• Bronchoalveolar lavage;
  • PCR;
  • pneumolysin;
  • pneumonia;
  • Streptococcus pneumoniae


  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results
  6. Discussion
  7. Transparency Declaration
  8. References

The pneumolysin (ply) gene is widely used as a target in PCR assays for Streptococcus pneumoniae in respiratory secretions. However, false-positive results with conventional ply-based PCR have been reported. The aim here was to study the performance of a quantitative ply-based PCR for the identification of pneumococcal lower respiratory tract infection (LRTI). In a prospective study, fibreoptic bronchoscopy was performed in 156 hospitalized adult patients with LRTI and 31 controls who underwent bronchoscopy because of suspicion of malignancy. Among the LRTI patients and controls, the quantitative ply-based PCR applied to bronchoalveolar lavage (BAL) fluid was positive at ≥103 genome copies/mL in 61% and 71% of the subjects, at ≥105 genome copies/mL in 40% and 58% of the subjects, and at ≥107 genome copies/mL in 15% and 3.2% of the subjects, respectively. Using BAL fluid culture, blood culture, and/or a urinary antigen test, S. pneumoniae was identified in 19 LRTI patients. As compared with these diagnostic methods used in combination, quantitative ply-based PCR showed sensitivities and specificities of 89% and 43% at a cut-off of 103 genome copies/mL, of 84% and 66% at a cut-off of 105 genome copies/mL, and of 53% and 90% at a cut-off of 107 genome copies/mL, respectively. In conclusion, a high cut-off with the quantitative ply-based PCR was required to reach acceptable specificity. However, as a high cut-off resulted in low sensitivity, quantitative ply-based PCR does not appear to be clinically useful. Quantitative PCR methods for S. pneumoniae using alternative gene targets should be evaluated.


  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results
  6. Discussion
  7. Transparency Declaration
  8. References

In lower respiratory tract infection (LRTI), identification of the aetiological agent can be useful for the selection of appropriate antimicrobial therapy [1]. Streptococcus pneumoniae is a major cause of severe LRTI [2,3]. However, a problem in clinical practice is that conventional cultures may give false-negative results for S. pneumoniae [3,4], especially in patients receiving ongoing antibiotic treatment [5]. Thus, for improvement of the diagnostic possibilities, nucleic acid detection methods have been developed for S. pneumoniae [6].

One of the most widely used PCR targets in S. pneumoniae is the pneumolysin (ply) gene [7–10]. However, specificity problems have been encountered with ply-based PCR. In two studies [11,12], conventional ply-based PCR applied to upper respiratory tract specimens was reported to give positive results in 58% and 73%, respectively, of healthy adult controls. Carriage of S. pneumoniae cannot explain these figures, as the carriage rate is low among adults in western countries [13,14]. Instead, a suggested explanation is false ply-based PCR positivity due to α-haemolytic streptococci [6], which are normally present in the respiratory flora. Streptococci such as Streptococcus mitis and Streptococcus oralis sometimes contain a ply gene [15–18].

In spite of these documented specificity problems, ply-based PCR is frequently used [9,10]. It has been assumed that ply-based PCR may be clinically useful, if quantitative PCR with appropriate cut-off limits is used and if the methods are applied to secretions from the lower respiratory tract [8,19]. However, so far, this assumption has not been tested appropriately.

The aim of the present study was to test the performance of a quantitative ply-based PCR applied to bronchoalveolar lavage (BAL) fluid for the identification of pneumococcal LRTI.

Materials and Methods

  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results
  6. Discussion
  7. Transparency Declaration
  8. References


One hundred and fifty-nine consecutively identified immunocompetent adult patients who were hospitalized because of LRTI at the Department of Internal Medicine, Silkeborg County Hospital, Silkeborg, Denmark, between September 1997 and August 2000, were enrolled in a prospective study. The criteria for LRTI were fever and/or an increased leukocyte count (≥11 × 109/L), together with increased focal symptoms from the lower airways with at least one of three newly developed symptoms of increased dyspnoea, increased coughing, and/or increased sputum purulence.

BAL fluid was available from 156 patients (median age, 63 years; range, 26–90 years), who were included in the present study. These patients have been described previously [20]. A chronic lung disease was documented in 72 patients (46%), 31% were current smokers, and 40% were previous smokers. New infiltrates were identified on chest X-ray films for 87 patients (56%). Antibiotics had been taken within 7 days prior to bronchoscopy in 103 cases (66%).

As controls, 31 adult patients (median age, 64 years; range, 30–77 years), who consecutively underwent bronchoscopy for suspected malignancy and who did not have pulmonary infection were included. Nineteen of them had lung malignancies, and 12 had no pathology identified by bronchoscopy or radiological examination. Twenty-seven controls (87%) were current or previous smokers.

Bronchoscopy and BAL fluid

The patients and controls underwent standardized fibreoptic bronchoscopy (FOB) with BAL [21] within 24 h of admission. In short, the fibreoptic bronchoscope was introduced through the nose or through the mouth. The tip of the bronchoscope was wedged into the segment of bronchus affected by a pulmonary infiltrate, or, if no infiltrate was available, into the middle lobe. A sterile, thin tube was then introduced into the working channel of the bronchoscope, and lavage was then performed. One to three portions of 60 mL of isotonic NaCl were used for lavage, and the aspirated fluid was collected in one single portion for microbiological analyses.

Conventional microbiological investigations

BAL fluid was analysed by culture at the Department of Clinical Microbiology, Aarhus University Hospital, Aalborg, Denmark within a maximum of 6 h from sampling. The specimens were cultured on horse blood (5%) agar with semiquantitative determination following dispersion of 1 and 10 μL each on one half of the plate. The plates were incubated in carbon dioxide (5%) at 35°C for 24–48 h. Bacterial identification was performed according to standard microbiological methods. S. pneumoniae was identified on the basis of colony morphology and optochin sensitivity. α-Haemolytic streptococci were identified in BAL culture, but were not subtyped. The cut-off limit for a positive BAL culture result was 102 CFUs/mL of sample. After culture, the BAL fluid was frozen at −20°C.

Blood culturing was performed with a Bactec blood-culturing system at the Department of Clinical Microbiology, Aarhus University Hospital. Urine samples were sent immediately to the Statens Serum Institute, Copenhagen, Denmark, and were analysed for pneumococcal urinary antigen by countercurrent immunoelectrophoresis [22]. This assay detects capsular polysaccharides, in contrast to the Binax NOW assay, which detects C polysaccharide.


The frozen BAL samples from the LRTI patients and controls were sent to the Department of Clinical Microbiology, Örebro University Hospital, Örebro, Sweden, for DNA extraction and lytA-based PCR in 2003–2004. Extracted DNA was stored and was sent to the Department of Clinical Microbiology, Uppsala University Hospital, Uppsala, Sweden, for quantitative ply-basedPCR in 2007.

DNA extraction DNA from 0.2–0.5 mL of BAL fluid was extracted using the automatic MagNa Pure LC DNA-Isolation system (Roche Diagnostics). DNA used for determination of the detection capacity of the ply-based PCR was purified using the Qiagen DNA mini kit (Qiagen, Hilden, Germany) and the concentration of DNA was determined using a Nanodrop instrument (NanoDrop Technologies, Inc. Wilmington, DE, USA). The genome copy number was determined according to conventional calculations based on molecular weight and one gene copy per genome.

LytA-based PCRLytA-based PCR was performed as previously described [23]. In short, extracted DNA (10 μL) was added to a PCR mixture containing the lytA primers 5′-CGGACTACCGCCTTTATATCG-3′ and 5′-GTTTCAATCGTCAAGCCGTT-3′. After 40 cycles, PCR products were detected by electrophoresis on an agarose gel containing ethidium bromide. A positive and negative control was included in all PCRs. To test for PCR inhibition, DNA (8 μL) extracted from a PCR-negative sample was spiked with 2 μL of DNA extracted from S. pneumoniae (CCUG  36696), as previously described [23], and the PCR was repeated.

Ply-based PCR The quantitative real-time PCR for ply was used as described by Corless et al. [24], except that 3.5 mmol/L MgCl2 was used instead of 5.5 mmol/L, and the elongation time was 40 s instead of 1 min. The following primers and probe were derived from a previously sequenced ply gene (S. pneumoniae strain NCTC7466, GenBank accession number X52474): primer Pnc  ply F, 5′-TGCAGAGCGTCCTTTGGTCTAT-3′ (position 894–915); and primer Pnc  ply R, 5′-CTCTTACTCGTGGTTTCCAAC TTG-3′ (position 974–950). These defined an amplicon of 80 bp. A Cy5-labeled probe (5′-TGGCGCCCATAAGCAACACTCGAA-3′) with black hole quencher was used. The primers and probe were obtained from Thermo Hybaid, Interactive Division (Ulm, Germany). In short, the optimized real-time PCR amplifications were performed in a 25-μL reaction volume, containing 0.3 μmol/L of each primer, 0.2 μmol/L of the probe, 3.5 mmol/L MgCl2, 0.2 mmol/L dNTP, and 1 U of HotStar Taq polymerase (Qiagen). In the assay, 5 μL of extracted DNA was used.

The PCR was performed in a Rotor-Gene 3000 instrument (Corbett Research, Mortlake, Sydney, Australia), according to the following program: 15 min of enzyme activation at 95°C, followed by 45 cycles of 94°C for 15 s, and 60°C for 40 s. A positive control (S. pneumoniaeCCUG28588) and a negative control were included in all PCRs. Standard curves for quantification were based on duplicates of three measured points with 500, 2000 and 10 000 genome copies per PCR reaction of the ply target.

The detection capacity of the ply-based PCR was determined with serial dilutions of target DNA in carrier tRNA (1 μg/mL). Two experiments were performed, with 5–600 genome copies per reaction tube and two to four tubes at each dilution.

The reproducibility was evaluated by testing DNA preparations with known concentrations (duplicates of 500, 2000 and 10 000 genome copies per PCR) in five consecutive runs.

Reference standard for pneumococcal aetiology

Our reference standard for pneumococcal aetiology was based on a combination of blood culture, urinary antigen test, and BAL culture with a cut-off of 104 CFUs/mL. If at least one of these tests gave a positive result, the reference standard was considered positive. If none of the tests gave a positive result, the reference standard was considered negative.


The study was performed according to the Declaration of Helsinki II and approved by the local ethical committee; all participating patients gave written consent.


The chi-square test was used for comparison of proportions. A p-value of <0.05 was considered to be significant.


  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results
  6. Discussion
  7. Transparency Declaration
  8. References

Detection limit and reproducibility of the ply-based PCR

Serial dilutions of target DNA of known concentration were tested to identify the detection capacity of the quantitative ply assay. The detection limit was 20 genome copies per reaction, which equals 103 genome copies/mL. Three known concentrations of the target DNA were tested in duplicate in five consecutive runs (mean of ten tubes for each concentration) to evaluate the reproducibility of the quantitative ply assay. For the concentration of 10 000 copies per reaction, the cycle of threshold value ranged from 27.2 to 27.7 cycles (average, 27.5 cycles), and the calculated concentration ranged from 9824 to 11 413 copies per reaction (average, 10 654 copies per reaction). For 2000 copies per reaction, the corresponding cycle of threshold values and copy numbers were 30.1–31.3 (average, 30.4) and 1431–2588 (average, 2020), respectively. For 500 copies per reaction, the corresponding values were 32.3–34.4 (average, 32.9) and 317–817 (average, 504), respectively.

Results concerning the patients with LRTI

Table 1 shows the frequencies of positive results of the different tests for S. pneumoniae, and Table 2 shows the different result combinations of the LRTI patients. According to the combined reference standard, 19 patients had pneumococcal LRTI.

Table 1.   Positive test results for Streptococcus pneumoniae in patients with lower respiratory tract infection (LRTI) and controls
TestCut-off limit LRTI (n = 156), no. (%) positiveControls (n = 31), no. (%) positive
  1. ND, not defined; NI, not investigated; BAL, bronchoalveolar lavage.

  2. aOne hundred and fifty-two LRTI patients were tested.

  3. bOne hundred and forty-two LRTI patients were tested.

Blood cultureaND6 (3.9)NI
Urinary antigen testbND9 (6.3)NI
BAL fluid culture≥102 CFUs/mL10 (6.4)2 (6.5)
≥104 CFUs/mL7 (4.4)0
BAL lytA-based PCRND44 (28)4 (13)
BAL ply-based PCR≥103 genome copies/mL95 (61)22 (71)
≥104 genome copies/mL84 (54)22 (71)
≥105 genome copies/mL63 (40)18 (58)
≥106 genome copies/mL41 (26)7 (23)
≥107 genome copies/mL24 (15)1 (3.2)
≥108 genome copies/mL2 (1.3)0
Table 2.   Combined results of tests for Streptococcus pneumoniae in 156 patients with lower respiratory tract infection
Blood cultureUrinary antigen testBAL culture, cut-off ≥104  CFUs/mLBAL lytA-based PCRBAL ply-based PCR, cut-off ≥103 copies/mLNumber of patients to whom the results of all preceeding columns apply
  1. BAL, bronchoalveolar lavage; ND, not done.

  2. aND, n = 1.

  3. bND, n = 2.

− or NDa− or NDb58

Altogether, ply DNA was found in BAL fluid from 95 patients. In Fig. 1, the quantitative data of ply-based PCR are presented in relation to the reference standard and lytA-based PCR. Among the 109 LRTI patients with negative reference standard and negative lytA-based PCR results, ply DNA was detected in 51 (47%), 27 of whom had taken antibiotics prior to FOB.


Figure 1.  Quantitative results of ply-based PCR applied to bronchoalveolar lavage fluid in 156 patients with lower respiratory tract infection (LRTI) and 31 controls, related to the results of other diagnostic tests. The reference standard of the LRTI patients was considered positive when at least one reference test (blood culture, urinary antigen test, or culture of bronchoalveolar lavage fluid, cut-off 104 CFUs/mL) gave a positive result, and negative when no reference test gave a positive result. In the control group, the cut-off of culture was 102 CFUs/mL.

Download figure to PowerPoint

Among the 103 LRTI patients who had taken antibiotics prior to FOB, the combined reference standard was positive in 11 cases, lytA-based PCR was positive in 32 cases, and ply-based PCR was positive in 58 cases.

Table 3 shows the performance of the quantitative ply-based PCR at different cut-offs. Although the negative predictive values were high, the positive predictive values for detection of pneumococcal LRTI were low. At a cut-off of ≥107 genome copies/mL, a specificity of 90% was obtained, but the sensitivity dropped to 53%. For comparison, the lytA-based PCR had a sensitivity of 84% (16/19) and a specificity of 80% (109/137). Analysis of the receiver operating characteristic curve for the quantitative ply-based PCR showed an area under the curve of 0.807 (95% CI  0.695–0.920).

Table 3.   Performance of quantitative ply-based PCR at different detection limits applied to bronchoalveolar lavage (BAL) fluid for identification of pneumococcal aetiology in lower respiratory tract infection
Ply-based PCR cut-off (genome copies/mL) Sensitivitya SpecificitybPositive predictive valuecNegative predictive valued
  1. Blood culture, urinary antigen test and BAL culture (cut-off 104 CFUs/mL) were used as reference tests.

  2. aReported as percentage (number with positive PCR/number with any reference test positive).

  3. bReported as percentage (number with negative PCR/number with no reference test positive).

  4. cReported as percentage (number with any reference test positive/number with positive PCR).

  5. dReported as percentage (number with no reference test positive/number with negative PCR).

≥10389 (17/19)43 (59/137)18 (17/95)97 (59/61)
≥10489 (17/19)51 (70/137)20 (17/84)97 (70/72)
≥10584 (16/19)66 (90/137)25 (16/63)97 (90/93)
≥10668 (13/19)80 (109/137)32 (13/41)95 (109/115)
≥10753 (10/19)90 (123/137)42 (10/24)93 (123/132)
≥1085.3 (1/19)99 (136/137)50 (1/2)88 (136/154)

α-Haemolytic streptococci were identified after culture of BAL fluid from 69 LRTI patients (44%). Among 135 patients in whom S. pneumoniae was not detected after BAL fluid culture, blood culture, or urinary antigen tests, those with and without α-haemolytic streptococci were, at similar frequencies, ply-based PCR-positive (61% (39/64) vs. 52% (37/71); p 0.30, chi-square test) and lytA-based PCR-positive (16% (10/64) vs. 23% (16/71); p 0.31).

Results concerning the control patients

Table 1 shows S. pneumoniae detection among the 31 controls. BAL fluid culture was positive in two cases. LytA-based PCR was positive in one of them and in three additional controls. BAL culture and/or lytA-based PCR gave positive results in two controls with lung malignancy and in three controls with no pathology identified. Ply-based PCR was positive in these five cases and additionally in 17 controls. Altogether, ply DNA was detected in 12 cases with lung malignancy and in ten cases with no pathology identified. The quantitative ply-based PCR results are shown in Fig. 1.


  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results
  6. Discussion
  7. Transparency Declaration
  8. References

Although a quantitative PCR technique and lower respiratory tract samples were used, the specificity problems with ply-based PCR could not be solved in the present study. In line with previous studies [11,12], there were similar positivity rates for ply-based PCR at the different cut-offs in LRTI patients and controls. The performance analysis of the quantitative ply-based PCR (Table 3) showed that a cut-off of 107 genome copies/mL was required for an acceptable specificity. At that cut-off, there was a higher positivity rate with quantitative ply-based PCR than with BAL culture (Table 1), but the sensitivity was low. Thus, no particular cut-off could make this method clinically useful.

The results of the present study are in agreement with the previous documentation of the non-specificity of ply-based PCR for the detection of pneumococcal LRTI [6]. It is important to note that non-specificity of detection using PCR has not been restricted to a single target sequence in the ply gene, but has been observed in several PCR studies in which different primer pairs have been used [15,24–27].

The question then arises of whether the α-haemolytic streptococci are responsible for the false-positive ply-based PCR results, as has been assumed [6]. In the present study, we could not find any correlation between the presence of α-haemolytic streptococci in BAL fluid culture and ply-based PCR positivity. As the α-haemolytic streptococci isolated were not typed to species level, we have no information on whether ply positivity was correlated with any particular species.

However, the ply-based PCR, as used here, recently yielded positive results with three of eight S. mitis isolates and with two of two Streptococcus pseudopneumoniae isolates, but negative results with 21 other isolates of α-haemolytic streptococci belonging to 11 different species [28]. These data are in agreement with those from other studies [16,18], and indicate that only the streptococcal species most closely related to S. pneumoniae may harbour the ply gene, whereas the remaining α-haemolytic streptococci do not. To our knowledge, the carriage rate of these species in the human respiratory tract has not been studied. Their importance for the false-positive results in the previous PCR studies targeting ply [11,12] is not known. However, the absence of correlation between α-haemolytic streptococci in BAL fluid culture and ply-based PCR positivity in the present study indicates that streptococci of the respiratory tract flora may not be the only reason for positive ply-based PCR results in samples devoid of S. pneumoniae. This leads to the question of whether the specificity problems encountered with ply-based PCR should discourage the application of PCR to respiratory tract secretions for the establishment of the diagnosis of pneumococcal LRTI. The answer to this should probably be no, as in vitro studies [15–17,29] have shown that some gene targets, e.g. lytA, are more specific for S. pneumoniae than ply. As previously discussed [20], the conventional lytA-based PCR of the present study could be a useful complement to BAL fluid culture in patients who have taken antibiotics prior to bronchoscopy. A quantitative lytA-based PCR would probably be even more clinically useful.

Another gene target that has been shown to be specific for S. pneumoniae is the Spn9802 fragment [12,17]. For this gene target, we have developed a quantitative real-time PCR [28], which showed promising results when applied to nasopharyngeal aspirates from pneumonia patients and controls. In a future study, this quantitative Spn9802 PCR will be applied to the BAL fluid samples analysed here.

In conclusion, a high cut-off of the quantitative ply-based PCR was required to obtain an acceptable specificity. However, as a high cut-off resulted in a low sensitivity, quantitative ply-based PCR does not appear to be clinically useful. Quantitative PCR methods for S. pneumoniae using alternative gene targets should be evaluated.

Transparency Declaration

  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results
  6. Discussion
  7. Transparency Declaration
  8. References

All authors declare the absence of competing interests.

Funding: The Uppsala-Örebro Regional Research Council; the Research Committee of Örebro County Council.


  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results
  6. Discussion
  7. Transparency Declaration
  8. References
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