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A LAMP-based system for rapid detection of eight common pathogens causing lower respiratory tract infections

Si, Yuying ; Zhang, Tong ; Chen, Nianzhen ; Cheng, Yu ; Wang, Lan ; Yuan, Jiayi ; Li, Gen ; Zong, Ming ; Sui, Guodong ; Fan, Lieying

Journal of microbiological methods, 2021-11, Vol.190, p.106339-106339, Article 106339 [Periódico revisado por pares]

Netherlands: Elsevier B.V

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A LAMP-based system for rapid detection of eight common pathogens causing lower respiratory tract infections
Autor: Si, Yuying ; Zhang, Tong ; Chen, Nianzhen ; Cheng, Yu ; Wang, Lan ; Yuan, Jiayi ; Li, Gen ; Zong, Ming ; Sui, Guodong ; Fan, Lieying
Assuntos: Acinetobacter baumannii - classification ; Acinetobacter baumannii - genetics ; Acinetobacter baumannii - isolation & purification ; Bacteria - classification ; Bacteria - genetics ; Bacteria - isolation & purification ; Colony Count, Microbial ; Escherichia coli - classification ; Escherichia coli - genetics ; Escherichia coli - isolation & purification ; Haemophilus influenzae - classification ; Haemophilus influenzae - genetics ; Haemophilus influenzae - isolation & purification ; High-Throughput Nucleotide Sequencing ; High-throughput sequencing ; Humans ; Klebsiella pneumoniae - classification ; Klebsiella pneumoniae - genetics ; Klebsiella pneumoniae - isolation & purification ; LAMP ; Lower respiratory tract infections ; Molecular Diagnostic Techniques - methods ; Moraxella catarrhalis - classification ; Moraxella catarrhalis - genetics ; Moraxella catarrhalis - isolation & purification ; Nucleic Acid Amplification Techniques - methods ; Pathogenic bacteria ; Pseudomonas aeruginosa - classification ; Pseudomonas aeruginosa - genetics ; Pseudomonas aeruginosa - isolation & purification ; Respiratory System - microbiology ; Respiratory Tract Infections - diagnosis ; Respiratory Tract Infections - microbiology ; Sanger sequencing ; Sensitivity and Specificity ; Sputum - microbiology ; Standard culture method ; Staphylococcus aureus - classification ; Staphylococcus aureus - genetics ; Staphylococcus aureus - isolation & purification ; Streptococcus pneumoniae - classification ; Streptococcus pneumoniae - genetics ; Streptococcus pneumoniae - isolation & purification
É parte de: Journal of microbiological methods, 2021-11, Vol.190, p.106339-106339, Article 106339
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
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Descrição: Lower respiratory tract infections (LRTIs) are a leading cause of morbidity and mortality worldwide and lack a rapid diagnostic method. To improve the diagnosis of LRTIs, we established an available loop-mediated isothermal amplification (LAMP) assay for the detection of eight common lower respiratory pathogens, including Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus aureus, Escherichia coli, Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis. The whole process can be achieved within 1 h (sample to results read out). We established an extraction free isothermal system. 528 sputum samples collected from patients suspected to have LRTIs were analyzed by the system (8 tests in each sample, a total of 4224 tests) and compared with the standard culture method (SCM). The samples with inconsistent results were further verified by Sanger sequencing and High-throughput sequencing (NGS). The detection limits of the LAMP assay for the 8 pathogens ranged from 103 to 104 CFU/mL. Upon testing 528 samples, the Kappa coefficients of all pathogens ranged between 0.5 and 0.7 indicated a moderate agreement between the LAMP assay and the SCM. All inconsistent samples were further verified by Sanger sequencing, we found that the developed LAMP assay had a higher consistency level with Sanger sequencing than the SCM for all pathogens. Additionally, when the NGS was set to a diagnostic gold standard, the specificity and sensitivity of the LAMP assay for LRTIs were 94.49% and 75.00%. The present study demonstrated that the developed LAMP has high consistency with the sequencing methods. Meanwhile, the LAMP assay has a higher detection rate compared to the SCM. It may be a powerful tool for rapid and reliable clinical diagnosis of LRTIs in primary hospitals. [Display omitted] •The whole process, from sample analysis to results read out can be achieved in 1 h.•528 sputum samples were analyzed to evaluate the consistency of two methods.•The samples with inconsistent results were further verified by Sanger sequencing.•High-throughput sequencing further evaluated the accuracy of the system.
Editor: Netherlands: Elsevier B.V
Idioma: Inglês

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A LAMP-based system for rapid detection of eight common pathogens causing lower respiratory tract infections

Si, Yuying ; Zhang, Tong ; Chen, Nianzhen ; Cheng, Yu ; Wang, Lan ; Yuan, Jiayi ; Li, Gen ; Zong, Ming ; Sui, Guodong ; Fan, Lieying

Netherlands: Elsevier B.V

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