) between about nucleotides 630 to 650, 637 to 656, 648 to 668, 671 to 690, 685 to 705, 704 to 724, 727 to 746, 745 to 764, 767 to 788 and 797 to 816. It is understood that other probes can be used for the present invention. One of ordinary skill in the art could design other probes appropriate in this context.
In another aspect, the present invention provides a method for diagnosing infection of a subject with Mycobacterium avium (M. avium) or Mycobacterium intracellulare (M. intracellulare), by contacting a biological sample containing nucleic acids from the subject with a first oligonucleotide specific for a first target nucleic acid sequence of M. avium, and a second oligonucleotide specific for a second target nucleic acid sequence of M. intracellulare; and determining if the first or second oligonucleotide has hybridized to the sample nucleic acids. The first and second target nucleic acid sequences are preferably from different genes and hybridization of the first oligonucleotide is indicative of infection by M. avium while hybridization of the second oligonucleotide is indicative of infection by M. intracellulare. 
Also provided are oligonucleotides useful in the method and kits containing the oligonucleotides.
Oligonucleotide primers may be designed for amplifying regions of the M. avium genome. In one approach, a primer pair is designed to hybridize to a specified segment of the mig gene, GenBank Accession No. U43598. The sequence of exemplary such oligo primers are shown highlighted in FIG. 1 (SEQ ID NO:10). Exemplary primer pairs for amplifying a region of the mig sequence are between about nucleotides 495 to 659; more specifically using a forward primer, SEQ ID NO:1 (5′-AGATGTCCGACACCACAACA-3′) and a reverse primer, SEQ ID NO:2 (5′-AGACCCTGGGAGTGCAGATA-3′) to amplify a 165 bp region of M. avium nucleic acid. Other preferred oligonucleotide primers are approximately 15-100 nucleotides in length and comprise a portion of SEQ ID NO:1 or SEQ ID NO:2. Still other preferred oligonucleotide primers include an oligonucleotide sequence that hybridizes to the complement of a 15-100 nucleotide sequence that comprises the complement of a portion of SEQ ID NO:1 or SEQ ID NO:2. Such oligonucleotides may be substantially purified.
In another approach, a primer pair is designed to hybridize to a specified segment of the mig gene, GenBank Accession No. L33879. The sequence of exemplary such oligonucleotide primers are shown highlighted in FIG. 2 (SEQ ID NO:11). Exemplary primer pairs for amplifying a region of the mig sequence are between about nucleotides 478 to 723; more specifically using a forward primer, SEQ ID NO:4 (5′-TCTGGTCAAGGCACTGGGTA-3′) and a reverse primer, SEQ ID NO:5 (5′-ACCTCAAAGCCCAGTACCTCG-3′) to amplify a 246 bp region of M. avium nucleic acid. Other preferred oligonucleotide primers are approximately 15-100 nucleotides in length and comprise a portion of SEQ ID NO:4 or SEQ ID NO:5. Still other preferred oligonucleotide primers include an oligonucleotide sequence that hybridizes to the complement of a 15-100 nucleotide sequence that comprises the complement of a portion of SEQ ID NO:4 or SEQ ID NO:5. Such oligonucleotides may be substantially purified.
Oligonucleotide primers may be designed for amplifying regions of a M. intracellulare genome. In one approach, a primer pair is designed to hybridize to a specified segment of the DT1 gene with unknown function, GenBank Accession No. L04543. The sequence of exemplary such oligo primers are shown highlighted in FIG. 3 (SEQ ID NO:12). One example is to use a primer pair to amplify a region of the DT1 sequence between about nucleotides 608 to 849; more specifically using a forward primer, SEQ ID NO:7 (5′-TCCATTCCCGTTCTTCACAC-3′) and a reverse primer, SEQ ID NO:8 (5′-GTTCGAAATGGCACACATCA-3′) to amplify a 242 by region of M. intracellulare nucleic acid. Other preferred nucleotide primers are approximately 15-100 nucleotides in length and comprise a portion of SEQ ID NO:7 or SEQ ID NO:8. Still other preferred oligonucleotide primers include an oligonucleotide sequence that hybridizes to the complement of a 15-100 nucleotide sequence that comprises the complement of a portion of SEQ ID NO:7 or SEQ ID NO:8. Such oligonucleotides may be substantially purified. Table 1 shows the sequence of exemplary primers and probes for amplifying and detecting a region of the mig gene, the IS1245 gene and the DT1 gene.







TABLE 1







Primer/probes for amplifying and detecting region


of the M. avium mig gene the M. avium IS1245 gene


and the M. intracellulare DT1 gene.









Sequence Name
SEQ ID NO:
Sequence













Forward Oligonucleotide
SEQ ID
5′-AGATGTCCGAC



Primer for M. avium
NO: 1
ACCACAACA-3′


(MIGL_01)


 


Reverse Oligonucleotide
SEQ ID
5′-AGACCCTGGGA


Primer for M. avium
NO: 2
GTGCAGATA-3′


(MIGR_01)


 


Oligonucleotide Probe
SEQ ID
5′-TCCAGGGCGAC


for M. avium
NO: 3
CGTCGCTAC-3′


(MIGP_01FT)


 


Forward Oligonucleotide
SEQ ID
5′-TCTGGTCAAGG


Primer for M. avium
NO: 4
CACTGGGTA-3′


(IS1245L_01)


 


Reverse Oligonucleotide
SEQ ID
5′-ACCTCAAAGCC


Primer for M. avium
NO: 5
CAGTACCTCG-3′


(IS1245R_01)


 


Oligonucleotide Probe
SEQ ID
5′-AGCCGGATCTG


for M. avium
NO: 6
CAAAGACCTCGAC-3′


(IS1245P_01)


 


Forward Oligonucleotide
SEQ ID
5′-TCCATTCCCGT


Primer for
NO: 7
TCTTCACAC-3′


M. intracellulare


(DT1L_01)


 


Reverse Oligonucleotide
SEQ ID
5′-GTTCGAAATGG


Primer for
NO: 8
CACACATCA-3′


M. intracellulare


(DT1R_01)


 


Oligonucleotide Probe
SEQ ID
5′-TAGGTGCCGCC


for M. intracellulare
NO: 9
TCCACTCCG-3′


(DTIP_01TT)









SEQ ID NO: 1, SEQ ID NO:4 and SEQ ID NO:7 can be used as forward PCR amplification primers for amplifying a region of MAC nucleic acid. SEQ ID NO:2, SEQ ID NO:5 and SEQ ID NO:8 can be used as reverse PCR amplification primers for amplifying a region of MAC nucleic acid.
SEQ ID NO:3, SEQ ID NO:6 and SEQ ID NO:9 can be used as an oligonucleotide probe to detect the target gene or an amplified sequence thereof. The probe may be labeled. Other oligonucleotide probes can be designed which are between about 10 and about 100 nucleotides in length and hybridize to the amplified region. Oligonucleotide probes are preferably 15-70 nucleotides in length; more preferably 15-60 nucleotides in length; and most preferably 15-25 nucleotides in length.
As used herein, the term “MAC” refers to DNA and/or RNA containing a contiguous sequence from a Mycobacterium avium complex genome, or the complement thereof. MAC consists of two predominant species, M avium and Mycobacterium intracellulare. More than 95% of infections in patients with AIDS are caused by M avium, while 40% of infections in immunocompetent patients are caused by M intracellulare. MAC is also sometimes called MAI, which stands for Mycobacterium avium intracellulare. 
As used herein, the term “sample” or “test sample” refers to any liquid or solid material which can contain nucleic acids. In preferred embodiments, a test sample is obtained from a biological source (i.e., a “biological sample”), such as cells in culture or a tissue sample from an animal, more preferably, a human. Preferred sample sources include, but are not limited to, sputum (processed or unprocessed), bronchial alveolar lavage (BAL), bronchial wash (BW), blood, bone marrow, bodily fluids, cerebrospinal fluid (CSF), urine, plasma, serum or tissue (e.g., biopsy material). More preferred samples include sputum, BAL, BW, CSF and urine. The term “patient sample” as used herein refers to a tissue sample obtained from a human seeking diagnosis or treatment of a disease related to MAC infection.
As used herein, the term “oligonucleotide” refers to a short polymer composed of deoxyribonucleotides, ribonucleotides or any combination thereof. Oligonucleotides are generally between about 10 and about 150 nt in length, more preferably about 15 to about 150 nt, more preferably about 15 to about 70 nt, and most preferably between about 20 to about 26 nt. The single letter code for nucleotides is as described in the U.S. Patent Office Manual of Patent Examining Procedure, section 2422, table 1. In this regard, the nucleotide designation “R” means guanine or adenine, “Y” means thymine (uracil if RNA) or cytosine; and “M” means adenine or cytosine. An oligonucleotide may be used as a primer or as a probe.
As used herein, the term “detecting” used in context of detecting a signal from a detectable label to indicate the presence of MT complex nucleic acids in the sample does not require the method to provide 100% sensitivity and 100% specificity. As is well known, “sensitivity” is the probability that a test is positive, given that the person has the disease, while “specificity” is the probability that a test is negative, given that the person does not have the disease. A sensitivity of at least 50% is preferred, although sensitivities of at least 60%, at least 70%, at least 80%, at least 90% and at least 99% are clearly more preferred. A specificity of at least 50% is preferred, although sensitivities of at least 60%, at least 70%, at least 80%, at least 90% and at least 99% are clearly more preferred. Detecting also encompasses assays with false positives and false negatives. False negative rates may be 1%, 5%, 10%, 15%, 20% or even higher. False positive rates may be 1%, 5%, 10%, 15%, 20% or even higher.
As used herein, the term “substantially purified” in reference to oligonucleotides does not require absolute purity. Instead, it represents an indication that the sequence is relatively more pure than in the natural environment. Such oligonucleotides may be obtained by a number of methods including, for example, laboratory synthesis, restriction enzyme digestion or PCR. A “substantially purified” oligonucleotide is preferably greater than 50% pure, more preferably at least 75% pure, and most preferably at least 95% pure.
As used herein, an oligonucleotide is “specific” for a nucleic acid if the oligonucleotide has at least 50% sequence identity with a portion of the nucleic acid when the oligonucleotide and the nucleic acid are aligned. An oligonucleotide that is specific for a nucleic acid is one that, under the appropriate hybridization or washing conditions, is capable of hybridizing to the target of interest and not substantially hybridizing to nucleic acids which are not of interest. Higher levels of sequence identity are preferred and include at least 75%, at least 80%, at least 85%, at least 90%, at least 95% and more preferably at least 98% sequence identity.
As used herein, the term “hybridize” or “specifically hybridize” refers to a process where two complementary nucleic acid strands anneal to each other under appropriately stringent conditions. Hybridizations are typically and preferably conducted with probe-length nucleic acid molecules, preferably 20-100 nucleotides in length, more preferably 18-50 nucleotides in length. Nucleic acid hybridization techniques are well known in the art. See, e.g., Sambrook, et al., 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press, Plainview, N.Y. Those skilled in the art understand how to estimate and adjust the stringency of hybridization conditions such that sequences having at least a desired level of complementarity will stably hybridize, while those having lower complementarity will not. For examples of hybridization conditions and parameters, see, e.g., Sambrook, et al., 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press, Plainview, N.Y.; Ausubel, F. M. et al. 1994, Current Protocols in Molecular Biology. John Wiley & Sons, Secaucus, N.J.
The term “target nucleic acid” or “target sequence” as used herein refer to M. avium and M. intracellulare sequences to be amplified and detected. These include the original M. avium or M. intracellulare nucleic acid to be amplified which includes either the coding or complementary strand and either strand of a copy of the original sequence which is produced by the amplification reaction. Copies of the target sequence which are generated during the amplification reaction are referred to as amplification products, amplimers, or amplicons. Target sequences may be composed of segments of a chromosome, a complete gene with or without intergenic sequence, segments or portions of a gene with or without intergenic sequence, or sequence of nucleic acids which probes or primers are designed. Target nucleic acids may include a wild type sequences, a nucleic acid sequence containing a mutation, deletion or duplication, tandem repeat regions, a gene of interest, a region of a gene of interest or any upstream or downstream region thereof. Target nucleic acids may represent alternative sequences or alleles of a particular gene. Target nucleic acids may be derived from genomic DNA, cDNA, or RNA. As used herein target nucleic acid may be native DNA or a PCR amplified product.
“Genomic nucleic acid” or “genomic DNA” refers to some or all of the DNA from a chromosome. Genomic DNA may be intact or fragmented (e.g., digested with restriction endonucleases by methods known in the art). In some embodiments, genomic DNA may include sequence from all or a portion of a single gene or from multiple genes. In contrast, the term “total genomic nucleic acid” is used herein to refer to the full complement of DNA contained in the genome. Methods of purifying DNA and/or RNA from a variety of samples are well-known in the art.
The term “flanking” as used herein means that a primer hybridizes to a target nucleic acid adjoining a region of interest sought to be amplified on the target. The skilled artisan will understand that preferred primers are pairs of primers that hybridize 3′ from a region of interest, one on each strand of a target double stranded DNA molecule, such that nucleotides may be add to the 3′ end of the primer by a suitable DNA polymerase.
The term “complement” “complementary” or “complementarity” as used herein with reference to polynucleotides (i.e., a sequence of nucleotides such as an oligonucleotide or a target nucleic acid) refers to standard Watson/Crick pairing rules. The complement of a nucleic acid sequence such that the 5′ end of one sequence is paired with the 3′ end of the other, is in “antiparallel association.” For example, the sequence “5′-A-G-T-3′” is complementary to the sequence “3′-T-C-A-5′.” Certain bases not commonly found in natural nucleic acids may be included in the nucleic acids described herein; these include, for example, inosine, 7-deazaguanine, Locked Nucleic Acids (LNA), and Peptide Nucleic Acids (PNA). Complementary need not be perfect; stable duplexes may contain mismatched base pairs, degenerative, or unmatched bases. Those skilled in the art of nucleic acid technology can determine duplex stability empirically considering a number of variables including, for example, the length of the oligonucleotide, base composition and sequence of the oligonucleotide, ionic strength and incidence of mismatched base pairs. A complement sequence can also be a sequence of RNA complementary to the DNA sequence or its complement sequence, and can also be a cDNA.
The term “substantially complementary” as used herein means that two sequences hybridize under stringent hybridization conditions. The skilled artisan will understand that substantially complementary sequences need not hybridize along their entire length. In particular, substantially complementary sequences comprise a contiguous sequence of bases that do not hybridize to a target sequence, positioned 3′ or 5′ to a contiguous sequence of bases that hybridize under stringent hybridization conditions to a target sequence.
The term “coding sequence” as used herein means a sequence of a nucleic acid or its complement, or a part thereof, that can be transcribed and/or translated to produce the mRNA for and/or the polypeptide or a fragment thereof. Coding sequences include exons in a genomic DNA or immature primary RNA transcripts, which are joined together by the cell's biochemical machinery to provide a mature mRNA. The anti-sense strand is the complement of such a nucleic acid, and the encoding sequence can be deduced from there.
The term “amplification” or “amplify” as used herein means one or more methods known in the art for copying a target nucleic acid, thereby increasing the number of copies of a selected nucleic acid sequence. Amplification may be exponential or linear. A target nucleic acid may be either DNA or RNA. The sequences amplified in this manner form an “amplicon.” While the exemplary methods described hereinafter relate to amplification using the polymerase chain reaction (PCR), numerous other methods are known in the art for amplification of nucleic acids (e.g., isothermal methods, rolling circle methods, etc.). The skilled artisan will understand that these other methods may be used either in place of, or together with, PCR methods. See, e.g., Saiki, “Amplification of Genomic DNA” in PCR Protocols, Innis et al., Eds., Academic Press, San Diego, Calif. 1990, pp 13-20; Wharam, et al., Nucleic Acids Res. 2001 Jun. 1; 29(11):E54-E54; Hafner, et al., Biotechniques 2001 April; 30(4):852-6, 858, 860 passim; Zhong, et al., Biotechniques 2001 April; 30(4):852-6, 858, 860 passim.
The term “multiplex PCR” as used herein refers to amplification of two or more products which are each primed using a distinct primer pair.
As used herein, a “primer” for amplification is an oligonucleotide that specifically anneals to a target nucleotide sequence. The 3′ nucleotide of the primer should be identical to the target sequence at a corresponding nucleotide position for optimal amplification. The term “primer” as used herein includes all forms of primers that may be synthesized including peptide nucleic acid primers, locked nucleic acid primers, phosphorothioate modified primers, labeled primers, and the like.
“Sense strand” means the strand of double-stranded DNA (dsDNA) that includes at least a portion of a coding sequence of a functional protein. “Anti-sense strand” means the strand of dsDNA that is the reverse complement of the sense strand.
As used herein, a “forward primer” is a primer that anneals to the anti-sense strand of dsDNA. A “reverse primer” anneals to the sense-strand of dsDNA.
As used herein, sequences that have “high sequence identity” have identical nucleotides at least at about 50% of aligned nucleotide positions, preferably at least at about 58% of aligned nucleotide positions, and more preferably at least at about 76% of aligned nucleotide positions.
As used herein “TaqMan® PCR detection system” refers to a method for real time PCR. In this method, a TaqMan® probe which hybridizes to the nucleic acid segment amplified is included in the PCR reaction mix. The TaqMan® probe comprises a donor and a quencher fluorophore on either end of the probe and in close enough proximity to each other so that the fluorescence of the donor is taken up by the quencher. However, when the probe hybridizes to the amplified segment, the 5′-exonuclease activity of the Taq polymerase cleaves the probe thereby allowing the donor fluorophore to emit fluorescence which can be detected.
As used herein, “about” means plus or minus 10%.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. Nucleotide sequence of Genbank Accession No. U43598 of the mig gene (SEQ ID NO:10) showing the preferred locations for hybridizing PCR primers (shaded regions corresponding to SEQ ID NO:1 and SEQ ID NO:2), and a preferred location for a hybridizing probe (bold underlined corresponding to SEQ ID N0:3).
FIG. 2. Nucleotide sequence of Genbank Accession No. L33879 of the insertion sequence transposase gene (SEQ ID NO:11) showing the preferred locations for hybridizing PCR primers (shaded regions corresponding to SEQ ID NO:4 and SEQ ID NO:5), and a preferred location for a hybridizing probe (bold underlined corresponding to SEQ ID NO:6).
FIG. 3. Nucleotide sequence of GenBank Accession No. L04543 of the DT1 gene (SEQ ID NO:12) showing the preferred locations for hybridizing PCR primers (shaded regions corresponding to SEQ ID NO:7 and SEQ ID NO:8), and a preferred location for a hybridizing probe (bold underlined corresponding to SEQ ID NO:9).



DETAILED DESCRIPTION OF THE INVENTION
In accordance with the present invention, there are provided methods for determining whether a sample contains nucleic acid from M. avium and/or M. intracellulare. 
Sample Preparation
The method may be performed using any biological sample. Biological samples may be obtained by standard procedures and may be used immediately or stored (e.g., the sample may be frozen between about −15° C. to about −100° C.) for later use. The presence of MAC nucleic acids in a sample can be determined by amplifying target regions within MAC nucleic acids. Thus, any liquid or solid material believed to contain MAC nucleic acids can be an appropriate sample. Preferred sample tissues include blood, bone marrow, body fluids, cerebrospinal fluid, urine and others. Heparin is known to inhibit PCR (Beutler, et al. BioTechniques 9:166, 1990), so samples containing heparin are not ideal for the uses contemplated herein. Nucleic acid extraction techniques that remove heparin are known in the art. These techniques may be used to remove heparin from samples to make the samples more suitable for amplification.
Biological samples may be obtained from patients suspected of having a MAC infection, or having any of a wide spectrum of diseases related to MAC infection. MAC is believed to be associated with diseases that have disseminated infections such as association with HIV infection. Less commonly, pulmonary disease in nonimmunocompromised persons is a result of infection with MAC. In children, the most common syndrome is cervical lymphadenitis.
The sample may be processed to release or otherwise make available a nucleic acid for detection as described herein. Such processing may include steps of nucleic acid manipulation, e.g., preparing a cDNA by reverse transcription of RNA from the biological sample. Thus, the nucleic acid to be amplified by the methods of the invention may be genomic DNA, cDNA, single stranded DNA or mRNA.
Nucleic acids from M. avium or M. intracellulare may be extracted from biological samples prior to amplification. Samples are pre-treated to lyse the mycobacteria, releasing the nucleic acids. Viscous samples such as sputum are generally liquefied by adding a solution of N-acetyl-1-cysteine (NALC) that is resuspended in a solution of citrate and NaOH. Addition of this solution to the sputum breaks it up and liquefies it. Alternatively, viscous samples are treated with DTT, incubated at 65° C. for 30 minutes, centrifuged, and the supernatant removed. Once the sample is liquefied, bacteria are pelleted, resuspended in a neutralizing buffer, and then can be subjected to lysis and nucleic acid extraction.
In an alternate pre-treatment protocol, lysis buffer (MagNA Pure System, Roche) is added in an equal volume of lysis buffer to the sputum. The sample is mixed by vortex and incubated for 15 min at 95° C. At this point, the sputum is sufficiently broken down (the viscosity is decreased enough to pipette), and it can be transferred to an automated DNA extraction instrument (e.g., MagNA Pure). Lysis of the mycobacteria can also be achieved by various methods known in the art (e.g., treatment with proteinase K and lysis buffer, freeze-thaw cycling, or sonication) (Buck et al. J. Clin. Microbiol. 30:1331-1334, 1992). Various commercial nucleic acid purification kits, such as MagNA Pure LC DNA Isolation Kit III or Total Nucleic Acid Isolation Kit (Roche) and related methods known to the skilled artisan and may be used to isolate MAC nucleic acids from the pre-treated samples.
Amplification of Nucleic Acids
Target samples or isolated nucleic acids may be amplified by various methods known to the skilled artisan. Preferably, PCR is used to amplify M. avium and/or M. intracellulare nucleic acids of interest. In this method, two or more oligonucleotide primers that flank and anneal to opposite strands of a nucleic acid of interest are repetitively annealed to their complementary sequences, extended by a DNA polymerase (e.g., AmpliTaq Gold polymerase), and heat denatured, resulting in exponential amplification of the target nucleic acid sequences. Cycling parameters can be varied, depending on the length of nucleic acids to be extended. The skilled artisan is capable of designing and preparing primers that are appropriate for amplifying a target sequence in view of this disclosure. The length of the amplification primers for use in the present invention depends on several factors including the nucleotide sequence identity and the temperature at which these nucleic acids are hybridized or used during in vitro nucleic acid amplification. The considerations necessary to determine a preferred length for an amplification primer of a particular sequence identity are well known to the person of ordinary skill. For example, the length of a short nucleic acid or oligonucleotide can relate to its hybridization specificity or selectivity.
Assay controls may be used in the assay for detecting MAC nucleic acid. An internal positive amplification control (IPC) can be included in the sample, utilizing oligonucleotide probes incorporating SEQ ID NO:3, SEQ ID NO:6 or SEQ ID NO:9, and may be introduced as part of a primer/probe mastermix.
Detection of Amplified Nucleic Acids
Amplification of nucleic acids can be detected by any of a number of methods well-known in the art such as gel electrophoresis, column chromatography, hybridization with a probe, or sequencing.
In a preferred approach, a target sequence from each of two genes is amplified in the same reaction vessel. In this case, the amplicon(s) could be detected by first size-separating the amplicons then detection of the size-separated amplicons. The separation of amplicons of different sizes can be accomplished by, for example, gel electrophoresis, column chromatography, or capillary electrophoresis. These and other separation methods are well-known in the art. In one example, amplicons of about 10 to about 150 base pairs whose sizes differ by 10 or more base pairs can be separated, for example, on a 4% to 5% agarose gel, (a 2% to 3% agarose gel for about 150 to about 300 base pair amplicons) or a 6% to 10% polyacrylamide gel. The separated nucleic acids can then be stained with a dye such as ethidium bromide and the size of the resulting stained band or bands can be compared to a standard DNA ladder.
In another embodiment, a target sequence from each of two genes is amplified in separate reaction vessels. If the amplification is specific, that is, one target sequence is amplified from one MAC organism but not the other, detection of amplification is sufficient to distinguish between the two types—size separation would not be required.
In some embodiments, amplified nucleic acids are detected by hybridization with a gene-specific probe. Probe oligonucleotides, complementary to a portion of the amplified target sequence may be used to detect amplified fragments. Amplified nucleic acids for each of the target sequences may be detected simultaneously (i.e., in the same reaction vessel) or individually (i.e., in separate reaction vessels). In preferred embodiments, the amplified DNA is detected simultaneously, using two distinguishably-labeled, gene-specific oligonucleotide probes, one which hybridizes to the first target sequence and one which hybridizes to the second target sequence.
The probe may be detectably labeled by methods known in the art. Useful labels include, e.g., fluorescent dyes (e.g., Cy5®, Cy3®, FITC, rhodamine, lanthamide phosphors, Texas red), 32P, 35S, 3H, 14C, 125I, 131I, electron-dense reagents (e.g., gold), enzymes, e.g., as commonly used in an ELISA (e.g., horseradish peroxidase, beta-galactosidase, luciferase, alkaline phosphatase), colorimetric labels (e.g., colloidal gold), magnetic labels (e.g., DynabeadsTM), biotin, dioxigenin, or haptens and proteins for which antisera or monoclonal antibodies are available. Other labels include ligands or oligonucleotides capable of forming a complex with the corresponding receptor or oligonucleotide complement, respectively. The label can be directly incorporated into the nucleic acid to be detected, or it can be attached to a probe (e.g., an oligonucleotide) or antibody that hybridizes or binds to the nucleic acid to be detected.
A probe oligonucleotide, complementary to the amplified region of MAC nucleic acid, is used to detect the amplification of MAC nucleic acids. The probe may be detectably labeled by methods known in the art. The binding of a probe to the amplified region of the MAC nucleic acid may be determined by hybridization as is well known in the art. Hybridization may be detected in real time or in non-real time.
One general method for real time PCR uses fluorescent probes such as the TaqMan® probes, molecular beacons and scorpions. Real-time reverse-transcriptase (RT) PCR quantitates the initial amount of the template with more specificity, sensitivity and reproducibility, than other forms of quantitative reverse transcriptase PCR, which detect the amount of final amplified product. Real-time RT-PCR does not detect the size of the amplicon. The probes employed in TaqMan® and molecular beacon technologies are based on the principle of fluorescence quenching and involve a donor fluorophore and a quenching moiety.
In a preferred embodiment, the detectable label is a fluorophore. The term “fluorophore” as used herein refers to a molecule that absorbs light at a particular wavelength (excitation frequency) and subsequently emits light of a longer wavelength (emission frequency). The term “donor fluorophore” as used herein means a fluorophore that, when in close proximity to a quencher moiety, donates or transfers emission energy to the quencher. As a result of donating energy to the quencher moiety, the donor fluorophore will itself emit less light at a particular emission frequency that it would have in the absence of a closely positioned quencher moiety.
The term “quencher moiety” as used herein means a molecule that, in close proximity to a donor fluorophore, takes up emission energy generated by the donor and either dissipates the energy as heat or emits light of a longer wavelength than the emission wavelength of the donor. In the latter case, the quencher is considered to be an acceptor fluorophore. The quenching moiety can act via proximal (i.e., collisional) quenching or by Förster or fluorescence resonance energy transfer (“FRET”). Quenching by FRET is generally used in TaqMan® probes while proximal quenching is used in molecular beacon and scorpion type probes.
In proximal quenching (a.k.a. “contact” or “collisional” quenching), the donor is in close proximity to the quencher moiety such that energy of the donor is transferred to the quencher, which dissipates the energy as heat as opposed to a fluorescence emission. In FRET quenching, the donor fluorophore transfers its energy to a quencher which releases the energy as fluorescence at a higher wavelength. Proximal quenching requires very close positioning of the donor and quencher moiety, while FRET quenching, also distance related, occurs over a greater distance (generally 1-10 nm, the energy transfer depending on R-6, where R is the distance between the donor and the acceptor). Thus, when FRET quenching is involved, the quenching moiety is an acceptor fluorophore that has an excitation frequency spectrum that overlaps with the donor emission frequency spectrum. When quenching by FRET is employed, the assay may detect an increase in donor fluorophore fluorescence resulting from increased distance between the donor and the quencher (acceptor fluorophore) or a decrease in acceptor fluorophore emission resulting from increased distance between the donor and the quencher (acceptor fluorophore).
Suitable fluorescent moieties include the following fluorophores known in the art:

    4-acetamido-4′-isothiocyanatostilbene-2,2′disulfonic acid
    acridine and derivatives:
    
        acridine
        acridine isothiocyanate
    
    
    Alexa Fluor® 350, Alexa Fluor® 488, Alexa Fluor® 546, Alexa Fluor® 555, Alexa Fluor® 568, Alexa Fluor® 594, Alexa Fluor® 647 (Molecular Probes)
    5-(2′-aminoethyl)aminonaphthalene-1-sulfonic acid (EDANS)
    4-amino-N-[3-vinylsulfonyl)phenyl]naphthalimide-3,5 disulfonate (Lucifer Yellow VS)
    N-(4-anilino-1-naphthyl)maleimide
    anthranilamide
    Black Hole QuencherTM (BHQTM) dyes (biosearch Technologies)
    BODIPYO® R-6G, BOPIPY® 530/550, BODIPY® FL
    Brilliant Yellow
    coumarin and derivatives:
    
        coumarin
        7-amino-4-methylcoumarin (AMC, Coumarin 120)
    
    
    7-amino-4-trifluoromethylcouluarin (Coumarin 151)
    Cy2®, Cy3®, Cy3.5®, Cy5®, Cy5.5®
    cyanosine
    4′,6-diaminidino-2-phenylindole (DAPI)
    5′,5′′-dibromopyrogallol-sulfonephthalein (Bromopyrogallol Red)
    7-diethylamino-3-(4′-isothiocyanatophenyl)-4-methylcoumarin
    diethylenetriamine pentaacetate
    4,4′-diisothiocyanatodihydro-stilbene-2,2′-disulfonic acid
    4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid
    5-[dimethylamino]naphthalene-1-sulfonyl chloride (DNS, dansyl chloride)
    4-(4′-dimethylaminophenylazo)benzoic acid (DABCYL)
    4-dimethylaminophenylazophenyl-4′-isothiocyanate (DABITC)
    EclipseTM (Epoch Biosciences Inc.)
    eosin and derivatives:
    
        eosin
        eosin isothiocyanate
    
    
    erythrosin and derivatives:
    
        erythrosin B
        erythrosin isothiocyanate
    
    
    ethidium
    fluorescein and derivatives:
    
        5-carboxyfluorescein (FAM)
        5-(4,6-dichlorotriazin-2-yl)aminofluorescein (DTAF)
        2′,7′-dimethoxy-4′5′-dichloro-6-carboxyfluorescein (JOE)
        fluorescein
        fluorescein isothiocyanate (FITC)
        hexachloro-6-carboxyfluorescein (HEX)
        QFITC (XRITC)
        tetrachlorofluorescein (TET)
    
    
    fluorescamine
    IR144
    IR1446
    Malachite Green isothiocyanate
    4-methylumbelliferone
    ortho cresolphthalein
    nitrotyrosine
    pararosaniline
    Phenol Red
    B-phycoerythrin, R-phycoerythrin
    o-phthaldialdehyde
    Oregon Green®
    propidium iodide
    pyrene and derivatives:
    
        pyrene
        pyrene butyrate
        succinimidyl 1-pyrene butyrate
    
    
    QSY®7, QSY® 9, QSY® 21, QSY® 35 (Molecular Probes)
    Reactive Red 4 (Cibacron® Brilliant Red 3B-A)
    rhodamine and derivatives:
    
        6-carboxy-X-rhodamine (ROX)
        6-carboxyrhodamine (R6G)
        lissamine rhodamine B sulfonyl chloride
        rhodamnine (Rhod)
        rhodamine B
        rhodamine 123
        rhodamine green
        rhodamine X isothiocyanate
        sulforhodamine B
        sulforhodamine 101
        sulfonyl chloride derivative of sulforhodamine 101 (Texas Red)
    
    
    N,N,N′,N′-tetramethyl-6-carboxyrhodamine (TAMRA)
    tetramethyl rhodamine
    tetramethyl rhodamine isothiocyanate (TRITC)
    riboflavin
    rosolic acid
    terbium chelate derivatives


Other fluorescent nucleotide analogs can be used, see, e.g., Jameson, Meth. Enzymol. 278:363-390, 1997; Zhu, Nucl. Acids Res. 22:3418-3422, 1994. U.S. Pat. Nos. 5,652,099 and 6,268,132 also describe nucleoside analogs for incorporation into nucleic acids, e.g., DNA and/or RNA, or oligonucleotides, via either enzymatic or chemical synthesis to produce fluorescent oligonucleotides. U.S. Pat. No. 5,135,717 describes phthalocyanine and tetrabenztriazaporphyrin reagents for use as fluorescent labels.
The detectable label can be incorporated into, associated with or conjugated to a nucleic acid. Label can be attached by spacer arms of various lengths to reduce potential steric hindrance or impact on other useful or desired properties. See, e.g., Mansfield, Mol. Cell. Probes 9:145-156, 1995.
Detectable labels can be incorporated into nucleic acids by covalent or non-covalent means, e.g., by transcription, such as by random-primer labeling using Klenow polymerase, or nick translation, or amplification, or equivalent as is known in the art. For example, a nucleotide base is conjugated to a detectable moiety, such as a fluorescent dye, e.g., Cy3® or Cy5® and then incorporated into genomic nucleic acids during nucleic acid synthesis or amplification. Nucleic acids can thereby be labeled when synthesized using Cy3®- or Cy5®-dCTP conjugates mixed with unlabeled dCTP.
Nucleic acid probes can be labeled by using PCR or nick translation in the presence of labeled precursor nucleotides, for example, modified nucleotides synthesized by coupling allylamine-dUTP to the succinimidyl-ester derivatives of the fluorescent dyes or haptens (such as biotin or digoxigenin) can be used; this method allows custom preparation of most common fluorescent nucleotides, see, e.g., Henegariu, Nat. Biotechnol. 18:345-348, 2000.
Nucleic acid probes may be labeled by non-covalent means known in the art. For example, Kreatech Biotechnology's Universal Linkage System® (ULS®) provides a non-enzymatic labeling technology, wherein a platinum group forms a co-ordinative bond with DNA, RNA or nucleotides by binding to the N7 position of guanosine. This technology may also be used to label proteins by binding to nitrogen and sulphur containing side chains of amino acids. See, e.g., U.S. Pat. Nos. 5,580,990; 5,714,327; and 5,985,566; and European Patent No. 0539466.
The binding of a probe to the marker sequence flanking the tandem repeat region may be determined by hybridization as is well known in the art. Hybridization may be detected in real time or in non-real time.
TaqMan® probes (Heid, et al., 1996) use the fluorogenic 5′ exonuclease activity of Taq polymerase to measure the amount of target sequences in cDNA samples. TaqMan® probes are oligonucleotides that contain a donor fluorophore usually at or near the 5′ base, and a quenching moiety typically at or near the 3′ base. The quencher moiety may be a dye such as TAMRA or may be a non-fluorescent molecule such as 4-(4-dimethylaminophenylazo) benzoic acid (DABCYL). See Tyagi, et al., Nature Biotechnology 16:49-53 (1998). When irradiated, the excited fluorescent donor transfers energy to the nearby quenching moiety by FRET rather than fluorescing. Thus, the close proximity of the donor and quencher prevents emission of donor fluorescence while the probe is intact.
TaqMan® probes are designed to anneal to an internal region of a PCR product. When the polymerase (e.g., reverse transcriptase) replicates a template on which a TaqMan® probe is bound, its 5′ exonuclease activity cleaves the probe. This ends the activity of quencher (no FRET) and the donor fluorophore starts to emit fluorescence which increases in each cycle proportional to the rate of probe cleavage. Accumulation of PCR product is detected by monitoring the increase in fluorescence of the reporter dye (note that primers are not labeled). If the quencher is an acceptor fluorophore, then accumulation of PCR product can be detected by monitoring the decrease in fluorescence of the acceptor fluorophore.
TaqMan® assay uses universal thermal cycling parameters and PCR reaction conditions. Because the cleavage occurs only if the probe hybridizes to the target, the fluorescence detected originates from specific amplification. The process of hybridization and cleavage does not interfere with the exponential accumulation of the product. One specific requirement for fluorogenic probes is that there be no G at the 5′ end. A ‘G’ adjacent to the reporter dye quenches reporter fluorescence even after cleavage.
Other methods of probe hybridization detected in real time can be used for detecting amplification of MAC nucleic acids. For example, the commercially available MGB EclipseTM probes (Epoch Biosciences), which do not rely on a probe degradation can be used. MGB EclipseTM probes work by a hybridization-triggered fluorescence mechanism. MGB EclipseTM probes have the EclipseTM Dark Quencher and the MGB positioned at the 5′-end of the probe. The fluorophore is located on the 3′-end of the probe. When the probe is in solution and not hybridized, the three dimensional conformation brings the quencher into close proximity of the fluorophore, and the fluorescence is quenched. However, when the probe anneals to a target sequence, the probe is unfolded, the quencher is moved from the fluorophore, and the resultant fluorescence can be detected.
Suitable donor fluorophores include 6-carboxyfluorescein (FAM), tetrachloro-6-carboxyfluorescein (TET), 2′-chloro-7′-phenyl-1,4-dichloro-6-carboxyfluorescein (VIC) and the like. Suitable quenchers include tetra-methylcarboxyrhodamine (TAMRA) 4-(4-dimethylaminophenylazo) benzoic acid (“DABCYL” or a DABCYL analog) and the like. Tetramethylrhodamine (TMR) or 5-carboxyrhodamine 6G (RHD) may be combined as donor fluorophores with DABCYL as quencher. Multiplex TaqMan® assays can be performed using multiple detectable labels each comprising a different donor and quencher combination. Probes for detecting amplified sequence in real time may be stored frozen (−10° to −30° C.) as 100 M stocks. TaqMan® probes are available from Applied BioSystems (4316032).
In a preferred embodiment, real time PCR is performed using TaqMan® probes in combination with a suitable amplification/analyzer such as the ABI Prism 7900HT Sequence Detection System. The ABI PRISM® 7900HT Sequence Detection System is a high-throughput real-time PCR system that detects and quantitates nucleic acid sequences. Briefly, TaqMan® probes specific for each allele are included in the PCR assay. These probes contain a reporter dye at the 5′ end and a quencher dye at the 3′ end. Each allele specific probe is conjugated with a different fluorescent reporter dye. During PCR, the fluorescently labeled probes bind specifically to their respective target sequences; the 5′ nuclease activity of Taq polymerase cleaves the reporter dye from the probe and a fluorescent signal is generated. The increase in fluorescence signal is detected only if the target sequence is complementary to the probe and is amplified during PCR. A mismatch between probe and target greatly reduces the efficiency of probe hybridization and cleavage. The ABI Prism 7700HT or 7900HT Sequence detection System measures the increase in fluorescence during PCR thermal cycling, providing “real time” detection of PCR product accumulation.
Real Time detection on the ABI Prism 7900HT or 7900HT Sequence Detector monitors fluorescence and calculates the measure of reporter signal, or Rn value, during each PCR cycle. The threshold cycle, or Ct value, is the cycle at which fluorescence intersects the threshold value. The threshold value is determined by the sequence detection system software or manually.
To minimize the potential for cross contamination, reagent and mastermix preparation, specimen processing and PCR setup, and amplification and detection are all carried out in physically separated areas. In addition, Uracil-N-Glycosylase is utilized (along with the incorporation of Uracil into PCR amplicons) to eliminate carry over contamination.
The examples below illustrate a standard protocol for performing PCR and analyzing in real time. The TaqMan® system of primer labeling is a preferred method of real time detection of PCR amplicons. The following examples serve to illustrate the present invention. These examples are in no way intended to limit the scope of the invention.
EXAMPLE 1
Primer/Probe Mastermix Preparation
A stock solution of primer and probe mastermix was prepared by mixing each of the stock solutions as shown in Table 1.







TABLE 1







Primer/Probe Mastermix.













Final




Volume/2000
Concentration



μl/reaction
reactions
per reaction
















Sterile Nuclease Free
6.90

13.8
ml



Water


10x Exo IPC Mix
5.0

10.0
ml
1x


50x Exo IPC DNA
1.0

2.0
ml
1x


MIGL_01 (100 μM)
0.25

500
μl
500 nM


MIGR_01 (100 μM)
0.25

500
μl
500 nM


MIGP_01FT (100 μM)
0.05

100
μl
100 nM


DT1L_01 (100 μM)
0.25

500
μl
500 nM


DT1R_01(100 μM)
0.25

500
μl
500 nM


DT1P_01TT (100 μM)
0.05

100
μl
100 nM


Total
14.0
μl
28.0
ml





*Exo IPC: Exogenous internal positive control






The mastermix stock solution was dispensed into 280 μl aliquots. Each aliquot is sufficient for up to 19 reactions. This solution can be stored at −20° C. for one year from the date of preparation.
EXAMPLE 2
Preparation of and DNA Extraction of Samples
Biological samples (e.g., sputum, BAL, CSF, blood, urine or pleural fluid) of a volume of 0.35-0.85 ml were collected. DNA was extracted from controls and biological samples using the MagNA Pure LC automated nucleic acid extraction system (Roche Cat # 2 236 931). 250 μl of MagNA pure Lysis buffer followed by 250 μl of control or specimen were placed into a sample tube and mixed thoroughly by vortexing for 10 seconds. The samples were incubated at 25° C. for 30 minutes. The entire volume, 500 μl, was added into the MagNA Pure sample cartridge.
EXAMPLE 3
DNA Amplification
To prepare the final mastermix, 500 μl of ABI 2× Mastermix (ABI #4304437) and 20 μl of AmpliTaq Gold was added to a sample tube. The resulting solution was mixed by pulse vortex and short spun in a microcentrifuge. 40 μl of the solution was dispensed into each well of a 96-well optical reaction plate to be used for PCR. The extracts from each control and clinical sample (10 μl/well) were added to individual wells containing the final mastermix. The sample were mixed by gently pipetting the sample up and down two times. The plate was sealed and transferred to the ABI 7900 Sequence Detector.
The thermocycler conditions were as follows:

    
    
        Stage 1: Hold at 50° C. for 2 minutes.
        Stage 2: Hold at 95° C. for 10 minutes.
        Stage 3: Cycle from 95° C. for 15 seconds to 60° C. for 1 minutes, 50 cycles.
        Sample volume set at 50 μl.
    
    


EXAMPLE 4
Data Analysis
The assay as described has been used to detect MAC nucleic acids in a variety of clinical specimens, including sputum, blood, CSF, BAL and urine. The assay results were reproducible over the course of multiple runs. Method comparison studies performed to detect MAC nucleic acids from samples submitted from patients showing symptoms of MAC infection were performed. This included verification studies which tested PCR efficiency, recovery of positive samples, intra-assay reproducibility, inter-assay reproducibility, limit of detection, target specificity, specimen stability, reagent stability and comparison with conventional culture methods. The results support the conclusion that the real-time PCR format described herein is both sensitive and specific, detecting specimens that were shown to be positive for M. avium and/or M. intracellulare by culture. In addition, the assay in a real-time PCR format was shown to be more sensitive than non-real time PCR format.
M. avium is positively identified if a positive result is obtained for mig and a negative result for DT1, except if M. avium is of serovar 2 or 3 in which case DT1 will also be positive. M. intracellulare is positively identified if a positive result is obtained for DT1 and a negative result for mig. If the sample is positive for both mig and DT1, then it is M. avium of serovar 2 or 3, but it is not M. intracellulare. The mig gene is also found in M. paratuberculosis, however the present assay methods will not detect M. paratuberculosis since neither gastric aspirate or stool are designated specimen types used in the present invention.
To ensure the absence of non-specific PCR inhibition of a sample, an internal positive amplification control (IPC) is included with each specimen. The positive control primers and probe are added with the target and sample primers. The IPC or control amplicon is detected by a probe labeled with VIC as the 5′ reporter dye. A sample can be interpreted as negative only if the analysis of the internal positive control indicates that DNA amplification has occurred in the reaction tube.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.
The inventions illustratively described herein may suitably be practiced in the absence of any element or elements, limitation or limitations, not specifically disclosed herein. Thus, for example, the terms “comprising,” “including,” “containing,” etc. shall be read expansively and without limitation. Additionally, the terms and expressions employed herein have been used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed.
Thus, it should be understood that although the present invention has been specifically disclosed by preferred embodiments and optional features, modification, improvement and variation of the inventions embodied therein herein disclosed may be resorted to by those skilled in the art, and that such modifications, improvements and variations are considered to be within the scope of this invention. The materials, methods, and examples provided here are representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention.
The invention has been described broadly and generically herein. Each of the narrower species and subgeneric groupings falling within the generic disclosure also form part of the invention. This includes the generic description of the invention with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein.
In addition, where features or aspects of the invention are described in terms of Markush groups, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group.
All publications, patent applications, patents, and other references mentioned herein are expressly incorporated by reference in their entirety, to the same extent as if each were incorporated by reference individually. In case of conflict, the present specification, including definitions, will control.
Other embodiments are set forth within the following claims.

## Claims

1. A method for detecting if a sample contains nucleic acid from Mycobacterium avium (M. avium) or Mycobacterium intracellulare (M. intracellulare), said method comprising:
assessing the presence or absence of a first target nucleic acid sequence in said sample; and
assessing the presence or absence of a second target nucleic acid sequence in said sample;
identifying the sample as containing nucleic acid from M. avium, M. intracellulare, or M. avium serovars 2/3, wherein the presence of said first target nucleic acid indicates that the sample contains M. avium, wherein the absence of said first target nucleic acid and the presence of said second target nucleic acid indicates that the sample contains M. intracellulare, and wherein the presence of said first and second target nucleic acids indicates that the sample contains M. avium serovar 2 or M. avium serovar 3,
wherein said first target nucleic acid sequence is specific for the macrophage-induced gene (mig) gene of M. avium and said second target nucleic acid sequence is specific for the DT1 gene of M. intracellulare, M. avium serovar 2 and M. avium serovar 3 and
wherein said sample is not a gastric aspirate or a stool sample.

2. A method according to claim 1, wherein said assessing the presence or absence of said target nucleic acid sequences further comprises amplifying said first and said second target nucleic acid sequences.

3. A method according to claim 2, wherein said amplifying is accomplished with polymerase chain reaction.

4. A method according to claim 1, wherein said assessing the presence or absence of said first and said second target nucleic acid sequences occurs in the same reaction vessel.

5. A method according to claim 1, wherein said assessing the presence or absence of said first and said second target nucleic acid sequences occurs in separate reaction vessels.

6. A method according to claim 1, wherein said assessing the presence or absence of said target nucleic acid sequences further comprises:
amplifying a region of the M. avium mig gene with a first pair of primers resulting in a first amplified region when M. avium nucleic acids are present in said sample;
amplifying a region of the M. intracellulare, M. avium serovar 2 or M. avium serovar 3 DT1 gene with a second pair of primers resulting in a second amplified region when M. intracellulare, M. avium serovar 2 or M. avium serovar 3 nucleic acids are present in said sample; and
assessing the presence or absence of said first and second amplified regions with a corresponding first gene-specific probe and a second gene-specific probe;
wherein the presence of said first amplified region indicates the presence of said first target nucleic acid sequence and wherein the presence of said second amplified region indicates the presence of said second target nucleic acid sequence.

7. A method according to claim 6, wherein said probes are labeled.

8. A method according to claim 7, wherein said probes are distinguishably labeled.

9. A method according to claim 6, wherein said first pair of primers comprises a forward primer comprising the sequence set forth in SEQ ID NO:1 and a reverse specific primer.

10. A method according to claim 6, wherein said first pair of primers comprises a reverse primer comprising the sequence set forth in SEQ ID NO:2 and a forward specific primer.

11. A method according to claim 6, wherein said second pair of primers comprises a forward primer comprising the sequence set forth in SEQ ID NO:7 and a reverse specific primer.

12. A method according to claim 6, wherein said second pair of primers comprises a reverse primer comprising the sequence set forth in SEQ ID NO:8 and a forward specific primer.

13. A method according to claim 6, wherein said first gene-specific probe comprises the sequence set forth in SEQ ID NO:3.

14. A method according to claim 6, wherein said second gene-specific probe comprises the sequence set forth in SEQ ID NO:9.

15. A method according to claim 6, wherein said amplifying of either region uses an oligonucleotide primer comprising a sequence of between 15-100 nucleotides in length.

16. A method according to claim 6, wherein said assessing the presence or absence of said first and second said amplified regions comprises:
a) hybridizing at least one of said amplified regions with at least one of said corresponding gene-specific probes wherein said gene-specific probe is an oligonucleotide probe in the presence of an enzyme that cleaves said probe when said probe hybridizes to said corresponding amplified region, wherein said probe is conjugated to a detectable label that generates an increase in its detectable signal upon said cleavage; and
b) detecting a signal from said detectable label, wherein an increased signal from said detectable label indicates the presence of said corresponding amplified region.

17. A method according to claim 16, wherein said oligonucleotide probe comprises the sequence set forth in SEQ ID NO:3.

18. A method according to claim 16, wherein said oligonucleotide probe comprises the sequence set forth in SEQ ID NO:9.

19. A method according to claim 16, wherein said oligonucleotide probe hybridizes to said amplified region of the M. avium mig gene and said probe is labeled with a fluorescent reporter dye and a quencher dye.

20. A method according to claim 19, wherein said reporter dye is 6-carboxyfluorescein (6-FAM) and said quencher dye is 6-carboxytetramethylrhodamine (TAMRA).

21. A method according to claim 16, wherein said oligonucleotide probe hybridizes to said amplified region of the DT1 gene and said probe is labeled with a fluorescent reporter dye and a quencher dye.

22. A method according to claim 21, wherein said reporter dye is tetrachloro-6-carboxyfluorescein (TET) and said quencher dye is 6-carboxytetramethylrhodamine (TAMRA).

23. A method according to claim 1, wherein said sample is biological and selected from the group consisting of sputum, bronchial alveolar lavage, bronchial wash, blood, bone marrow, bodily fluid, cerebrospinal fluid, urine, plasma, serum or tissue.

24. A method for diagnosing a subject infected with Mycobacterium avium (M. avium) or Mycobacterium intracellulare (M. intracellulare), comprising:
contacting a biological sample containing nucleic acids from the subject with a first oligonucleotide specific for a first target nucleic acid sequence and a second oligonucleotide specific for a second target nucleic acid sequence; and
determining if said first or second oligonucleotide has hybridized to said sample nucleic acids,
diagnosing the subject as infected with M. avium, M. intracellular, or M. avium serovar 2/3 wherein hybridization of the first oligonucleotide is indicative of infection by M. avium, hybridization of the second oligonucleotide but not the first oligonucleotide is indicative of infection by M. intracellulare, and hybridization of the first and second oligonucleotides is indicative of infection by M. avium serovar 2 or M. avium serovar 3; and
wherein said first target nucleic acid sequence is specific for the macrophage-induced gene (mig) gene of M. avium and said second target nucleic acid sequence is specific for the DT1 gene of M. intracellulare, M. avium serovar 2 and M. avium serovar 3 and
wherein said sample is not a gastric aspirate or stool sample.

25. A method according to claim 24, wherein said determining of hybridization further comprises amplifying said first and said second target nucleic acid sequences.

26. A method according to claim 25, wherein said amplifying is accomplished with polymerase chain reaction.

27. A method according to claim 24, wherein said determining of hybridization of said first and said second target nucleic acid sequences occurs in the same reaction vessel.

28. A method according to claim 24, wherein said determining of hybridization of said first and said second target nucleic acid sequences occurs in separate reaction vessels.

29. A method according to claim 24, wherein prior to contacting said nucleic acids from the subject with said first and second oligonucleotides further comprises:
amplifying a region of the M. avium mig gene with a first pair of primers when M. avium nucleic acids are present in said sample resulting in a first amplified region;
amplifying a region of the M. intracellulare, M. avium serovar 2 or M. avium serovar 3 DT1 gene with a second pair of primers when M. intracellulare, M. avium serovar 2 or M. avium serovar 3 nucleic acids are present in said sample resulting in a second amplified region; and
wherein said resulting first and second amplified regions correspond to said first and second target nucleic acid sequences.

30. A method according to claim 29, wherein said first pair of primers comprises a forward primer comprising the sequence set forth in SEQ ID NO:1 and a reverse specific primer.

31. A method according to claim 29, wherein said first pair of primers comprises a reverse primer comprising the sequence set forth in SEQ ID NO:2 and a forward specific primer.

32. A method according to claim 29, wherein said second pair of primers comprises a forward primer comprising the sequence set forth in SEQ ID NO:7 and a reverse specific primer.

33. A method according to claim 29, wherein said second pair of primers comprises a reverse primer comprising the sequence set forth in SEQ ID NO:8 and a forward specific primer.

34. A method according to claim 29, wherein said first oligonucleotide comprises the sequence set forth in SEQ ID NO:3.

35. A method according to claim 29, wherein said second oligonucleotide comprises the sequence set forth in SEQ ID NO:9.

36. The method of claim 29, wherein said amplifying of either region uses an oligonucleotide primer comprising a sequence of between 15-100 nucleotides in length.

37. The method of claim 29, wherein said determining of hybridization comprises:
a) hybridizing at least one of said amplified regions with an oligonucleotide probe in the presence of an enzyme that cleaves said probe when said probe hybridizes to said corresponding amplified region, wherein said probe is conjugated to a detectable label that generates an increase in its detectable signal upon said cleavage; and
b) detecting a signal from said detectable label, wherein an increased signal from said detectable label indicates the presence of said corresponding amplified region.

38. A method according to claim 24, wherein said oligonucleotides are labeled.

39. A method according to claim 24, wherein said oligonucleotides are distinguishably labeled.

40. The method of claim 24, wherein said biological sample is selected from the group consisting of sputum, bronchial alveolar lavage, bronchial wash, blood, bone marrow, bodily fluid, cerebrospinal fluid, urine, plasma, serum or tissue.