Assess the Diagnostic Accuracy of GeneXpert to Detect Mycobacterium tuberculosis and Rifampicin-Resistant Tuberculosis among Presumptive Tuberculosis and Presumptive Drug Resistant Tuberculosis Patients
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Setting, Period, and Design
2.2. Sample Processing for Light-Emitting Diode Fluorescent Microscopy
2.3. Expectorated Sputum Sample Processing for GeneXpert MTB/RIF Assay
2.4. Lymph Nodes and Other Tissues Sample Processing for GeneXpert MTB/RIF Assay
2.5. Processing of Non-Sterile Lymph Nodes and Tissues for GeneXpert MTB/RIF Assay
2.6. Processing of CSF Samples for GeneXpert MTB/RIF Assay
2.7. DNA Extraction Using GenoLyse for MTBDRplus VER 2.0 Assay
2.8. Hybridization for First-Line Drugs
2.9. DNA Extraction Using GenoLyse for MTBDRsl VER 2.0 Assay
2.10. Hybridization for Second-Line Drugs
2.11. Statistics
3. Results
4. Discussion
- Early diagnosis.
- Novel case-finding methods beyond healthcare facilities.
- Shorter and simpler successful treatment regimens for drug-sensitive and drug-resistant tuberculosis.
- A greater focus on prevention strategies.
- Steps to reduce mortality and transmission in adults and children.
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
References
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State | Districts | Samples (n) from | Cumulative (n) | % among the Total Samples | |
---|---|---|---|---|---|
Public Sector | Private Sector | ||||
Tamil Nadu | Villupuram (VPM) | 2801 | 36 | 2837 | 7.53 |
Tanjavore (TAN) | 1791 | 286 | 2077 | 5.51 | |
Prembalore (PBR) | 1790 | 374 | 2164 | 5.74 | |
Cuddalore (CUD) | 2224 | 188 | 2412 | 6.4 | |
Kallakuruchi (KKL) | 3011 | 232 | 3243 | 8.6 | |
Nagapattinam (NAG) | 839 | 182 | 1021 | 2.71 | |
Thiruvannamali (TVM) | 2427 | 647 | 3074 | 8.15 | |
Thiruvarur (TVR) | 3596 | 125 | 3721 | 9.87 | |
Thiruchirapalli (TRY) | 6781 | 811 | 7592 | 20.14 | |
Puducherry | Puducherry (PD) | 9554 | 0 | 9554 | 25.35 |
Total samples | 34,814 | 2881 | 37,695 | 100 |
Stratification of Patients | Total | MTB Not Detected (MTB−) | MTB Detected (MTB+) | RIF Resistance Not Detected | RIF Resistance Detected | % of MTB Positive | % of RIF Resistant | |
---|---|---|---|---|---|---|---|---|
Presumptive TB | PL-HIV out of presumptive TB | 2374 | 2195 | 179 | 155 | 10 | 7.54 | 5.59 |
Pediatric out of presumptive TB | 2257 | 2207 | 50 | 49 | 0 | 2.22 | 0.00 | |
Smear-negative, X-ray suggestive of TB | 11,233 | 8927 | 2306 | 2088 | 113 | 20.53 | 4.90 | |
Other vulnerable group | 1820 | 1557 | 263 | 197 | 10 | 14.45 | 3.80 | |
Contacts of TB and DR-TB patients | 595 | 494 | 101 | 77 | 24 | 16.97 | 23.76 | |
EPTB | 7639 | 6892 | 747 | 669 | 26 | 9.78 | 3.48 | |
Upfront molecular test offered | 4026 | 3427 | 599 | 191 | 6 | 14.88 | 1.00 | |
Presumptive DR-TB (Pulmonary) | Notified TB patients (New)—UDST | 3846 | 2273 | 1573 | 1210 | 268 | 40.90 | 17.04 |
Notified TB patients (Pre-treated)—UDST | 462 | 275 | 187 | 165 | 19 | 40.48 | 10.16 | |
Non-responders (DS-TB and Hr TB) | 562 | 93 | 469 | 282 | 14 | 83.45 | 2.99 | |
Private sector | Pulmonary TB | 1939 | 1430 | 509 | 472 | 15 | 26.25 | 2.95 |
EPTB | 942 | 769 | 173 | 134 | 4 | 18.37 | 2.31 | |
37,695 | 30,539 | 7156 | 5689 | 509 | 18.98 | 7.11 |
Number | % | Sensitivity (%) with 95%CI | Specificity (%) with 95%CI | PPV (%) with 95%CI | NPV (%) with 95%CI | Prevalence (%) with 95%CI | Accuracy (%) with 95%CI | Kappa with 95%CI | |
---|---|---|---|---|---|---|---|---|---|
PTB | 29,114 | 74.45 | 99.87 (0.12–0.07) | 99.92 (0.04–0.03) | 99.71 (0.17–0.11) | 99.97 (0.04–0.01) | 21.38 (0.46–0.48) | 99.91 (0.04–0.03) | 0.997 (0.996–0.998) |
EPTB | 8581 | 21.94 | 99.45 (0.72–0.37) | 99.84 (0.11–0.08) | 98.70 (0.97–0.55) | 99.93 (0.09–0.04) | 10.64 (0.65–0.67) | 99.80 (0.12–0.08) | 0.990 (0.985–0.995) |
Presumptive TB | 32,825 | 87.08 | 99.82 (0.17–0.10) | 99.91 (0.04–0.03) | 99.51 (0.23–0.16) | 99.97 (0.03–0.01) | 14.96 (0.38–0.39) | 99.93 (0.04–0.02) | 0.996 (0.995–0.997) |
Presumptive DR-TB (Pulmonary) | 4870 | 12.92 | 99.82 (0.28–0.13) | 99.77 (0.26–0.15) | 99.73 (0.33–0.15) | 99.85 (0.25–0.09) | 45.73 (1.41–2.41) | 99.92 (0.10–0.05) | 0.996 (0.993–0.998) |
Presumptive TB | |||||||||
PLHIV out of presumptive TB | 2374 | 6.07 | 99.44 (2.53–0.55) | 99.91 (0.24–0.08) | 98.88 (3.20–0.84) | 99.95 (0.27–0.04) | 7.50 (1.03–1.13) | 99.87 (0.24–0.10) | 0.991 (0.981–1.00) |
Pediatric out of presumptive TB | 2257 | 5.77 | 97.96 (8.81–1.99.) | 99.91 (0.24–0.08) | 96.00 (10.28–2.27) | 99.95 (0.26–0.04) | 2.17 (0.56–0.69) | 99.87 (0.26–0.10) | 0.969 (0.934–1.00) |
Smear-negative, X-ray suggestive of TB | 11,233 | 28.72 | 100.00 (0.16–0.0) | 99.99 (0.05–0.01) | 99.96 (0.27–0.03) | 100.00 (0.04–0.00) | 20.52 (0.74–0.76) | 99.99 (0.04–0.01) | 0.999 (0.999–1.00) |
Other vulnerable group | 1820 | 4.65 | 99.62 (1.73–0.37) | 99.87 (0.33–0.11) | 99.24 (2.21–0.57) | 99.94 (0.39–0.05) | 14.40 (1.59–1.69) | 99.84 (0.32–0.13) | 0.993 (0.986–1.00) |
Contacts of TB and DR-TB patients | 595 | 1.52 | 100.00 (3.69–0.00) | 99.40 (1.15–0.48) | 97.03 (5.67–1.99) | 100.00 (0.74–0.00) | 16.47 (2.89–3.23) | 99.50 (0.97–0.40) | 0.982 (0.961–1.00) |
EP TB | 7639 | 19.53 | 99.60 (0.78–0.32) | 99.90 (0.11–0.06) | 99.06 (1.00–0.39) | 99.96 (0.09–0.03) | 9.73 (0.66–0.68) | 99.87 (0.11–0.07) | 0.993 (0.988–0.997) |
Upfront molecular test offered | 4026 | 10.29 | 99.83 (0.76–0.17) | 99.97 (0.13–0.03) | 99.83 (1.00–0.15) | 99.97 (0.18–0.03) | 14.88 (1.09–1.54) | 99.95 (0.13–0.04) | 0.998 (0.995–1.00) |
Presumptive DR-TB | |||||||||
Notified TB patients (New)—UDST | 3846 | 9.83 | 99.94 (0.34–0.06) | 99.87 (0.25–0.10) | 99.81 (0.40–0.13) | 99.96 (0.27–0.03) | 40.85 (1.56–1.57) | 99.90 (0.17–0.07) | 0.998 (0.996–0.999) |
Notified (previously treated)—UDST | 462 | 1.18 | 99.47 (2.41–0.52) | 99.64 (1.65–0.35) | 99.47 (3.13–0.45) | 99.64 (2.15–0.31) | 40.48 (4.51–4.63) | 99.57 (1.12–0.38) | 0.991 (0.979–1.00) |
Non-responders (DS-TB and H Resistant TB) | 562 | 1.44 | 99.57 (1.10–0.38) | 97.85 (5.40–1.89) | 99.57 (1.23–0.32) | 97.85 (5.91–1.60) | 83.45 (3.33–2.98) | 99.29 (1.10–0.62) | 0.974 (0.949–0.999) |
Private sector | |||||||||
Pulmonary TB | 1939 | 4.96 | 100.00 (0.78–0.00) | 99.93 (0.32–0.07) | 99.80 (0.18–0.17) | 100.00 (0.26–0.00) | 26.20 (1.95–2.02) | 99.95 (0.24–0.05) | 0.999 (0.996–1.00) |
EPTB | 942 | 2.41 | 98.82 (3.01–1.04) | 99.35 (0.85–0.44) | 97.11 (3.77–1.66) | 99.74 (0.76–0.19) | 18.05 (1.41–2.60) | 99.26 (0.79–0.44) | 0.975 (0.957–0.993) |
GeneXpert Results | R-Resistance Detected | Resistant Probes | |||||
---|---|---|---|---|---|---|---|
Probe A | Probe B | Probe C | Probe D | Probe E | ΔCT Value > 4 | ||
Very low | 212 (41.65%) | 9 | 27 | 19 | 22 | 29 | 106 |
Low | 163 (32.02%) | 13 | 15 | 17 | 21 | 28 | 69 |
Medium | 98 (19.25%) | 13 | 12 | 9 | 12 | 10 | 42 |
High | 36 (7.07%) | 2 | 1 | 4 | 2 | 1 | 26 |
Total | 509 | 37 (7.27%) | 55 (10.81%) | 49 (9.63%) | 57 (11.20%) | 68 (13.36%) | 243 (47.74%) |
FL Gene Target | Type of Resistant | SL Gene Target | Type of Resistant | Mutation Probe | Missing WT Probe | Phenotypic Susceptibility | Mutation | Frequency n = (47) |
---|---|---|---|---|---|---|---|---|
rpoB | True Resistant | gyrA | True Resistant | MUT1 | WT2 | Resistant | A90V | 5 |
n = (157) | (91.7%) | MUT2 | WT2 | Resistant | S91P | 1 | ||
MUT3A | WT3 | Resistant | D94A | 2 | ||||
MUT3B | WT3 | Resistant | D94N/Y | 2 | ||||
MUT3C | WT3 | Resistant | D94G | 7 | ||||
MUT3D | WT3 | Resistant | D94H | 1 | ||||
Inferred Resistant | -- | WT1 | Resistant | -- | 2 | |||
-- | WT2 | Resistant | -- | 2 | ||||
gyrB | Inferred Resistant | -- | WT3 | Resistant | -- | 1 | ||
Inferred Resistant | gyrA | True Resistant | MUT1 | WT2 | Resistant | A90V | 2 | |
(8.3%) | MUT3C | WT3 | Resistant | D94H | 2 | |||
katG | True Resistant | gyrA | True Resistant | MUT1 | WT2 | Resistant | A90V | 2 |
n = (438) | (98.6%) | MUT3A | WT3 | Resistant | D94A | 1 | ||
MUT3C | WT3 | Resistant | D94G | 5 | ||||
MUT3D | WT3 | Resistant | D94H | 1 | ||||
Inferred Resistant | -- | WT1 | Resistant | -- | 1 | |||
-- | WT2 | Resistant | -- | 2 | ||||
gyrB | Inferred Resistant | -- | WT3 | Resistant | -- | 1 | ||
Inferred Resistant | gyrA | True Resistant | MUT3C | WT3 | Resistant | D94G | 1 | |
(1.4%) | ||||||||
inhA | True Resistant | gyrA | True Resistant | MUT1 | WT2 | Resistant | A90V | 1 |
n = (60) | (81.7%) | MUT3C | WT3 | Resistant | D94G | 2 | ||
Inferred Resistant | -- | WT1 | Resistant | -- | 1 | |||
Inferred Resistant | gyrA | True Resistant | MUT3C | WT3 | Resistant | D94G | 2 | |
(18.3%) |
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Ramachandra, V.; Brammacharry, U.; Muralidhar, A.; Muthukumar, A.; Mani, R.; Muthaiah, M.; Soundappan, G.; Frederick, A. Assess the Diagnostic Accuracy of GeneXpert to Detect Mycobacterium tuberculosis and Rifampicin-Resistant Tuberculosis among Presumptive Tuberculosis and Presumptive Drug Resistant Tuberculosis Patients. Microbiol. Res. 2024, 15, 91-108. https://doi.org/10.3390/microbiolres15010006
Ramachandra V, Brammacharry U, Muralidhar A, Muthukumar A, Mani R, Muthaiah M, Soundappan G, Frederick A. Assess the Diagnostic Accuracy of GeneXpert to Detect Mycobacterium tuberculosis and Rifampicin-Resistant Tuberculosis among Presumptive Tuberculosis and Presumptive Drug Resistant Tuberculosis Patients. Microbiology Research. 2024; 15(1):91-108. https://doi.org/10.3390/microbiolres15010006
Chicago/Turabian StyleRamachandra, Venkateswari, Usharani Brammacharry, Aaina Muralidhar, Anbazhagi Muthukumar, Revathi Mani, Muthuraj Muthaiah, Govindarajan Soundappan, and Asha Frederick. 2024. "Assess the Diagnostic Accuracy of GeneXpert to Detect Mycobacterium tuberculosis and Rifampicin-Resistant Tuberculosis among Presumptive Tuberculosis and Presumptive Drug Resistant Tuberculosis Patients" Microbiology Research 15, no. 1: 91-108. https://doi.org/10.3390/microbiolres15010006
APA StyleRamachandra, V., Brammacharry, U., Muralidhar, A., Muthukumar, A., Mani, R., Muthaiah, M., Soundappan, G., & Frederick, A. (2024). Assess the Diagnostic Accuracy of GeneXpert to Detect Mycobacterium tuberculosis and Rifampicin-Resistant Tuberculosis among Presumptive Tuberculosis and Presumptive Drug Resistant Tuberculosis Patients. Microbiology Research, 15(1), 91-108. https://doi.org/10.3390/microbiolres15010006