Fig 1.
Enrolment and samples obtained in this study.
In total 810 samples were analysed.
Fig 2.
Detection of Streptococcus pneumoniae in all samples analysed in the study.
Figure shows the distribution of samples classified in the study as positive for S. pneumoniae based on (A) isolation of live S. pneumoniae from cultured samples or (B) detection of S. pneumoniae by qPCR in DNA extracted from culture-enriched samples of trans-nasal swabs (n = 270), culture-enriched trans-oral swabs (n = 270) and culture-enriched saliva samples (n = 270) tested. Each circle represents sample type as labelled. Numbers next to sample type depict number (% of 270) of positive samples. Overlapping areas depict matching positive samples (detection of S. pneumoniae simultaneously in more than one of three samples collected per sampling event).
Fig 3.
qPCR-based detection of Streptococcus pneumoniae versus isolation of live pneumococci from trans-nasal (n = 270), trans-oral (n = 270) and saliva (n = 270) samples analysed in the study.
Figure depicts results of qPCR-based detection of S. pneumoniae-specific genes lytA and piaA and results of live Streptococcus pneumoniae isolation from culture-enriched trans-nasal samples (A), culture-enriched trans-oral samples (B) and culture-enriched saliva samples (C) from 135 elderly. Each symbol (dot or cross) represents an individual sample. Position of the symbol corresponds to CT values for lytA- and piaA-specific signals as marked on corresponding axes. Red dots represent samples from which live pneumococci were isolated by conventional culture at primary diagnostic step or from re-culture of samples qPCR-positive for S. pneumoniae. Open dots represent samples classified with qPCR as positive yet culture-negative for S. pneumoniae. Crosses represent samples classified as negative for S. pneumoniae in the study. Dotted lines mark the threshold of sample positivity based on presence of signals for both lytA and piaA CT <40 and the continuous lines represent total number of 45 cycles in each qPCR reaction. Number depicts number of samples identified as positive for S. pneumoniae by culture (in red) and by molecular method (in black). Spearman’s rank correlation coefficient (rho) and the associated P value (p) are shown.
Table 1.
Sensitivity of methods used to detect Streptococcus pneumoniae carriage in this study.
Table 2.
Patient characteristics related to Streptococcus pneumoniae carriage detected in the study.
Fig 4.
Stretococcus pneumoniae serotypes of pneumococcal strains detected in the study.
Each row represents one of 31 individual study subjects either culture-positive for S. pneumoniae in any of the six samples collected in the study, or positive for carriage of PCV13-serotypes detected by qPCR (results for remaining 34 carriers of S. pneumoniae not shown). Serotype of cultured strain or serotype-specific signal detected depicted. Empty grey squares depict samples positive for S. pneumoniae by qPCR but negative for any of the serotypes tested for in the study.