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The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults.

Boelsen, LK; Dunne, EM; Gould, KA; Ratu, FT; Vidal, JE; Russell, FM; Mulholland, EK; Hinds, J; Satzke, C (2020) The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults. mSphere, 5 (4). e00478-20. ISSN 2379-5042 https://doi.org/10.1128/mSphere.00478-20
SGUL Authors: Gould, Katherine Ann Hinds, Jason

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Abstract

Streptococcus pneumoniae (the pneumococcus) carriage is commonly used to measure effects of pneumococcal vaccines. Based on findings from culture-based studies, the World Health Organization recommends both nasopharyngeal (NP) and oropharyngeal (OP) sampling for detecting adult carriage. Given evidence of potential confounding by other streptococci, we evaluated molecular methods for pneumococcal identification and serotyping from 250 OP samples collected from adults in Fiji, using paired NP samples for comparison. Samples were screened using lytA quantitative PCR (qPCR), as well as pneumococcal identification and serotyping conducted by DNA microarray. A subset of OP samples were characterized by latex sweep agglutination and multiplex PCR. Alternate qPCR assays (piaB and bguR) for pneumococcal identification were evaluated. The lytA qPCR was less specific and had poor positive predictive value (PPV) in OP samples (88% and 26%, respectively) compared with NP samples (95% and 64%, respectively). Using additional targets piaB and/or bguR improved qPCR specificity in OP, although the PPV (42 to 53%) was still poor. Using microarray, we found that 102/107 (95%) of OP samples contained nonpneumococcal streptococci with partial or divergent complements of pneumococcal capsule genes. We explored 91 colonies isolated from 11 OP samples using various techniques, including multiplex PCR, latex agglutination, and microarray. We found that nonpneumococcal streptococci contribute to false positives in pneumococcal serotyping and may also contribute to spurious identification by qPCR. Our results highlight that molecular approaches should include multiple loci to minimize false-positive results when testing OP samples. Regardless of method, pneumococcal identification and serotyping results from OP samples should be interpreted with caution.IMPORTANCEStreptococcus pneumoniae (the pneumococcus) is a significant global pathogen. Accurate identification and serotyping are vital. In contrast with World Health Organization recommendations based on culture methods, we demonstrate that pneumococcal identification and serotyping with molecular methods are affected by sample type. Results from oropharyngeal samples from adults were often inaccurate. This is particularly important for assessment of vaccine impact using carriage studies, particularly in low- and middle-income countries where there are significant barriers for disease surveillance.

Item Type: Article
Additional Information: Copyright © 2020 Boelsen et al. This content is distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/).
Keywords: PCR, Streptococcus pneumoniae, carriage, genotypic, identification, nasopharyngeal, oropharyngeal, serotyping
SGUL Research Institute / Research Centre: Academic Structure > Infection and Immunity Research Institute (INII)
Journal or Publication Title: mSphere
ISSN: 2379-5042
Language: eng
Dates:
DateEvent
29 July 2020Published
1 July 2020Accepted
Publisher License: Creative Commons: Attribution 4.0
Projects:
Project IDFunderFunder ID
OPP126272Bill and Melinda Gates Foundationhttp://dx.doi.org/10.13039/100000865
OPP1084341Bill and Melinda Gates Foundationhttp://dx.doi.org/10.13039/100000865
1087957National Health and Medical Research Councilhttp://dx.doi.org/10.13039/501100000925
R21AI112768-01A1National Institutes of Healthhttp://dx.doi.org/10.13039/100000002
1R21AI144571-01National Institutes of Healthhttp://dx.doi.org/10.13039/100000002
PubMed ID: 32727860
Go to PubMed abstract
URI: https://openaccess.sgul.ac.uk/id/eprint/112225
Publisher's version: https://doi.org/10.1128/mSphere.00478-20

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