Streptococcus pneumoniae
(
Spn
) is a bacterial pathogen that causes a range of disease manifestations in children, from acute otitis media to pneumonia, septicemia, and meningitis. Primary
Spn
laboratory diagnostic identification methods include culture, antigen testing, single-plex real-time PCR, and syndromic PCR panels. However, each method lacks sensitivity, specificity, and/or cost efficiency. We developed and validated a quantitative, multiplex PCR assay using three
Spn
genomic targets (
lytA, piaB
, and SP2020) for improved sensitivity and specificity to detect
Spn
in pleural fluid (PF), bronchoalveolar lavage (BAL), tracheal aspirate (TA), and upper respiratory (UR, research only) samples. Validation testing included analytical sensitivity (limit of detection), specimen storage, analytical specificity (cross-reactivity), and accuracy studies. Limit of detection is 500 genome copies/mL in lower respiratory samples and 100 copies/mL in upper respiratory specimens, with a quantification range of 1,000 to 10,000,000 copies/mL. Specimens can be stored frozen at least 60 days and
Spn
DNA is stable through three freeze-thaw cycles. No cross-reactivity was observed against 20 closely related microorganisms and/or microorganisms that can be detected in similar sample types, including
Streptococcus pseudopneumoniae
. In testing of residual clinical specimens,
Spn
was detected in 5 of 23 (21.7%) PF, 2 of 19 (10.5%) BAL, 1 of 20 (5.0%) TA, and 44 of 178 (24.7%) UR residual specimens. For accuracy studies, 98 specimens were tested and overall percent agreement with a qualitative,
lytA
-based comparator assay was 96.9% across all sample types. This multiplex, quantitative PCR assay is a sensitive and specific method for
Spn
detection in pediatric respiratory samples.
IMPORTANCE
Streptococcus pneumoniae
(
Spn
) is the world’s leading cause of lower respiratory tract infection morbidity and mortality in children. However, current clinical microbiological methods have disadvantages.
Spn
can be difficult to grow in laboratory conditions if a patient is pre-treated, and
Spn
antigen testing has unclear clinical utility in children. Syndromic panel testing is less cost-effective than targeted PCR if clinical suspicion is high for a single pathogen. Also, such testing entails a full, expensive validation for each panel target if used for multiple respiratory sources. Therefore, better diagnostic modalities are needed. Our study validates a multiplex PCR assay with three genomic targets for semi-quantitative and quantitative
Spn
molecular detection from lower respiratory sources for clinical testing and from upper respiratory sources for research investigation.