Nasopharyngeal Swabs Most Sensitive for Pneumococcal Detection in Infants


Study authors suggest that saliva samples can be a complementary testing method to provide additional information on pneumococcal carriage and serotypes that may be undetected by nasopharyngeal testing.

Key Takeaways

  1. Pneumococcal Carriage Detection in Children: In children, detecting pneumococcal carriage is commonly done through nasopharyngeal swabs; however, saliva has shown to be a sensitive method for surveying pneumococcal colonization, particularly in older age groups. The study authors aimed to investigate whether nasopharyngeal sampling might be underdetecting carriage prevalence in 24-month-old children.
  2. Sensitivity of Different Detection Methods: The study compared culture-based methods, quantitative polymerase chain reaction (qPCR), and saliva samples for detecting pneumococcal carriage in children. The results indicated that culture-based detection from nasopharyngeal swabs had relatively high sensitivity.
  3. Benefits of qPCR and Saliva Sampling: Testing culture-enriched nasopharyngeal samples by qPCR was proven to be the most sensitive method because it detected more carriers compared to either conventional culture or qPCR detection of saliva alone. Saliva sampling can serve as a complementary method of testing that can provide additional information on carriage and serotypes undetected in the nasopharynx, benefiting research on upper respiratory tract commensals, pathogens, immune responses, and overall tolerability.

Detecting pneumococcal carriage in children is performed with a nasopharyngeal swab; however, saliva has been shown to be a very sensitive method of surveying pneumococcal colonization and has improved detection in older age groups. Children are typically the focus of surveillance in pneumococcal carriage prior to or following updated vaccination strategies. To investigate whether nasopharyngeal sampling was underdetecting carriage prevalence, a cross-sectional study published in Microbiology evaluated the sensitivity of culture and molecular (quantitative polymerase chain reaction [qPCR]) methods for pneumococcal carriage detection in nasopharyngeal swabs and saliva samples collected from children aged 24 months.

Paired nasopharyngeal swabs and saliva samples were collected from 288 children aged 24 months. Nasopharyngeal swabs were processed by a conventional diagnostic culture for pneumococcal carriage detection with isolates serotyped. Further, the DNA extracted from plate harvests was tested using qPCR and saliva samples from the participants who were tested using qPCR for the presence of sequences specific to pneumococcal serotypes or serogroups (1; 3; 6A, 6B, 6C, and 6D; 7 A and 7F; 8; 9 A, 9N, and 9V; 10A and 10B; 12A, 12B, and 12F; 14; 15A, 15B, and 15C; 19A; 20; 23F; 33A and 33F; 37; 11A and 11D; 16F; 18B and 18C; and 19F).

Further, pneumococcus-positive samples were categorized as positive for pneumococcal serotype or serogroup from assessments determined to be specific for pneumococcus, when CT values for targeted genes were less than 40. The results from the detection of pneumococcus in saliva samples obtained in the current study were analyzed together alongside the results of pneumococcal carriage and serotype detection in their paired nasopharyngeal swabs.

Results indicated that culture-based detection of pneumococcal carriers when testing nasopharyngeal swabs was of relatively high sensitivity; however, isolation of live pneumococci from saliva at the initial culture step was impossible due to abundant polymicrobial growth on plates. A total of 161 (60%) nasopharyngeal swabs tested positive for pneumococcus by culture; however, detection was not possible from saliva due to the abundant polymicrobial growth on the culture plates.

Health care worker testing a nasal swab

Image credit: RomanR |

Testing of culture-enriched nasopharyngeal samples by qPCR was the most sensitive, with 187 (65%) of 288 nasopharyngeal swabs testing positive, compared to 155 (54%) detected with saliva alone. The authors note that culture enrichment can enhance carriage detection in low-density carriers of secondary—or lesser—serotypes co-carried in a sample when serotype surveillance is taken into consideration.

A total of 219 (76%) infants had tested positive for pneumococcus, with qPCR-based carriage detection of culture-enriched nasopharyngeal swabs detecting significantly more carriers compared to either conventional culture or qPCR detection of saliva. In addition, 32 (15%) of the 219 infants that tested positive were only positive in saliva. The overall serotype detection in saliva samples had correlated well with qPCR detection in nasopharyngeal swabs, according to the study authors.

A limitation of the study was that it included the use of qPCR to test saliva for pneumococcal carriage detection due to its potential for confounding assessments as a result of the presence of closely-related homologous genetic sequences. The authors note that it is impossible to specifically test for all pneumococcal serotypes in polymicrobial oral samples; however, future vaccines may surpass pneumococcal serotypes by protecting all pneumococci, which are independent of the capsular polysaccharide that is expressed.

Although testing nasopharyngeal swabs by qPCR demonstrated to be the most sensitive for detecting pneumococcus in infants, the study authors note that saliva sampling may serve as a complementary method to provide additional information on carriage and serotypes that may be undetected in the nasopharynx. Further, the authors suggest that saliva samples may benefit broader research because of its potential to be used for other upper respiratory tract commensals or pathogens, immune responses, as well as its general tolerability.


Wyllie AL, Rots NY, Wijmenga-Monsuur AJ, et al. Saliva as an alternative sample type for detection of pneumococcal carriage in young children. Microbiology. 2023;169(10). doi:10.1099/mic.0.001394

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