Toward a quantitative DNA-based definition of pneumococcal pneumonia: a comparison of Streptococcus pneumoniae target genes, with special reference to the Spn9802 fragment

Abdeldaim, Guma; Strålin, Kristoffer; Olcén, Per; Blomberg, Jonas; Herrmann, Björn

doi:10.1016/j.diagmicrobio.2007.08.010

Cited by 67 publications

(88 citation statements)

References 32 publications

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“…This is the first study that investigated the presence of S. pneumoniae and S. pseudopneumoniae in respiratory specimens. Two recent studies described the presence of S. pneumoniae in respiratory samples with the Spn9802 real-time PCR that detects both S. pneumoniae and S. pseudopneumoniae, without a discrimination of the two species (3,4). The data described in this paper show that for all respiratory samples from which S. pneumoniae or S. pseudopneumoniae isolates were cultured, S. pneumoniae or S. pseudopneumoniae was detected by real-time PCR with C T values lower than 30.…”

Section: Discussionmentioning

confidence: 70%

“…Several previous studies showed that a PCR assay targeting the Spn9802 fragment detects only S. pneumoniae and S. pseudopneumoniae but not S. mitis (4,10,32). False-positive results with Spn9802 primers have been described, and therefore, it remains unknown whether the Spn9802 DNA fragment is specific for S. pneumoniae and S. pseudopneumoniae or whether specificity is obtained by particular signatures (26).…”

Section: Discussionmentioning

confidence: 99%

“…S. pneumoniae belongs to the mitis group of streptococci, and several molecular assays have been applied in an attempt to discriminate S. pneumoniae from other mitis group streptococci. A variety of genes has been used as target for a (real-time) PCR assay to detect S. pneumoniae, including genes encoding the virulence factors autolysin (lytA) and pneumolysin (ply) and the DNA fragment Spn9802 (1,4,7,16,22,25,32). However, most of these PCR assays are not able to discriminate S. pneumoniae from the recently discovered Streptococcus pseudopneumoniae and other mitis group streptococci.…”

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confidence: 99%

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Evaluation of Several Biochemical and Molecular Techniques for Identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and Their Detection in Respiratory Samples

et al. 2012

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The identification and detection of mitis group streptococci, which contain Streptococcus pneumoniae, have been hampered by the lack of sensitive and specific assays. In this study, we evaluated several biochemical and molecular assays for the identification of S. pneumoniae and Streptococcus pseudopneumoniae and their distinction from other mitis group streptococci using a collection of 54 isolates obtained by the routine culturing of 53 respiratory specimens from patients with community-acquired pneumonia. The combined results of the biochemical and molecular assays indicated the presence of 23 S. pneumoniae, 2 S. pseudopneumoniae, and 29 other mitis group streptococcal isolates. The tube bile solubility test that is considered gold standard for the identification of S. pneumoniae showed concordant results with optochin susceptibility testing (CO 2 atmosphere) and a real-time multiplex PCR assay targeting the Spn9802 fragment and the autolysin gene. Optochin susceptibility testing upon incubation in an O 2 atmosphere, bile solubility testing by oxgall disk, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and sequence analysis of the tuf and rpoB genes resulted in several false-positive, false-negative, or inconclusive results. The S. pseudopneumoniae isolates could be identified only by molecular assays, and the multiplex real-time PCR assay was concluded to be most convenient for the identification of S. pneumoniae and S. pseudopneumoniae isolates. Using this method, S. pneumoniae and S. pseudopneumoniae DNA could be detected in the respiratory samples from which they were isolated and in an additional 11 samples from which only other streptococci were isolated. S treptococcus pneumoniae is a major cause of community-acquired pneumonia (CAP). There is no true gold standard for S. pneumoniae identification, but the bile solubility test has been shown to have a high level of accuracy and is frequently used for the identification of S. pneumoniae (18). Since this test is relatively time-consuming and sometimes difficult to interpret, several other conventional biochemical and phenotypic tests, like Gram stain morphology, optochin susceptibility, colony morphology, and alpha-hemolysis on sheep blood agar, are currently applied as part of routine procedures in the clinical microbiology laboratory. S. pneumoniae belongs to the mitis group of streptococci, and several molecular assays have been applied in an attempt to discriminate S. pneumoniae from other mitis group streptococci. A variety of genes has been used as target for a (real-time) PCR assay to detect S. pneumoniae, including genes encoding the virulence factors autolysin (lytA) and pneumolysin (ply) and the DNA fragment Spn9802 (1,4,7,16,22,25,32). However, most of these PCR assays are not able to discriminate S. pneumoniae from the recently discovered Streptococcus pseudopneumoniae and other mitis group streptococci. As an alternative approach, sequence analysis of several genes has been used for the species-level identifica...

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Section: Discussionmentioning

confidence: 70%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Evaluation of Several Biochemical and Molecular Techniques for Identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and Their Detection in Respiratory Samples

et al. 2012

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“…One limitation of our study is that we used ply gene of pneumococcal for detection (diagnosis) and quantification of pneumococcal DNA bacterial load (DBL). Ply gene may be unspecific because some other strains closely related with S.pneumoniae may share the virulent genes encoding by S.pneumoniae such as ply or lytA genes [27]. Carvalho et al [20] tested two ply based PCR assays against 10…”

Section: P=04)mentioning

confidence: 99%

DNA bacterial load in children and adolescents with pneumococcal pneumonia and empyema

Muñoz-Almagro

Gala

Selva

et al. 2010

Eur J Clin Microbiol Infect Dis

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“…Advantages of nonculture techniques include increased sensitivity and shorter turnaround time. We and others previously reported quantitative nasopharyngeal (NP) colonization density as a novel diagnostic tool for determining pneumococcal etiology in HIV-infected adults with pneumonia (4,5). Testing of sputum samples with quantitative PCR was initially reported with the less specific pneumococcal target ply (6)(7)(8).…”

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confidence: 99%

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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Toward a quantitative DNA-based definition of pneumococcal pneumonia: a comparison of Streptococcus pneumoniae target genes, with special reference to the Spn9802 fragment

Cited by 67 publications

References 32 publications

Evaluation of Several Biochemical and Molecular Techniques for Identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and Their Detection in Respiratory Samples

Evaluation of Several Biochemical and Molecular Techniques for Identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and Their Detection in Respiratory Samples

DNA bacterial load in children and adolescents with pneumococcal pneumonia and empyema

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

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