196. Agreement Between Nasal Mid-turbinate And Nasopharyngeal Swab to Detect Streptococcus pneumoniae by Polymerase Chain Reaction in Children And Adults.
Session: Poster Abstract Session: Diagnostics: Bacteriology, Sequencing, and Resistance
Thursday, October 27, 2016
Room: Poster Hall
  • Poster_Agreement between nasal and nasopharyngeal swabs_IDWEEK_20161024(3)_DV.pdf (610.2 kB)
  • Background:

    Polymerase chain reaction (PCR) is a reliable method for detecting S. pneumoniae (SPN) carriage and the nasopharynx is the sampling site recommend by the WHO. Correct sampling from the nasopharynx is uncomfortable and requires execution by trained staff. Nasal mid-turbinate 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 (RTI). Our goal was to determine the agreement between the NP and nasal swab to detect SPN carriage in children and adults using PCR.


    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 analysed 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 log10copies/ml SPN using the paired sample t-test.


    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 one 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 6-15 year olds. The difference in proportions of subjects positive in the NP swab (29.3%) compared to those with a positive nasal swab (25.7%) was not statistically significant (P=.54). The difference in mean SPN log10copies/ml was -0.06 (SD 1.4) (P=.83).


    PCR 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.

    Danielle Vuichard, MD, Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada, Pardeep Singh, BSc, Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada, Kathy Luinstra, ,, St. Joseph's Healthcare, Hamilton, ON, Canada, Jennifer Newton, ,, Michael G. Degroote Institute for Infectious Diseases Research, McMaster University, Hamilton, ON, Canada, Mark Loeb, MD, MSc, McMaster University, Hamilton, ON, Canada and Marek Smieja, MD, PhD, St. Joseph's Healthcare/McMaster University, Hamilton, ON, Canada


    D. Vuichard, None

    P. Singh, None

    K. Luinstra, None

    J. Newton, None

    M. Loeb, None

    M. Smieja, None

    Findings in the abstracts are embargoed until 12:01 a.m. CDT, Wednesday Oct. 26th with the exception of research findings presented at the IDWeek press conferences.