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Combined nasopharyngeal and oropharyngeal sampling improves pathogen detection in community-acquired pneumonia

Hansen, Karin LU orcid ; Wasserstrom, Lisa LU orcid ; Ahl, Jonas LU ; Su, Yu Ching LU ; Nilsson, Anna C. LU and Riesbeck, Kristian LU orcid (2026) In Frontiers in Microbiology 17.
Abstract

Introduction – Determining the etiology of community-acquired pneumonia (CAP) is essential for targeted treatment and optimal care. Reliable results require selection of the appropriate sampling site. Methods – Paired nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from 484 patients with CAP between September 2016 and September 2018. The samples were analyzed by PCRs for Streptococcus pneumoniae, Haemophilus influenzae, 6 atypical bacterial species, and 14 viral agents. Results – The most common pathogen was S. pneumoniae (24%), followed by H. influenzae (23%). Both were more frequently detected in the oropharynx, with 29% and 40% respectively, identified only in OP swabs. Respiratory viruses were found in 32% of the... (More)

Introduction – Determining the etiology of community-acquired pneumonia (CAP) is essential for targeted treatment and optimal care. Reliable results require selection of the appropriate sampling site. Methods – Paired nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from 484 patients with CAP between September 2016 and September 2018. The samples were analyzed by PCRs for Streptococcus pneumoniae, Haemophilus influenzae, 6 atypical bacterial species, and 14 viral agents. Results – The most common pathogen was S. pneumoniae (24%), followed by H. influenzae (23%). Both were more frequently detected in the oropharynx, with 29% and 40% respectively, identified only in OP swabs. Respiratory viruses were found in 32% of the patients; of these, 65% were present in both NP and OP samples. Notably, 21% were detected only in NP samples, and 15% only in OP samples. Mycoplasma pneumoniae was identified in 6% of all patients, predominantly in OP samples (89%) compared with NP samples (70%). Cq-values were lower in NP swabs for all pathogens except M. pneumoniae, suggesting a higher microbial load in the nasopharynx. Discussion – This study highlights the importance of sampling site selection in the diagnosis and management of CAP. Nasopharyngeal sampling was more effective for detecting respiratory viruses, whereas OP samples yielded more cases of S. pneumoniae, H. influenzae and M. pneumoniae. To maximize the diagnostic yield, a combined NP/OP-sampling strategy can thus be recommended.

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author
; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
community-acquired pneumonia, Haemophilus influenzae, influenza virus, Mycoplasma pneumoniae, PCR, Streptococcus pneumoniae
in
Frontiers in Microbiology
volume
17
article number
1774447
publisher
Frontiers Media S. A.
external identifiers
  • pmid:42027462
  • scopus:105039693202
ISSN
1664-302X
DOI
10.3389/fmicb.2026.1774447
language
English
LU publication?
yes
id
63563f7e-959a-421c-8ed2-a3f0c51da787
date added to LUP
2026-06-30 11:06:32
date last changed
2026-09-09 21:00:59
@article{63563f7e-959a-421c-8ed2-a3f0c51da787,
  abstract     = {{<p>Introduction – Determining the etiology of community-acquired pneumonia (CAP) is essential for targeted treatment and optimal care. Reliable results require selection of the appropriate sampling site. Methods – Paired nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from 484 patients with CAP between September 2016 and September 2018. The samples were analyzed by PCRs for Streptococcus pneumoniae, Haemophilus influenzae, 6 atypical bacterial species, and 14 viral agents. Results – The most common pathogen was S. pneumoniae (24%), followed by H. influenzae (23%). Both were more frequently detected in the oropharynx, with 29% and 40% respectively, identified only in OP swabs. Respiratory viruses were found in 32% of the patients; of these, 65% were present in both NP and OP samples. Notably, 21% were detected only in NP samples, and 15% only in OP samples. Mycoplasma pneumoniae was identified in 6% of all patients, predominantly in OP samples (89%) compared with NP samples (70%). Cq-values were lower in NP swabs for all pathogens except M. pneumoniae, suggesting a higher microbial load in the nasopharynx. Discussion – This study highlights the importance of sampling site selection in the diagnosis and management of CAP. Nasopharyngeal sampling was more effective for detecting respiratory viruses, whereas OP samples yielded more cases of S. pneumoniae, H. influenzae and M. pneumoniae. To maximize the diagnostic yield, a combined NP/OP-sampling strategy can thus be recommended.</p>}},
  author       = {{Hansen, Karin and Wasserstrom, Lisa and Ahl, Jonas and Su, Yu Ching and Nilsson, Anna C. and Riesbeck, Kristian}},
  issn         = {{1664-302X}},
  keywords     = {{community-acquired pneumonia; Haemophilus influenzae; influenza virus; Mycoplasma pneumoniae; PCR; Streptococcus pneumoniae}},
  language     = {{eng}},
  publisher    = {{Frontiers Media S. A.}},
  series       = {{Frontiers in Microbiology}},
  title        = {{Combined nasopharyngeal and oropharyngeal sampling improves pathogen detection in community-acquired pneumonia}},
  url          = {{http://dx.doi.org/10.3389/fmicb.2026.1774447}},
  doi          = {{10.3389/fmicb.2026.1774447}},
  volume       = {{17}},
  year         = {{2026}},
}