Evaluation of Each Three Entamoeba histolytica- and Strongyloides stercoralis-Specific Real-Time PCR Assays Applying Test Comparisons Without Reference Standards
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethics
2.2. Study Design and Sample Materials
2.3. Laboratory Diagnostics
2.4. Statistics
3. Results
3.1. Latent Class Analysis-Based Diagnostic Accuracy Assessment and Diagnostic Accuracy Adjusted Prevalences
3.2. Effects of Cycle Threshold Values
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
0.95 CI | 95% confidence interval |
AIDS | acquired immunodeficiency syndrome |
Ct | cycle threshold |
ddPCR | digital droplet polymerase chain reaction |
HIV | human immunodeficiency virus |
LAMP | loop-mediated isothermal amplification |
LCA | latent class analysis |
n | number |
n.e. | not estimable |
NGS | next generation sequencing |
max | maximum |
min | minimum, minute |
PCR | polymerase chain reaction |
RNA | ribosomal nucleic acid |
SD | standard deviation |
sec | second |
SREPH | small-subunit RNA episomal repeat sequence |
SSU | small subunit |
Appendix A
PCR Target | Strongyloides stercoralis (PCR 1) |
Target gene | Small-subunit rRNA gene |
Detection limit | 1.3 × 102 copies/µL |
Amplicon size | 101 base pairs |
Forward primer | 5′-GAA-TTC-CAA-GTA-AAC-GTA-AGT-CAT-TAG-C-3′ |
Reverse primer | 5′-TGC-CTC-TGG-ATA-TTG-CTC-AGT-TC-3′ |
Probe and modifications | 5′-CY5-ACA-CAC-CGG-CCG-TCG-CTG-C-BHQ2-3′ |
Positive control plasmid insert | 5′-AAC-GAG-GAA-TTC-CAA-GTA-AAC-GTA-AGT-CAT-TAG-CTT-ACA-TTG-ATT-ACG-TCC-CTG-CCC-TTT-GTA-CAC-ACC-GGC-CGT-CGC-TGC-CCG-GAA-CTG-AGC-AAT-ATC-CAG-AGG-CAG-GAA-GA-3′ |
GenBank accession number used for the insert | AF279916.2 |
Reference | [73] |
PCR target | Strongyloides stercoralis (PCR 2) |
Target gene | Small-subunit rRNA gene |
Amplicon size | 471 base pairs |
Detection limit | 4.0 × 101 copies/µL |
Forward primer | 5′-GGG-CCG-GAC-ACT-ATA-AGG-AT-3′ |
Reverse primer | 5′-TGC-CTC-TGG-ATA-TTG-CTC-AGT-TC-3′ |
Probe and modifications | 5′-Cy5-ACA-CAC-CGG-CCG-TCG-CTG-C-BHQ2-3′ |
Positive control plasmid insert | 5′-AAA-CTC-ACC-CGG-GCC-GGA-CAC-TAT-AAG-GAT-TGA-CAG-ATT-GAT-AGC-TCT-TTC-ATG-ATT-TAG-TGG-TTG-GTG-GTG-CAT-GGC-CGT-TCT-TAG-TTC-GTG-GAT-ATG-ATT-TGT-CTG-GTT-GAT-TCC-GAT-AAC-GAG-CGA-GAC-TTT-TAT-GTT-ATA-TTA-AAT-ATT-ATT-ATT-TTG-TTT-ATT-TTA-ATA-TAA-ATA-ATT-AAT-ATT-TTA-ATA-ACA-GAT-TAA-TAG-TGT-TTA-ACT-ATT-TGA-GAG-AGA-GCG-ATA-ACA-GGT-CTG-TGA-TGC-CCT-TAG-ATG-TCC-GGG-GCT-GCA-CGC-GCG-CTA-CAA-TGT-AGT-GAT-CAT-TAT-GTT-CCT-GTT-TAG-AGA-TAA-ATG-GGT-AAA-CAT-TGA-AAA-CAT-TAC-GTA-ACT-GGG-AAT-GAA-AAT-TGC-AAT-TAT-TTT-TCA-TGA-ACG-AGG-AAT-TCC-AAG-TAA-ACG-TAA-GTC-ATT-AGC-TTA-CAT-TGA-TTA-CGT-CCC-TGC-CCT-TTG-TAC-ACA-CCG-GCC-GTC-GCT-GCC-CGG-AAC-TGA-GCA-ATA-TCC-AGA-GGC-AGG-AAG-AGA-T-3′ |
GenBank accession number used for the insert | AF279916.2 |
Reference | [74] |
PCR target | Strongyloides stercoralis (PCR 3) |
Target gene | Strongyloides stercoralis dispersed repetitive sequence |
Amplicon size | 136 base pairs |
Detection limit | 7.5 × 101 copies/µL |
Forward primer | 5′-CGC-TCC-AGA-ATT-AGT-TCC-AGT-T-3′ |
Reverse primer | 5′-GCA-GCT-TAG-TCG-AAA-GCA-TAG-A-3′ |
Probe and modifications | 5′-6-FAM-ACA-GTC-TCC-AGT-TCA-CTC-CAG-AAG-AGT-BMN-Q535-3′ |
Positive control plasmid insert | 5′-ACA-GCT-CTC-ACG-CTC-CAG-AAT-TAG-TTC-CAG-TTG-AAT-AAC-AGT-CTC-CAG-TTC-ACT-CCA-GAA-GAG-TTC-CTA-TAA-TCC-TAA-CTC-AGC-TCC-AGT-AAA-GCA-ACA-GTT-TCC-AAC-CCC-TCA-CAA-AAG-AGC-TTC-TAT-GCT-TTC-GAC-TAA-GCT-GCA-GTA-TAG-GTA-3′ |
GenBank accession number used for the insert | AY028262.1 |
Reference | [75] |
Strongyloides stercoralis PCR 1 | Strongyloides stercoralis PCR 2 | Strongyloides stercoralis PCR 3 | |
---|---|---|---|
Reaction chemistry | |||
Master Mix | HotStar (Qiagen, Hilden, Germany) | HotStar (Qiagen, Hilden, Germany) | HotStar (Qiagen, Hilden, Germany) |
Reaction volume (µL) | 20.0 | 20.0 | 20.0 |
Forward primer concentration (nM) | 60.0 | 100.0 | 250.0 |
Reverse primer concentration (nM) | 60.0 | 100.0 | 250.0 |
Probe concentration (nM) | 250.0 | 100.0 | 125.0 |
Final Mg2+ concentration (mM) | 5.0 | 5.0 | 5.0 |
Eluate volume (µL) | 2.0 | 2.0 | 2.0 |
Run conditions | |||
Initial denaturation | 15 min. at 95 °C | 15 min. at 95 °C | 15 min. at 95 °C |
Cycle numbers | 50 | 45 | 45 |
Denaturation | 9 s at 95 °C | 15 s at 95 °C | 15 s at 95 °C |
Annealing and amplification | 60 s at 60 °C | 60 s at 59 °C | 60 s at 59 °C |
Hold | 30 s at 40 °C | 20 s at 30 °C | 20 s at 30 °C |
PCR Target | Entamoeba histolytica (PCR 1) |
Target gene | Small-subunit rRNA gene |
Detection limit | 1.0 × 103 copies/µL |
Amplicon size | 173 base pairs |
Forward primer | 5′-ATT-GTC-GTG-GCA-TCC-TAA-CTC-A-3′ |
Reverse primer | 5′-GCG-GAC-GGC-TCA-TTA-TAA-CA-3′ |
Probe and modifications | 5′-JOE-TCA-TTG-AAT-GAA-TTG-GCC-ATT-T-BHQ1-3′ |
Positive control plasmid insert | 5′-GGA-TGA-AAC-TGC-GGA-CGG-CTC-ATT-ATA-ACA-GTA-ATA-GTT-TCT-TTG-GTT-AGT-AAA-ATA-CAA-GGA-TAG-CTT-TGT-GAA-TGA-TAA-AGA-TAA-TAC-TTG-AGA-CGA-TCC-AGT-TTG-TAT-TAG-TAC-AAA-ATG-GCC-AAT-TCA-TTC-AAT-GAA-TTG-AGA-AAT-GAC-ATT-CTA-AGT-GAG-TTA-GGA-TGC-CAC-GAC-AAT-TGT-AGA-ACA-C-3′ |
GenBank accession number used for the insert | X64142 |
Reference | [48] |
PCR target | Entamoeba histolytica (PCR 2) |
Target gene | Small-subunit rRNA gene |
Amplicon size | 108 base pairs |
Detection limit | 7.0 × 100 copies/µL |
Forward primer | 5′-GGA-CAC-ATT-TCA-ATT-GTC-CTA-3′ |
Reverse primer | 5′-CAT-CAC-AGA-CCT-GTT-ATT-GCT-G-3′ |
Probe and modifications | 5′-Cy5-TGT-AGT-TAT-CTA-ATT-TCG-GTT-AGA-CC-BHQ2-3′ |
Positive control plasmid insert | 5′-CTT-CTT-AAA-GGG-ACA-CAT-TTC-AAT-TGT-CCT-ATT-TTA-ATT-GTA-GTT-ATC-TAA-TTT-CGG-TTA-GAC-CTC-TTT-TAA-CGT-GGG-AAA-AAG-AAA-AAG-GAA-GCA-TTC-AGC-AAT-AAC-AGG-TCT-GTG-ATG-CCC-TTA-GAC-A-3′ |
GenBank accession number used for the insert | X64142 |
Reference | [43] |
PCR target | Entamoeba histolytica (PCR 3) |
Target gene | small-subunit RNA episomal repeat sequence (SREPH) |
Amplicon size | 83 base pairs |
Detection limit | 4.6 × 101 copies/µL |
Forward primer | 5′-CAT-TAA-AAA-TGG-TGA-GGT-TCT-TAG-GAA-3′ |
Reverse primer | 5′-TGG-TCG-TCG-TCT-AGG-CAA-AAT-ATT-3′ |
Probe and modifications | 5′-FAM-TTG-ACC-AAT-TTA-CAC-CGT-TGA-TTT-TCG-BHQ1-3′ |
Positive control plasmid insert | 5′-TAG-TAC-TTT-TCA-TTA-AAA-ATG-GTG-AGG-TTC-TTA-GGA-AAT-CCG-AAA-ATC-AAC-GGT-GTA-AAT-TGG-TCA-AAA-AAT-ATT-TTG-CCT-AGA-CGA-CGA-CCA-TTT-TGA-ATA-A-3′ |
GenBank accession number used for the insert | no GenBank accession number, sequence from [91] |
Reference | [48] |
Entamoeba histolytica PCR 1 | Entamoeba histolytica PCR 2 | Entamoeba histolytica PCR 3 | |
---|---|---|---|
Reaction chemistry | |||
Master Mix | HotStarTaq (Qiagen, Hilden, Germany) | HotStarTaq (Qiagen, Hilden, Germany) | HotStarTaq (Qiagen, Hilden, Germany) |
Reaction volume (µL) | 20 | 20 | 20 |
Forward primer concentration (pmol/µL) | 125 | 500 | 500 |
Reverse primer concentration (pmol/µL) | 125 | 500 | 500 |
Probe concentration (pmol/µL) | 175 | 200 | 200 |
Final Mg2+ concentration (mM) | 5.0 | 1.5 | 1.5 |
Bovine serum albumin (mg/mL) | - | 2.0 | 2.0 |
Eluate volume (µL) | 2.0 | 2.0 | 2.0 |
Run conditions | |||
Initial denaturation | 95 °C for 15 min. | 95 °C for 15 min. | 95 °C for 15 min. |
Cycle numbers | 45 | 40 | 40 |
Denaturation | 95 °C for 15 s | 95 °C for 15 s | 95 °C for 15 s |
Annealing | Touchdown from 72 °C to 67 °C in 0.5 °C steps for 30 s | Touchdown from 60 °C to 52 °C in 0.5 °C steps for 30 s | Touchdown from 60 °C to 52 °C in 0.5 °C steps for 30 s |
Amplification | together with annealing | 72 °C for 30 s | 72 °C for 30 s |
Hold | 40 °C for 30 s | 30 °C for 20 s | 30 °C for 20 s |
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Assay | N | Positives (%) | Sensitivity (0.95 CI) | Specificity (0.95 CI) | Kappa (0.95 CI) |
---|---|---|---|---|---|
Strongyloides stercoralis PCR 1 | 873 | 15 (1.72) | 1 (0, 1) | 0.99 (0.86, 1) | 0.680 (0.475, 0.856) |
Strongyloides stercoralis PCR 2 | 873 | 13 (1.49) | 0.89 (0.50, 0.98) | 1 (0.88, 1) | |
Strongyloides stercoralis PCR 3 | 873 | 10 (1.15) | 0.89 (0.49, 0.99) | 1 (0.99, 1) | |
Prevalence of Strongyloides stercoralis | 1.15% |
Strongyloides Stercoralis PCR 1 | Strongyloides Stercoralis PCR 2 | Strongyloides Stercoralis PCR 3 | |||||
---|---|---|---|---|---|---|---|
Negative | Positive | Negative | Positive | Negative | Positive | ||
Strongyloides stercoralis PCR 1 | Negative | 854 | 4 | 857 | 1 | ||
Positive | 6 | 9 | 6 | 9 | |||
Strongyloides stercoralis PCR 2 | Negative | 858 | 2 | ||||
Positive | 5 | 8 | |||||
Strongyloides stercoralis PCR 3 | Negative | ||||||
Positive |
Assay | N | Positives (%) | Sensitivity (0.95 CI) | Specificity (0.95 CI) | Kappa (0.95 CI) |
---|---|---|---|---|---|
Entamoeba histolytica PCR 1 | 873 | 54 (6.19) | 0.75 (0.24, 0.97) | 0.94 (0.92, 0.96) | 0.108 (0.018, 0.313) |
Entamoeba histolytica PCR 2 | 873 | 4 (0.46) | 1 (0, 1) | 1 (n.e.) | |
Entamoeba histolytica PCR 3 | 873 | 4 (0.46) | 0.75 (0.24, 0.97) | 1 (0.99, 1) | |
Prevalence of Entamoeba histolytica | 0.46% |
Entamoeba Histolytica PCR 1 | Entamoeba Histolytica PCR 2 | Entamoeba Histolytica PCR 3 | |||||
---|---|---|---|---|---|---|---|
Negative | Positive | Negative | Positive | Negative | Positive | ||
Entamoeba histolytica PCR 1 | Negative | 818 | 1 | 817 | 2 | ||
Positive | 51 | 3 | 52 | 2 | |||
Entamoeba histolytica PCR 2 | Negative | 868 | 1 | ||||
Positive | 1 | 3 | |||||
Entamoeba histolytica PCR 3 | Negative | ||||||
Positive |
n | Mean (SD) | Median (Min., Max.) | Significance P (t-Test) | |
---|---|---|---|---|
Strongyloides stercoralis PCR 1—concordantly positive results with PCR 2 | 9 | 25.59 (3.12) | 25.19 (23.32, 32.4) | 0.0004 |
Strongyloides stercoralis PCR 1—discordantly positive results with PCR 2 | 6 | 32.36 (2.02) | 32.88 (29.22, 34.88) | |
Strongyloides stercoralis PCR 1—concordantly positive results with PCR 3 | 9 | 27.29 (3.30) | 26.17 (23.32, 32.40) | 0.0490 |
Strongyloides stercoralis PCR 1—discordantly positive results with PCR 3 | 6 | 31.31 (3.83) | 32.88 (24.5, 34.88) | |
Strongyloides stercoralis PCR 2—concordantly positive results with PCR 1 | 9 | 33.33 (2.45) | 33 (30, 37) | <0.0001 |
Strongyloides stercoralis PCR 2—discordantly positive results with PCR 1 | 4 | 42.25 (1.26) | 42 (41, 44) | |
Strongyloides stercoralis PCR 2—concordantly positive results with PCR 3 | 8 | 33.5 (2.56) | 33.5 (30, 37) | 0.0064 |
Strongyloides stercoralis PCR 2—discordantly positive results with PCR 3 | 5 | 40.2 (4.71) | 42 (32, 44) | |
Strongyloides stercoralis PCR 3—concordantly positive results with PCR 1 | 9 | 31.44 (2.07) | 31 (29, 36) | n.e. |
Strongyloides stercoralis PCR 3—discordantly positive results with PCR 1 | 1 | 35 (-) | 35 (35, 35) | |
Strongyloides stercoralis PCR 3—concordantly positive results with PCR 2 | 8 | 30.88 (1.25) | 31 (29, 33) | 0.0012 |
Strongyloides stercoralis PCR 3—discordantly positive results with PCR 2 | 2 | 35.5 (0.71) | 35.5 (35, 36) |
n | Mean (SD) | Median (Min., Max.) | Significance P (t-Test) | |
---|---|---|---|---|
Entamoeba histolytica PCR 1—concordantly positive results with PCR 2 | 3 | 23.75 (9.57) | 24.09 (14.01, 33.15) | 0.1218 |
Entamoeba histolytica PCR 1—discordantly positive results with PCR 2 | 51 | 37.83 (3.71) | 38.33 (18.1, 43.97) | |
Entamoeba histolytica PCR 1—concordantly positive results with PCR 3 | 2 | 19.05 (7.13) | 19.05 (14.01, 24.09) | <0.0001 |
Entamoeba histolytica PCR 1—discordantly positive results with PCR 3 | 52 | 37.74 (3.73) | 38.30 (18.1, 43.97) | |
Entamoeba histolytica PCR 2—concordantly positive results with PCR 1 | 3 | 27 (12.12) | 29 (14, 38) | n.e. |
Entamoeba histolytica PCR 2—discordantly positive results with PCR 1 | 1 | 21 (-) | 21 (21, 21) | |
Entamoeba histolytica PCR 2—concordantly positive results with PCR 3 | 3 | 21.33 (7.51) | 21 (14, 29) | n.e. |
Entamoeba histolytica PCR 2—discordantly positive results with PCR 3 | 1 | 38 (-) | 38 (38, 38) | |
Entamoeba histolytica PCR 3—concordantly positive results with PCR 1 | 2 | 21 (5.66) | 21 (17, 25) | 0.5084 |
Entamoeba histolytica PCR 3—discordantly positive results with PCR 1 | 2 | 28.5 (12.02) | 28.5 (20, 37) | |
Entamoeba histolytica PCR 3—concordantly positive results with PCR 2 | 3 | 20.67 (4.04) | 20 (17, 25) | n.e. |
Entamoeba histolytica PCR 3—discordantly positive results with PCR 2 | 1 | 37 (-) | 37 (37, 37) |
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Zautner, A.E.; Frickmann, H.; Hahn, A.; Sarfo, F.S.; Norman, B.R.; Dompreh, A.; Agyei, M.K.; Asibey, S.O.; Boateng, R.; Kuffour, E.O.; et al. Evaluation of Each Three Entamoeba histolytica- and Strongyloides stercoralis-Specific Real-Time PCR Assays Applying Test Comparisons Without Reference Standards. Microorganisms 2025, 13, 1976. https://doi.org/10.3390/microorganisms13091976
Zautner AE, Frickmann H, Hahn A, Sarfo FS, Norman BR, Dompreh A, Agyei MK, Asibey SO, Boateng R, Kuffour EO, et al. Evaluation of Each Three Entamoeba histolytica- and Strongyloides stercoralis-Specific Real-Time PCR Assays Applying Test Comparisons Without Reference Standards. Microorganisms. 2025; 13(9):1976. https://doi.org/10.3390/microorganisms13091976
Chicago/Turabian StyleZautner, Andreas Erich, Hagen Frickmann, Andreas Hahn, Fred Stephen Sarfo, Betty Roberta Norman, Albert Dompreh, Martin Kofi Agyei, Shadrack Osei Asibey, Richard Boateng, Edmund Osei Kuffour, and et al. 2025. "Evaluation of Each Three Entamoeba histolytica- and Strongyloides stercoralis-Specific Real-Time PCR Assays Applying Test Comparisons Without Reference Standards" Microorganisms 13, no. 9: 1976. https://doi.org/10.3390/microorganisms13091976
APA StyleZautner, A. E., Frickmann, H., Hahn, A., Sarfo, F. S., Norman, B. R., Dompreh, A., Agyei, M. K., Asibey, S. O., Boateng, R., Kuffour, E. O., Di Cristanziano, V., Tufa, T. B., Feldt, T., & Eberhardt, K. A. (2025). Evaluation of Each Three Entamoeba histolytica- and Strongyloides stercoralis-Specific Real-Time PCR Assays Applying Test Comparisons Without Reference Standards. Microorganisms, 13(9), 1976. https://doi.org/10.3390/microorganisms13091976