Dataset Information

Performance of Biochip system in detecting drug resistant and multidrug-resistant tuberculosis using sputum collected from multiple clinical settings in Zhejiang, China.

ABSTRACT: The objective of the present study was to conduct a multicentre, prospective evaluation of the diagnostic performance of the Biochip system for the detection of drug-resistant tuberculosis using smear-positive sputum specimens. This prospective study evaluated the diagnostic performance of this new platform for drug resistant and multidrug-resistant tuberculosis (MDR-TB) using 1491 smear-positive sputum specimens collected from multiple clinical settings. Using conventional culture-based culturing and drug-susceptibility testing as reference standards, the biochip system had a sensitivity of 86.08% and a specificity of 97.7% for rifampicin (RIF) detection, in detecting isoniazid (INH) resistance, it had a sensitivity of 79.36% and a specificity of 98.71%. With respect to MDR-TB detection, the sensitivity was 78.01% and the specificity was 98.86%. The performance only varies among different sites for RIF resistance, and there are no other statistically difference in diagnostic performance for other variables considered. The Biochip system shows favourable sensitivity and specificity for RIF and INH resistance, along with MDR-TB detection, directly using clinical smear-positive sputum samples. It is an alternative to conventional drug-susceptibility testing (DST) for detecting drug resistance or MDR-TB and is a method worth expanding to clinical settings in China.

SUBMITTER: Xu K

PROVIDER: S-EPMC6043617 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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Performance of Biochip system in detecting drug resistant and multidrug-resistant tuberculosis using sputum collected from multiple clinical settings in Zhejiang, China.

Xu Kaijin K Wang Shuting S Wu Jie J Liu Zhengwei Z Ji Zhongkang Z Zheng Lin L Jin Xiuyuan X Ren Jingjing J Yang Shigui S Li Zhaoxia Z Yuan Jing J Zhao Yanlin Y Li Lanjuan L

Scientific reports 20180712 1

The objective of the present study was to conduct a multicentre, prospective evaluation of the diagnostic performance of the Biochip system for the detection of drug-resistant tuberculosis using smear-positive sputum specimens. This prospective study evaluated the diagnostic performance of this new platform for drug resistant and multidrug-resistant tuberculosis (MDR-TB) using 1491 smear-positive sputum specimens collected from multiple clinical settings. Using conventional culture-based culturi ...[more]

PMID: 30002508

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Project description:In South Africa and other high prevalence countries, transmission is a significant contributor to rising rates of multidrug resistant tuberculosis (MDR-TB). Thus, there is a need to develop an early detection system for transmission clusters suitable for high burden settings. We have evaluated the discriminatory power and clustering concordance of a novel and simple genotyping approach, combining spoligotyping with pncA sequencing (SpoNC), against two well-established methods: IS6110-RFLP and 24-loci MIRU-VNTR.A total of 216 MDR-TB isolates collected from January to June 2010 from the NHLS Central TB referral laboratory in Braamfontein, Johannesburg, representing a diversity of strains from South Africa, were included. The isolates were submitted for genotyping, pncA sequencing and analysis to the Centre for Tuberculosis in South Africa and the Public Health Research Institute Tuberculosis Center at Rutgers University in the United States. Clustering rates, Hunter-Gaston Discriminatory Indexes (HGI) and Wallace coefficients were compared between the methods.Overall clustering rates were high by both IS6110-RFLP (52.8%) and MIRU-VNTR (45.8%), indicative of on-going transmission. Both 24-loci MIRU-VNTR and IS6110-RFLP had similar HGI (0.972 and 0.973, respectively), with close numbers of unique profiles (87 vs. 70), clustered isolates (129 vs. 146), and cluster sizes (2 to 26 vs. 2 to 25 isolates). Spoligotyping alone was the least discriminatory (80.1% clustering, HGI 0.903), with 28 unique types. However, the discriminatory power of spoligotyping was improved when combined with pncA sequencing using the SpoNC approach (61.8% clustering, HGI 0.958). A high proportion of MDR-TB isolates had mutations in pncA (68%, n = 145), and pncA mutations were significantly associated with clustering (p = 0.007 and p = 0.0013 by 24-loci MIRU-VNTR and IS6110-RFLP, respectively), suggesting high rates of resistance to pyrazinamide among all MDR-TB cases and particularly among clustered cases.We conclude that SpoNC provides good discrimination for MDR-TB surveillance and early identification of outbreaks in South Africa, with 24-loci MIRU-VNTR applied for pncA wild-type strains as needed.

Project description:There is a growing awareness that molecular diagnostics for detect-to-treat applications will soon need a highly multiplexed mutation detection and identification capability. In this study, we converted an open-amplicon microarray hybridization test for multidrug-resistant (MDR) Mycobacterium tuberculosis into an entirely closed-amplicon consumable (an amplification microarray) and evaluated its performance with matched sputum and sediment extracts. Reproducible genotyping (the limit of detection) was achieved with ?25 M. tuberculosis genomes (100 fg of M. tuberculosis DNA) per reaction; the estimated shelf life of the test was at least 18 months when it was stored at 4°C. The test detected M. tuberculosis in 99.1% of sputum extracts and 100% of sediment extracts and showed 100% concordance with the results of real-time PCR. The levels of concordance between M. tuberculosis and resistance-associated gene detection were 99.1% and 98.4% for sputum and sediment extracts, respectively. Genotyping results were 100% concordant between sputum and sediment extracts. Relative to the results of culture-based drug susceptibility testing, the test was 97.1% specific and 75.0% sensitive for the detection of rifampin resistance in both sputum and sediment extracts. The specificity for the detection of isoniazid (INH) resistance was 98.4% and 96.8% for sputum and sediment extracts, respectively, and the sensitivity for the detection of INH resistance was 63.6%. The amplification microarray reported the correct genotype for all discordant phenotype/genotype results. On the basis of these data, primary sputum may be considered a preferred specimen for the test. The amplification microarray design, shelf life, and analytical performance metrics are well aligned with consensus product profiles for next-generation drug-resistant M. tuberculosis diagnostics and represent a significant ease-of-use advantage over other hybridization-based tests for diagnosing MDR tuberculosis.

Dataset Information

Performance of Biochip system in detecting drug resistant and multidrug-resistant tuberculosis using sputum collected from multiple clinical settings in Zhejiang, China.

Publications

Performance of Biochip system in detecting drug resistant and multidrug-resistant tuberculosis using sputum collected from multiple clinical settings in Zhejiang, China.

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