Comparison of Sputum and Nasopharyngeal Aspirate Samples and of the PCR Gene Targets
            <i>lytA</i>
            and Spn9802 for Quantitative PCR for Rapid Detection of Pneumococcal Pneumonia

Strålin, Kristoffer; Herrmann, Björn; Abdeldaim, Guma; Olcén, Per; Holmberg, Hans; Mölling, Paula

doi:10.1128/jcm.01742-13

Cited by 56 publications

(78 citation statements)

References 26 publications

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“…While the diagnostic accuracy of our optimal sputum lytA rtPCR cutoff value was 83% in patients with good-quality sputum, it was still lower than that recently published by Stralin et al in a Swedish pneumonia cohort (10). Of note, their optimal cutoff value was comparable to and only 1 log higher than ours and within the same range as that reported from a New Zealand study by Werno et al (9).…”

Section: Discussioncontrasting

confidence: 50%

“…In addition, the optimal lytA rtPCR cutoff values for NP specimens differed in the two studies, with 8,000 copies/ml for NP swabs in our study (4) and 10 2 copies/ml for NP aspirates in Stralin's study (10). Even though there might be some dilution with aspirates compared to swabs, this alone does not explain an almost 3-log difference in the cutoff values.…”

Section: Discussioncontrasting

confidence: 47%

“…One might speculate that without sputum induction, there would be an even greater proportion of patients with suboptimal sputum quality. Our results indirectly suggest that lytA rtPCR can be applied to those specimens as well, as shown by Stralin, who used expectorated sputum and likely had a higher proportion of suboptimal-quality samples (10). We initially used NP swabs as a diagnostic tool to diagnose pneumococcal pneumonia, in part because of the ease of obtaining these noninvasive specimens and because many pneumonia patients have a dry cough and are unable to produce sputum.…”

Section: Discussionmentioning

confidence: 99%

“…Most recently, Stralin et al performed a direct comparison of sputum and nasopharyngeal aspirates using lytA and another pneumococcus-specific gene target (Spn9802) to identify pneumococcal pneumonia in Swedish adults with quantitative PCR (qPCR). In their study, sputum lytA qPCR had the best sensitivity and specificity with a cutoff value of 10 5 DNA copies/ml (10). The prevalence and density of pneumococcal nasopharyngeal colonization vary with age, with HIV serostatus, and in different geographic areas (11)(12)(13).…”

mentioning

confidence: 99%

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Genomic Load from Sputum Samples and Nasopharyngeal Swabs for Diagnosis of Pneumococcal Pneumonia in HIV-Infected Adults

et al. 2014

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Quantitative lytA real-time PCR (rtPCR) results from nasopharyngeal (NP) swabs distinguish community-acquired pneumococcal pneumonia (CAP) from asymptomatic colonization. The use of an optimized cutoff value improved pneumococcal etiology determination compared to that of traditional diagnostic methods. Here, we compare the utility of lytA rtPCR from induced sputum and from NP swabs. Pneumococcus was considered the cause of CAP in HIV-infected South African adults if blood culture, induced-sputum culture or Gram stain, urine antigen test, or whole-blood lytA rtPCR revealed pneumococcus or if lytA rtPCR from NP swabs gave a result of >8,000 copies/ml. lytA rtPCR was also performed on induced sputum. Pneumococcus was detected by lytA rtPCR from sputum in 149 (67.1%) of 222 patients with available induced sputum, whereas the results of either Gram stain or culture of sputum were positive in 105 of 229 patients (45.9%; P < 0.001). The mean copy numbers from sputum were higher when the sputum cultures were positive than when the sputum cultures were negative (7.9 versus 5.6 log 10 copies/ ml; P < 0.001). Against the composite diagnostic standard, a cutoff value of 10,000 copies/ml for good-quality sputum lytA rtPCR had a sensitivity of 78.1% and a specificity of 80.0%. This cutoff value performed similarly to the previously identified cutoff value of 8,000 copies/ml for NP swab lytA rtPCR (area under the curve receiver operating characteristic [AUC-ROC], 80.4% for sputum of any quality versus 79.6% for NP swabs). The AUC-ROC for good-quality sputum was 83.2%. Overall, lytA rtPCR performs similarly well on induced sputum as on NP swabs for most patients but performs slightly better if good-quality sputum can be obtained. Due to the ease of specimen collection, NP swabs may be preferable for the diagnosis of pneumococcal pneumonia.

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Section: Discussioncontrasting

confidence: 50%

Section: Discussioncontrasting

confidence: 47%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Genomic Load from Sputum Samples and Nasopharyngeal Swabs for Diagnosis of Pneumococcal Pneumonia in HIV-Infected Adults

et al. 2014

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“…[4][5][6][7][8] While traditional methods of serotyping (Quellung reaction) require live organism, PCR-based detection and serotyping of S. pneumoniae can be performed on a variety of clinical specimens without culture. [9][10][11][12][13][14][15] Our laboratory previously demonstrated the feasibility of these PCR methods on nasopharyngeal (NP) swabs routinely collected for respiratory virus studies. 9 The serotype distribution mirrored trends obtained with traditional Quellung serotyping, but the PCR methods were not thoroughly validated with specimens collected from patients with pneumococcal disease.…”

Section: Introductionmentioning

confidence: 99%

Assessing the diagnostic accuracy of PCR-based detection ofStreptococcus pneumoniaefrom nasopharyngeal swabs collected for viral studies in Canadian adults hospitalised with community-acquired pneumonia: a Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research (CIRN) study

et al. 2017

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Study designDetection and serotyping of Streptococcus pneumoniae are important to assess the impact of pneumococcal vaccines. This study describes the diagnostic accuracy of PCR-based detection of S. pneumoniae directly from nasopharyngeal (NP) swabs collected for respiratory virus studies.MethodsActive surveillance for community-acquired pneumonia (CAP) in hospitalised adults was performed from December 2010 to 2013. Detection of pneumococcal CAP (CAPSpn) was performed by urine antigen detection (UAD), identification of S. pneumoniae in sputum or blood cultures. S. pneumoniae was detected in NP swabs using lytA and cpsA real-time PCR, and serotyping was performed using conventional and real-time multiplex PCRs. For serotyping, the Quellung reaction, PCR-based serotyping or a serotype-specific UAD was used.ResultsNP swab results were compared against CAP cases where all pneumococcal tests were performed (n=434), or where at least one test was performed (n=1616). CAPSpn was identified in 22.1% (96/434) and 14.9% (240/1616), respectively. The sensitivity of NP swab PCR for the detection of S. pneumoniae was poor for CAPSpn (35.4% (34/96) and 34.17% (82/240)), but high specificity was observed (99.4% (336/338) and 97.89% (1347/1376)). Of the positive NP swabs, a serotype could be deduced by PCR in 88.2% (30/34) and 93.9% (77/82), respectively.ConclusionsWhile further optimisation may be needed to increase the sensitivity of PCR-based detection, its high specificity suggests there is a value for pneumococcal surveillance. With many laboratories archiving specimens for influenza virus surveillance, this specimen type could provide a non-culture-based method for pneumococcal surveillance.

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Bronchoalveolar Lavage: Microbial Evaluation

Downes

Bouso

Planet

2020

Respiratory Medicine

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Comparison of Sputum and Nasopharyngeal Aspirate Samples and of the PCR Gene Targets lytA and Spn9802 for Quantitative PCR for Rapid Detection of Pneumococcal Pneumonia

Cited by 56 publications

References 26 publications

Genomic Load from Sputum Samples and Nasopharyngeal Swabs for Diagnosis of Pneumococcal Pneumonia in HIV-Infected Adults

Genomic Load from Sputum Samples and Nasopharyngeal Swabs for Diagnosis of Pneumococcal Pneumonia in HIV-Infected Adults

Assessing the diagnostic accuracy of PCR-based detection ofStreptococcus pneumoniaefrom nasopharyngeal swabs collected for viral studies in Canadian adults hospitalised with community-acquired pneumonia: a Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research (CIRN) study

Bronchoalveolar Lavage: Microbial Evaluation

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