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

In 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 surveillances on pneumococcal colonisation and has recently been shown to improve carriage detection in older age groups. Here, we compared the sensitivity of nasopharyngeal and saliva samples from PCV7-vaccinated 24-month-old children for pneumococcal carriage detection using conventional and molecular diagnostic 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 techniques. Next, DNA extracted from all plate growth was tested by qPCR for the presence of pneumococcal genes piaB and lytA and a subset of serotypes. By culture, 164/288 (57%) nasopharyngeal swabs tested positive for pneumococcus, but detection was not possible from saliva due to abundant polymicrobial growth on culture-plates. Molecular methods increased the number of children pneumococci-positive to 172/288 (60%) when testing culture-enriched saliva and to 212/288 (73%) when testing nasopharyngeal samples. Altogether, by molecular methods 239/288 (83%) infants were positive, with qPCR-based carriage detection of culture-enriched nasopharyngeal swabs significantly detecting more carriers compared to either conventional culture (p<0.001) or qPCR-detection of saliva (p<0.001). However, 27/240 (11%) carriers were positive only in saliva, significantly contributing to the overall number of carriers detected (p<0.01). While testing nasopharyngeal swabs with qPCR proved most sensitive for pneumococcal detection in infants, saliva sampling could be considered as complementary to provide additional information on carriage and serotypes which may not be detected in the nasopharynx and may be particularly useful in longitudinal studies, requiring repeated sampling events.