Agreement Between Nasal Midturbinate and Nasopharyngeal Swab to Detect Streptococcus pneumoniae by Polymerase Chain Reaction in Children and Adults
Bibliographic record
Abstract
Background. Polymerase chain reaction (PCR) is a reliable method for detecting Streptococcus pneumoniae (SPN) carriage, and the nasopharynx is the sampling site recommend by the World Health Organization. Correct sampling from the nasopharynx is uncomfortable and requires execution by trained staff. Nasal midturbinate sampling is more convenient and feasible. Comparison of nasal and nasopharyngeal (NP) swabs using culture methods showed high concordance in detecting SPN carriage in youngest children with prevalent respiratory tract infections (RTIs). Our goal was to determine the agreement between the NP and nasal swab to detect SPN carriage in children and adults using PCR. Methods. In a prospective cohort study on influenza viral shedding in Canadian Hutterite communities, pairs of NP and nasal flocked swabs were obtained in participants with and without RTI. The stored samples were analyzed for the presence of SPN using a real-time PCR assay targeting lytA gene. We determined sensitivity and specificity of the nasal swab with the NP swab as reference standard and applied McNemar's test for differences in proportions. We assessed the difference in means of log10 copies/mL SPN using the paired sample t test. Results. Of 152 individuals, 53 (34.9%) tested positive for SPN. Median age (range) was 11 (0–74) years. Ninety-seven (63.8%) subjects had at least 1 symptom suggesting ARI with the highest proportion (91%) among children <6 years of age. Overall sensitivity of the nasal swab was 67.4% (95% confidence interval [CI], 51.5–80.9), and specificity was 90.8% (95% CI, 83.8–95.5). Sensitivity was 95.2% (95% CI, 76.2–99.9) in children <6 years of age but was only 52.6 (95% CI, 28.9–75.6) in 6- to 15-year-olds. The difference in proportions of subjects positive in the NP swab (29.3%) compared with those with a positive nasal swab (25.7%) was not statistically significant (P = .54). The difference in mean SPN log10 copies/mL was −0.06 (standard deviation = 1.4; P = .83). Conclusion. Polymerase chain reaction from nasal and NP specimen yielded similar SPN log amounts. Consistent with previous studies, agreement between NP and nasal swab was high in youngest children where the less convenient NP swab could be substituted by a nasal swab. This did not hold true for older children and adults. Disclosures. All authors: No reported disclosures.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".