Saliva as an alternative sample type for detection of pneumococcal carriage in young children

Abstract

For children, the gold standard for the detection of pneumococcal carriage is conventional culture of a nasopharyngeal swab. Saliva, however, has a history as one of the most sensitive methods for surveillance of pneumococcal colonization and has recently been shown to improve carriage detection in older age groups. Here, we compared the sensitivity of paired nasopharyngeal and saliva samples from PCV7-vaccinated 24-month-old children for pneumococcal carriage detection using conventional and molecular detection methods. Nasopharyngeal and saliva samples were collected from 288 24-month-old children during the autumn/winter, 2012/2013. All samples were first processed by conventional diagnostic culture. Next, DNA extracted from all plate growth was tested by qPCR for the presence of the pneumococcal genes piaB and lytA and a subset of serotypes. By culture, 161/288 (60 %) nasopharyngeal swabs tested positive for pneumococcus, but detection was not possible from saliva due to abundant polymicrobial growth on culture plates. By qPCR, 155/288 (54 %) culture-enriched saliva samples and 187/288 (65 %) nasopharyngeal swabs tested positive. Altogether, 219/288 (76 %) infants tested positive for pneumococcus, with qPCR-based carriage detection of culture-enriched nasopharyngeal swabs detecting significantly more carriers compared to either conventional culture (P<0.001) or qPCR detection of saliva (P=0.002). However, 32/219 (15 %) carriers were only positive in saliva, contributing significantly to the overall number of carriers detected (P=0.002). While testing nasopharyngeal swabs by qPCR proved most sensitive for pneumococcal detection in infants, saliva sampling could be considered as complementary to provide additional information on carriage and serotypes that may not be detected in the nasopharynx and may be particularly useful in longitudinal studies, requiring repeated sampling of study participants.

A low-cost culture- and DNA extraction-free method for the molecular detection of pneumococcal carriage in saliva

“…A total of 759 saliva samples collected from 92 children attending child care centers (median age: 3.23 years, IQR: 1.8-4.5 years) were used to compare the performance of two pneumococcal detection protocols: a well-established method in which DNA is extracted following sample cultureenrichment 3,13,25,26 and an extraction-free method, originally developed and extensively used for the detection of SARS-CoV-2 (Figure 1). 17 Of the 759 samples, pneumococcus was detected in 378 (49.8%) samples using at least one of the methods, with a near-perfect agreement between the two protocols (Cohen's kappa=0.92, 95%CI: 0.90-0.95; Table 1) the culture-enrichment protocol detected slightly more positive samples (369/759, 48.6%) compared to the extraction-free method (358/759, 47.1%).…”