Development and clinical validation of a loop mediated isothermal amplification (LAMP) method for the rapid detection of Neisseria meningitidis
Bibliographic record
Abstract
Loop mediated isothermal amplification (LAMP) is an innovative technique which allows the rapid detection of target nucleic acid sequences under isothermal conditions without the need for complex instrumentation. The development, systematic optimisation and clinical validation of a LAMP assay targeting the ctrA gene for the rapid detect ion of capsular N. meningitidis is described. Highly specific detection of capsular N. meningitidis type strains and clinical isolates was demonstrated, with no cross reactivity with other Neisseria spp., or with a comprehensive panel of other common human pathogens. The lower limit of detection was determined as 6 ctrA gene copies detectable in 48 minutes, with positive reactions readily identifiable visually via a simple colour change. High copy numbers could be detected in 22 minutes. Clinical Validation was carried out by retrospectively and prospectively analysing a total of 935 clinical specimens from a total of 603 patients. The level of agreement between the ctrA LAMP assay and a confirmatory test result (Culture, MRU PCR, ctrA RT-PCR) for each patient was used to evaluate the performance of LAMP for the detection of capsular N. meningitidis. The overall sensitivity and specificity of the designed ctrA LAMP assay was determined as 94.6% and 99.6% with positive and negative predictive values of 96.4% and 99.5% respectively. The potential utility of a positive ctrA LAMP respiratory specimen result to indicate MD was investigated. The sensitivity and specificity of respiratory• specimens in this regard was 89.3% and 97.7% with positive and negative predictive values of 80.7% and 98.9% respectively. Rapid LAMP testing of non-invasive respiratory specimens has significant potential to accelerate the diagnosis of MD. The LAMP method represents a simple, rapid, sensitive, and highly specific technique for the detection of N. meningitidis, and has the potential to be used as a POC molecular test and in resource poor settings.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.006 | 0.007 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".