Abstract:
This invention provides probes, chip, kit and method for detection the species of  Mycobacterium tuberculosis  (MTB), non-tuberculosis mycobacteria (NTM) and drug resistant of  Mycobacterium tuberculosis . The purpose of this present invention is archived by hybridization reaction of said probes being selected from the group consisting of SEQ ID NO: 3˜23 and 26˜36. Efficient and one-step detection for determining the species of NTM, MTB and drug resistance of MTB is achieved via hybridization of probes with specific DNA fragments in MTB, NTM and MTB B acquiring drug resistance potency.

Description:
BACKGROUND OF THE INVENTION 
       [0001]    1. Field of the Invention 
         [0002]    This invention relates to the field of mycobacteria detection, specially relates to probe, chip, kit and method for detection of mycobacterial nucleic acid in biological sample. 
         [0003]    2. Description of the Related Art 
         [0004]      Mycobacterium  genus includes  Mycobacterium tuberculosis  complex (MTB) and non-tuberculous mycobacteria (NTM). MTB includes  M. tuberculosis, M. africanum, M. bovis  etc, and the other species in  Mycobacterium  genus are all categorized in NTM. So far, there are more than one hundred of identified species of NTM. 
         [0005]    MTB is a major pathogen for human pulmonary tuberculosis, which is a epidemic disease causing the most infected and dead patients in the world. In Taiwan, pulmonary tuberculosis is one of legal infectious diseases. Once a diagnosed patient with pulmonary tuberculosis or a MTB infected patient, it has to be notified to the Department of Health and treated with antibiotics. 
         [0006]    In the treatment of pulmonary tuberculosis, gradually increased ratio of MTB with drug resistance elevated difficulty in curing, either in Taiwan or worldwide, according statistic reports from World Health Organization and Center of Disease Control in Taiwan. Especially, patients having multidrug resistant tuberculosis (MDR-TB) and extensively drug resistant tuberculosis (XDR-TB) require cautious drug delivering approach. 
         [0007]    NTM is a low pathogenic bacteria to human and typically present in the environment. They usually infect human through environmental water, such as condensate water from air conditioner or medical instruments such as ventilator. In clinical, NTM infected patients need not to be announced to the Department of Health. Clinicans have to identify the species of infectious NTM for chosen of appropriated treatment with suitable antibiotics. 
         [0008]    Taken together, diagnosis and identification of  mycobacterium  species and drug resistance are important for clinical management. Therefore, it is helpful to rapidly determine whether MTB drug resistance or identify  mycobacterium  species for clinicans trying to select an adequate regiment for patients. 
         [0009]    Traditionally, species determination of MTB or NTM in sample isolated from respiratory specimen, mainly sputum, in hospital is achieved by biochemical method which spends 1˜2 months with complex processes. Recently, large-scale hospitals identify MTB and NTM in samples by using BACTEC MGIT 960 system and BD ProbeTec™ ET  Mycobacterium tuberculosis  Complex (CTB) Culture Identification Reagent Pack (Becton Dickinson) within 1˜2 weeks. However, bacterial culture and biochemical identifying method are required to identify the species of NTM. Conventional biochemical methods take times and also frequently interfered by artificial interpretation. In addition, the cost in instruments and reagents for automatic detection, bacterial culture and analysis are too expensive to generally apply in all hospitals. 
         [0010]    In previous study, Telenti et al. had established database of NTM restriction map by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP), which is also known as fragment restriction enzyme analysis (PRA), of NTM hsp65 gene, 65-kilodalton heat shock protein. Species of unknown  mycobacterium  can be identified by comparison of PRA result from unknown  mycobacterium  with this database. (Telenti A, Marchesi F, Balz M, Bally F, Bottger E C, Bodmer T. 1993. Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol 31(2):175-178.) 
         [0011]    Kim et al. had analyzed rpoB gene, polymerase β-subunit-encoding, with PRA (Kim B J, Lee K H, Park B N, Kim S J, Bai G H, Kim S J, Kook Y H. 2001. Differentiation of mycobacterial species by PCR-restriction analysis of DNA (342 base pairs) of the RNA polymerase gene (rpoB). J Clin Microbiol. 39:2102-2109; Kim B J, Hong S K, Lee K H, Yun Y J, Kim E C, Park Y G, Bai G H, Kook Y H. 2004. Differential identification of  Mycobacterium tuberculosis  complex and nontuberculous mycobacteria by duplex PCR assay using the RNA polymerase gene (rpoB). J Clin Microbiol 42(3):1308-12.); and then, cross-reference with growth rate, phenotypic characters and two biochemical tests including Tween 80 hydrolysis test and nitrate reduction test to precisely determine the species of  mycobacterium  (G-H. Shen, C-H. Hung, K-M. Wu, C-H, Chen, C-F. Lin, Y-W. Sun J-H. Chen. Combining the Capilia T B assay with smear morphology for the identification of  Mycobacterium tuberculosis  complex. Int. J. Tuberc. Lung Dis. 2009; 13(3):371-376). However, practical experiences revealed that the erroneous interpretation occurred in determination of the species of NTM resulted from similar size of PCR-RFLP fragments. 
         [0012]    16S-23S rRNA internal transcribed spacer region (ITS) is a transcription region between loci of 16S rRNA and 23S rRNA. There are conserved regions at 5′-end and 3′-end and variant region at central which could be utilized as identification targets for determination of  mycobacterium  species. 
         [0013]    Rifampicin (RIF) could terminate the elongation of translation through binding to the β-subunit of bacterial RNA polymerase encoded from rpoB gene. Previous reports have suggested that the MTB stains exhibiting drug resistance to RIF usually contain mutations in rpoB gene. Therefore, rpoB gene could be utilized as targets to determine the presence of drug resistance in MTB. 
         [0014]    Taiwan Pub, No. 201002825, China Pub. No. 101413031 and China Pub. No. 100368559 disclosed detection techniques using PCR with specific primer sets or probes to identify the species of MTB or NTM; however, these techniques comprise many steps and distinguish MTB and NTM roughly without to identify the species of NTM. U.S. Pat. No. 6,025,132 disclosed specific multiple nucleotide probes to identify the specific  mycobacterium  species exhibiting infectious and pathogenic potential. However, this invention is unable to identify drug resistance of MTB, U.S. Pat. Nos. 6,329,138, 6,632,607 and 7,252,936 also disclosed specific nucleotide probes to determine the sensitivity and resistance of MTB with RIF; however, these inventions are unable to detect the species of NTM at the same time. 
       SUMMARY OF THE INVENTION 
       [0015]    In order to improve said problem, this present invention discloses probe, chip, kit and method for detection the species of  Mycobacterium tuberculosis , non-tuberculosis mycobacteria and drug resistant of  Mycobacterium tuberculosis  to achieve the goal for distinguishing MTB or NTM, identifying the species of NTM, and detecting the drug resistance of MTB by one step manipulation. 
         [0016]    In order to achieve the goal, this present invention provides a composition for detection of  Mycobacterium tuberculosis , non-tuberculosis mycobacteria and drug resistant of  Mycobacterium tuberculosis , comprising a plurality of probes being selected from the group consisting of: SEQ ID NO: 3˜23, 26˜36. 
         [0017]    Wherein, said non-tuberculosis mycobacteria is selected from the group consisting of:  M. abscessus, M. asiaticum, M. avium, M. chelonae, M. fortuitum, M. gordonae, M. intracellulare, M. kansasii, M. lentiflavum, M. malmoense, M. marinum, M. scrofulaceum, M. shimodei, M. szulgai  and  M. xenopi.    
         [0018]    In order to achieve the purpose, this present invention provides a chip for detection of  Mycobacterium tuberculosis , non-tuberculosis mycobacteria and drug resistant of  Mycobacterium tuberculosis , comprising a solid matrix; and a plurality of probes setting on said matrix, and said probes being selected from the group consisting of: SEQ ID NO: 3˜23, 26˜36. 
         [0019]    Wherein, said non-tuberculosis mycobacteria is selected from the group consisting of:  M. abscessus, M. asiaticum, M. avium, M. chelonae, M. fortuitum, M. gordonae, M. intracellulare, M. kansasii, M. lentiflavum, M. malmoense, M. marinum, M. scrofulaceum, M. shimodei, M. szulgai  and  M. xenopi.    
         [0020]    To achieve the purpose, this present invention provides a kit for detection of  Mycobacterium tuberculosis , non-tuberculosis mycobacteria and drug resistant of  Mycobacterium tuberculosis , comprising a plurality of probes being selected from the group consisting of: SEQ ID NO: 3˜23, 26˜36. 
         [0021]    Wherein, said non-tuberculosis mycobacteria is selected from the group consisting of  M. abscessus, M. asiaticum, M. avium, M. chelonae, M. fortuitum, M. gordonae, M. intracellulare, M. kansasii, M. lentiflavum, M. malmoense, M. marinum, M. scrofulaceum, M. shimodei, M. szulgai  and  M. xenopi.    
         [0022]    According to a preferred embodiment of said kit, further comprises a solid matrix for setting said probes, wherein said matrix is polystyrene. 
         [0023]    According to a preferred embodiment of said kit, further comprises a primer set SEQ ID NO:1 and 2. 
         [0024]    According to a preferred embodiment of said kit, further comprises a primer set SEQ ID NO: 24 and 25. 
         [0025]    According to a preferred embodiment of said kit, further comprises a hybridization buffer for appropriate environment to perform hybridization reaction of said probes. 
         [0026]    According to a preferred embodiment of said kit, further comprises a wash buffer to remove residues which do not hybridize with said probes. 
         [0027]    According to a preferred embodiment of said kit, further comprises a streptavidin conjugate alkaline phosphatase to label hybridization products. 
         [0028]    According to a preferred embodiment of said kit, further comprises a dilution buffer for said streptavidin conjugate alkaline phosphatase to avoid non-specific binding with said hybridization products. 
         [0029]    According to a preferred embodiment of said kit, further comprises a detection reagent to present color via interacting with said streptavidin conjugate alkaline phosphatase. 
         [0030]    According to a preferred embodiment of said kit, further comprises a detection buffer to provide required environment for the reaction of color development. 
         [0031]    In order to achieve the purposes, this present invention further provides a method for detection of  Mycobacterium tuberculosis , non-tuberculosis mycobacteria and drug resistant of  Mycobacterium tuberculosis , comprising following steps: (a) amplifying 16S-23S rRNA ITS gene and rpoB gene from sample; (b) providing a plurality of probes to hybridize product from step (a), wherein said probes being selected from the group consisting of: SEQ ID NO: 3˜23, 26˜36; and (c) measuring result of hybridization reaction. 
         [0032]    Wherein, said non-tuberculosis mycobacteria is selected from the group consisting of:  M. abscessus, M. asiaticum, M. avium, M. chelonae, M. fortuitum, M. gordonae, M. intracellulare, M. kansasii, M. lentiflavum, M. malmoense, M. marinum, M. scrofulaceum, M. shimodei, M. szulgai  and  M. xenopi.    
         [0033]    According to a preferred embodiment of said method, wherein two primer sets SEQ ID NO: 1 and 2, 24 and 25 were used for amplification in step (a). 
         [0034]    According to a preferred embodiment of said method, further comprises following steps: (d) spotting said probes on a solid matrix. 
         [0035]    According to these features, this present invention integrates specific probes designed for specific sequence to distinguish MTB versus NTM and the species of NTM. Furthermore, this present invention also provides specific probe for the mutation of drug-resistant MTB. Therefore, this present invention provides a detection technique to determine the species and drug resistance of MTB and NTM in one assay. 
         [0036]    The details about structure, features, assembling or utilizing method of this present invention will further explain in following text. However, above-mentioned specification is only for detailed description with the embodiment of this present invention and shall not be construed as a scope limitation of this present invention 
     
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         [0037]      FIG. 1 . The illustration of probes which are used for determining the  mycobacterium  species and MDR-TB. 
           [0038]    A1, A6, F1 and F6 were positive control spots for hybridization to make sure whether all steps of hybridization reactions were archived. A4 was positive control spot which was utilized for confirming the successful reaction of PCR reaction. C6 was negative control spot to detect the contamination of reagents in different steps. 
           [0039]    B1 was ABS position spotted with ABS probe to detect  M. abscessus. C 1 was ASI position spotted with ASI probe to detect  M. asiaticum . D1 was AVI position spotted with AVI probe to detect  M. avium  spp.  avium . E1 was INT position spotted with INT4 and INT5 probes to detect  M. intracellulare.    
           [0040]    A2 was CHE position spotted with CHE4 probe to detect  M. chelonae . B2 was FOR position spotted with FOR2 and FOR7 probes to detect  M. fortuitum . C2 was GOR position spotted with GOR probe to detect  M. gordonae . D2 was KAN position spotted with KAN1-1 and KAN4 probes to detect  M. kansasii . E2 was LEN position spotted with LEN2 probe to detect  M. lentiflavum . F2 was MAL position spotted with MAL probe to detect  M. malmoense.    
           [0041]    A3 was MAR position spotted with MAR probe to detect  M. marinum . B3 was SCR position spotted with SCR probe to detect  M. scrofulaceum . C3 was SHI position spotted with SHI2 probe to detect  M. shimodei . D3 was SZU position spotted with SZU probe to detect  M. szulgai . E3 was XEN position spotted with XEN probe to detect  M. xenopi . F3 was MYC position spotted with MYC-a and MYC-c probes to detect  Mycobacterium  genus. 
           [0042]    F5 was MTBC position spotted with MTBC probe to detect  M. tuberculosis  complex, A5, B5, C5, D5 and E5 were position on chip to detect wild type  M. tuberculosis  complex. These indicated positions were spotted with probes RW1-1, RW2-1, RW3-4, RW4-3 and RW5-3, respectively. 
           [0043]    C4, D4, E4, B6, D6 and E6 were position on chip to detect the drug resistant strains of  M. tuberculosis  complex with mutations in rpoB gene. These indicated positions were spotted with probes RW4-3, RW4-3a, RW5-2a, RW2-3, RW4-2b and RM5-2b, respectively. 
           [0044]      FIG. 2 . (A) Hybridization reactions of the common probes for MTB and the specific probes for following species:  M. abscessus, M. asiaticum, M. avium, M. intracellulare, M. chelonae, M. fortuitum, M. gordonae, M. kansasii  and  M. lentiflavum.    
           [0045]      FIG. 2 . (B) Hybridization reactions of the common probes for  mycobacterium  genus and the specific probes for following species:  M. malmoense, M. marinum, M. scrofulaceum, M. shimoidei, M. szulgai, M. xenopi, M. mucogenicum, M. flavescens, M. senegalense  and  M. terrae.    
           [0046]      FIG. 3 . Hybridization reactions of the common probes for  mycobacterium  genus, the specific probes for  M. tuberculosis  complex and MDR-TB. 
           [0047]    FIG.  4 .(A) Hybridization reactions of the common probes for  mycobacterium  genus and various specific probes including a probe for mutant rpoB gene of  M. tuberculosis  complex with mutations on codon 511 and codon 526, a probe for mutant rpoB gene of  M. tuberculosis  complex with mutation on codon 516, and a probe for mutant rpoB gene of  M. tuberculosis  complex with mutation on codon 526. 
           [0048]    FIG.  4 .(B) Hybridization reactions of the common probes for  mycobacterium  genus and various specific probes including a probe for mutant rpoB gene of  M. tuberculosis  complex with mutation on codon 526 and codon 529, and a probe for mutant rpoB gene of  M. tuberculosis  complex with mutation on codon 531. 
       
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
       [0049]    The features of this present invention are described in the following examples and figures. 
       Example 1 
     Collection of Mycobacteria Strains 
       [0050]    Reference mycobacteria strains were purchased from American Type Culture Collection (ATCC), MTB strain and comparative strain names were showed in Table 1. Clinical strains were collected from Taichung Veterans General Hospital (Taichung, Taiwan), Chung-Shan Hospital (Taichung, Taiwan), Changhua Christian Hospital (Changhua, Taiwan) and Reference-lab (Taichung, Taiwan). 
         [0051]      Mycobacteria  strains, wherein clinical samples from the respiratory tract of patient in these indicated hospitals or lab, identified by traditional biochemical and molecular methods include 9  M. tuberculosis  complex, 9  M. abscessus,  1  M. asiaticum,  3  M. avium,  3  M. chelonae,  9  M. fortuitum,  9  M. gordonae,  9  M. intracellulare,  9  M. kansasii,  2  M. lentiflavum,  1  M. malmoense,  2  M. marinum,  1  M. scrofulaceum,  2  M. shimodei,  1  M. szulgai and  2  M. xenopi . The strains and species of those strains were shown in Table 1. 
         [0052]    The identification methods utilized including pre-processes of respiratory tract specimens, culture of bacterial clones, identification of acid-fast  bacillus,  traditional biochemical methods and molecular biological methods were briefly described as below. 
         [0053]    1. Pre-Processes of the Samples from Respiratory Tract 
         [0054]    Samples collected from the respiratory tract of patients were digested by NALC (N-acety-L-cysyeine)-2% NaOH decontamination procedure, centrifugal concentration, and sputum dissolving agents first. The processed specimens were culture on Löwenstein-Jensen medium (hereafter “L-J medium”) or Middlebrook 7H11 medium (hereafter “7H11 medium”) in BD BACTEC 960 MGIT tubes (mycobacterial growth indicator tube, hereafter “MGIT tube”). 
         [0055]    2. Culture of Bacterial Strains 
         [0056]    L-J medium and 7H11 medium were incubated at 37° C., 5% CO 2  microbiological incubator. After scanning labels of MGIT tubes by BACTEC MGIT 960 system, MGIT tubes were incubated in incubator. The culture period of BD BACTEC MGIT 960 system is 42 days. Generally, positive signal indicating growth of  mycobacterium  in medium would presence within 7˜10 days while  mycobacterium  exists in samples. 
         [0057]    3. Identification of Acid-Fast  Bacillus    
         [0058]    Acid-fast stain was performed to confirm the existence of mycobacteria when MGIT instrument detected positive signal for the growth of mycobacteria. Morphology of acid-fast  bacillus  was recorded when the existence of  mycobacterium  in MGIT tube was present by positive staining of acid-fast stain. Growth of colony in L-J medium was also compared with the bacterial growth in MGIT tube. Consistent result of colony formation on L-J medium would be utilized to assist the result of bacterial growth in MGIT tube. 
         [0059]    3.1 CTB Analysis 
         [0060]    CTB analysis is utilized a detection kit, BD ProbeTec™ ET  Mycobacterium tuberculosis  complex (CTB) Culture Identification Reagent Pack, developed by Becton Dickinson company for detecting the presence of MTB. In CTB analysis, the existence of MTB was detected by strand displacement amplification (SDA) which amplifies specific repeated sequence IS6110 in MTB and labels amplified DNA fragment with luminescence for detection. The growth of MTB in MGIT tube was detected by manufacturer&#39;s instruction. Positive signal from this assay suggests that existing DNA of MTB in sample tested. 
         [0061]    3.2 Biochemical Assays 
         [0062]    Traditional biochemical assay will be performed to confirm the species of  mycobacterium  when there were more than two specimens detected from the colony in MGIT tube collected from the respiratory specimens of patients. Biochemical assays including Arysulfatase assay, Catalase assay, Tolerance to 5% NaCl assay, Niacin accumulation test, Tween 80 hydrolysis assay, urease assay were performed following the  mycobacterium  laboratory handbook published from Centers for Disease Control, R.O.C., Taiwan, in 2004. 
         [0063]    3.3 PCR-RFLP Identification 
         [0064]    Chromosomal DNA extracted from each bacterial colonies were subjected for PCR to amplify hsp65 gene for restriction enzyme digestion by BstEII and HaeIII. The comparison between the restriction enzyme digestion map with the hsp65 RFLP pattern in the database, which established by Telenti et al., was performed to identify the MTB species (http://app.chuv.ch/prasite/index.html). 
       Experiment 2: PCR Amplification of 16S-23S rRNA ITS Gene in MTB 
       [0065]    Amplification of the region in 16S-23S rRNA ITS locus by PCR reaction was performed with the primer sets Sp1 (SEQ ID NO: 1) and Sp2 (SEQ ID NO: 2) to amplify the common region for all mycobacteria species (Xiong L, Kong F, Yang Y, Cheng J, Gilbert G L. 2006. Use of PCR and reverse line blot hybridization macroarray based on 16S-23S rRNA gene internal transcribed spacer sequences for rapid identification of 34  mycobacterium  species. J Clin Microbiol 44(10):3544-50). 
         [0066]    The single colony of NTM was sampled and re-suspended in 40 μL ddH 2 O which was further heated for 10 minutes to obtain DNA containing supernatant. In addition, DNA of MTB was prepared by  M. tuberculosis  Complex (CTB) Culture Identification Reagent Pack purification kit, BD ProbeTec™ ET, for the further PCR reaction. Total volume of PCR reaction was up to 50 μL which was sequentially added with 28.75 μL of ddH 2 O, 5 μL of DNA template, 1 μL 10 μM. Sp1 primer (SEQ ID NO:1), 1 μL of 10 μM Sp4 (SEQ ID NO:2, wherein Y means T or C), 4 μL of 2.5 mM dNTP, 10 μL of 5× buffer (Promega) and 0.25 μL GO Taq polymerase (5000 units/mL, Promega). Following PCR reaction, gel electrophoresis was performed to detect PCR products which might be 212-300 base pairs dependent on different species of the bacterial colonies (Roth A, Reischl U, Streubel A, Naumann L, Kroppenstedt R M, Habic Fischer M, Mauch H. 2000. Novel diagnostic algorithm for identification of mycobacteriausing genus-specific amplification of the 165-235 rRNA gene spacer and restriction endonucleases. J. Clin Microbiol 38(3):1094-1104.). 
         [0067]    In this experiment, DNA extracted from 16 reference mycobacteria bacterial strain and clinical strains were subjected for PCR reaction. Species, number of strains and size of PCR product were shown in Table 1. below. 
         [0000]    
       
         
               
             
               
               
             
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 The PCR product of ITS gene in the MTB 
               
               
                 standard clone and clinical clone. 
               
             
          
           
               
                   
                 Size 
               
             
          
           
               
                   
                 Analyzed Clone 
                 of PCR 
               
             
          
           
               
                 Species 
                 Clinical clone 
                 Standard clone 
                 product 
               
               
                   
               
               
                 
                   M. tuberculosis 
                 
                 O151            P36            Q136            
                 H37Rv 
                 221 
               
               
                 complex 
                 R54            R195            R205            
               
               
                   
                 S63            S10            S12 
               
               
                 
                   M. abscessus 
                 
                                        4871            type II 
                 ATCC 19977 
                 257 
               
               
                   
                 S19            IS 1-2            type I 
               
               
                   
                 S21            95 CAP-9                       
               
               
                   
                                                              IS 3-2 
               
               
                 
                   M. asiaticum 
                 
                 96-CAP-5 
                 ATCC 25276 
                 220 
               
               
                 
                   M. avium 
                 
                 cch7            cch10            V213 
                 ATCC 25291 
                 219 
               
               
                 
                   M. chelonae 
                 
                 cch 39            V200            95-7 
                 ATCC 35752 
                 257 
               
               
                 
                   M. fortuitum 
                 
                 V61 
                 — 
                 257 
               
               
                   
                 V9            V13            V65 
                 — 
                 280            300 
               
               
                   
                 V7            V12            V16            V23 
                 — 
                 257            300 
               
               
                   
                 V205 
                 — 
                 280 
               
               
                   
                 — 
                 ATCC 6841 
                 257            280 
               
               
                 
                   M. gordonae 
                 
                 V43            V45            V121            
                 ATCC 14470 
                 211 
               
               
                   
                 V132            V138            V142            
               
               
                   
                 V147            V155            V167 
               
               
                 
                   M. intracellulare 
                 
                 V17            V19            V193            
                 ATCC 13950 
                 219 
               
               
                   
                 V194            V195            cch11            
               
               
                   
                 cch12            cch21            cch37 
               
               
                 
                   M. kansasii 
                 
                 V128            V168            V169            
                 ATCC 12478 
                 220 
               
               
                   
                 V179            V182            V185            
               
               
                   
                 cch1            cch14            cch23 
               
               
                 
                   M. lentiflavum 
                 
                 cch24            cch30 
                 — 
                 225 
               
               
                 
                   M. malmoense 
                 
                 cch13 
                 ATCC 29571 
                 219 
               
               
                 
                   M. marinum 
                 
                 V74            97-CAP-1 
                 ATCC 927 
                 220 
               
               
                 
                   M. scrofulaceum 
                 
                 96-CAP-2 
                 ATCC 19981 
                 220 
               
               
                 
                   M. shimodei 
                 
                 V219            V229 
                 ATCC 27962 
                 230 
               
               
                 
                   M. szulgai 
                 
                 cch34 
                 ATCC 29716 
                 220 
               
               
                 
                   M. xenopi 
                 
                 95-CAP-1            
                 ATCC 19250 
                 205 
               
               
                   
                 97-CAP-11 
               
               
                   
               
             
          
         
       
     
       Experiment 3: Sequencing Analysis of 16S-23S rRNA ITS Gene of Mycobacteria 
       [0068]    Since gel electrophoresis showed two PCR products amplified from 16S-23S rRNA ITS of  M. fortuitum  with similar size. Therefore, these bands were further eluted and cloned by yT&amp;A cloning for DNA sequencing. First, the bands containing gel were purified by QIA quick Gel Extraction kit (QIAGEN, Germany) to prepare the inset DNA. Following, ligation was performed with 3:1 molar ratio of insert DNA to vector DNA for the transformation. 
         [0069]    The PCR products amplified from 16S-23S rRNA ITS gene of one colony of  M. asiaticum, M. malmoense, M. scrofulaceum  and  M. szulgai ; three colonies of  M. avium  and  M. chelonae ; two colonies of  M. lentiflavum, M. marinum, M. shimodei  and  M. xenopi ; and four colonies of other strains among these 16 clinical strains were sequenced by Tri-i biotech, Inc. (Taiwan). The primer sets used for the DNA sequencing is Sp1 (SEQ ID NO: 1). The PCR product of 16S-23S rRNA ITS gene from  M. fortuitum  was cloned by yT&amp;A cloning for DNA sequencing with T7 primer. 
       Experiment 4: Designing Specific Probes for Identifying Mycobacteria 
       [0070]    The acquired sequences were further analyzed by DNAMAN (version 4.11). Comparison analysis was performed to find out sequences of specific probes and common probes among these 16 mycobacteria strains. Poly (T) containing 15 T at the 5′-end was followed by sequences of specific probes for each mycobacteria strains. Probes and corresponding mycobacteria strains were shown in the Table 2. Wherein, identification of  Mycobacterium  genus,  M. fortuitum, M. intracellulare  and  M. kansasii  required two independent probes, and the identification of other mycobacteria strains required one probe. 
         [0000]    
       
         
               
             
               
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 The sequence of common and specific probes  
               
               
                 for MTB 
               
             
          
           
               
                   
                   
                   
                 SEQ 
               
               
                 Identified 
                   
                   
                 ID 
               
               
                 species 
                 Probe 
                 Sequence (5′-&gt;3′) 
                 NO. 
               
               
                   
               
               
                   M .  
                 MTBC 
                 TGCATGACAACAAAGTTGGCC 
                  3 
               
               
                 
                   tuberculosis 
                 
                   
                   
                   
               
               
                 complex 
                   
                   
                   
               
               
                   
               
               
                 
                   Mycobacterium 
                 
                 MYC-c 
                 GTGGTGGGGTGTGGTSTTTG 
                  4 
               
               
                 genus 
                   
                   
                   
               
               
                   
               
               
                 
                   Mycobacterium 
                 
                 MYC-a 
                 GTGGTGGGGTGTGGACTTTG 
                  5 
               
               
                 genus 
                   
                   
                   
               
               
                   
               
               
                   M .  abscessus   
                 ABS 
                 GGGAACATAAAGTAGGCATCTGTAG 
                  6 
               
               
                   
                   
                 TG 
                   
               
               
                   
               
               
                   M .  asiaticum   
                 ASI 
                 TGCAGGCCGTGTGGAGTTCTC 
                  7 
               
               
                   
               
               
                   M .  avium   
                 AVI2 
                 CACTCGGTCCGTCCGTGTG 
                  8 
               
               
                   
               
               
                   M .  chelonae   
                 CHE4 
                 GGAACATAAAGCGAGTTTCTGTAGT 
                  9 
               
               
                   
                   
                 GGTTAC 
                   
               
               
                   
               
               
                   M .  fortuitum   
                 FOR2 
                 TTTGCGGTGATGGGACTGCC 
                 10 
               
               
                   
                 FOR7 
                 AGCGCGGGTGATGGAACTGC 
                 11 
               
               
                   
               
               
                   M .  gordonae   
                 GOR 
                 GGCAACACCCTCGGGTGCTG 
                 12 
               
               
                   
               
               
                   M .  
                 INT4 
                 CACTCGGTCGATCCGTGTGG 
                 13 
               
               
                 
                   intracellulare 
                 
                 INT5 
                 ACTCGGTCAGTCCGTGT 
                 14 
               
               
                   
               
               
                   M .  kansasii   
                 KAN1-1 
                 TCGGACTTGTCTGGGTCGTT 
                 15 
               
               
                   
                 KAN4 
                 TCGGGCTCTGTTCGAGAGTT 
                 16 
               
               
                   
               
               
                   M .  lentiflavum   
                 LEN2 
                 ACAACAGGCAATCGCCAGAC 
                 17 
               
               
                   
               
               
                   M .  malmoense   
                 MAL 
                 AACACTCGGCCAGTCCGCGT 
                 18 
               
               
                   
               
               
                   M .  marinum   
                 MAR 
                 AACATCTCTGTTGGTTTCGG 
                 19 
               
               
                   
               
               
                   M .  
                 SCR 
                 ACTCGGCTCGTTCTGAGTGGT 
                 20 
               
               
                 
                   scrofulaceum 
                 
                   
                   
                   
               
               
                   
               
               
                   M .  shimodei   
                 SHI2 
                 AACAACAAGCGAGAAGCCGAG 
                 21 
               
               
                   
               
               
                   M .  szulgai   
                 SZU 
                 AGGCTTGGCCAGAGCTGTTGT 
                 22 
               
               
                   
               
               
                   M .  xenopi   
                 XEN 
                 TGTTGGGCAGCAGGCAGTAAC 
                 23 
               
               
                   
               
             
          
         
       
     
       Experiment 5: Collection of MTB Exhibiting Drug Resistance 
       [0071]    Reference strain of MTB (H37Rv) was purchased from ATCC and clinical strains of MTB exhibiting drug resistance were collected by Reference-lab. Those clinical strains exhibiting tested and confirmed drug resistance were showed in Table 3, Preparation of samples from respiratory specimens, bacterial culture, acid-fast staining, biochemical assays and molecular biological methods were described in Experiment 1. 
         [0072]    Drug sensitivity test was performed while MTB was isolated according indicated methods and processes. The first line drug for the drug sensitivity test was streptomycin (SM), isoniazid (INH), rifampicin (RIF) and ethambutol (EMB). Culture medium plates purchased from Bio Concept (Taiwan, Taipei) were used for the drug sensitivity test of MTB with manufacturer&#39;s instruction. The concentration of test drugs in culture medium plates is 0.2 μg/ml and 1.0 μg/ml for INH; 1.0 μg/ml for RIF; 2.0 μg/ml and 10 μg/ml for SM; 5 μg/ml and 10 μg/ml for EMB. 
       Experiment 6: PCR Amplification of rpoB Gene in Drug Resistant Strain of MTB 
       [0073]    The primer sets, rpoF-1 (SEQ ID NO: 24) and rpo8-1 (SEQ ID NO: 25), were used to amplify rpoB gene. Total volume of PCR reaction was 50 μL which was sequentially added with 18 μL of ddH 2 O, 5 μL of DNA template, 1 μL 10 μM rpoF-1 (SEQ ID NO: 24), 1 μL 10 μM rpo8-1 (SEQ ID NO: 25), 25 μL 2×GO Taq Colorless Master MIX (Promega). PCR conditions are 95° C. for 5 minutes; 95° C. for 30 seconds, 60° C. for 30 seconds, and 72° C. for 45 seconds for 30 cycles; 72° C. for 5 minutes. After PCR reaction, gel electrophoresis was performed in 2% agarose gel to detect PCR product with predicted size at 196 base-pairs. The results show in Table 3. 
         [0000]    
       
         
               
             
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 3 
               
             
             
               
                   
               
               
                 PCR amplification of rpoB gene from standard MTB strains 
               
               
                 and clinical MTB strains with drug resistance 
               
             
          
           
               
                   
                 Selected strain 
                 PCR 
               
             
          
           
               
                 Drug resistance 
                 Clinical strain 
                 Standard strain 
                 product (bp) 
               
               
                   
               
               
                 None 
                 — 
                 H37Rv 
                 196 
               
               
                 Rifampicin 
                 MDR TB 
                 — 
                 196 
               
               
                   
                 1~39            41~49 
               
               
                   
               
             
          
         
       
     
       Experiment 7: Sequences Analysis of rpoB Gene in MTB with Drug Resistance 
       [0074]    The amplified DNA from 48 colonies of MTB with drug resistance were further sequenced and analyzed by BLAST system on the National Center of Biotechnology Information (NCBI) website (http://blast.ncbi.nlm.nih.gov/Blast.cgi). The results were further compared with the rpoB gene sequence of MTB (H37Rv) standard strain to identify the position and sequence of mutations occurred in each drug-resistant MTB strains. The results show in Table 4 below. 
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 4 
               
             
             
               
                   
               
               
                 Positions and sequence alterations of the  
               
               
                 mutations in each drug-resistant MTB  
               
               
                 strains 
               
             
          
           
               
                   
                 Mutation 
                 Sequence 
               
               
                 Bacterial strains 
                 position 
                 alteration 
               
               
                   
               
               
                 MDR TB 41 
                 511 
                 CTG→CCG 
               
               
                   
               
               
                 MDR TB 27 
                 513 
                 CAA→CTA 
               
               
                   
               
               
                 MDR TB 6, 32, 34 
                 516 
                 GAC→TTC 
               
               
                   
               
               
                 MDR TB 21, 45 
                 516 
                 GAC→TAC 
               
               
                   
               
               
                 MDR TB 49 
                 522 
                 TCG→TTG 
               
               
                   
               
               
                 MDR TB 1, 3, 19 
                 526 
                 CAC→TAC 
               
               
                   
               
               
                 MDR TB 25 
                 526 
                 CAC→GAC 
               
               
                   
               
               
                 MDR TB 13 
                 526 
                 CAC→CGC 
               
               
                   
                 529 
                 CGA→CAA 
               
               
                   
               
               
                 MDR TB 39 
                 511 
                 CTG→CCG 
               
               
                   
                 526 
                 CAC→CAG 
               
               
                   
               
               
                 MDR TB 44 
                 526 
                 CAC→CTC 
               
               
                   
               
               
                 MDR TB 35 
                 529 
                 CGA→CTA 
               
               
                   
               
               
                 MDR TB 2, 4, 5, 7, 8,  
                 531 
                 TCG→TTG 
               
               
                 9, 10, 12, 14, 15, 16, 
                   
                   
               
               
                 17, 18, 22, 23, 24, 26,  
                   
                   
               
               
                 29, 30, 31, 33, 37, 38,  
                   
                   
               
               
                 43, 46, 47, 48 
                   
                   
               
               
                   
               
               
                 MDR TB 11, 20, 28, 42 
                 531 
                 TCG→TGG 
               
               
                   
               
               
                 MDR TB 36 
                 533 
                 CTG→CCG 
               
               
                   
               
             
          
         
       
     
         [0075]    The results revealed that the mutations occurred in 48 drug-resistant MTB strains were all point mutation locating at codon 511 to 533. There were 31 strains (31/48) exhibiting mutation on codon 531, 27 stains revealed TCG→TTG mutation and other 4 strains showed were TCG→TGG mutation. 5 strains (5/48) showed mutations on codon 526, 3 strains showed the CAC→TAC mutation, 1 strain showed CAC→GAC mutation and another one strain showed CAC→CTC mutation. 5 strains (5/48) exhibited mutations on codon 516, 3 strains showed the GAC→TTC dinucleotides mutation and 2 strains showed the GAC→TAC mutation, 1 out of 48 strains showed CTG→CCG mutation on codon 511. 1 strain showed the CAA→CTA mutation on codon 513. 1 strain showed the TCG→TTG mutation on codon 522. 1 strain showed the CGA→CTA mutation on codon 529. 1 strain showed the CTG→CCG mutation on codon 533. In addition, there were 2 strains contain two mutations on different position. There were one strain showed CAC→CGC mutation on codon 526 and CGA→CAA mutation on codon 529, another strain showed CTG→CCG mutation on codon 511 and CAC→CAG mutation on codon 526. 
       Experiment 8. Probe Design for Drug-Resistant MTB 
       [0076]    Probes were designed according to the mutation positions and sequences in rpoB gene of various drug-resistant MTB strains and synthesized with poly (T) comprising 15 T at the 5′-end. The probes were shown in Table 5 below. 
         [0000]    
       
         
               
             
               
               
               
               
             
           
               
                 TABLE 5 
               
             
             
               
                   
               
               
                 The probe sequences for drug-resistant MTB 
               
             
          
           
               
                   
                   
                 SEQ  
                   
               
               
                   
                   
                 ID 
                 Detecting 
               
               
                 Probe 
                 Sequence (5′-&gt;3′) 
                 NO. 
                 position 
               
               
                   
               
               
                 RW1-1 
                 CCAGCTG AGC CAATTCAT 
                 26 
                 510, 511,  512 , 
               
               
                   
                   
                   
                 513, 514 
               
               
                   
               
               
                 RW2-1 
                 CAATTCATG GAC CAGAACA 
                 27 
                 513, 514, 515, 
               
               
                   
                   
                   
                   516 , 517, 518 
               
               
                   
               
               
                 RM2-3 
                 CCAATTCATG TTC CAGAACA 
                 28 
                 513, 514, 515, 
               
               
                   
                   
                   
                   516 , 517, 518 
               
               
                   
               
               
                 RW3-4 
                 CCGCTGTCG GGG TTGACC 
                 29 
                 520, 521, 522, 
               
               
                   
                   
                   
                   523 , 524, 525 
               
               
                   
               
               
                 RW4-3 
                 GGTTGACC CAC AAGCGCC 
                 30 
                 524, 525,  526 , 
               
               
                   
                   
                   
                 527, 528 
               
               
                   
               
               
                 RM4-3 
                 GTTGACC CGC AAGCGC 
                 31 
                 524, 525,  526 , 
               
               
                   
                   
                   
                 527, 528 
               
               
                   
               
               
                 RM4-3a 
                 GGGTTGACCT AC AAGCGC 
                 32 
                 523, 524, 525, 
               
               
                   
                   
                   
                   526 , 527, 528 
               
               
                   
               
               
                 RM4-2b 
                 GGTTGACC GAC AAGCGC 
                 33 
                 524, 525,  526 , 
               
               
                   
                   
                   
                 527, 528 
               
               
                   
               
               
                 RW5-3 
                 GCCGACTG TCG GCGCTGG 
                 34 
                 529, 530,  531 , 
               
               
                   
                   
                   
                 532, 533 
               
               
                   
               
               
                 RM5-2a 
                 CCGACTG TTG GCGCTG 
                 35 
                 529, 530,  531 , 
               
               
                   
                   
                   
                 532, 533 
               
               
                   
               
               
                 RM5-2b 
                 CCGACTG TGG GCGCTG 
                 36 
                 529, 530,  531 , 
               
               
                   
                   
                   
                 532, 533 
               
               
                   
               
             
          
         
       
     
         [0077]    RW1-1 probe was designed for the position between codon 510 to 514 of rpoB in H37Rv reference MTB strain. RW2-1 probe was designed for the position between codon 513 to 518 of rpoB in H37Rv reference MTB strain. In addition, RM2-3 probe was designed for the mutation on codon 516 and covered the region from codon 513 to 518 according to the sequencing result of MDR TB 6, 32 and 34 shown in Table 4. 
         [0078]    RW3-4 probe was designed for the position between codon 520 to 525 of rpoB in H37Rv reference MTB strain. RW4-3 probe was designed for the position between codon 524 to 528 of rpoB in H37Rv reference MTB B strain. RM4-3 probe was designed for the mutation on codon 526 and covered the region from codon 524 to codon 528 according to the sequencing result from MDR TB 13 in Table 4. Moreover, RM4-3a probe was designed for the mutation on codon 526 and covered the region from codon 523 to 528 according to the sequencing result from MDR TB 1, 3 and 19 in Table 4. RM4-3b probe was designed for the mutation on codon 526 and covered the region from codon 524 to 528 according the sequencing result from MDR TB 25 in Table 4. 
         [0079]    RW5-3 probe was designed for the position between codon 529 to 533 of rpoB in H37Rv reference MTB strain. Moreover, RW5-2a probe was designed for codon 529 to 533 to detect mutation on codon 531 according to the sequencing results of MDR TB 2, 4, 5, 7˜10, 12, 14˜18, 22˜24, 26, 29˜31, 33, 37, 38, 43, 43 and 46˜48 in Table 4. In addition, RM5-2b was designed for codon 529 to 533 to detect mutation on codon 531 according to the sequencing results of MDR TB 11, 20, 28 and 42 in Table 4. 
       Experiment 9: Duplex PCR Reaction for Amplifying 16S-23S rRNA and rpoB Genes 
       [0080]    The primer set Sp1 (SEQ ID NO: 1) and Sp4 (SEQ ID NO: 2) for 16S-23S rRNA ITS and another primer set, rpoF-1 (SEQ ID NO: 24) and rpo8-1 (SEQ ID NO: 25) for rpoB genes, were utilized for duplex PCR reaction to amplify 16S-23S rRNA ITS and rpoB gene in the same PCR reaction. Notably, the primers including Sp4 (SEQ ID NO: 2) and rpo8-1 (SEQ ID NO: 25) were labeled with biotin for the duplex PCR. Equal amount of two primer sets including rpoF-1 (SEQ ID NO: 24) and rpo8-1 (SEQ ID NO: 25), Sp1 (SEQ ID NO: 1) and Sp4 (SEQ ID NO: 2), were added for the duplex PCR reaction. Total volume of PCR reaction was 25 μL which contains DNA template, 0.4 μM of rpoF-1 and rpo8-1, 0.4 μM of Sp1 and Sp4, 0.2 mM dNTP, 1.5 mM MgCl2, 1×PCR buffer, 2×10 2  copies/μL control DNA template and 0.3 μL DNA polymerase. The heating condition for duplex PCR reaction is 95° C. for 5 minutes; 95° C. for 30 seconds, 60° C. for 30 seconds, and 72° C. for 1 minute for 35 cycles; 72° C. for 10 minutes. Products of duplex PCR reaction should amplify DAN fragments with 212-300 bp (16S-23S rRNA ITS gene) dependent on detected strains. Furthermore, DNA fragment with 196 bp (rpoB gene) would be amplified while MTB exists in the detecting sample. 
       Experiment 10: Preparation of Chip 
       [0081]    Preparation of probe containing reagent by dissolving 100 μmole synthesized probes by 1× probe buffer (DR.Chip Biotech, Inc, Miaoli, Taiwan) with concentration at 10 μM. Probes were spotted on the destined positions of polystyrene plates by automatic spotting machine (DR. Fast Spot, DR.Chip Biotech, Inc). Positions of the spotted probes on chip were showed in  FIG. 1 . Wherein, there were 36 probe spots including 28 detecting probe spots, 4 positive control spots for hybridization reaction, 1 negative control spot for hybridization reaction and 1 positive control spot for PCR reaction on chip. Spotted chip was treated with UV to fix probes on plate and then washed by ddH 2 O and dried. Finally, prepared chip was stored at 4° C. 
       Experiment 11: Hybridization Reaction 
       [0082]    25 μL biotinated PCR production from duplex PCR was heat at 95° C. for 5 minutes to denature and chilled on ice for 2 minutes. Spotted chip was loaded with 200 μL hybridization buffer (DR.Hyb™ buffer, DR.Chip Biotech, Inc) in each well and followed by loading with 5 μL of PCR product. Chip was sealed with cellophane to prevent contamination between wells. After that, chip was shacked and incubated in the hybridization oven at 55° C. for 40 minutes. 
         [0083]    After hybridization reaction, cellophane was removed from chip and discarded the hybridization buffer. Then, wells were wash by adding 200 μL wash buffer (DR.Chip Biotech, Inc) and incubating for 3 minutes, thrice. Wash buffer was discard carefully as complete as possible in the last wash. 200 μL blocking reagent (DR.Chip Biotech, Inc.) which contains 0.24 Strep-AP (DR.Chip Biotech, Inc.) was added into each well and incubated for 20 minutes at room-temperature. After the incubation, Strep-AP reagent was discarded and added wash buffer for 3 minutes to wash, thrice. Washing buffer had to be completely discarded in the last wash. 200 μL of detection buffer (DR.Chip Biotech, Inc.) was added into wells for rinse and discarded. 200 μL of detection buffer which contains 4 μL detection reagent (NBT/BCIP, DR.Chip Biotech, Inc.) was added into wells and incubated in dark for 7 minutes. After reaction, detection reagent was discarded from wells which were followed by wash with ddH 2 O. Finally, wash ddH 2 O was removed for analysis by eye or DR. AiM reader (DR.Chip Biotech, Inc.). 
       Experiment 12: Chip Analysis for the Clinical Samples 
       [0084]    Among 216 strains from clinical samples for this test, 209 strains were correctly determined, 1 strain was not successfully cultured but diagnosed by chip, 6 stains revealed inconsistent results in bacterial culture and chip analysis. Taken together, overall reaction sensitivity is 97.2% and specificity is 96.8%. In TB test, reaction sensitivity is 100% and specificity is 98.9%. Analyzing results are shown in Table 6 below. 
         [0000]    
       
         
               
             
               
               
             
           
               
                 TABLE 6 
               
             
             
               
                   
               
               
                 Comparison of chip analysis and bacterial culture 
               
             
          
           
               
                 chip analysis (strain number) 
                 Culture (strain number) 
               
               
                   
               
               
                   M. abscessus  (21) 
                   M. abscessus  (15) 
               
               
                   
                 RGM (2) 
               
               
                   
                 NTM (4) 
               
               
                   M. avium  (6) 
                   M. avium  (1) 
               
               
                   
                 MAC (1) 
               
               
                   
                 NTM (4) 
               
               
                   M. chelonae  (7) 
                   M. chelonae  (1) 
               
               
                   
                 NTM (6) 
               
               
                   M. fortuitum  (9) 
                   M. fortuitum  (9) 
               
               
                   M. gordonae  (9) 
                   M. gordonae  (7) 
               
               
                   
                   M. haemophilum  (1) 
               
               
                   
                 NTM (1) 
               
               
                   M. intracellulare  (7) 
                   M. intracellulare  (2) 
               
               
                   
                 MAC (1) 
               
               
                   
                 NTM (4) 
               
               
                   M. kansasii  (11) 
                   M. kansasii  (8) 
               
               
                   
                 NTM (3) 
               
               
                   M. lentiflavum  (1) 
                   M. gordonae  (1) 
               
               
                   M. malmoense  (1) 
                   M. malmoense  (1) 
               
               
                   M. marinum  (1) 
                 NTM (1) 
               
               
                   M. scrofulaceum  (2) 
                   M. scrofulaceum  (1) 
               
               
                   
                 NTM (1) 
               
               
                   M. szulgai  (4) 
                   M. kansasii  (2) 
               
               
                   
                 NTM (2) 
               
               
                   M. xenopi  (3) 
                   M. xenopi  (1) 
               
               
                   
                 NTM (2) 
               
               
                   M. tuberculosis  complex (109) 
                   M. tuberculosis  complex (109) 
               
               
                   M. tuberculosis  complex &amp; 
                   M. tuberculosis  complex (4) 
               
               
                   M. intracellulare  (4) 
               
               
                   M. tuberculosis  complex &amp; 
                   M. tuberculosis  complex &amp; 
               
               
                   M. lentiflavum  (2) 
                 NTM (1) 
               
               
                   
                 no growth (1) 
               
               
                   M. avium  &amp;  M. chelonae  (1) 
                 NTM (1) 
               
               
                   M. abscessus  &amp;  M. chelonae  (1) 
                 NTM (1) 
               
               
                   M. intracellulare  &amp;  M. fortuitum  (1) 
                 NTM (1) 
               
               
                   M. intracellulare  &amp;  M. szulgai  (1) 
                 NTM (1) 
               
               
                   M. avium  &amp;  M. kansasii  (1) 
                   M. kansasii  (1) 
               
               
                 NTM (12) 
                   M. fortuitum  (2) 
               
               
                   
                   M. mucogenicum  (1) 
               
               
                   
                   M. peregrinum  (1) 
               
               
                   
                 NTM (8) 
               
               
                 No signal (2) 
                   Tsukamurella  (1) 
               
               
                   
                   Nocardia  (1) 
               
               
                   
               
             
          
         
       
     
         [0085]    There were 21 strains determined as  M. abscessus  according to hybridization result in chip assay shown in  FIG. 2A . In addition, comparing results from bacterial culture revealed that 15 strains were  M. abscessus,  2 strains were Rapid Growing  Mycobacteria  (RGM), and 4 strains were NTM. 
         [0086]    6 strains were determined as  M. avium  according to hybridization result in chip assay in  FIG. 2A . Comparing results from bacterial culture showed that I strain was  M. avium,  1 strain was  Mycobacterium avium  complex (MAC), and 4 strains were NTM. 
         [0087]    7 strains were determined as  M. chelonae  according to hybridization result in chip assay shown in  FIG. 2A . Comparing results from bacterial culture showed that 1 strain was  M. chelonae , and 6 strains were NTM. 
         [0088]    9 strains were determined as  M. fortuitum  according to hybridization result in chip assay shown in  FIG. 2A  which was consistent with the bacterial culture assay. 
         [0089]    9 strains were determined as  M. gordonae  according to hybridization result in chip assay shown in  FIG. 2A . Comparing results from bacterial culture showed that 7 strains were  M. gordonae,  1 strain was  M. haemophilum  and 1 strain was NTM. Result of  M. haemophilum  was inconsistent between hybridization result in chip assay and bacterial culture assay. 
         [0090]    7 strains were determined as  M. intracellulare  according to hybridization result in chip assay shown in  FIG. 2A . Comparing results from bacterial culture showed that 2 strains  M. intracellulare,  1 strain was MAC and 4 strains were NTM. 
         [0091]    11 strains were determined as  M. kansasii  according to hybridization result in chip assay shown in  FIG. 2A . Comparing results from bacterial culture showed that 8 strains  M. kansasii  and 3 strains were NTM. 
         [0092]    1 strain was determined as  M. lentiflavum  according to hybridization result in chip assay shown in  FIG. 2A . However, culture assay showed that the testing bacterium was  M. gordonae . Results of chip analysis and bacterial culture assay were inconsistent. 
         [0093]    1 strain was determined as  M. malmoense  according to chip hybridization shown in  FIG. 2A . In addition, bacterial culture assay also showed that this strain was  M. malmoense.    
         [0094]    1 strain was determined as  M. marinum  according to chip hybridization shown in  FIG. 2A . In addition, bacterial culture assay also showed that this strain was  M. marinum.    
         [0095]    2 strains were determined as  M. scrofulaceum  according to chip hybridization shown in  FIG. 2A . Comparing results from bacterial culture showed that 1 strain was  M. scrofulaceum  and another one was NTM. 
         [0096]    4 strains were determined as  M. szulgai  according to chip hybridization shown in  FIG. 2A . Comparing results from culture showed that 2 strains were  M. kansasiiand  and 2 were NTM. Results of chip analysis and bacterial culture assay were inconsistent. 
         [0097]    1 strain was determined as  M. xenopi  according to chip hybridization shown in  FIG. 2A . In addition, comparing results from bacterial culture showed that 1 strain was  M. xenopi  and 2 strains were NTM. 
         [0098]    109 strains were determined as  M. tuberculosis  complex according to chip analysis shown in  FIG. 3B  and bacterial culture assay showed consistent result as chip analysis. 
         [0099]    4 strains were diagnosed as  M. tuberculosis  complex and  M. intracellulare  according to chip analysis. In addition, results of bacterial culture assay showed that 4 strains were  M. tuberculosis  complex. 
         [0100]    2 strains were diagnosed as  M. tuberculosis  complex and  M. lentiflavum  according to chip analysis. Result of culture assay showed that 1 strain was mixed with  M. tuberculosis  complex and NTM, and another strain did not grew in bacterial culture assay. 
         [0101]    1 strain showed positive signal in chip assay for  M. avium  and  M. chelonae . In addition, results of bacterial culture assay showed that this strain was NTM. 1 strain showed positive signal in chip assay that determined this strain as  M. abscessus  and  M. chelonae . Moreover, results of bacterial culture assay showed that this strain was NTM. 
         [0102]    1 strain showed positive in chip assay that determine this strain as  M. intracellulare  and  M. fortuitum . In addition, results of bacterial culture assay showed that this strain was NTM. 
         [0103]    1 strain showed positive in chip assay that determine this strain as  M. intracellulare  and  M. szulgai . In addition, results of bacterial culture assay showed that this strain was NTM. 
         [0104]    1 strain showed positive in chip assay that determined this strain as  M. avium  and  M. kansasii . In addition, results of bacterial culture assay showed that this strain was  M. kansasii.    
         [0105]    12 strains were determined as NTM according to chip analysis. 2 strains were  M. fortuitum,  1 stain was  M. inucogenicum,  1 stain was  M. peregrinum  and 8 strains were NTM according to biochemical assays. Result from biochemical assay which indicated this strain as  M. fortuitum  was inconsistent from result of chip analysis. 
         [0106]    There were 2 strains revealed negative in chip analysis, 1 strain was  Tsukamurella  and the another was  Nocardia . Both of them belong to bacteria that could not be detected by this chip platform which did not include specific probe for these two bacteria species. Hence, these two strains revealed negative result in chip analysis. 
         [0107]    Furthermore, clinical strain  M. mucogenicum , standard strains including  M. flavescens  (ATCC 14474),  M. senegalense  (ATCC 35796) and  M. terrae  (ATCC 15755) were subjected for chip analysis to obtain hybridization result shown in  FIG. 2B . Since the designed chip in this invention did not include specific probes for these indicated bacterial strains. Therefore, chip analysis of these strains just revealed positive hybridization signal from common probe for  mycobacterium . This result suggests that even strain wants to be tested not belonged to 16  mycobacterium  species in this assay; present chip could still determine whether it belongs to  mycobacterium  genus. 
         [0108]    In addition, RIF drug resistance test performed on 109 strains of  M. tuberculosis  complex in Table 6 by this chip platform. Hybridization results showed in  FIGS. 4A and 4B . Comparison of chip analysis and drug sensitivity test was showed in Table 7. There were 15 RIF resistant strains determined by chip assay including 14 RIF resistant strains and 1 INH resistant strain examined by drug sensitivity test. Other 94 stains were determined as non-drug resistant MTB according to chip analysis and bacterial culture test. 
         [0000]    
       
         
               
             
               
               
             
           
               
                 TABLE 7 
               
             
             
               
                   
               
               
                 Comparison of chip analysis and drug sensitivity 
               
               
                 test of drug sensitive test 
               
             
          
           
               
                 Chip analysis (strains number) 
                 Drug sensitivity test (strains number) 
               
               
                   
               
               
                   M. tuberculosis  complex (94) 
                   M. tuberculosis  complex (94) 
               
               
                 MDR TB (15) 
                 MTB- RIF resistance (14) 
               
               
                   
                 MTB- INH resistance (1) 
               
               
                   
               
             
          
         
       
     
         [0109]    Detection technique based on molecular biology provides a platform to rapidly determine the species and drug resistance of bacteria to be tested. The chip platform in this invention could determine 16  mycobacterium  species and RIF resistance strains. In addition, existence of RIF resistant strains probably exhibiting INH resistance. There will be multiple drug resistance if both RIF and INH resistant to be determined. This information is helpful for clinicians to appropriately modify the management for patient treatment. 
         [0110]    The above-mentioned specification is only for detailed description with the examples of this present invention and shall not be construed as a scope limitation of this present invention. Any modification or change without departing from the features of this present invention or any equivalent thereof shall be included in the scope of this present invention defined in the following claims.