Contribution of the Rapid LAMP-Based Diagnostic Test (RLDT) to the Evaluation of Enterotoxigenic Escherichia coli (ETEC) and Shigella in Childhood Diarrhea in the Peri-Urban Area of Ouagadougou, Burkina Faso
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Design and Participants
2.2. Laboratory Methods
- Collection of stool specimens, isolation, and identification of Shigella and ETEC
- ETEC and Shigella RLDTs analysis.
2.3. Statistical Analysis
3. Results
3.1. Stool Samples Used for Shigella and ETEC Testing
3.2. Stool Samples Positivity for Shigella and ETEC According to Diagnostic Tool
- Coinfection of Shigella and ETEC
3.3. ETEC Toxins Genes Distribution using RLDT
3.4. Performance of the RLDT against Culture for Shigella and ETEC Detection
- Performance of RLDT against culture for Shigella detection
- Performance of the RLDT against culture followed by PCR for ETEC detection
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
EDCTP | European and Developing countries Clinical trial Partnership |
ETEC | Enterotoxigenic Escherichia coli |
LT | Heat-labile enterotoxin |
STp | Heat-stable enterotoxin Porcine |
STh | Heat-stable enterotoxin Human |
PCR | Polymerase chain reaction |
RLDT | Rapid LAMP-based diagnostic test |
Sd | Standard deviation |
WHO | World Health Organisation |
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ETEC Toxin/Virulence Factor | Target Gene | Primer Name | Primer Sequences (5′ to 3′) | Amplicon Size (bp) |
---|---|---|---|---|
LT | eltB | LTF | ACG GCG TTA CTA TCC TCT C | 274 |
LTR | TGG TCT CGG TCA GAT ATG TG | |||
STp | estA1 | STpF1 | TCT TTC CCC TCT TTT AGT CAG | 166 |
STpR2 | ACA GGC AGG ATT ACA ACA AAG | |||
STh | estA2 | SThnyF | TTCACCTTTCCCTCAGGATG | 120 |
SThnyR | CTATTATTCATGCTTTCAGGACCA |
Well | A | B | C | D | E | F | G | H |
Gene | ipaH | control | ipaH | control | ipaH | control | ipaH | control |
Well | A | B | C | D | E | F | G | H |
Gene | LT | STh | STp | control | LT | STh | STp | control |
Shigella n = 263 (44.87) | ETEC n = 165 (23.19) | |
Characteristics | ||
Age (Months) | ||
0–11 | 57 (21.7) | 38 (23.0) |
12–23 | 81 (30.8) | 49 (29.7) |
24+ | 125 (47.5) | 78 (47.3) |
Gender | ||
Male | 134 (51.0) | 79 (47.9) |
Female | 129 (49.1) | 86 (52.1) |
Type of stool | ||
Diarrheal | 155 (58.9) | 104 (63.0) |
Non-diarrheal | 108 (41.1) | 61 (37.0) |
Severity scoring (Vesikari score for diarrheal cases) | ||
Mild | 144 (93.0) | 98 (24.6) |
Moderate | 5 (3.2) | 2 (24.6) |
Severe | 6 (3.9) | 4 (24.6) |
Stunted (HAZ < −2.0) | ||
Yes | 67 (25.5) | 48 (29.1) |
No | 196 (74.5) | 117 (70.9) |
RLDT | Culture | ||
---|---|---|---|
Characteristics | Proportion of Positive Shigella using RLDT | Proportion of Positive Shigella by Culture | p-Value |
Overall | 118 (44.9 *) | 61 (23.2 *) | <0.001 |
Age (Months) | |||
0–11 | 29 (50.9) | 13 (22.8) | <0.001 |
12–23 | 41 (50.6) | 17 (21.0) | |
24+ | 48 (38.4) | 31 (24.8) | |
Gender | |||
Male | 61 (45.5) | 27 (20.2) | <0.001 |
Female | 57 (44.2) | 34 (26.4) | |
Type of stool | |||
Diarrheal | 75 (48.4) | 29 (18.7) | <0.001 |
Non-diarrheal | 43 (39.8) | 32 (29.6) | |
Severity scoring (Vesikari score for diarrheal cases) | |||
Mild | 69 (47.9) | 28 (19.4) | <0.001 |
Moderate | 2 (40.0) | 0 | |
Severe | 4 (66.7) | 1 (16.7) | |
Stunted (HAZ < −2.0) | |||
Yes | 29 (43.3) | 13 (19.4) | <0.001 |
No | 89 (45.4) | 48 (24.5) |
Shigella Culture (as the Gold Standard) vs. RLDT | ||||||||
---|---|---|---|---|---|---|---|---|
Total Samples Screened | Samples Positive via RLDT (%) | Samples Positive via Culture (%) | False Positive | False Negative | Sensitivity (95%CI) | Specificity (95%CI) | PPV (95%CI) | NPV (95%CI) |
263 | 118 | 57 | 61 | 4 | 93.4 (90.5, 96.4) | 69.8 (64.3, 75.4) | 48.3 (42.3, 54.3) | 97.2 (95.3, 99.2) |
Cohen’s Kappa RLDT Stool Culture for Shigella Detection | |||||
---|---|---|---|---|---|
Agreement | Expected Agreement | Kappa | Std. error | z | p Value |
75.29% | 52.75% | 0.4769 | 0.0548 | 8.70 | <0.001 |
Cohen’s Kappa RLDT Stool Culture for ETEC Detection | |||||
---|---|---|---|---|---|
Agreement | Expected Agreement | Kappa | Std. err. | z | p Value |
78.18% | 73.02% | 0.1914 | 0.0503 | 3.81 | <0.001 |
ETEC Culture (as the Gold Standard *) vs. RLDT | ||||||||
---|---|---|---|---|---|---|---|---|
Total Samples Screened | Samples Positive via ETEC RLDT | Samples Positive via Culture | False Positive | False Negative | Sensitivity (95%CI) | Specificity (95%CI) | PPV (95%CI) | NPV (95%CI) |
165 | 41 | 7 | 35 | 1 | 83.7 (80.37, 91.1) | 77.9 (71.5, 84.2) | 14.6 (9.2, 20.0) | 99.2 (97.8, 100.6) |
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Héma, A.; Sermé, S.S.; Sawadogo, J.; Diarra, A.; Barry, A.; Ouédraogo, A.Z.; Nébié, I.; Tiono, A.B.; Houard, S.; Chakraborty, S.; et al. Contribution of the Rapid LAMP-Based Diagnostic Test (RLDT) to the Evaluation of Enterotoxigenic Escherichia coli (ETEC) and Shigella in Childhood Diarrhea in the Peri-Urban Area of Ouagadougou, Burkina Faso. Microorganisms 2023, 11, 2809. https://doi.org/10.3390/microorganisms11112809
Héma A, Sermé SS, Sawadogo J, Diarra A, Barry A, Ouédraogo AZ, Nébié I, Tiono AB, Houard S, Chakraborty S, et al. Contribution of the Rapid LAMP-Based Diagnostic Test (RLDT) to the Evaluation of Enterotoxigenic Escherichia coli (ETEC) and Shigella in Childhood Diarrhea in the Peri-Urban Area of Ouagadougou, Burkina Faso. Microorganisms. 2023; 11(11):2809. https://doi.org/10.3390/microorganisms11112809
Chicago/Turabian StyleHéma, Alimatou, Samuel S. Sermé, Jean Sawadogo, Amidou Diarra, Aissata Barry, Amidou Z. Ouédraogo, Issa Nébié, Alfred B. Tiono, Sophie Houard, Subhra Chakraborty, and et al. 2023. "Contribution of the Rapid LAMP-Based Diagnostic Test (RLDT) to the Evaluation of Enterotoxigenic Escherichia coli (ETEC) and Shigella in Childhood Diarrhea in the Peri-Urban Area of Ouagadougou, Burkina Faso" Microorganisms 11, no. 11: 2809. https://doi.org/10.3390/microorganisms11112809
APA StyleHéma, A., Sermé, S. S., Sawadogo, J., Diarra, A., Barry, A., Ouédraogo, A. Z., Nébié, I., Tiono, A. B., Houard, S., Chakraborty, S., Ouédraogo, A., & Sirima, S. B. (2023). Contribution of the Rapid LAMP-Based Diagnostic Test (RLDT) to the Evaluation of Enterotoxigenic Escherichia coli (ETEC) and Shigella in Childhood Diarrhea in the Peri-Urban Area of Ouagadougou, Burkina Faso. Microorganisms, 11(11), 2809. https://doi.org/10.3390/microorganisms11112809