The Enhanced Pneumococcal LAMP Assay: A Clinical Tool for the Diagnosis of Meningitis Due to Streptococcus pneumoniae
Open accessAbstract
BACKGROUND: Streptococcus pneumoniae is a leading cause of invasive bacterial disease in developed and developing countries. We studied the loop-mediated isothermal amplification (LAMP) technique to assess its suitability for detecting S. pneumoniae nucleic acid in cerebrospinal fluid (CSF). METHODOLOGY/PRINCIPAL FINDINGS: We established an improved LAMP assay targeting the lytA gene (Streptococcus pneumoniae [Sp] LAMP). The analytical specificity of the primers was validated by using 32 reference strains (10 Streptococcus and seven non-Streptococcus species) plus 25 clinical alpha-hemolytic streptococcal strains, including four S. pneumoniae strains and 21 other strains (3 S. oralis, 17 S. mitis, and one Streptococcus species) harboring virulence factor-encoding genes (lytA or ply). Within 30 minutes, the assay could detect as few as 10 copies of both purified DNA and spiked CSF specimens with greater sensitivity than conventional polymerase chain reaction (PCR). The linear determination range for this assay is 10 to 1,000,000 microorganisms per reaction mixture using real-time turbidimetry. We evaluated the clinical sensitivity and specificity of the Sp LAMP assay using 106 randomly selected CSF specimens from children with suspected meningitis in Korea, China and Vietnam. For comparison, CSF specimens were also tested against conventional PCR and culture tests. The detection rate of the LAMP method was substantially higher than the rates of PCR and culture tests. In this small sample, relative to the LAMP assay, the clinical sensitivity of PCR and culture tests was 54.5% and 33.3%, respectively, while clinical specificity of the two tests was 100%. CONCLUSIONS/SIGNIFICANCE: Compared to PCR, Sp LAMP detected S. pneumoniae with higher analytical and clinical sensitivity. This specific and sensitive LAMP method offers significant advantages for screening patients on a population basis and for diagnosis in clinical settings.
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.
Integrity signals
Registry
Cites
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.
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 [55]
The Results and Discussion (Sp LAMP and Sp PCR Analysis of CSF Specimens; page unavailable) report PCR clinical sensitivity of 54.5% relative to LAMP, below the claimed 79%–100% range. The paper's 100% figure refers to PCR specificity; it also notes that PCR detected every culture-positive specimen, but does not report 100% overall clinical sensitivity. (LLM, conf=0.88)
Checked by a reasoning model — may be wrong.
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
Loop-mediated isothermal amplification of DNA
Notomi, T. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.12.e63 · Cited by 8,805 · see citing works
O'Brien, K. L., Wolfson, L. J., Watt, J. P., Henkle, E., Deloria-Knoll, M., McCall, N., Lee, E., Mulholland, K., Levine, O. S., & Cherian, T. (2009) · The Lancet · doi:10.1016/s0140-6736(09)61204-6 · Cited by 2,398 · see citing works
Accelerated reaction by loop-mediated isothermal amplification using loop primers
Nagamine, K., Hase, T., & Notomi, T. (2002) · Molecular and Cellular Probes · doi:10.1006/mcpr.2002.0415 · Cited by 2,049 · see citing works
Mori, Y., & Notomi, T. (2009) · Journal of Infection and Chemotherapy · doi:10.1007/s10156-009-0669-9 · Cited by 1,031 · see citing works
Tolerance of loop-mediated isothermal amplification to a culture medium and biological substances
Kaneko, H., Kawana, T., Fukushima, E., et al. (2006) · Journal of Biochemical and Biophysical Methods · doi:10.1016/j.jbbm.2006.08.008 · Cited by 710 · see citing works
Real-time turbidimetry of LAMP reaction for quantifying template DNA
Mori, Y., Kitao, M., Tomita, N., & Notomi, T. (2004) · Journal of Biochemical and Biophysical Methods · doi:10.1016/j.jbbm.2003.12.005 · Cited by 627 · see citing works
Robustness of a loop-mediated isothermal amplification reaction for diagnostic applications
François, P., Tangomo, M., Hibbs, J. R., et al. (2011) · FEMS Immunology & Medical Microbiology · doi:10.1111/j.1574-695x.2011.00785.x · Cited by 504 · see citing works
Acute bacterial meningitis in infants and children
Kim, K. S. (2010) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(09)70306-8 · Cited by 454 · see citing works
Ribosa, T. F. D. S., Ferrer, V. F., & Jm, M. V. (2010) · CRC Press eBooks · doi:10.1201/9781785231025-47 · Cited by 333 · see citing works
Whatmore, A. M., Efstratiou, A., Pickerill, A. P., Broughton, K., Woodard, G., Sturgeon, D., George, R. C., & Dowson, C. G. (2000) · Infection and Immunity · doi:10.1128/iai.68.3.1374-1382.2000 · Cited by 280 · see citing works
Essential procedures for clinical microbiology
Isenberg, H. D. (1998) · ASM Press eBooks · Cited by 160 · see citing works
Brown, P. D., & Lerner, S. A. (1998) · The Lancet · doi:10.1016/s0140-6736(98)02239-9 · Cited by 156 · see citing works
Salo, P., Örtqvist, Å., & Leinonen, M. (1995) · The Journal of Infectious Diseases · doi:10.1093/infdis/171.2.479 · Cited by 155 · see citing works
Essential Procedures for Clinical Microbiology
Fraise, A. P. (1999) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/43.1.167a · Cited by 143 · see citing works
Nagai, K. (2001) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/48.6.915 · Cited by 128 · see citing works
Seki, M., Yamashita, Y., Torigoe, H., Tsuda, H., Sato, S., & Maeno, M. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.4.1581-1586.2005 · Cited by 101 · see citing works
Self-citationAcute Bacterial Meningitis in Infants and Children: Epidemiology and Management
Agrawal, S., & Nadel, S. (2011) · Pediatric Drugs · doi:10.2165/11593340-000000000-00000 · Cited by 99 · see citing works
Interpreting Assays for the Detection of Streptococcus pneumoniae
Blaschke, A. J. (2011) · Clinical Infectious Diseases · doi:10.1093/cid/cir048 · Cited by 97 · see citing works
Llull, D., López, R., & Garcı́a, E. (2006) · Journal of Clinical Microbiology · doi:10.1128/jcm.44.4.1250-1256.2006 · Cited by 92 · see citing works
Sheppard, C. L., Harrison, T. G., Morris, R., et al. (2004) · Journal of Medical Microbiology · doi:10.1099/jmm.0.05460-0 · Cited by 86 · see citing works
KENNEDY, W. A., CHANG, S.-J., PURDY, K., LE, T., KILGORE, P. E., KIM, J. S., ANH, D. D., HUONG, P. L. T., DONG, B. Q., TAN, D. M., et al. (2007) · Epidemiology and Infection · doi:10.1017/s0950268806007734 · Cited by 66 · see citing works
Self-citationANTIMICROBIAL-RESISTANT PATHOGENS IN THE 1990s
Jacoby, G. A. (1996) · Annual Review of Medicine · doi:10.1146/annurev.med.47.1.169 · Cited by 64 · see citing works
Laboratory-based diagnosis of pneumococcal pneumonia: state of the art and unmet needs
Vernet, G., Saha, S. K., Satzke, C., Burgess, D. C. H., Alderson, M. R., Maisonneuve, J., Beall, B., Steinhoff, M. C., & Klugman, K. P. (2011) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.2011.03496.x · Cited by 59 · see citing works
Kim, D. W., Kilgore, P. E., Kim, E. J., Kim, S. A., Anh, D. D., & Seki, M. (2011) · Journal of Clinical Microbiology · doi:10.1128/jcm.00515-11 · Cited by 50 · see citing works
Self-citationReal-time turbidimetry of LAMP reaction for quantifying template DNA
Mori, Y. (2004) · Journal of Biochemical and Biophysical Methods · doi:10.1016/s0165-022x(03)00217-3 · Cited by 38 · see citing works
Wester, C. W., Ariga, D., Nathan, C., et al. (2002) · Diagnostic Microbiology and Infectious Disease · doi:10.1016/s0732-8893(01)00358-3 · Cited by 30 · see citing works
Identification of selected respiratory pathogens in endodontic infections
Nandakumar, R., Whiting, J., & FOUAD, A. F. (2008) · Oral Surgery Oral Medicine Oral Pathology Oral Radiology and Endodontology · doi:10.1016/j.tripleo.2008.01.036 · Cited by 13 · see citing works
Flume, P. A. (1998) · Journal of Infectious Disease Pharmacotherapy · doi:10.1300/j100v03n01_04 · Cited by 11 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Acute bacterial meningitis in adults
McGill, F., Heyderman, R. S., Panagiotou, S., Tunkel, A. R., & Solomon, T. (2016) · The Lancet · doi:10.1016/s0140-6736(16)30654-7 · Cited by 274 · see citing works
Laboratory diagnosis of central nervous system infection
He, T., Kaplan, S., Kamboj, M., & Tang, Y.-W. (2016) · Current Infectious Disease Reports · doi:10.1007/s11908-016-0545-6 · Cited by 81 · see citing works
Loop-mediated isothermal amplification methods for diagnosis of bacterial meningitis
Seki, M., Kilgore, P. E., Kim, E. J., Ohnishi, M., Hayakawa, S., & Kim, D. W. (2018) · Frontiers in Pediatrics · doi:10.3389/fped.2018.00057 · Cited by 60 · see citing works
Self-citationDiallo, K., Feteh, V. F., Ibe, L., Antonio, M., Caugant, D. A., du Plessis, M., Deghmane, A.-E., Feavers, I. M., Fernandez, K., Fox, L. M., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103274 · Cited by 51 · see citing works
Molecular diagnostics in cerebrospinal fluid for the diagnosis of central nervous system infections
Olie, S. E., Andersen, C. Ø., van de Beek, D., & Brouwer, M. C. (2024) · Clinical Microbiology Reviews · doi:10.1128/cmr.00021-24 · Cited by 38 · see citing works
“Several studies found that PCR for S. pneumoniae provided additional diagnostic value in culture-negative bacterial meningitis (49, 50, 53, 55).”
- Authors
- Kim, D. W., Kilgore, P. E., Kim, E. J., Kim, S. A., Anh, D. D., Dong, B. Q., Kim, J. S., & Seki, M.
- Affiliations
- International Vaccine Institute (KR)
- Eugene Applebaum College of Pharmacy and Health Sciences (US)
- Guangxi Center for Disease Prevention and Control (CN)
- Jeonbuk National University (KR)
- Nihon University (JP)
- Corresponding author
- Seki, Mitsuko
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-08-10
- Volume
- 7
- Issue
- 8
- Pages
- e42954
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3416792
- OpenAlex
- W2053220097
- Cited by
- 50
- References
- 28
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 5 · 2023: 2 · 2022: 1 · 2021: 7 · 2020: 4 · 2019: 1 · 2018: 4 · 2017: 6 · 2016: 5 · 2015: 6 · 2014: 3 · 2013: 2
- FWCI
- 2.26
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- The Royal Society of Chemistry’s Journals, Books and Databases (The Royal Society of Chemistry) (submittedVersion, cc-by)
- Human Biology (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Greater South Information System
- Funders
- Nihon University
- Ministry of Education, Culture, Sports, Science and Technology
- Hanyang University (HY-2011, HY-2011-N)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
- Life Sciences › Immunology and Microbiology › Microbiology › Bacterial Infections and Vaccines
- Physical Sciences › Engineering › Biomedical Engineering › Biosensors and Analytical Detection
- Keywords
- Streptococcus pneumoniae, pneumococcal meningitis, loop-mediated isothermal amplification, lytA gene, cerebrospinal fluid, rapid molecular diagnostics, sensitivity and specificity, alpha-hemolytic streptococci, invasive pneumococcal disease
- MeSH terms
- Child, Preschool, DNA, Bacterial, Genes, Bacterial, Humans, Infant, Meningitis, Pneumococcal, N-Acetylmuramoyl-L-alanine Amidase, Sensitivity and Specificity, Streptococcus pneumoniae, Reproducibility of Results, Nucleic Acid Amplification Techniques
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
