Detection of Streptococcus pneumoniae from Different Types of Nasopharyngeal Swabs in Children

PLOS ONE, Dec 2019

Background A better understanding of the epidemiology of nasopharyngeal carriage of Streptococcus pneumoniae is important to assess the impact of vaccination and the pathogenesis of pneumococcal disease. We compared the recovery of S. pneumoniae from nylon flocked, Dacron and rayon swabs. Methods The recovery of S. pneumoniae from mocked specimens using flocked, Dacron and rayon swabs were compared by culture. The yield from paired nasopharyngeal (NP) samples obtained from healthy children sampled with flocked and Dacron swabs was also determined using culture and lytA-targeted real-time polymerase chain reaction (qPCR). Results Using mock specimen, the percentage recovery of S. pneumoniae ATCC 49619 (serotype 19F) strain from the flocked swabs was 100%, while it was 41% from Dacron swabs and 7% from rayon swabs. Similar results were observed for S. pneumoniae serotypes 1 and 5. S. pneumoniae was cultured from 18 of 42 (43%) paired NP samples from the healthy children (median age 8 [interquartile range (IQR) 5–16] months). The median number of colony-forming units (CFU) recovered from flocked swabs was two-fold higher (8.8×104 CFU/mL [IQR, 2.0×102 – 4.0×105 CFU/mL]) than Dacron swabs (3.7×104 CFU/mL [IQR, 4.0×102–3.2×105 CFU/mL], p = 0.17). Using lytA-targeted qPCR from paired NP samples, the median copy number of S. pneumoniae detected from flocked swabs was significantly higher than from Dacron swabs (3.0×105 genome copies/mL [IQR, 1.3×102−1.8×106] vs. 9.3×104 genome copies/mL [IQR, 7.0×101−1.1×106]; p = 0.005). Conclusion Flocked swabs released more S. pneumoniae compared to both Dacron and rayon swabs from mock specimens. Similarly, higher bacterial loads were detected by qPCR from flocked swabs compared with Dacron swabs from healthy children.

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Detection of Streptococcus pneumoniae from Different Types of Nasopharyngeal Swabs in Children

Nicol MP (2013) Detection of Streptococcus pneumoniae from Different Types of Nasopharyngeal Swabs in Children. PLoS ONE 8(6): e68097. doi:10.1371/journal.pone.0068097 Detection of Streptococcus pneumoniae from Different Types of Nasopharyngeal Swabs in Children Felix S. Dube 0 Mamadou Kaba 0 Elizabeth Whittaker 0 Heather J. Zar 0 Mark P. Nicol 0 Bernard Beall, Centers for Disease Control & Prevention, United States of America 0 1 Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town , Cape Town , South Africa , 2 Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town , South Africa , 3 Academic Department of Paediatrics, Wright-Fleming Institute, Imperial College London, St Mary's Campus , London , United Kingdom , 4 Department of Paediatrics and Child Health, University of Cape Town, South Africa, 5 Red Cross War Memorial Children's Hospital , Cape Town , South Africa , 6 National Health Laboratory Service, Groote Schuur Hospital , Cape Town , South Africa Background: A better understanding of the epidemiology of nasopharyngeal carriage of Streptococcus pneumoniae is important to assess the impact of vaccination and the pathogenesis of pneumococcal disease. We compared the recovery of S. pneumoniae from nylon flocked, Dacron and rayon swabs. Methods: The recovery of S. pneumoniae from mocked specimens using flocked, Dacron and rayon swabs were compared by culture. The yield from paired nasopharyngeal (NP) samples obtained from healthy children sampled with flocked and Dacron swabs was also determined using culture and lytA-targeted real-time polymerase chain reaction (qPCR). Results: Using mock specimen, the percentage recovery of S. pneumoniae ATCC 49619 (serotype 19F) strain from the flocked swabs was 100%, while it was 41% from Dacron swabs and 7% from rayon swabs. Similar results were observed for S. pneumoniae serotypes 1 and 5. S. pneumoniae was cultured from 18 of 42 (43%) paired NP samples from the healthy children (median age 8 [interquartile range (IQR) 5-16] months). The median number of colony-forming units (CFU) recovered from flocked swabs was two-fold higher (8.86104 CFU/mL [IQR, 2.06102 - 4.06105 CFU/mL]) than Dacron swabs (3.76104 CFU/mL [IQR, 4.06102-3.26105 CFU/mL], p = 0.17). Using lytA-targeted qPCR from paired NP samples, the median copy number of S. pneumoniae detected from flocked swabs was significantly higher than from Dacron swabs (3.06105 genome copies/mL [IQR, 1.3610221.86106] vs. 9.36104 genome copies/mL [IQR, 7.0610121.16106]; p = 0.005). Conclusion: Flocked swabs released more S. pneumoniae compared to both Dacron and rayon swabs from mock specimens. Similarly, higher bacterial loads were detected by qPCR from flocked swabs compared with Dacron swabs from healthy children. - Funding: This work was funded in part by grants from the National Institutes of Health, USA (1R01HD058971-01), the Medical Research Council of South Africa, the Wellcome Trust and the Bill and Mellinda Gates Foundation Global Health Grant (OPP1017641). Felix S. Dube is supported by the National Research Foundation of South Africa; Mamadou Kaba is a recipient of Carnegie Corporation of New York (USA) fellowship; Elizabeth Whittaker is supported by the Wellcome Trust, UK. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: Prof. Heather J. Zar and Prof. Mark P. Nicol are members of the PLOS ONE Editorial Board. This does not alter the authors adherence to all the PLOS ONE policies on sharing data and materials. Streptococcus pneumoniae is the leading bacterial cause of childhood pneumonia worldwide [1,2]. S. pneumoniae colonizes the nasopharynx of many healthy young children and only causes pneumonia in a small proportion of those colonized [36]. The timing of acquisition, intensity of colonization and interaction of S. pneumoniae with other respiratory pathogens are likely to be key determinants for progression to pneumonia [710]. Since nasopharyngeal (NP) colonization by S. pneumoniae is key to understanding the pathogenesis of pneumococcal disease and is increasingly used as an endpoint for pneumococcal vaccine studies, it is important to establish the optimal strategy for recovery of S. pneumoniae from NP specimens. Sampling of the NP may be achieved using an NP swab or aspirate. NP swabs are preferred as the procedure is simpler, quicker and better tolerated by children. The ideal swab would be highly absorbent, maintain the viability of microorganisms present, release most of the specimen material into culture broth or transport medium and not inhibit culture or nucleic acid amplification. Traditionally used swabs, such as Dacron and rayon swabs are constructed by winding the respective fibres onto the tip of the swab shaft. This swab design may potentially trap a large proportion of clinical material (...truncated)


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Felix S. Dube, Mamadou Kaba, Elizabeth Whittaker, Heather J. Zar, Mark P. Nicol. Detection of Streptococcus pneumoniae from Different Types of Nasopharyngeal Swabs in Children, PLOS ONE, 2013, Volume 8, Issue 6, DOI: 10.1371/journal.pone.0068097