Rapid, accurate, and novel diagnostic technique for respiratory pathogens: Clinical application of loop-mediated isothermal amplification assay in older patients with pneumonia, a multicenter prospective observational study

Abstract

BackgroundLoop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method using only one type of enzyme that can amplify DNA with high specificity, efficiency and rapidity under isothermal conditions. Chips for Complicated Infection Detection (CCID) is based on LAMP. This study translate CCID into clinical application and evaluate its diagnostic value for pneumonia.MethodsEighty one older patients with pneumonia were prospectively enrolled from January 1 to July 23, 2021, and 57 sputum/airway secretion and 35 bronchoalveolar lavage fluid samples were collected and analyzed by CCID and conventional microbiological tests (CMTs). Samples were collected, transported, monitored, and managed by a multidisciplinary team using a sample management information system.ResultsCCID turnaround time was 50 min, and the detection limit was 500 copies/reaction. The percentage of positive samples was significantly higher using CCID than CMTs, especially for Klebsiella pneumoniae (odds ratio [OR], 9.0; 95% confidence interval [CI], 1.1–70.5; p < 0.05), Enterococcus faecalis (OR, ∞; p < 0.01), Stenotrophomonas maltophilia (OR, ∞; p < 0.01), fungi (OR, 26.0; 95% CI, 3.6–190.0; p < 0.01), and viruses (CCID only; p < 0.01). In addition, the percentage of positive results was significantly higher using CCID than CMTs in patients who used antibiotics for more than 3 days (91.9% vs. 64.9%; p < 0.01). Analyzing clinical impact, 55 cases (59.8%) benefited from CCID.ConclusionCCID allows the rapid and accurate detection of pneumonia in older patients. Moreover, this technique is less affected by previous antibiotic treatment and can improve patient care.

Microbiological Profile of Patients with Aspiration Pneumonia Identified by Combined Detection Methods

“…The chip was able to identify 47 bacterial species, 22 fungal species and 21 viruses. 12 The workflow of mNGS includes sample pretreatment and nucleic acid extraction, library preparation, highthroughput sequencing, and bioinformatics analysis. Nucleic acid extraction and library preparation were performed.…”

“…Chips for complicated infection detection (CCID) is a novel technique for rapid detection of pathogenic microorganisms. 12 Our previous multicenter prospective observational study has shown that CCID was promising in elderly patients with pneumonia due to its potential to rapidly and accurately detect multiple pathogenic microorganisms and was less affected by prior antimicrobial therapy. 12 In addition, metagenomic next-generation sequencing (mNGS), as a hypothesis-free, unbiased, and culture-independent modality, has been progressively applied in the etiological diagnosis of respiratory tract infection.…”

“… 12 Our previous multicenter prospective observational study has shown that CCID was promising in elderly patients with pneumonia due to its potential to rapidly and accurately detect multiple pathogenic microorganisms and was less affected by prior antimicrobial therapy. 12 In addition, metagenomic next-generation sequencing (mNGS), as a hypothesis-free, unbiased, and culture-independent modality, has been progressively applied in the etiological diagnosis of respiratory tract infection. 13 , 14 In view of the complexity of the etiology of AP and AspRF-CAP and the unsatisfactory detection techniques of pathogens, multiplexed detection techniques with high sensitivity and accuracy are required.…”