Epidemiology of Streptococcus pneumoniae Serotypes in Jordan Amongst Children Younger than the Age of 5: A National Cross-Sectional Study
Abstract
:1. Introduction
2. Methods
2.1. Case Definition [20,21]
2.2. Inclusion Criteria
3. Exclusion Criteria
- Children receiving routine pneumococcal vaccination as part of the private sector vaccination program or as high-risk groups. Only one case was excluded from the study due to receiving PCV-13 in a private clinic.
- Not permanently resident in the study area.
Sample Size Calculations [22,23,24]
4. Microbiology
- PCR-positive cases: For cases with radiological findings suggestive of lobar pneumonia, as described in the radiology section below, blood samples were collected on admission. PCR was used to identify Streptococcus pneumoniae and for serotyping.
- Culture-positive cases: For invasive pneumococcal disease cases (pneumonia, meningitis, septicemia, etc.) identified during the study period at study sites, a Quellung test was performed for serotyping.
5. Sample Collection and PCR Analysis
6. Culture and Identification
7. Serotyping for Culture-Positive Cases
8. Radiological Findings
9. Results
10. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Serotype | Primer Name | Sequence (5′-3′) | Frequency for All Participants | Frequency for Cases < 2 Year of Age, N = 754 | Mean Age | Age SD | Presence of Congenital Disease | Presence of Chronic Illness | Percentage in Pneumonia Cases |
---|---|---|---|---|---|---|---|---|---|
PCV-10 | 45.32% | 45.23% | 15.5 | 16.2 | 1.77% | 7.09% | 44.63% | ||
1 | 1-F,1-R [51] | 5′-TTTCATCCCTATGTGTGGTATAG-3′, 5′-GCTTTAGAAGGTAGAGTTAACAAC-3′ | 3.84% | 3.32% | 19.6 | 18.3 | 0.30% | 0.89% | 3.74% |
4 | 4-F,4-R [51] | 5′-GCTTCTGCTGTAACTGTTGTGC-3′, 5′-CACCACCATAGTAACCAAAGTTCC-3′ | 0.79% | 0.66% | 16.5 | 17.9 | 0.00% | 0.20% | 0.79% |
5 | 5-F,5R [51] | 5′-CATGATTTATGCCCTCTTGCAA-3′, 5′-GACAGTATAAGAAAAAGCAAGGGCTAA-3′ | 0.99% | 0.93% | 17 | 14.5 | 0.00% | 0.10% | 0.99% |
6B | 6B-F, 6B-R [52] | CGA CGT AAC AAA GAA CTA GGT GCT GAA AC, AAG TAT ATA ACC ACG CTG TAA AAC TCT GAC | 16.45% | 15.65% | 16.2 | 16.9 | 0.49% | 2.86% | 16.45% |
7F | 7F-F, 7F-R [53] | 5′-CCTACGGGAGGATATAAAATTATTTTTGAG-3′, 5′-CAAATACACCATATAGGCTGTTGAGACTAAC-3′ | 0.30% | 0.40% | 8.6 | 12.5 | 0.00% | 0.10% | 0.30% |
9V | 9V-F, 9V-R [53] | 5′-CTTCGTTAGTTAAAATTCTAAATTTTTCTAAG-3′, 5′-GTCCCAATACCAGTCCTTGCAACACAAG-3′ | 0.10% | 0.13% | 1 | 0 | 0.00% | 0.00% | 0.10% |
14 | 14-F, 14-R [51] | 5′-AGAGTGTATGAGGAATCC-3′, 5′-ATATATCTACTGTAGAGGGAAT-3′ | 12.12% | 12.60% | 14.5 | 16.3 | 0.59% | 1.38% | 11.72% |
18C | 18C-F, 18C-R [54] | 5′-CTTAATAGCTCTCATTATTCTTTTTTTAAGCC-3′, 5′-TTATCTGTAAACCATATCAGCATCTGAAAC-3′ | 1.08% | 1.19% | 12.7 | 16.1 | 0.00% | 0.10% | 1.08% |
19F | 19F-F, 19F-R [51] | 5′-TGAGGTTAAGATTGCTGATCG-3′, 5′-CACGAATGAGAACTCGAATAAAAG-3′ | 8.18% | 8.62% | 15.3 | 14.5 | 0.30% | 1.18% | 8.08% |
23F | 23F-F, 23F-R [51] | 5′-GACAGCAACGACAATAGTCATCTC-3′, 5′-TCCATCCCAACCTAACACACTTC-3′ | 1.48% | 1.72% | 9.7 | 12.6 | 0.10% | 0.30% | 1.38% |
PCV-13 | 61.87% | 61.54% | 15.5 | 16.6 | 2.76% | 8.57% | 60.79% | ||
3 | 3-F, 3-R [51] | 5′-CCACTAAAGCTTTGGCAAAAGAAA-3′, 5′-CCCGAACGTAAAGCTTCTTCA-3′ | 1.18% | 0.93% | 20 | 17.5 | 0.10% | 0.10% | 1.08% |
6A | 6A-F, 6A-R [52] | AAT TTG TAT TTT ATT CAT GCC TAT ATC TGG, TTA GCG GAG ATA ATT TAA AAT GAT GAC TA | 13.60% | 14.06% | 14.5 | 17.6 | 0.79% | 1.28% | 13.50% |
19A | 19A-F, 19A-R [51] | 5′-CGCCTAGTCTAAATACCA-3′, 5′-GAGGTCAACTATAATAGTAAGAG-3′ | 1.77% | 1.33% | 18.7 | 17.9 | 0.10% | 0.10% | 1.58% |
PCV-15 | 64.14% | 63.79% | 15.5 | 16.6 | 2.76% | 8.77% | 63.05% | ||
22F | 22F-F, 22F-R [51] | 5′-CTTGTCAAGTATGCTGAGGATTTG-3′, 5′-AGATTTCTCCTGGATATAATGCGAT-3′ | 1.58% | 1.59% | 15.7 | 16.6 | 0.00% | 0.20% | 1.58% |
33F | 33F-F, 33F-R [55] | 5′-GAAGGCAATCAATGTGATTGTGTCGCG-3′, 5′-CTTCAAAATGAAGATTATAGTACCCTTCTAC-3′ | 0.69% | 0.66% | 15.9 | 17 | 0.00% | 0.00% | 0.69% |
PCV-20 | 68.47% | 68.44% | 15.3 | 16.6 | 2.96% | 9.36% | 67.39% | ||
8 | 8-F, 8-R [51] | 5′-ATTCTAATTACTACATTACTGCTTTATACTA-3′, 5′-TCTTCTTAAATCATAATGAATCGTACC-3′ | |||||||
10A | 10A-F, 10A-R [51] | 5′-TAGTGTCGGCAGACAAATTAT-3′, 5′-CACGCTCATACACTTTATTTGA-3′ | 0.20% | 0.13% | 34.5 | 29 | 0.00% | 0.00% | 0.20% |
11A | 11A-F, 11A-R [55] | 5′-GGACATGTTCAGGTGATTTCCCAATATAGTG-3′, 5′-GATTATGAGTGTAATTTATTCCAACTTCTCCC-3′ | 1.77% | 1.86% | 12.9 | 15.9 | 0.00% | 0.30% | 1.77% |
12F | 12F-F, 12F-R [55] | 5′-GCAACAAACGGCGTGAAAGTAGTTG-3′, 5′-CAAGATGAATATCACTACCAATAACAAAAC-3′ | 1.87% | 1.99% | 11.9 | 15.9 | 0.00% | 0.10% | 1.87% |
15B | 15B-F, 15B-R [54] | 5′-ATTAGTACAGCTGCTGGAATATCTCTTC-3′, 5′-GATCTAGTGAACGTACTATTCCAAAC-3′ | 0.49% | 0.66% | 4.4 | 6.2 | 0.20% | 0.20% | 0.49% |
Total other serotypes | 31.53% | 31.56% | 14.3 | 15.2 | 1.28% | 3.25% | 31.43% | ||
11 Non-A subserotypes | Quellung test for culture-positive cases | 1.08% | 1.06% | 15.6 | 16.6 | 0.10% | 0.20% | 1.08% | |
15 Non-B subserotypes | Quellung test for culture-positive cases | 0.30% | 0.13% | 20 | 9.5 | 0.00% | 0.10% | 0.30% | |
16 | Quellung test for culture-positive cases | 0.59% | 0.53% | 20.7 | 15.3 | 0.10% | 0.20% | 0.59% | |
18 Non-C subserotypes | Quellung test for culture-positive cases | 0.39% | 0.40% | 14.8 | 17.3 | 0.00% | 0.00% | 0.39% | |
22 Non-F subserotypes | Quellung test for culture-positive cases | 0.69% | 0.53% | 21.4 | 13.3 | 0.00% | 0.10% | 0.69% | |
28 | Quellung test for culture-positive cases | 0.10% | 0.13% | 6 | 0 | 0.00% | 0.10% | 0.00% | |
33 Other subserotypes | Quellung test for culture-positive cases | 0.10% | 0.13% | 20 | 0 | 0.00% | 0.10% | 0.10% | |
3F | Quellung test for culture-positive cases | 0.10% | 0.13% | 5 | 0 | 0.00% | 0.00% | 0.10% | |
5A | Quellung test for culture-positive cases | 0.10% | 0.00% | 26 | 0 | 0.00% | 0.00% | 0.10% | |
6C/6D | Quellung test for culture-positive cases | 0.10% | 0.13% | 7 | 0 | 0.00% | 0.00% | 0.10% | |
7 Non-F subserotypes | Quellung test for culture-positive cases | 0.49% | 0.40% | 22 | 20.7 | 0.00% | 0.00% | 0.49% | |
other serotype | Not identified through above primers for PCR-positive cases | 27.49% | 27.98% | 13.8 | 15.3 | 1.08% | 2.46% | 27.49% |
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Pneumococcal Vaccine | Covered Serotypes |
---|---|
PCV-7 [8] | 4, 6B, 9V, 14, 18C, 19F, and 23F |
PCV-10 [9] | PCV-7 plus 1, 5, and 7F |
PCV-13 [10] | PCV-10 plus 3, 6A, and 19A |
PCV-15 [14] | PCV-13 plus 22F and 33F |
PCV-20 [17] | PCV-15 plus 8, 10A, 11A, 12F, and 15 |
Variable | Category | N (%) |
---|---|---|
Sex | Male | 584 (57.5%) |
Female | 431 (42.5%) | |
Birth history | Full term | 937 (92.3%) |
Preterm | 78 (7.7%) | |
Mode of delivery | Normal VD | 683 (67.3%) |
Caesarean section | 332 (32.2%) | |
Congenital conditions | Yes | 78 (7.7%) |
Congenital heart disease | Yes | 43 (4.2%) |
Chronic illness | Yes | 128 (12.6%) |
Asthma | Yes | 25 (2.5%) |
Family members’ smoking place | Inside home | 438 (43.2%) |
Only outside home | 42 (4.1%) | |
Not smoker | 535 (52.7%) | |
Patient received antibiotics within a week of admission | Yes | 213 (21.0%) |
Previous hospitalization | Yes | 220 (21.7%) |
Patient receives regular medications | Yes | 59 (5.8%) |
Fever | Yes | 715 (70.4%) |
Blood culture | Positive | 23 (2.2%) |
Negative | 987 (97.3%) | |
Not performed | 5 (0.5%) | |
Complications during admission | Yes | 117 (11.5%) |
Required ICU admission | Not admitted | 774 (76.2%) |
Admitted and intubated | 95 (9.4%) | |
Admitted and not intubated | 146 (14.4%) | |
WBC (leukocytosis) | Negative | 255 (25.1%) |
Positive | 760 (74.9%) |
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Abu-Helalah, M.; Al-Mnayyis, A.; Alzoubi, H.; Al-Abdallah, R.; Jdaitawi, H.; Nafi, O.; Abu-Sal, K.; Altawalbeh, A.; Khlaifat, A.; Al-Zayadneh, E.; et al. Epidemiology of Streptococcus pneumoniae Serotypes in Jordan Amongst Children Younger than the Age of 5: A National Cross-Sectional Study. Vaccines 2023, 11, 1396. https://doi.org/10.3390/vaccines11091396
Abu-Helalah M, Al-Mnayyis A, Alzoubi H, Al-Abdallah R, Jdaitawi H, Nafi O, Abu-Sal K, Altawalbeh A, Khlaifat A, Al-Zayadneh E, et al. Epidemiology of Streptococcus pneumoniae Serotypes in Jordan Amongst Children Younger than the Age of 5: A National Cross-Sectional Study. Vaccines. 2023; 11(9):1396. https://doi.org/10.3390/vaccines11091396
Chicago/Turabian StyleAbu-Helalah, Munir, Asma’a Al-Mnayyis, Hamed Alzoubi, Ruba Al-Abdallah, Hussein Jdaitawi, Omar Nafi, Kamel Abu-Sal, Alaa Altawalbeh, Alia Khlaifat, Enas Al-Zayadneh, and et al. 2023. "Epidemiology of Streptococcus pneumoniae Serotypes in Jordan Amongst Children Younger than the Age of 5: A National Cross-Sectional Study" Vaccines 11, no. 9: 1396. https://doi.org/10.3390/vaccines11091396
APA StyleAbu-Helalah, M., Al-Mnayyis, A., Alzoubi, H., Al-Abdallah, R., Jdaitawi, H., Nafi, O., Abu-Sal, K., Altawalbeh, A., Khlaifat, A., Al-Zayadneh, E., Almaaitah, I., Borghol, I., Batarseh, F., Okkeh, O., Dalal, A., Alhendi, A., Almaaitah, M., Al-Lahham, A., Gazo, M., ... Elnasser, Z. (2023). Epidemiology of Streptococcus pneumoniae Serotypes in Jordan Amongst Children Younger than the Age of 5: A National Cross-Sectional Study. Vaccines, 11(9), 1396. https://doi.org/10.3390/vaccines11091396