Targeted next generation sequencing is comparable with metagenomic next generation sequencing in adults with pneumonia for pathogenic microorganism detection

Li, Shiying; Tong, Jin; Liu, Yi; Shen, Wei; Hu, Ping

doi:10.1016/j.jinf.2022.08.022

Cited by 27 publications

(20 citation statements)

References 8 publications

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“…Mycoplasma pneumonia and Macrolide-resistant gene detection. [5,6] Anti-MP IgM titrations were performed at the time of admission. At the same time, tNGS was completed once BALF and other pertinent samples were obtained.…”

Section: Study Populationmentioning

confidence: 99%

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Clinical Efficacy of Macrolide Antibiotics in Mycoplasma Pneumoniae Pneumonia Carrying a Macrolide-resistant Mutation in the 23S rRNA Gene in Pediatric Patients

He,

Xie,

Rui

et al. 2024

Preprint

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Background. These global prospective surveillance data showed the re-emergence of mycoplasma pneumoniae pneumonia (MPP) in Europe and Asia after the coronavirus disease 2019 pandemic. We sought to observe the effect of macrolide antibiotics in the treatment of MPP carrying a macrolide-resistant mutation gene and the potential of targeted next-generation sequencing (tNGS) as a front-line diagnostic in MPP patients. Methods. The baseline characteristics of 91 children with MPP hospitalized from January to October 2023 were retrospectively analyzed. They were divided into two groups according to whether carrying the macrolide-resistant mutation or not. The logistic and linear regression analyses were used to determine whether the mutation was a standalone predictive predictor of the duration of fever and hospital length of stay. Results. First, no patients had a fever for ≥ 7 days after macrolide treatment. But length of stay and hormone concentration were significantly different between the two groups (P < 0.05). There were also no statistical association between the mutation and the duration of fever and hospital length of stay. Conclusion. Macrolides can be administered to MPP children carrying a macrolide-resistant mutation. tNGS can be seen as a front-line diagnostic in MPP.

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Section: Study Populationmentioning

confidence: 99%

“…Targeted next-generation sequencing(tNGS), which is based on ultra-multiplex polymerase chain reaction (PCR) ampli cation and high-throughput sequencing technology, is more rapid and economical than metagenomic next-generation sequencing [5,6] . It can achieve an early diagnosis of respiratory infection, including MP [5] .…”

Section: Introductionmentioning

confidence: 99%

Clinical Efficacy of Macrolide Antibiotics in Mycoplasma Pneumoniae Pneumonia Carrying a Macrolide-resistant Mutation in the 23S rRNA Gene in Pediatric Patients

He,

Xie,

Rui

et al. 2024

Preprint

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“…14,18 Prof. Peng Hu's team's research has demonstrated that tNGS can achieve comparable efficacy to mNGS in identifying pneumonia pathogens. 19 Nevertheless, there need to be more studies examining the use of tNGS in critically ill pediatric children. [20][21][22] Furthermore, there currently needs to be more research focused on the pathogens responsible for CNS infections in children undergoing neurosurgery, making it difficult to understand the range of infections affecting this population entirely.…”

Section: Introductionmentioning

confidence: 99%

Diagnostic Significance of Targeted Next-Generation Sequencing in Central Nervous System Infections in Neurosurgery of Pediatrics

Li¹,

Zhang²,

Yang³

et al. 2023

IDR

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Background Cerebrospinal fluid (CSF) pathogen culture suffers from the drawbacks of prolonged cycle time and a low positivity rate in diagnosing intracranial infections in children. This study aims to investigate the diagnostic potential of targeted next-generation sequencing (tNGS) in pediatric neurosurgery for central nervous system (CNS) infections. Methods A retrospective study was conducted on children under 14 with suspected intracranial infections following craniocerebral trauma or surgery between November 2018 and August 2020. Routine, biochemical, smear, and pathogen culture tests were performed on CSF during treatment. The main parameters of CSF analysis encompassed white blood cells (WBC, ×10 6 /L) count, percentage of multinucleated cells (%), protein levels (g/L), glucose concentration (GLU, mmol/L), chloride levels (mmol/L), and pressure (mmH2O). The outcomes of tNGS were assessed through the Receiver Operating Characteristic (ROC) curve and pertinent diagnostic parameters. Results Among the 35 included pediatric patients, 22 were clinically diagnosed with CNS infection in neurosurgery, tNGS was confirmed in 18 cases. The sensitivity and specificity of tNGS were 81.8% and 76.9%, respectively, while the traditional method of CSF cultures and smears exhibited a sensitivity of 13.6% and a specificity of 100%. ROC curve analysis indicated an area under the curve (AUC) of 0.794 for tNGS and 0.568 for the CSF cultures and smears. CSF analysis indicated that the two groups exhibited statistically significant differences in terms of WBC count [330.0 (110.00–2639.75) vs 14.00 (4.50–26.50), P<0.001] and percentage of multinuclear cells (%) [87.50 (39.75–90.00) vs 0 (0–10.00), P<0.001]. However, the remaining parameters did not statistically significant differences between the groups (all P>0.05). Conclusion tNGS demonstrates a high degree of diagnostic accuracy when detecting infections within the CNS of pediatric neurosurgery patients. tNGS can effectively establish for diagnosing CNS infections by detecting pathogenic microorganisms and their corresponding virulence and/or resistance genes within the test samples.

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“…Nevertheless, the complexity, high cost, and challenging interpretation of both techniques make them unsuitable for widespread clinical use in the short term. In contrast, Polymerase chain reaction (PCR)-based targeted next-generation sequencing (tNGS) (ElSharawy et al, 2012;Li et al, 2022) is a simple and cost-effective method that simultaneously enriches multiplex targets for sequencing (Gaston et al, 2022). It has the ability to simultaneously detect numerous known pathogenic microorganisms, virulence, or drug resistance genes of pathogens, including the vast majority of pandemic pathogens, making it a powerful tool for known pathogen detection (Cabibbe et al, 2020;Kambli et al, 2021;Quick et al, 2017;Wu et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Targeted Next-Generation Sequencing with MultiPrime A Reliable and Efficient Tool for Global Pathogen Detection

Yang

2023

Preprint

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Targeted next-generation sequencing (tNGS) offers a cost-effective option for pathogen diagnostics and therapeutics. Nevertheless, the design of multiplex primers constrains its wide-spectrum target coverage. Herein, we present multiPrime, which enables a more extensive coverage of pathogen spectra while maintaining high multiplexing compatibility. Our study demonstrates that multiPrime outperforms DegePrime with fewer primers and greater coverage on 8 viruses. Furthermore, multiPrime-designed primers successfully amplified all target amplicons across these viruses. We utilized multiPrime to design primers for a tNGS panel that covers 30 viruses, validating the panel's performance in 80 clinical specimens, achieving 94% sensitivity and 89% specificity.

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Targeted next generation sequencing is comparable with metagenomic next generation sequencing in adults with pneumonia for pathogenic microorganism detection

Cited by 27 publications

References 8 publications

Clinical Efficacy of Macrolide Antibiotics in Mycoplasma Pneumoniae Pneumonia Carrying a Macrolide-resistant Mutation in the 23S rRNA Gene in Pediatric Patients

Clinical Efficacy of Macrolide Antibiotics in Mycoplasma Pneumoniae Pneumonia Carrying a Macrolide-resistant Mutation in the 23S rRNA Gene in Pediatric Patients

Diagnostic Significance of Targeted Next-Generation Sequencing in Central Nervous System Infections in Neurosurgery of Pediatrics

Targeted Next-Generation Sequencing with MultiPrime A Reliable and Efficient Tool for Global Pathogen Detection

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