Evaluating the Impact of a Molecular Diagnostic Algorithm on Tuberculosis and Nontuberculous Mycobacterial Infections in Newfoundland and Labrador, Canada
Abstract
1. Introduction
2. Materials and Methods
2.1. Culture and AFB Smear
2.2. Molecular Diagnostics
2.3. Data Collection and Analysis
- Empiric: Treatment began before any diagnostic results were available.
- Rapid Diagnostics: Treatment was initiated after rapid diagnostics, smear, and/or LDT m-qPCR, results but before culture results were available.
- Culture-Based: Treatment was started after culture results were available.
3. Results
3.1. Diagnostic Assay Performance
3.2. Impact of Panel Approach on Case Management
3.3. Days to Diagnosis for MTBC
3.4. Days to Treatment for MTBC
3.5. Impact of Panel Approach on Cost
4. Discussion
4.1. Diagnostic Assay Performance
4.2. Impact on Case Management
4.3. Cost and Operational Considerations
4.4. Limitations and Confounders
4.5. Tuberculosis Control and Elimination
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
NAAT | Nucleic acid amplification testing |
MTBC | Mycobacterium tuberculosis complex |
TB | Tuberculosis |
NTM | Nontuberculous mycobacteria |
NL | Newfoundland and Labrador |
PHML | Provincial Public Health and Microbiology Laboratory |
NRCM | National Reference Center for Mycobacteriology |
Myco spp. | Mycobacterium spp. |
AFB | Acid-fast bacilli |
m-qPCR | Multiplex real-time polymerase chain reaction |
NALC | N-acetyl-l-cysteine |
MGIT | Mycobacteria Growth Indicator Tube |
NML | National Microbiology Laboratory |
LJ | Lowenstein–Jensen |
LDT | Laboratory-developed test |
ITS | Internal transcribed spacer |
GAPDH | Glyceraldehyde-3-phosphate dehydrogenase |
Ct | Cycle threshold |
PPV | Positive predictive value |
NPV | Negative predictive value |
N/A | Not applicable |
ID | Identification |
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Name | Sequence (5′ to 3′) | Final Conc. | Amplicon Length | Ref. |
---|---|---|---|---|
IS6110-F | CGGGACAACGCCGAATT | 300 | 53 | This Study |
IS6110-R | GCCGACGCGGTCTTTAAAA | 300 | ||
IS6110-P | /56-FAM/CGAAGGGCGAACGC/3MGBEC/ | 200 | ||
ITS-F | GGTGGGGTGTGGTGTTTGA | 200 | 147 | [18] |
ITS-R | TGGATAGTGGTTGCGAGCA | 200 | ||
ITS-P | /5HEX/TGGATAGTGGTTGCGAGCA/3MGBEC/ | 250 | ||
T4-F | ATCCAACACTAGGTTCTAACTGGACTG | 250 | 164 | This Study |
T4-R | CGCTGTCATAGCAGCTTCAG | 250 | ||
T4-P | /56-ROXN/CGGAAATTTCTTCATCTTCCTCTGG/3IABRQSP/ | 250 | ||
GAPDH-F | GGTGGTCTCCTCTGACTTCAACA | 100 | 71 | Modified from [19] |
GAPDH-R | TGAGGGCAATGCCAGCC | 100 | ||
GAPDH-P | /5CY5/CCACTCCTC/TAO/CACCTTTGACGCTGG/3IABRQSP/ | 100 |
Reflex Algorithm | Panel Approach | p-Value | |
---|---|---|---|
Total Patients Male/Female Median Age in Years (Range) | 2507 | 2071 | |
1372/1135 | 1098/973 | 0.25 | |
68 (1–104) | 67 (1–99) | <0.001 | |
MTBC Patients Male/Female Median Age in Years (Range) | 33 | 30 | |
21/12 | 21/10 | 0.80 | |
32 (1–79) | 42.5 (13–90) | 0.04 | |
NTM Patients | 40 | 64 | |
Male/Female | 10/30 | 18/46 | 0.82 |
Median Age in Years (Range) | 67 (2–91) | 67 (2–84) | 0.86 |
Smear (MTBC, NTM) | LDT m-qPCR MTBC Result | LDT m-qPCR Myco spp. Result 1 | Culture (MTBC, NTM) | |
---|---|---|---|---|
True Positive | 17 (11, 6) | 29 | 17 | 91 (27, 64) |
True Negative | 1922 | 2038 | 1956 | 1978 |
False Positive | 0 | 3 | 0 | 0 |
False Negative | 77 (19, 58) | 1 | 33 | 3 (3, 0) |
True Inconclusive 2 | N/A | N/A | 13 | N/A |
False Inconclusive 2 | N/A | N/A | 19 | N/A |
Sensitivity | 18.1% (36.7, 9.4) | 96.7% | 47.6% | 96.8% (90.0, 100) |
Specificity | 100% | 99.8% | 99.0% | 100% |
PPV | 100% | 90.6% | 61.2% | 100% |
NPV | 96.1% (99.0, 97.1) | 99.95% | 98.3% | 99.8% (99.9, 100) |
Number of MTBC Cases (%) | Number of NTM Cases (%) | |
---|---|---|
No Treatment | 0 (0%) | 45 (70%) |
Empiric | 1 (3%) | 0 (0%) |
m-qPCR+/Smear− | 17 (57%) | 0 (0%) |
m-qPCR+/Smear+ | 11 (37%) | 1 (2%) |
m-qPCR−/Smear+ | 0 (0%) | 0 (0%) |
Culture | 1 (3%) | 18 (28%) |
Reflex Median (n, Range) | Panel Median (n, Range) | Difference | p-Value | |
---|---|---|---|---|
Days to Diagnosis MTBC | 31 (33, 2–71) | 2 (30, 2–61) | 29 | p < 0.0001 |
Days to Diagnosis AFB+ | 6 (8, 2–23) | 2 (11, 1–5) | 4 | p = 0.08 |
Days to Diagnosis AFB− | 31 (25, 2–71) | 3 (19, 1–61) | 28 | p < 0.0001 |
Days to Diagnosis w/Rapid Culture ID | 16 (33, 1–59) | 2 (30, 1–42) | 14 | p = 0.003 |
Day to Treatment, All Cases | 18 (33, −1–103) | 5 (30, 0–62) | 13 | p = 0.002 |
Days to Treatment, Non-Empiric Only | 31 (25, 7–103) | 5.5 (29, 2–62) | 25.5 | p < 0.001 |
Days to Treatment, AFB+, Non-Empiric Only | 7 (5, 2–36) | 4 (11, 2–20) | 3 | p = 0.610 |
Days to Treatment, AFB−, Non-Empiric Only | 32 (20, 6–103) | 7.5 (18, 2–62) | 24.5 | p = 0.004 |
Cost Components | LDT Assay (CAD) | Commercial Assay (CAD) |
---|---|---|
Materials | CAD 13.26 | CAD 68.25 |
Labor | CAD 11.36 | CAD 1.36 |
Total | CAD 23.62 | CAD 69.61 |
Sputum Sensitivity (95% CI) | Respiratory 1 Sensitivity (95% CI) | |
---|---|---|
First Specimen Only | 94.74 (73.97–99.87) | 92.6% (75.71–99.09) |
First and Second | 94.74 (73.97–99.87) | 96.3% (81.03–99.91) |
All Specimens 2 | 94.74 (73.97–99.87) | 96.3% (81.03–99.91) |
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Needle, R.; Yu, Y.; Soualhine, H.; Yoshida, C.; Jiao, L.; Russell, R. Evaluating the Impact of a Molecular Diagnostic Algorithm on Tuberculosis and Nontuberculous Mycobacterial Infections in Newfoundland and Labrador, Canada. Biomedicines 2025, 13, 2416. https://doi.org/10.3390/biomedicines13102416
Needle R, Yu Y, Soualhine H, Yoshida C, Jiao L, Russell R. Evaluating the Impact of a Molecular Diagnostic Algorithm on Tuberculosis and Nontuberculous Mycobacterial Infections in Newfoundland and Labrador, Canada. Biomedicines. 2025; 13(10):2416. https://doi.org/10.3390/biomedicines13102416
Chicago/Turabian StyleNeedle, Robert, Yang Yu, Hafid Soualhine, Catherine Yoshida, Lei Jiao, and Rodney Russell. 2025. "Evaluating the Impact of a Molecular Diagnostic Algorithm on Tuberculosis and Nontuberculous Mycobacterial Infections in Newfoundland and Labrador, Canada" Biomedicines 13, no. 10: 2416. https://doi.org/10.3390/biomedicines13102416
APA StyleNeedle, R., Yu, Y., Soualhine, H., Yoshida, C., Jiao, L., & Russell, R. (2025). Evaluating the Impact of a Molecular Diagnostic Algorithm on Tuberculosis and Nontuberculous Mycobacterial Infections in Newfoundland and Labrador, Canada. Biomedicines, 13(10), 2416. https://doi.org/10.3390/biomedicines13102416