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

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. Gi...

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Autores principales:	Laura K. Boelsen, Eileen M. Dunne, Katherine A. Gould, F. Tupou Ratu, Jorge E. Vidal, Fiona M. Russell, E. Kim Mulholland, Jason Hinds, Catherine Satzke
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	PCR Streptococcus pneumoniae carriage genotypic identification nasopharyngeal Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/741b3450085e435092368323d4a32e65
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spelling	oai:doaj.org-article:741b3450085e435092368323d4a32e652021-11-15T15:30:50ZThe Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults10.1128/mSphere.00478-202379-5042https://doaj.org/article/741b3450085e435092368323d4a32e652020-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00478-20https://doaj.org/toc/2379-5042ABSTRACT 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. IMPORTANCE Streptococcus 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.Laura K. BoelsenEileen M. DunneKatherine A. GouldF. Tupou RatuJorge E. VidalFiona M. RussellE. Kim MulhollandJason HindsCatherine SatzkeAmerican Society for MicrobiologyarticlePCRStreptococcus pneumoniaecarriagegenotypicidentificationnasopharyngealMicrobiologyQR1-502ENmSphere, Vol 5, Iss 4 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	PCR Streptococcus pneumoniae carriage genotypic identification nasopharyngeal Microbiology QR1-502
spellingShingle	PCR Streptococcus pneumoniae carriage genotypic identification nasopharyngeal Microbiology QR1-502 Laura K. Boelsen Eileen M. Dunne Katherine A. Gould F. Tupou Ratu Jorge E. Vidal Fiona M. Russell E. Kim Mulholland Jason Hinds Catherine Satzke The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults
description	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. IMPORTANCE Streptococcus 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.
format	article
author	Laura K. Boelsen Eileen M. Dunne Katherine A. Gould F. Tupou Ratu Jorge E. Vidal Fiona M. Russell E. Kim Mulholland Jason Hinds Catherine Satzke
author_facet	Laura K. Boelsen Eileen M. Dunne Katherine A. Gould F. Tupou Ratu Jorge E. Vidal Fiona M. Russell E. Kim Mulholland Jason Hinds Catherine Satzke
author_sort	Laura K. Boelsen
title	The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults
title_short	The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults
title_full	The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults
title_fullStr	The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults
title_full_unstemmed	The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults
title_sort	challenges of using oropharyngeal samples to measure pneumococcal carriage in adults
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/741b3450085e435092368323d4a32e65
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The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults

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