CoChat
Sign Up
Cited by 588Pneumonia and Respiratory InfectionsBacterial Identification and Susceptibility TestingMicrobial infections and disease research

Evaluation and Improvement of Real-Time PCR Assays Targeting lytA , ply , and psaA Genes for Detection of Pneumococcal DNA

Open access
Carvalho, Maria da Gloria S., Tondella, Maria Lucia, McCaustland, Karen, Weidlich, Luciana, McGee, Lesley, Mayer, Leonard W., Steigerwalt, Arnold, Whaley, Melissa +6 more·2007·Journal of Clinical Microbiology
DOI 10.1128/jcm.02498-06PMC PMC1951257
Open this paper in CoChat — free account

Abstract

The accurate diagnosis of pneumococcal disease has frequently been hampered not only by the difficulties in obtaining isolates of the organism from patient specimens but also by the misidentification of pneumococcus-like viridans group streptococci (P-LVS) as Streptococcus pneumoniae. This is especially critical when the specimen comes from the respiratory tract. In this study, three novel real-time PCR assays designed for the detection of specific sequence regions of the lytA, ply, and psaA genes were developed (lytA-CDC, ply-CDC, and psaA, respectively). These assays showed high sensitivity (<10 copies for lytA-CDC and ply-CDC and an approximately twofold less sensitivity for psaA). Two additional real-time PCR assays for lytA and ply described previously for pneumococcal DNA detection were also evaluated. A panel of isolates consisting of 67 S. pneumoniae isolates (44 different serotypes and 3 nonencapsulated S. pneumoniae isolates from conjunctivitis outbreaks) and 104 nonpneumococcal isolates was used. The 67 S. pneumoniae isolates were reactive in all five assays. The new real-time detection assays targeting the lytA and psaA genes were the most specific for the detection of isolates confirmed to be S. pneumoniae, with lytA-CDC showing the greatest specificity. Both ply PCRs were positive for all isolates of S. pseudopneumoniae, along with 13 other isolates of other P-LVS isolates confirmed to be non-S. pneumoniae by DNA-DNA reassociation. Thus, the use of the ply gene for the detection of pneumococci can lead to false-positive reactions in the presence of P-LVS. The five assays were applied to 15 culture-positive cerebrospinal fluid specimens with 100% sensitivity; and serum and ear fluid specimens were also evaluated. Both the lytA-CDC and psaA assays, particularly the lytA-CDC assay, have improved specificities compared with those of currently available assays and should therefore be considered the assays of choice for the detection of pneumococcal DNA, particularly when upper respiratory P-LVS might be present in the clinical specimen.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1128/jcm.02498-06

Cites

34 of 34 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The reported sensitivity of PCR for pneumococcal meningitis is high and reached 100% in the majority of studies, with a median of 100% and range 79%-100%.

    “The reported sensitivity of PCR for pneumococcal meningitis is high and reached 100% in the majority of conducted studies (median of 100%, range 79%–100%) (Table 1; see also Table S1 in the supplemental material) (49–58).”

    From Molecular diagnostics in cerebrospinal fluid for the diagnosis of central nervous system infections (2024) · cites this paper as [51]

    The Materials and Methods identify the CSF specimens as coming from meningitis patients, and the Results report 100% sensitivity for all five assays in 15 pneumococcus-positive CSF specimens. This supports the paper as one example of a 100% result, but it does not establish that most studies reached 100% or report the stated median and 79%–100% range. Page numbers are unavailable in our copy. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 1

  1. [14]Facklam, R. R., and N. Pigott. 1994. Description of phenotypic characteristics to aid in the identification of Streptococcus pneumoniae. In A. Totollan (ed.), Pathogenic streptococci: present and future. Lancer Publications, St. Petersburg, Russia.

Cited by

Sorted by citations

Related

Authors
Carvalho, M. D. G. S., Tondella, M. L., McCaustland, K., Weidlich, L., McGee, L., Mayer, L. W., Steigerwalt, A., Whaley, M., Facklam, R. R., Fields, B., Carlone, G., Ades, E. W., Dagan, R., & Sampson, J. S.
Affiliations
  • Division of Bacterial Diseases
  • Centers for Disease Control and Prevention (US)
  • Fundação Estadual de Produção e Pesquisa em Saúde (BR)
  • Emory University (US)
  • Soroka Medical Center (IL)
ORCID
Venue
Journal of Clinical Microbiology
Publisher
American Society for Microbiology
Published
2007-08
Volume
45
Issue
8
Pages
2460-2466
ISSN
  • 0095-1137 (ISSN-L)
  • 1098-660X
DOI
10.1128/jcm.02498-06
PMC
PMC1951257
OpenAlex
W2110005071
Cited by
588
References
34
Citations by year
2026: 23 · 2025: 40 · 2024: 34 · 2023: 32 · 2022: 34 · 2021: 49 · 2020: 27 · 2019: 37 · 2018: 30 · 2017: 43 · 2016: 43 · 2015: 42 · 2014: 26 · 2013: 33 · 2012: 23
FWCI
9.63
Type
journal article
Language
en
Open access
Licence
journals.asm.org/non-commercial-tdm-license (tdm)
Locations
  • Journal of Clinical Microbiology (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • U.S. Department of Energy
  • Centers for Disease Control and Prevention
  • Oak Ridge Institute for Science and Education
Topics
  • Health Sciences › Medicine › Epidemiology › Pneumonia and Respiratory Infections
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
  • Life Sciences › Immunology and Microbiology › Microbiology › Microbial infections and disease research
Keywords
Streptococcus pneumoniae, lytA gene, psaA gene, Streptococcus viridans, false positives, cerebrospinal fluid, serotype diversity, conjunctivitis, respiratory tract isolates
MeSH terms
Cerebrospinal Fluid, Child, DNA, Bacterial, False Positive Reactions, Genes, Bacterial, Humans, Nucleic Acid Hybridization, Otitis Media with Effusion, Pneumococcal Infections, Sensitivity and Specificity, Streptococcus pneumoniae, Polymerase Chain Reaction, Serum

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review