GeneChip analysis of resistant Mycobacterium tuberculosis with previously treated tuberculosis in Changchun

Zhang, Ming-Jin; Ren, Wenzhi; Sun, Xiaoduan; Liu, Yang; Liu, Kewei; Ji, Zhong-Hao; Gao, Wei; Yuan, Bao

doi:10.1186/s12879-018-3131-8

Cited by 9 publications

(4 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…[ 29 , 30 ] Previous studies also showed a relatively high diagnostic value for TB. [ 27 , 31 ] Nevertheless, the low sensitivity of the GeneXpert MTB/RIF assay in the present study might be related to the selection of the comparator. A previous study suggested that the GeneXpert MTB/RIF assay and culture had similar results in sputum-negative patients, [ 13 ] while another study showed higher performance of the GeneXpert MTB/RIF assay compared to culture in sputum.…”

Section: Discussionmentioning

confidence: 83%

Comparison of 3 diagnostic methods for pulmonary tuberculosis in suspected patients with negative sputum smear or no sputum

Cheng,

Chen,

Wan

et al. 2024

Medicine

View full text Add to dashboard Cite

Study design: To explore the diagnostic value of 3 methods for sputum smear-negative and non-sputum patients with suspected pulmonary tuberculosis (TB). Methods: This prospective study enrolled sputum smear-negative and non-sputum patients with suspected TB admitted to Jiangxi Chest Hospital between January 2020 and December 2022. The 3 methods were bronchoalveolar lavage fluid (BALF)-acid-fast bacillus (AFB) smear, GeneXpert MTB/RIF, and gene chip for Mycobacterium strain identification. The diagnostic performance of the 3 tests was evaluated with BALF Mycobacterium culture + BALF-AFB smear + GeneXpert MTB/RIF + Gene chip as the gold standard. Results: A total of 456 samples were collected from 114 patients with suspected TB. Twenty-four patients were diagnosed with TB. The combination of GeneXpert MTB/RIF and gene chip for Mycobacterium strain identification yielded the highest area under the receiver operating characteristics curve (AUC) of 0.953 and had sensitivity of 90.57%, specificity of 100%, positive predictive value (PPV) of 100%, negative predictive value (NPV) of 92.42%, accuracy of 95.61%. GeneXpert MTB/RIF achieved AUC of 0.906, sensitivity of 81.13%, specificity of 100%, PPV of 100%, NPV of 85.92%, accuracy of 91.23%. BALF-AFB smear had AUC of 0.519, sensitivity of 3.77%, specificity of 100%, PPV of 100%, NPV of 54.46%, and accuracy of 55.26%. The combination of GeneXpert MTB/RIF and gene chip for Mycobacterium strain identification yielded the highest κ of 0.911, while BALF-AFB smear had the lowest κ value of 0.040. Conclusion: For TB in sputum smear-negative and non-sputum patients using BALF Mycobacterium culture + BALF-AFB smear + GeneXpert MTB/RIF + Gene chip as the gold standard, BALF-AFB smear showed low diagnostic performance, while, though GeneXpert MTB/RIF and gene chip had good diagnostic performance, combining GeneXpert MTB/RIF and gene chip improved the diagnostic value to a great extent.

show abstract

Section: Discussionmentioning

confidence: 83%

Comparison of 3 diagnostic methods for pulmonary tuberculosis in suspected patients with negative sputum smear or no sputum

Cheng,

Chen,

Wan

et al. 2024

Medicine

View full text Add to dashboard Cite

show abstract

“…A meta-analysis (including 15 studies) in 2014 showed that the overall sensitivity of DNA microarray for detecting RFP resistance was 0.91 (95% CI: 0.89-0.92), the overall specificity was 0.96 (95% CI: 0.96-0.97), and the AUC was 0.97 (21). A recently published study by Zhang et al (22) showed that the sensitivity and specificity of DNA microarray for detecting RFP resistance in patients with previously treated TB were 83.1% and 98.7%, respectively. Our results were consistent with the findings of previous studies.…”

Section: Detection Of Rfp-resistant M Tuberculosis With Dna Microarraymentioning

confidence: 99%

Diagnostic performance of DNA microarray for detecting rifampicin and isoniazid resistance in Mycobacterium tuberculosis

Sun¹,

Sun²

2021

J Thorac Dis

View full text Add to dashboard Cite

Background: While rifampicin (RFP) and isoniazid (INH) are the most commonly used first-line antituberculosis drugs, multidrug resistance in Mycobacterium tuberculosis poses a threat to the success of tuberculosis (TB) control programs. Clinical practice guidelines and expert consensuses recommend drug susceptibility testing (DST) before the initiation of antituberculosis treatment. However, traditional DST is time-consuming and has high requirements for laboratory conditions. The recently developed molecular diagnostic techniques, such as DNA microarray, offer new options. We thus investigated the diagnostic value of DNA microarray in detecting RFP + INH-resistant TB, with an attempt to identify simple, efficient, and accurate drug-resistant TB testing methods. Methods: The clinical features and DST results of patients diagnosed with pulmonary tuberculosis by Bactec MGIT 960 liquid culture system (Becton, Dickinson and Company, Franklin Lakes, NJ, USA) who received DNA microarray analysis in our center from July 2019 to July 2020 were retrospectively analyzed.Level of agreement between liquid culture and DNA microarray technology was assessed by using the Cohen kappa coefficient. With the results of liquid culture as the gold standard, the sensitivity and specificity of the DNA microarray were calculated, and the receiver operating characteristic (ROC) curves were used to assess the diagnostic values of the DNA microarray in detecting RFP + INH-resistant TB. Results: A total of 825 patients were enrolled. The sensitivity and specificity of DNA microarray were 0.84 and 0.94, respectively, in the detection of RFP resistance, with an area under the curve (AUC) of 0.89 [95% confidence interval (CI): 0.87-0.91)] and a Cohen kappa coefficient of 0.78 (95% CI: 0.72-0.83). For INH resistance, the sensitivity and specificity of the DNA microarray were 0.73 and 0.97, respectively, with an AUC of 0.85 (95% CI: 0.82-0.87) and a Cohen kappa coefficient of 0.75 (95% CI: 0.70-0.80). Conclusions:The DNA microarray had high specificity and sensitivity in detecting RFP + INH-resistant TB. As a rapid, accurate, and practical technique, it can be routinely performed in clinical laboratories.

show abstract

“…In the last decade, next-generation sequencing (NGS) has been extensively used in human, livestock and plant research [ 1 – 5 ]. An increasing number of single nucleotide polymorphisms (SNPs) have been detected in NGS datasets using various calling pipelines [ 6 – 8 ].…”

Section: Introductionmentioning

confidence: 99%

Comparison of seven SNP calling pipelines for the next-generation sequencing data of chickens

2022

View full text Add to dashboard Cite

Single nucleotide polymorphisms (SNPs) are widely used in genome-wide association studies and population genetics analyses. Next-generation sequencing (NGS) has become convenient, and many SNP-calling pipelines have been developed for human NGS data. We took advantage of a gap knowledge in selecting the appropriated SNP calling pipeline to handle with high-throughput NGS data. To fill this gap, we studied and compared seven SNP calling pipelines, which include 16GT, genome analysis toolkit (GATK), Bcftools-single (Bcftools single sample mode), Bcftools-multiple (Bcftools multiple sample mode), VarScan2-single (VarScan2 single sample mode), VarScan2-multiple (VarScan2 multiple sample mode) and Freebayes pipelines, using 96 NGS data with the different depth gradients of approximately 5X, 10X, 20X, 30X, 40X, and 50X coverage from 16 Rhode Island Red chickens. The sixteen chickens were also genotyped with a 50K SNP array, and the sensitivity and specificity of each pipeline were assessed by comparison to the results of SNP arrays. For each pipeline, except Freebayes, the number of detected SNPs increased as the input read depth increased. In comparison with other pipelines, 16GT, followed by Bcftools-multiple, obtained the most SNPs when the input coverage exceeded 10X, and Bcftools-multiple obtained the most when the input was 5X and 10X. The sensitivity and specificity of each pipeline increased with increasing input. Bcftools-multiple had the highest sensitivity numerically when the input ranged from 5X to 30X, and 16GT showed the highest sensitivity when the input was 40X and 50X. Bcftools-multiple also had the highest specificity, followed by GATK, at almost all input levels. For most calling pipelines, there were no obvious changes in SNP numbers, sensitivities or specificities beyond 20X. In conclusion, (1) if only SNPs were detected, the sequencing depth did not need to exceed 20X; (2) the Bcftools-multiple may be the best choice for detecting SNPs from chicken NGS data, but for a single sample or sequencing depth greater than 20X, 16GT was recommended. Our findings provide a reference for researchers to select suitable pipelines to obtain SNPs from the NGS data of chickens or nonhuman animals.

show abstract

GeneChip analysis of resistant Mycobacterium tuberculosis with previously treated tuberculosis in Changchun

Cited by 9 publications

References 27 publications

Comparison of 3 diagnostic methods for pulmonary tuberculosis in suspected patients with negative sputum smear or no sputum

Comparison of 3 diagnostic methods for pulmonary tuberculosis in suspected patients with negative sputum smear or no sputum

Diagnostic performance of DNA microarray for detecting rifampicin and isoniazid resistance in Mycobacterium tuberculosis

Comparison of seven SNP calling pipelines for the next-generation sequencing data of chickens

Contact Info

Product

Resources

About