Superiority of Trans-Oral over Trans-Nasal Sampling in Detecting Streptococcus pneumoniae Colonization in Adults

Abstract

The human nasopharynx is the main reservoir for Streptococcus pneumoniae. We applied conventional and molecular methods to determine the prevalence of S. pneumoniae nasopharyngeal colonization in adults. Paired trans-orally and trans-nasally obtained nasopharyngeal samples from 268 parents of 24-month-old children were assessed for pneumococcal presence. Parents were classified as colonized when live pneumococci were recovered from either sample cultured on medium selective for S. pneumoniae. Of the 52 (19%) colonized parents 49 (18%) were culture-positive in trans-nasal and 10 (4%) in trans-oral samples. Bacterial growth was harvested from these cultures, DNA isolated and tested by quantitative-PCR (qPCR) targeting lytA and piaA genes specific for S. pneumoniae. A sample was considered positive if signals for both genes were detected. Altogether 105 (39%) individuals were classified as positive for pneumococcus by qPCR including 50 (19%) in trans-nasal and 94 (35%) in trans-oral settings. Although significantly more trans-nasal compared to trans-oral samples were culture-positive for S. pneumoniae at the primary diagnostic step (p<0.001) the opposite was observed in qPCR results (p<0.001). To confirm the presence of live pneumococcus in samples positive by qPCR but negative at the initial diagnostic step, we serially-diluted cell harvests, re-cultured and carefully examined for S. pneumoniae presence. Live pneumococci were recovered from an additional 43 parents including 42 positive in trans-oral and 4 in trans-nasal samples increasing the number of individuals culture- and qPCR-positive to 93 (35%) and positive by either of two methods to 107 (40%). There were significantly more trans-oral than trans-nasal samples positive for pneumococcus by both culture and qPCR (n = 71; 27%; vs. n = 50; 19%; p<0.05). Our data suggest that pneumococcal colonization is more common in adults than previously estimated and point towards the superiority of a trans-oral over a trans-nasal approach when testing adults for colonization with S. pneumoniae.

Streptococcus pneumoniae oropharyngeal colonization in children and adolescents with cystic fibrosis

“…In contrast, this study was conducted by means of molecular methods which, albeit with some exceptions, have been found to be significantly more reliable than traditional non-enriched cultures in routine practice [9,[12][13][14]. Oropharyngeal sampling was used to collect the pharyngeal secretions; it has recently been shown that it is a significantly better means of detecting the colonization by S. pneumoniae in adolescents, and young adults than the nasopharyngeal sampling used in the previous studies of younger children [13,15,16]. Finally, a flocked nylon fiber tip was used for sampling because previous studies have shown that this ensures the highest rate of detection of S. pneumoniae, particularly when compared with the more widely used Dacron and rayon swabs [17].…”

Pharyngeal Colonization by Streptococcus pneumoniae in Older Children and Adolescents in a Geographical Area Characterized by Relatively Limited Pneumococcal Vaccination Coverage

“…17 In addition, S. pneumoniae was identified by means of molecular methods which, albeit with some exceptions, 18 have been found to be significantly more reliable than traditional non-enriched cultures in routine practice. 17,19 Furthermore, to improve the detection of S. pneumoniae without increasing the risk of false-positive results, both the lytA and cpsA genes were amplified, 17 and only the samples in which both genes were detected in 2 out of 3 consecutive tests of the same swab were considered positive. This permitted to avoid falsepositive results because only S. pneumoniae has both these genes, whereas different streptococci that are not capsulated but that could colonies oropharynx possess only lytA gene but not cpsA gene.…”

“…This permitted to avoid falsepositive results because only S. pneumoniae has both these genes, whereas different streptococci that are not capsulated but that could colonies oropharynx possess only lytA gene but not cpsA gene. 17 Finally, a flocked nylon fiber tip was used for the sampling because previous studies have shown that this ensures the highest rate of detection of S. pneumoniae, particularly in comparison with the more widely used Dacron and rayon swabs. 20 We did not observe differences in cycle threshold values comparing pneumococcal colonization in vaccinated and unvaccinated children, although it may be technically challenging to compare density of carriage using bacteria recovered on a small nylon tip as the size of the tip may be a limiting factor in assessing the magnitude of colonization.…”

Assessing the diagnostic accuracy of PCR-based detection ofStreptococcus pneumoniaefrom nasopharyngeal swabs collected for viral studies in Canadian adults hospitalised with community-acquired pneumonia: a Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research (CIRN) study

“…[24][25][26][27] While this study evaluated the performance for S. pneumoniae detection by PCR in NP swab collected for viral studies, it was recognised that other specimen types, such as oral and oropharyngeal swabs, were previously shown to perform better than sampling from the nasopharynx to assess pneumococcal colonisation. [28][29][30] Since the performance of NP swab PCR is affected by the results of its comparator, a future studies would benefit from a direct comparison between PCR-based detection of pneumococcal DNA in NP swabs and concurrent quantitative S. pneumoniae from culture swabs collected from the nasopharynx. 31 Other studies have also suggested broth enrichment prior to lytA real-time PCR can enhance the detection of S. pneumoniae, particularly for low density colonisation.…”