title: Identification and evaluation of a new nucleic acid amplification test target for specific detection of Mycobacterium tuberculosis.
abstract: BACKGROUND
  Accurate and early diagnosis of tuberculosis (TB) is of major importance in the management and control of TB. Because the conventional bacteriological diagnosis of TB has several limitations, nucleic acid amplification (NAA) tests have emerged as promising alternatives. A potential problem with NAA tests is that some strains lack a target, which may be the one of main reasons for the much lower and highly variable accuracy in diagnosis. A possible solution may be to use more valid and applicable targets to increase detection accuracy.
  
  
  METHODS
  In this paper, we designed a two-step program to obtain NAA test targets. Inter-simple sequence repeats (ISSR) based on oligonucleotide (GTG)(5) were first constructed to genotype Mycobacterium strains to obtain Mycobacterium tuberculosis (MTB)-specific fragment. Second, sequence characterized amplified region (SCAR) markers were developed from these species-specific sequences to identify MTB. Some 312 Mycobacterium strains were used to evaluate the efficacy of the SCAR markers, IS6110 element [specific identification of Mycobacterium tuberculosis complex (MTC)] and 16SrRNA gene (specific identification of Mycobacterium) amplification, together with traditional bacteriology testing was used as a control.
  
  
  RESULTS
  MTB-specific sequences located in a gene coding for Rv1508c, as a new NAA test target, were obtained using ISSR-PCR genotyping. Based on these sequences, the SCAR primer pairs MISP1 and MISP2 were designed. All 312 strains from Mycobacterium accurately produced the genus-specific 16SrRNA amplicon. 271 MTB strains and M. africanum were positive. However, all nontuberculous mycobacteria (NTM) strains and 1 MTB strain named 1143 were negative in both SCAR and IS6110 PCR amplification. M. bovis, bacille Calmette-Guérin (BCG) were IS6110-PCR positive, while SCAR-PCR was negative. Strain 1143 was defined as M. arupense with 99% identity by 16SrRNA gene sequencing identification, despite being diagnosed as MTB using traditional testing.
  
  
  CONCLUSIONS
  SCAR markers developed with this two-step program can be used as a new NAA test target to correctly detect MTB.
authors.affiliation: Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China.
authors.forename: Lianhua
authors.initials: L
authors.lastname: Qin
authors.forename: Ruijuan
authors.initials: R
authors.lastname: Zheng
authors.forename: Chao
authors.initials: C
authors.lastname: Fan
authors.forename: Jiangli
authors.initials: J
authors.lastname: Cai
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Liu
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.forename: Junmei
authors.initials: J
authors.lastname: Lu
authors.forename: Ruiliang
authors.initials: R
authors.lastname: Jin
authors.forename: Hua
authors.initials: H
authors.lastname: Yang
authors.forename: Zhenling
authors.initials: Z
authors.lastname: Cui
authors.forename: Yonghong
authors.initials: Y
authors.lastname: Feng
authors.forename: Zhongyi
authors.initials: Z
authors.lastname: Hu
mesh_terms: D005838:Genotype; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000302:isolation & purification*; D021141:Nucleic Acid Amplification Techniques; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012680:Sensitivity and Specificity; D014376:Tuberculosis / Q000175:diagnosis*
chemical_list: D012336:RNA, Ribosomal, 16S