# Patent

## Title
Mycobacterial rpoB sequences

## Abstract

This invention provides polynucleotide probes, sequences and methods for speciating and phenotyping organisms, for example, using probes based on the Mycobacterium tuberculosis rpoB gene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application derives priority from U.S. Ser. No. 60/080,616, filed Apr. 3, 1998, and incorporated by reference. Applications U.S. Ser. No. 08/797,812, filed Feb. 7, 1997, now U.S. Pat. No. 6,228,575; U.S. Ser. No. 60/011,339, filed Feb. Feb. 8, 1996; U.S. Ser. No. 60/012,631, filed Mar. 1, 1996; U.S. Ser. No. 08/629,031, filed Apr. 8, 1996, now abandoned; and 60/017,765, filed 15 May 15, 1996 are directed to related subject matter. These applications are specifically incorporated by reference in their entirety for all purposes.


STATEMENT OF GOVERNMENT INTEREST
The work described in this application was supported in part by grant number 1R43a140400 by the NIAID. The Government may have certain rights in this invention.


BACKGROUND OF THE INVENTION
1. Field of the Invention
This invention is directed to polymorphisms in rpoB genes of mycobacteria and use of the same in the identification and characterization of microorganisms.
2. Background of the Invention
Multidrug resistance and human immunodeficiency virus (HIV-1) infections are factors which have had a profound impact on the tuberculosis problem. An increase in the frequency of Mycobacterium tuberculosis strains resistant to one or more anti-mycobacterial agents has been reported, Block, et al., (1994) JAMA 271:665–671. Immunocompromised HIV-1 infected patients not infected with M. tuberculosis are frequently infected with M. avium complex (MAC) or M. avium-M. intracellulare (MAI) complex. These mycobacteria species are often resistant to the drugs used to treat M. tuberculosis. These factors have re-emphasized the importance for the accurate determination of drug sensitivities and mycobacteria species identification.
In HIV-1 infected patients, the correct diagnosis of the mycobacterial disease is essential since treatment of M. tuberculosis infections differs from that called for by other mycobacteria infections, Hoffner, S. E. (1994) Eur. J. Clin. Microbiol. Inf. Dis. 13:937–941. Non-tuberculosis mycobacteria commonly associated with HIV-1 infections include M. kansasii, M. xenopi, M. fortuitum, M. avium and M. intracellulare, Wolinsky, E., (1992) Clin. Infect. Dis. 15:1–12, Shafer, R. W. and Sierra, M. F. 1992 Clin. Infect. Dis. 15:161–162. Additionally, 13% of new cases (HIV-1 infected and non-infected) of M. tuberculosis are resistant to one of the primary anti-tuberculosis drugs (isoniazid [INH], rifampin [RIF], streptomycin [STR], ethambutol [EMB] and pyrazinamide [PZA] and 3.2% are resistant to both RIF and INH, Block, et al., JAMA 271:665–671, (1994). Consequently, mycobacterial species identification and the determination of drug resistance have become central concerns during the diagnosis of mycobacterial diseases.
Methods used to detect, and to identify Mycobacterium species vary considerably. For detection of Mycobacterium tuberculosis, microscopic examination of acid-fast stained smears and cultures are still the methods of choice in most microbiological clinical laboratories. However, culture of clinical samples is hampered by the slow growth of mycobacteria. A mean time of four weeks is required before sufficient growth is obtained to enable detection and possible identification. Recently, two more rapid methods for culture have been developed involving a radiometric, Stager, C. E. et al., (1991) J. Clin. Microbiol. 29:154–157, and a biphasic (broth/agar) system Sewell, et al., (1993) J. Clin. Microbiol. 29:2689–2472. Once grown, cultured mycobacteria can be analyzed by lipid composition, the use of species specific antibodies, species specific DNA or RNA probes and PCR-based sequence analysis of 16S rRNA gene (Schirm, et al. (1995) J. Clin. Microbiol. 33:3221–3224; Kox, et al. (1995) J. Clin. Microbiol. 33:3225–3233) and IS6110 specific repetitive sequence analysis (For a review see, e.g., Small et al., P. M. and van Embden, J. D. A. (1994) Am. Society for Microbiology, pp. 569–582). The analysis of 16S rRNA sequences (RNA and DNA) has been the most informative molecular approach to identify Mycobacteria species (Jonas, et al., J. Clin. Microbiol. 31:2410–2416 (1993)). However, to obtain drug sensitivity information for the same isolate, additional protocols (culture) or alternative gene analysis is necessary.
To determine drug sensitivity information, culture methods are still the protocols of choice. Mycobacteria are judged to be resistant to particular drugs by use of either the standard proportional plate method or minimal inhibitory concentration (MIC) method. However, given the inherent lengthy times required by culture methods, approaches to determine drug sensitivity based on molecular genetics have been recently developed.
Because resistance to RIF in E. coli strains was observed to arise as a result of mutations in the rpoB gene, Telenti, et al., id., identified a 69 base pair (bp) region of the M. tuberculosis rpoB gene as the locus where RIF resistant mutations were focused. Kapur, et al., (1995) Arch. Pathol. Lab. Med. 119:131–138, identified additional novel mutations in the M. tuberculosis rpoB gene which extended this core region to 81 bp. In a detailed review on antimicrobial agent resistance in mycobacteria, Musser (Clin. Microbiol. Rev., 8:496–514 (1995)), summarized all the characterized mutations and their relative frequency of occurrence in this 81 bp region of rpoB. Missense mutations comprise 88% of all known mutations while insertions (3 or 6 bp) and deletions (3, 6 and 9 bp) account for 4% and 8% of the remaining mutations, respectively. Approximately 90% of all RIF resistant tuberculosis isolates have been shown to have mutations in this 81 bp region. The remaining 10% are thought possibly to involve genes other than rpoB.
For the above reasons, it would be desirable to have simpler methods which identify and characterize microorganisms, such as Mycobacteria, both at the phenotypic and genotypic level. This invention fulfills that and related needs.
SUMMARY OF THE INVENTION
In one aspect, the invention provides isolated nucleic acids comprising at least 25, 50, 75, 100, or 200 contiguous bases from an rpoB sequence shown in Table 1 (SEQ ID NOS: 1–181). Some nucleic acid comprise a complete sequence shown in Table 1.
The invention further provides a set of probes perfectly complementary to and spanning such nucleic acids, preferably spanning one of the complete sequences shown in Table 1 (SEQ ID NOS: 1–181).
The invention further provides methods of classifying mycobacteria. Some such methods entail providing a sample comprising a mycobacterial rpoB target nucleic acid from a mycobacteria, determining the sequence of a segment of at least 50 contiguous bases from the target nucleic acid; comparing the determined sequence to at least one sequence shown in Table 1; and classifying the mycobacteria from the extent of similarity of the compared sequences. Preferably, at least 100 or 200 contiguous bases are determined from the target nucleic acid. Preferably, the determined sequence is compared with a plurality of sequences from Table 1, for example, 10, 20, 50 or all of the sequence from Table 1 (SEQ ID NOS: 1–181).
In other methods of classification, the identity of one or more bases in the target sequence at one or more positions corresponding to one or more of the highlighted positions in a sequence shown in Table 1 is determined. The identity of the one or more bases characterizing the species of mycobacteria that is present in the sample. In some methods, the identity of at least 10 bases in the target nucleic acid at positions corresponding to highlighted positions in a sequence shown in Table 1 is determined. In some methods, the identity of at least 20 bases in the target sequence at highlighted positions shown in Table 1 are identified. In some methods, at least 20 determined bases are compared with 20 bases occupying corresponding positions in each of at least ten sequences from Table 1.
In another aspect, the invention provides sequence-specific polynucleotide probes or primers that hybridizes to a segment of a mycobacterial rpoB sequence shown in Table 1 or its complement without hybridizing to the M. tuberculosis sequence designated ATCC9-Mtb in Table 1 or its complement, the segment including a highlighted nucleotide position shown in Table 1. In some such probes, a central position of the probe aligns with a highlighted nucleotide position shown in Table 1. In some such primers, the 3′ end of the primer aligns with a highlighted nucleotide position shown in Table 1. Some probes and primers are between 10 and 50 bases long.
In another aspect, the invention provides a computer-readable storage medium for storing data for access by an application program being executed on a data processing system. Such a system comprises a data structure stored in the computer-readable storage medium. The data structure includes information resident in a database used by the application program and includes a plurality of records, each record comprising information identifying a polymorphism or sequence shown in Table 1. Some records have a field identifying a base occupying a polymorphic site and a field identifying location of the polymorphic site. Some records record a contiguous segment of at least 50, 100, or 200 bases from an rpoB sequence shown in Table 1. Some storage medium comprise at least ten records each recording a contiguous segment of at least 50 bases from at least ten rpoB sequences shown in Table 1.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1: Computer that may be utilized to execute software embodiments of the present invention.
FIG. 2: A system block diagram of a typical computer system that may be used to execute software embodiments of the invention.



DEFINITIONS
A polynucleotide can be DNA or RNA, and single- or double-stranded. Polynucleotide can be naturally occurring or synthetic, and can be of any length. Preferred polynucleotide probes of the invention include contiguous segments of DNA, or their complements including any of the highlighted bases shown in Table 1. The segments are usually between 5 and 100 bases, and often between 5–10, 5–20, 10–20, 10–50, 20–50 or 20–100 bases. The highlighted site can occur within any position of the segment. Preferred polynucleotide probes are capable of binding in a base-specific manner to a complementary strand of nucleic acid. Such probes include peptide nucleic acids, as described in Nielsen et al., Science 254, 1497–1500 (1991), and probes having nonnaturally occurring bases.
The term primer refers to a single-stranded polynucleotide capable of acting as a point of initiation of template-directed DNA synthesis under appropriate conditions (i.e., in the presence of four different nucleoside triphosphates and an agent for polymerization, such as, DNA or RNA polymerase or reverse transcriptase) in an appropriate buffer and at a suitable temperature. The appropriate length of a primer depends on the intended use of the primer but typically ranges from 15 to 30 nucleotides. Short primer molecules generally require cooler temperatures to form sufficiently stable hybrid complexes with the template. The term primer site refers to the area of the target DNA to which a primer hybridizes. The term primer pair means a set of primers including a 5′ upstream primer that hybridizes with the 5′ end of the DNA sequence to be amplified and a 3′, downstream primer that hybridizes with the complement of the 3′ end of the sequence to be amplified.
A cDNA or cRNA is derived from an RNA if it produced by a process in which the RNA serves as a template for production of the cDNA or cRNA.
Hybridizations are usually performed under stringent conditions, for example, at a salt concentration of no more than 1 M and a temperature of at least 25° C. For example, conditions of 5×SSPE (750 mM NaCl, 50 mM Na Phosphate, 5 mM EDTA, pH 7.4) and a temperature of 25–30° C. are suitable for allele-specific probe hybridizations.
An isolated nucleic acid means an object species invention that is the predominant species present (i.e., on a molar basis it is more abundant than any other individual species in the composition). Preferably, an isolated nucleic acid comprises at least about 50, 80 or 90 percent (on a molar basis) of all macromolecular species present. Most preferably, the object species is purified to essential homogeneity (contaminant species cannot be detected in the composition by conventional detection methods).
For sequence comparison and homology determination, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see generally, Ausubel et al., infra).
One example of algorithm that is suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm, which is described in Altschul et al., J. Mol. Biol. 215:403–410 (1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915).
In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul (1993) Proc. Nat'l. Acad. Sci. USA 90:5873–5787). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
The term “target nucleic acid” refers to a nucleic acid (often derived from a biological sample), to which the probe nucleic acid is designed to specifically hybridize. It is the presence or expression level of the target nucleic acid that is to be detected or quantified. The target nucleic acid has a sequence that is complementary to the nucleic acid sequence of the corresponding probe directed to the target. The term target nucleic acid may refer to the specific subsequence of a larger nucleic acid to which the probe is directed or to the overall sequence (e.g. gene or mRNA) whose expression level it is desired to detect. The difference in usage will be apparent from context.
“Subsequence” refers to a sequence of nucleic acids that comprise a part of a longer sequence of nucleic acids.
DETAILED DESCRIPTION
I. Mycobacterial Sequences of rpoB Genes
Table 1 shows a comparison of a substantial collection of mycobacterial strains of an about 700-nucleotide conserved region of an rpoB gene. The sequences shown in Table 1 are identified as follows: SEQ ID NOS: 1–56, respectively, are shown on pages 21, 25, 29, 33, 37, 41, 45, 49, 53, 57, 61 and 65; SEQ ID NOS: 57–112, respectively, are shown on pages 22, 26, 30, 34, 38, 42, 46, 50, 54, 58, 62 and 65; SEQ ID NOS: 113–168, respectively, are shown on pages 23, 27, 31, 35, 39, 43, 47, 51, 55, 59, 63 and 66; SEQ ID NOS: 169–181, respectively, are shown on pages 24, 28, 32, 36, 40, 44, 52, 56, 60, 64 and 68. The first sequence, designated as a reference sequence, is from M. tuberculosis. Nucleotides are numbered consecutively starting from the first nucleotide of the reference sequences. Other sequences are from other strains of mycobacteria. For example, the sequences designated ATCC-av, M29, M30 . . . M104 are from M. avium. Sequences designated from ATT-chelnew, M11, M13, and 17 are from M. chelonae. Sequences designated ATCC—for, M53, M55, M56, and M74 are from M. fortuitum, and so forth. Complete correspondence between strain designations and strain types is shown in Table 2. Nucleotides in a mycobacterial sequence are accorded the same number as the corresponding position of the reference sequence when the two are maximally aligned. Differences between a sequence and the reference sequences are shown in highlighted type. Many of the highlighted positions are common to all tested members of a species. Other highlighted positions vary among different isolates in a species. Both types of variation can be useful in speciation analysis.
II. Analysis of Species Variations
A. Preparation of Samples
An rpoB sequence is isolated from a sample of an unknown mycobacteria being tested. Nucleic acids can be isolated from myobacteria by standard methods as described in WO 97/29212 (incorporated by reference in its entirety for all purposes). The rpoB sequences to be analyzed can then be isolated and amplified by means of PCR. See generally PCR Technology: Principles and Applications for DNA Amplification (ed. H. A. Erlich, Freeman Press, NY, N.Y., 1992); PCR Protocols: A Guide to Methods and Applications (eds. Innis, et al., Academic Press, San Diego, Calif., 1990); Mattila et al., Nucleic Acids Res. 19, 4967 (1991); Eckert et al., PCR Methods and Applications 1, 17 (1991); PCR (eds. McPherson et al., IRL Press, Oxford); and U.S. Pat. No. 4,683,202 (each of which is incorporated by reference for all purposes). Primers for PCR preferably flank the regions of interest rpoB genes, although primers to internal sites can be used if it is intended to analyze only certain sites of potential species variation. Exemplary primers are described in WO 97/29212. If necessary, additional sequences flanking the sequences shown in Table 1 can be determined using probes based on the sequences in Table 1 to isolate full-length rpoB sequences from the appropriate mycobacterial species.
B. Detection of Species-Specific Variations in Target DNA
1. Sequence-Specific Probes
The design and use of sequence-specific probes for analyzing polymorphisms is described by e.g., Saiki et al., Nature 324, 163–166 (1986); Dattagupta, E P 235,726, Saiki, WO 89/11548. Sequence-specific probes can be designed that hybridize to a segment of target DNA in one isolate of mycobacteria that do not isolate to a corresponding isolate in another due to the presence of allelic or species variations in the respective segments from the two sequences. Hybridization conditions should be sufficiently stringent that there is a significant difference in hybridization intensity between alleles, and preferably an essentially binary response, whereby a probe hybridizes to only one of the sequences. Some probes are designed to hybridize to a segment of target DNA such that the site of potential sequence variation aligns with a central position (e.g., in a 15 mer at the 7 position; in a 16 mer, at either the 8 or 9 position) of the probe. This design of probe achieves good discrimination in hybridization between different allelic and species variants.
Sequence-specific probes are often used in pairs, one member of a pair showing a perfect match to a reference form of a target sequence and the other member showing a perfect match to a variant form. Several pairs of probes can then be immobilized on the same support for simultaneous analysis of multiple potential variations within the same target sequence.
2. Tiling Arrays
The bases occupying sites of potential variation can also be identified by hybridization to nucleic acid arrays, some example of which are described by WO 95/11995 (incorporated by reference in its entirety for all purposes). Such arrays contain a series of overlapping probes spanning a reference sequence. Any of the rpoB sequences shown in Table 1, or contiguous segments of, for example, at least 25, 50, 100 or 200 bases thereof, can serve as a reference sequence. WO 95/11995 also describes subarrays that are optimized for detection of a variant forms of a precharacterized polymorphism. Such a subarray contains probes designed to be complementary to a second reference sequence, which is a variant of the first reference sequence. The inclusion of a second group (or further groups) can be particular useful for analyzing short subsequences of the primary reference sequence in which multiple mutations are expected to occur within a short distance commensurate with the length of the probes (i.e., two or more mutations within 9 to 21 bases).
3. Sequence-Specific Primers
A sequence-specific primer hybridizes to a site on target DNA overlapping a polymorphism and only primes amplification of a variant form to which the primer exhibits perfect complementarily. See Gibbs, Nucleic Acid Res. 17, 2427–2448 (1989). This primer is used in conjunction with a second primer which hybridizes at a distal site. Amplification proceeds from the two primers leading to a detectable product signifying the particular variant form is present. A control is usually performed with a second pair of primers, one of which shows a single base mismatch at the site of variation and the other of which exhibits perfect complementarily to a distal site. The single-base mismatch prevents amplification and no detectable product is formed. The method works best when the mismatch is included in the 3′-most position of the primer aligned with the point of variation because this position is most destabilizing to elongation from the primer. See, e.g., WO 93/22456.
4. Direct-Sequencing
The direct analysis of mycobacterial sequences can be accomplished using either the dideoxy chain termination method or the Maxam Gilbert method (see Sambrook et al., Molecular Cloning, A Laboratory Manual (2nd Ed., CSHP, New York 1989); Zyskind et al., Recombinant DNA Laboratory Manual, (Acad. Press, 1988)).
III. Methods of Use
The sequences and polymorphisms shown in Table 1 are useful for identifying the presence of myobacteria in samples, and optionally, classifying the mycobacteria. The sample can be obtained from a patient or from a biological source, such as a food product.
The sequences shown in Table 1 can be used for design of sequence-specific probes or primers encompassing polymorphic sites as described above. These probes or primers can then be used to determine the base occupying a corresponding position in an rpoB sequence from an isolate in a sample under test. A base in one sequence corresponds with a base in another when the two bases occupy the same position when the two sequences are maximally aligned by one of the criteria described in Definitions.
Alternatively, the sequences shown in Table 1 can be used for design of tiling arrays in which one or more of the sequences serves as a reference sequence. At least one set of overlapping probes is designed spanning a segment of the reference sequence, as described in WO95/11995 or EP 717,113. Target sequences from samples under test can be hybridized to such arrays, optionally in combination with controls of known rpoB sequences. The hybridization pattern of a target sequence to such an array can be analyzed to determine the identity of bases at which the target sequence differs from the reference sequence, as described in WO 95/11995.
One or more of the above methods, or direct sequencing, can be used to identify the base occupying at least one and usually several (e.g., 5, 10, 15, 25, 50 or 100) sites of potential variation between the 16S RNA and/or rpoB gene in an unknown mycobacteria relative to bases occupying corresponding sites in one or more known strains of mycobacteria, such as those shown in Table 1. This analysis results in a profile of bases occupying particular sites that characterizes the mycobacterial strain under test. The profile is compared with the corresponding profiles of different mycobacterial isolates shown in e.g., Table 1. In general, the unknown mycobacterium isolate is characterized as being from the same mycobacterial species as the precharacterized isolate with which it shares the greatest similarity in base profile.
In some methods, the sequence of a contiguous segment of the rpoB target nucleic acid is determined in a sample under test for comparison with one or more of the sequences shown in Table 1. The mycobacteria is classified by the extent of similarity. For example, if a target nucleic acid shows greater sequence identity to rpoB sequences from one species than any other, the sample from which the target was obtained is typically classified as arising from that species.
Alternatively, an array of tiled probes based on a reference sequence shown in Table 1 can be used for identifying and characterizing mycobacterial sequences based on comparison of hybridization patterns. Such an array is hybridized to a 16S RNA or rpoB target sequence from a sample, and the hybridization pattern compared with the hybridization pattern of one or more control sequences. The hybridization patterns of control sequences can be historic controls, stored, for example, in a computer database, or can be contemporaneous controls performed at or near the same time as the hybridization to the target sequence. Optionally, hybridization of target and reference sequence can be performed simultaneously using different labels.
Method of classifying unknown mycobacterial isolate by matching the hybridization pattern of a target sequence with those of control sequences from characterized species are described in more detail in WO 97/29212 (incorporated by reference in its entirety for all purposes). In an idealized case, the detection of a particular hybridization pattern in an isolate characterizes that isolate as belonging to a particular species. This can occur when the hybridization pattern detected in the isolate is uniquely associated with a specific species. More frequently however, such an unique one-to-one correspondence is not present. Instead, the hybridization pattern observed in an isolate does not bear a unique correspondence with a previously characterized species. However, the hybridization pattern detected is associated with a probability of the organism being screened belonging to a particular species (or not) or carrying a particular phenotypic trait (or not). As a result, analysis of an increasing number of polymorphic sites in an isolate, allows one to classify the isolated with an increasing level of confidence. Algorithms can be used to derive such composite probabilities from the comparison of multiple polymorphic forms between an isolate and references. Typically, the mathematical algorithm makes a call of the identity of the species and assign a confidence level to that call. One can determine the confidence level (>90%, >95% etc.) that one desires and the algorithm will analyze the hybridization pattern and either provide an identification or not. Occasionally, the call is that the sample may be one of two, three or more species, in which case a specific identification is not be possible. However, one of the strengths of this technique is that the rapid screening made possible by the chip-based hybridization allows one to continuously expand a database of patterns ultimately to enable the identification of species previously unidentifiable due to lack of sufficient information.
IV. Modified Polypeptides and Gene Sequences
The invention further provides variant forms of nucleic acids and corresponding proteins. The nucleic acids comprise one of the sequences described in Table 1. Some nucleic acid encode full-length variant forms of proteins. Variant proteins have the prototypical amino acid sequences of encoded by nucleic acid sequence shown in Table 1 (read so as to be in-frame with the full-length coding sequence of which it is a component).
Variant genes can be expressed in an expression vector in which a variant gene is operably linked to a native or other promoter. Usually, the promoter is a eukaryotic promoter for expression in a mammalian cell. The transcription regulation sequences typically include a heterologous promoter and optionally an enhancer which is recognized by the host. The selection of an appropriate promoter, for example trp, lac, phage promoters, glycolytic enzyme promoters and tRNA promoters, depends on the host selected. Commercially available expression vectors can be used. Vectors can include host-recognized replication systems, amplifiable genes, selectable markers, host sequences useful for insertion into the host genome, and the like.
The means of introducing the expression construct into a host cell varies depending upon the particular construction and the target host. Suitable means include fusion, conjugation, transfection, transduction, electroporation or injection, as described in Sambrook, supra. A wide variety of host cells can be employed for expression of the variant gene, both prokaryotic and eukaryotic. Suitable host cells include bacteria such as E. coli, yeast, filamentous fungi, insect cells, mammalian cells, typically immortalized, e.g., mouse, CHO, human and monkey cell lines and derivatives thereof. Preferred host cells are able to process the variant gene product to produce an appropriate mature polypeptide. Processing includes glycosylation, ubiquitination, disulfide bond formation, general post-translational modification, and the like.
The protein may be isolated by conventional means of protein biochemistry and purification to obtain a substantially pure product, i.e., 80, 95 or 99% free of cell component contaminants, as described in Jacoby, Methods in Enzymology Volume 104, Academic Press, New York (1984); Scopes, Protein Purification, Principles and Practice, 2nd Edition, Springer-Verlag, New York (1987); and Deutscher (ed), Guide to Protein Purification, Methods in Enzymology, Vol. 182 (1990). If the protein is secreted, it can be isolated from the supernatant in which the host cell is grown. If not secreted, the protein can be isolated from a lysate of the host cells.
In addition to substantially full-length polypeptides expressed by variant genes, the present invention includes biologically active fragments of the polypeptides, or analogs thereof, including organic molecules which simulate the interactions of the peptides. Biologically active fragments include any portion of the full-length polypeptide which confers a biological function on the variant gene product, including ligand binding, and antibody binding. Ligand binding includes binding by nucleic acids, proteins or polypeptides, small biologically active molecules, or large cellular structures.
Polyclonal and/or monoclonal antibodies that specifically bind to variant gene products but not to corresponding prototypical gene products are also provided. Antibodies can be made by injecting mice or other animals with the variant gene product or synthetic peptide fragments thereof. Monoclonal antibodies are screened as are described, for example, in Harlow & Lane, Antibodies, A Laboratory Manual, Cold Spring Harbor Press, New York (1988); Goding, Monoclonal antibodies, Principles and Practice (2d ed.) Academic Press, New York (1986). Monoclonal antibodies are tested for specific immunoreactivity with a variant gene product and lack of immunoreactivity to the corresponding prototypical gene product. These antibodies are useful in diagnostic assays for detection of the variant form, or as an active ingredient in a pharmaceutical composition.
V. Kits
The invention further provides kits comprising at least one sequence-specific probe as described above. Often, the kits contain one or more pairs of sequence-specific probes hybridizing to different forms of a polymorphism. In some kits, the sequence-specific probes are provided immobilized to a substrate. For example, the same substrate can comprise sequence-specific probes for detecting at least 10, 100 or all of the variations shown in Table 1. Optional additional components of the kit include, for example, restriction enzymes, reverse-transcriptase or polymerase, the substrate nucleoside triphosphates, means used to label (for example, an avidin-enzyme conjugate and enzyme substrate and chromogen if the label is biotin), and the appropriate buffers for reverse transcription, PCR, or hybridization reactions. Usually, the kit also contains instructions for carrying out the methods.
VI. Computer Databases
FIG. 1 illustrates an example of a computer system that can be used to store records relating to polymorphisms of the invention and perform algorithms comparing polymorphic profiles and to classify species. FIG. 2 shows a computer system 100 which includes a monitor 102, screen 104, cabinet 106, keyboard 108, and mouse 110. Mouse 110 may have one or more buttons such as mouse buttons 112. Cabinet 106 houses a CD-ROM drive 114, a system memory and a hard drive (see FIG. 2) which can be utilized to store and retrieve software programs incorporating code that implements the present invention, data for use with the present invention, and the like. Although a CD-ROM 116 is shown as an exemplary computer readable storage medium, other computer readable storage media including floppy disks, tape, flash memory, system memory, and hard drives may be utilized. Cabinet 106 also houses familiar computer components such as a central processor, system memory, hard disk, and the like.
FIG. 2 shows a system block diagram of computer system 100 that may be used to execute software embodiments of the present invention. As in FIG. 1, computer system 100 includes monitor 102 and keyboard 108. Computer system 100 further includes subsystems such as a central processor 102, system memory 120, I/O controller 122, display adapter 124, removable disk 126 (e.g., CD-ROM drive), fixed disk 128 (e.g., hard drive), network interface 130, and speaker 132. Other computer systems suitable for use with the present invention may include additional or fewer subsystems. For example, another computer system can include more than one processor 102 (i.e., a multi-processor system) or a cache memory.
Arrows such as 134 represent the system bus architecture of computer system 100. However, these arrows are illustrative of any interconnection scheme serving to link the subsystems. For example, a local bus can be utilized to connect the central processor to the system memory and display adapter. Computer system 100 shown in FIG. 1 is but an example of a computer system suitable for use with the present invention.
The computer stores records relating to the polymorphisms of the record. Some such records record a polymorphism by reference to the position of a polymorphic site and the identity of base(s) occupying that site in one or more species. Some databases include records for at least ten polymorphic sites in at least ten of the sequences shown in Table 1. Some databases include records for all of the polymorphic sites in at least one of the sequences shown in Table 1. Some databases includes records for at least 100, 1000, or 2000 polymorphic sites shown in Table 1. Some databases include records for all of the polymorphic sites shown in Table 1.
The foregoing invention has been described in some detail by way of illustration and example, for purposes of clarity and understanding. It will be obvious to one of skill in the art that changes and modifications may be practiced within the scope of the appended claims. Therefore, it is to be understood that the above description is intended to be illustrative and not restrictive. The scope of the invention should, therefore, be determined not with reference to the above description, but should instead be determined with reference to the following appended claims, along with the full scope of equivalents to which such claims are entitled.
All patents, patent applications and publications cited in this application are hereby incorporated by reference in their entirety for all purposes to the same extent as if each individual patent, patent application or publication were so individually denoted.







TABLE 1







BASE NOS 1–60

















































 







BASE NOS 61–120

















































 







BASE NOS 121–180

















































 







BASE NOS 181–240

















































 







BASE NOS 241–300

















































 







BASE NOS 301–360

















































 







BASE NOS 361–420

















































 







BASE NOS 421–480

















































 







BASE NOS 481–540

















































 







BASE NOS 541–600

















































 







BASE NOS 600–660

















































 







BASE NOS 660–720


































































TABLE 2





Affy#
SAMPLE ID#
Alt. ID
SPECIES







MY621

ATCC
M. abscessus


ATCC1
25291
ATCC-av
M. avium


M100
60300
MAC
M. avium


M101
60112
MAC
M. avium


M102
60268
MAC
M. avium


M103
60270
MAC
M. avium


M104
60272
MAC
M. avium


M105
60293
MAC
M. avium


M106
60313
MAC
M. avium


M107
60345
MAC
M. avium


M29
95-1764

M. avium


M30
95-1766

M. avium


M31
95-1768

M. avium


M32
95-1770

M. avium


M33
95-1775

M. avium


M34
95-1776

M. avium


M48
95-1765

M. avium


M49
95-1769

M. avium


M63
MAC #1
MAC
M. avium


M64
MAC #2
MAC
M. avium


M65
MAC #3
MAC
M. avium


M67
MAC #5
MAC
M. avium


M69
MAC #7
MAC
M. avium


M70
MAC #8
MAC
M. avium


M71
MAC #9
MAC
M. avium


M72
MAC #10
MAC
M. avium


M91
FM
avium-intracell.
M. avium




FM(MAC)


M92
60040
MAC
M. avium


M93
60042
MAC
M. avium


M94
60049
MAC
M. avium


M95
60051
MAC
M. avium


M96
60110
MAC
M. avium


M97
60116
MAC
M. avium


M98
60123
MAC
M. avium


M99
60176
MAC
M. avium


M76
92-773

M. bovis


MY451


M. bovis


ATCC2
35752
ATCC-chel(new)
M. chelonae


M10
95A9151

M. chelonae


M11
95A0477

M. chelonae


M115
60121

M. chelonae


M116
52942

M. chelonae


M117
43192

M. chelonae


M118
53180

M. chelonae


M119
53131

M. chelonae


M12
95A4883

M. chelonae


M120
52923

M. chelonae


M121
52919

M. chelonae


M13
95A2611

M. chelonae


M14
95A0779

M. chelonae


M15
95A8654

M. chelonae


M16
95A8882

M. chelonae


M17
95A8881

M. chelonae


M50
95A11814

M. chelonae


M51
95A1102

M. chelonae


M75
#13
MAC#13
M. chelonae


MY109


M. chelonae


MY200


M. chelonae


MY207


M. chelonae


MY209


M. chelonae


M122
60025

M. flavescens


M123
60076

M. flavescens


M124
60252

M. flavescens


ATCC3
6841
ATCC-for
M. fortuitum


M53
60305

M. fortuitum


M54
60344

M. fortuitum


M55
60435

M. fortuitum


M56
60447

M. fortuitum


M74
#12
MAC#12
M. fortuitum


M88
CH
fort. CH
M. fortuitum


MY221


M. fortuitum


MY223


M. fortuitum


MY225


M. fortuitum


MY341


M. fortuitum


MY715


M. fortuitum


MY470


M. genevese


ATCC4
14470
ATCC-go
M. gordonae


ATCC4-0

gord.
M. gordonae


M125
60068

M. gordonae


M126
60182

M. gordonae


M127
60214

M. gordonae


M128
60283

M. gordonae


M78
92-942
gord. LZ
M. gordonae


M79
93-692
gord. JD
M. gordonae


M80
94-94
gord. LG
M. gordonae


M81
93-1231
gord. LL
M. gordonae


M82
93-463
gord. RM
M. gordonae


M83
92-1219
gord. MB
M. gordonae


M84
91-1131
gord. OW
M. gordonae


M85
91-1478
gord. LB
M. gordonae


M86
92-642
gord. RB
M. gordonae


M87
93-1180
gord. WN
M. gordonae


M90
DB
gord. DB
M. gordonae


MY103


M. gordonae


MY475


M. gordonae


MY476


M. gordonae


MY746


M. gordonae


MY830


M. gordonae


ATCC5

ATCC-int
M. intracellulare


ATCC5-0

intra
M. intracellulare


M16
95-1778

M. intracellulare


M19
95-1780

M. intracellulare


M20
95-1781

M. intracellulare


M21
95-1782

M. intracellulare


M22
95-1790

M. intracellulare


M23
95-1794

M. intracellulare


M24
95-1796

M. intracellulare


M25
95-1777

M. intracellulare


M26
95-1779

M. intracellulare


M27
95-1760

M. intracellulare


M28
95-1761

M. intracellulare


ATCC6
12478
ATCC-kan
M. kansasii


ATCC6-0

kans.
M. kansasii


M1
95A5375

M. kansasii


M2
95A10299

M. kansasii


M3
95A0020

M. kansasii


M4
95A3977

M. kansasii


M5
95A4739

M. kansasii


M52
95A5381

M. kansasii


M57
60163

M. kansasii


M58
60180

M. kansasii


M59
60207

M. kansasii


M6
95A2695

M. kansasii


M60
60294

M. kansasii


M61
60308

M. kansasii


M62
60314

M. kansasii


M7
95A2694

M. kansasii


M73
#11
MAC#11
M. kansasii


M8
94A9042

M. kansasii


M9
95A1275

M. kansasii


MY106


M. kansasii


MY141


M. kansasii


MY216


M. kansasii


MY226


M. kansasii


M108
60044

M. maimoense


M109
60149

M. maimoense


M110
60211

M. maimoense


M111
60202

M. maimoense


M112
60085

M. maimoense


M113
60047

M. maimoense


M114
60185

M. maimoense


MY325

ATCC
M. maimoense


MY718

maimo
M. maimoense


MY214


M. marinum


MY224


M. marinum


MY244


M. marinum


MY339


M. marinum


MY343


M. marinum


MY458

ATCC
M. mucogenicum


MY809


M. mucogenicum


MY817


M. mucogenicum


MY821


M. mucogenicum


MY824


M. mucogenicum


MY102


M. nonchromagenicum


MY105


M. nonchromagenicum


MY251


M. nonchromagenicum


MY256


M. nonchromagenicum


MY294


M. nonchromagenicum


ATCC7
19981
ATCC-scr
M. scrofulaceum


ATCC7-0

scrof.
M. scrofulaceum


MY121


M. scrofulaceum


MY249


M. scrofulaceum


MY372


M. scrofulaceum


MY378


M. scrofulaceum


MY484


M. simiae


MY555


M. simiae


MY563


M. simiae


MY586


M. simiae


ATCC8
19420
ATCC-sme
M. smegmatis


M35
95A1072

M. smegmatis


M36
95A8183

M. smegmatis


M37
95A4990

M. smegmatis


M77
92-144
smeg. JL
M. smegmatis


MY143

ATCC
M. smegmatis


MY104


M. szulgai


MY196


M. szulgai


MY357


M. szulgai


MY358


M. szulgai


MY480


M. szulgai


TB74
C.17.96.5

M. tab M160 DR


MY387


M. tb


MY418


M. tb


MY437


M. tb


MY462


M. tb


TB59
C.18.96.1

M. tb H37rv DR


TB67
C.18.96.1

M. tb H37rv DR


TB73
C.17.96.1

M. tb H37rv DR


TB60
C.18.96.2

M. tb J35 DR


TB65
C.22.96.9

M. tb M101 DR


TB62
C.18.96.4

M. tb M104 DR


TB69
C.18.96.3

M. tb M104 DR


TB72
C.18.96.7

M. tb M104 DR


TB66
C.22.96.10

M. tb M112 DR


TB63
C.18.96.5

M. tb M140 DR


TB64
C.18.96.6

M. tb M160 DR


TB70
C.18.96.4

M. tb M160 DR


TB61
C.18.96.3

M. tb M60 DR


TB68
C.18.96.2

M. tb M60 DR


TB71
C.18.96.6

M. tb M60 DR


MY212


M. terrae


MY354


M. terrae


MY491


M. terrae


MY497


M. terrae


MY816


M. triplex


ATCC9
27294
Mtb
M. tuberculosis


ATCC9-0

TB2020
M. tuberculosis


N/A
93-1071

M. tuberculosis


N/A
93-336

M. tuberculosis


N/A
92-852

M. tuberculosis


N/A
92-1005

M. tuberculosis


N/A
92-243

M. tuberculosis


N/A
92-304

M. tuberculosis


N/A
92-199

M. tuberculosis


N/A
92-197

M. tuberculosis


N/A
92-484

M. tuberculosis


N/A
94-577

M. tuberculosis


TB1
936

M. tuberculosis


TB10
1122

M. tuberculosis


TB11
3407

M. tuberculosis


TB12
978

M. tuberculosis


TB13
3553

M. tuberculosis


TB14
3468

M. tuberculosis


TB15
2163

M. tuberculosis


TB16
DW
DW
M. tuberculosis


TB17
CB
CB
M. tuberculosis


TB18
PB
PB
M. tuberculosis


TB19
AA
AA
M. tuberculosis


TB2
M0404A

M. tuberculosis


TB20
3492

M. tuberculosis


TB21
1435

M. tuberculosis


TB22
896

M. tuberculosis


TB23
2268

M. tuberculosis


TB24
3455

M. tuberculosis


TB25
37

M. tuberculosis


TB26
173

M. tuberculosis


TB27
230

M. tuberculosis


TB28
2519

M. tuberculosis


TB29
T29233

M. tuberculosis


TB3
1231

M. tuberculosis


TB30
SP
SP
M. tuberculosis


TB31
3201

M. tuberculosis


TB32
3219

M. tuberculosis


TB33
80

M. tuberculosis


TB34
3442

M. tuberculosis


TB35
3502

M. tuberculosis


TB36
3759

M. tuberculosis


TB37
1295

M. tuberculosis


TB38
337

M. tuberculosis


TB39
394

M. tuberculosis


TB4
914

M. tuberculosis


TB40
499

M. tuberculosis


TB41
535

M. tuberculosis


TB42
607

M. tuberculosis


TB43
707

M. tuberculosis


TB44
692

M. tuberculosis


TB45
2408

M. tuberculosis


TB46
1069

M. tuberculosis


TB47
M3262A

M. tuberculosis


TB48
1338

M. tuberculosis


TB49
1368

M. tuberculosis


TB5
1145

M. tuberculosis


TB50
65

M. tuberculosis


TB51
727

M. tuberculosis


TB52
3455

M. tuberculosis


TB53
3506

M. tuberculosis


TB54
9600387

M. tuberculosis


TB55
9600173

M. tuberculosis


TB56
9503471

M. tuberculosis


TB57
9600309

M. tuberculosis


TB58
9600230

M. tuberculosis


TB6
1417

M. tuberculosis


TB7
SM2341

M. tuberculosis


TB75
2098

M. tuberculosis


TB76
173/1

M. tuberculosis


TB77
1122/1

M. tuberculosis


TB78
1417/1

M. tuberculosis


TB8
1587

M. tuberculosis


TB9
M7032A

M. tuberculosis


ATCC10
19250
ATCC-xen
M. xenopi


M129
60133

M. xenopi


M130
60200

M. xenopi


M131
60365

M. xenopi


M132
60387

M. xenopi


M38
95A5208

M. xenopi


M39
95A5399

M. xenopi


M40
95A3938

M. xenopi


M41
95A6762

M. xenopi


M42
95A0933

M. xenopi


M43
95A4320

M. xenopi


M44
95A3478

M. xenopi


M45
95A2997

M. xenopi


M46
95A8383

M. xenopi


M47
95A4319

M. xenopi


M68
MAC #6
MAC #6
M. xenopi


M69
SG
xen. SG
M. xenopi


MY219


M. xenopi


MY250


M. xenopi


MY252


M. xenopi


MY254


M. xenopi


MY255


M. xenopi


MY107


MAC


MY111


MAC


MY112


MAC


MY312


MAC


M66
MAC #4
MAC #4
unique

## Claims

1. An isolated rpoB nucleic acid fragment of a molecule consisting of a sequence selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5, 6, 8, 9 and 10, wherein said fragment consists of at least about 100 contiguous bases of said sequence.

2. An isolated nucleic acid molecule consisting of a rpoB sequence selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9 and 10.

3. An isolated probe which is the full complement of a rpoB sequence selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9, and 10.

4. A method of classifying a mycobacteria, comprising
providing a sample comprising a mycobacterial rpoB target nucleic acid from a mycobacteria;
determining the sequence of a segment of at least 50 contiguous bases from the target nucleic acid;
comparing the determined sequence to at least one sequence selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9, and 10; and
classifying the mycobacteria from the extent of similarity of the compared sequences.

5. The method of claim 4, wherein at least 100 contiguous bases are determined from the target nucleic acid.

6. The method of claim 4, wherein the determined sequence is compared with at least nine sequences selected from the group consisting SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9, and 10.

7. A method of classifying a mycobacteria, comprising
providing a sample comprising a mycobacterial rpoB target nucleic acid;
determining the identity of one or more bases in the target sequence at one or more positions corresponding to one or more bases in a sequence selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9, and 10, wherein the one or more bases of the sequence selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9, and 10 differ from the corresponding one or more bases in SEQ ID NO: 1 when the sequences are maximally aligned, the identity of the one or more bases characterizing the species of mycobacteria that is present in the sample;
comparing the identified one or more bases in the target sequence to at least one sequence selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9, and 10; and
classifying the mycobacteria from the extent of similarity between the one or more bases identified in the target sequence and the corresponding one or more bases in the compared sequences.

8. The method of claim 7, wherein the identity of at least 10 bases in the target nucleic acid at positions corresponding to the one or more bases in the sequence selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9, and 10 is determined.

9. The method of claim 8, wherein the identity of at least 20 bases in the target sequence at positions corresponding to the one or more bases in the sequence selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9, and 10 is determined.

10. The method of claim 9, further comprising comparing the at least 20 determined bases with at least 20 bases occupying corresponding positions in each of at least nine sequences selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9, and 10.