title: Clinical efficacy of direct DNA sequencing analysis on sputum specimens for early detection of drug-resistant Mycobacterium tuberculosis in a clinical setting.
abstract: BACKGROUND
  Early detection of drug-resistant Mycobacterium tuberculosis is important for the control and prevention of disease transmission. However, conventional drug susceptibility tests for drug-resistant M tuberculosis take at least 3 to 8 weeks. Here, we report the clinical efficacy of direct DNA sequencing analysis for detecting drug-resistant TB on sputum specimens in a clinical setting.
  
  
  METHODS
  A total of 113 sputum specimens from 111 patients, who were suspected of having drug-resistant TB by clinicians, were used for DNA sequencing of katG, rpoB, embB, and pncA genes for isoniazid (INH), rifampin (RIF), ethambutol (EMB), and pyrazinamide (PZA) resistance, respectively, and the results were compared with drug susceptibility tests. The optimization of antituberculosis drugs according to the results of DNA sequencing and the treatment outcomes of the patients were also analyzed.
  
  
  RESULTS
  Turnaround time of the direct DNA sequencing analysis was 3.8 +/- 1.8 days. We found mutations related to drug resistance in 30 clinical specimens for katG, 39 for rpoB, 13 for embB, and 24 for pncA. The sensitivity and specificity of the assay were 63.6% and 94.6% for INH, 96.2 and 93.9% for RIF, 69.2% and 97.5% for EMB, and 100% and 92.6% for PZA, respectively. Of the patients with RIF resistance, including multidrug-resistant TB by the assay, 92.5% of the patients with initial first-line antituberculosis drugs were changed to second-line antituberculosis drugs, and treatment was successful in 61.9% of these cases.
  
  
  CONCLUSIONS
  Direct DNA sequencing analysis of clinical sputum specimens is a rapid and useful method for the detection and treatment of drug-resistant TB.
authors.affiliation: Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Hallym University Medical Center, Gangwon-do, Korea.
authors.forename: Jeong-Hee
authors.initials: JH
authors.lastname: Choi
authors.forename: Kyung Wha
authors.initials: KW
authors.lastname: Lee
authors.forename: Hye-Ryun
authors.initials: HR
authors.lastname: Kang
authors.forename: Yong Il
authors.initials: YI
authors.lastname: Hwang
authors.forename: SeungHun
authors.initials: S
authors.lastname: Jang
authors.forename: Dong-Gyu
authors.initials: DG
authors.lastname: Kim
authors.forename: Cheol-Hong
authors.initials: CH
authors.lastname: Kim
authors.forename: In-Gyu
authors.initials: IG
authors.lastname: Hyun
authors.forename: Tae-Rim
authors.initials: TR
authors.lastname: Shin
authors.forename: Sang-Myeon
authors.initials: SM
authors.lastname: Park
authors.forename: Myung-Goo
authors.initials: MG
authors.lastname: Lee
authors.forename: Chang-Youl
authors.initials: CY
authors.lastname: Lee
authors.forename: Yong-Bum
authors.initials: YB
authors.lastname: Park
authors.forename: Ki-Suck
authors.initials: KS
authors.lastname: Jung
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000581:Amidohydrolases / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D002374:Catalase / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods*; D004269:DNA, Bacterial / Q000032:analysis*; D012321:DNA-Directed RNA Polymerases; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D010430:Pentosyltransferases / Q000235:genetics; D016133:Polymerase Chain Reaction; D012189:Retrospective Studies; D012680:Sensitivity and Specificity; D013183:Sputum / Q000382:microbiology*; D018088:Tuberculosis, Multidrug-Resistant / Q000175:diagnosis* / Q000382:microbiology; D055815:Young Adult
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; C505805:rpoB protein, Mycobacterium tuberculosis; D002374:Catalase; C480353:katG protein, Mycobacterium tuberculosis; C540269:EmbB protein, Mycobacterium tuberculosis; D010430:Pentosyltransferases; D012321:DNA-Directed RNA Polymerases; D000581:Amidohydrolases; C487496:PncA protein, Mycobacterium tuberculosis