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. 2025 Jun 12:15:1552236.
doi: 10.3389/fcimb.2025.1552236. eCollection 2025.

The significance of metagenomic next-generation sequencing and targeted next-generation sequencing in the diagnostic evaluation of patients with suspected pulmonary infections

Yucong Tang  1 , Shujin Tang  1 , Yingchao Zhang  1 , Zhentao Lin  1 , Shuxiang Shan  1
Affiliations

The significance of metagenomic next-generation sequencing and targeted next-generation sequencing in the diagnostic evaluation of patients with suspected pulmonary infections

Yucong Tang et al. Front Cell Infect Microbiol. .

Abstract

Objective: To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in identifying pathogens in patients with pulmonary infections.

Methods: A retrospective analysis was conducted on 155 patients with suspected lung infections who underwent alveolar lavage and were admitted to the Department of Respiratory and Critical Care Medicine at Baodi Hospital, Tianjin Medical University, from July 2023 to December 2023. The bronchoalveolar lavage fluid (BALF) samples obtained were subjected to mNGS, tNGS and culture methods to compare their diagnostic efficacy in identifying lung infection pathogens.

Results: The results indicated that both tNGS and mNGS methods exhibit comparable detection efficiencies in identifying pathogens in patients with pulmonary infections, significantly outperforming BALF culture approach. In terms of diagnostic accuracy, tNGS exhibited a higher sensitivity than mNGS, with rates of 96.1% and 75.7% respectively (P>0.05). However, the specificity of tNGS was slightly lower than that of mNGS, with rates of 59.1% and 68.2% respectively (P>0.05). It is noteworthy that this difference in specificity was not statistically significant.

Conclusion: tNGS exhibits a diagnostic efficacy comparable to mNGS, particularly in its sensitivity for identifying lung infections, as evidenced by expert insights and clinical applications. Furthermore, tNGS offers advantages in convenience, time efficiency, and cost-effectiveness, hinting at its potential to serve as an alternative to mNGS in clinical settings.

Keywords: bronchoalveolar lavage fluid; mNGS; pathogens; pulmonary infection; tNGS.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
An evaluation of the efficacy in identifying pathogens utilizing mNGS, tNGS, and culture methods. (A) A categorization of the distribution of microorganisms detected in more than two samples through the application of mNGS, tNGS, and culture assays. (B) The distribution of potential pathogens and the respective contributions of tNGS, mNGS, and culture in the detection of these pathogens. (C) A comparison of the number of positive samples for bacteria, fungi, DNA viruses, and atypical pathogens among tNGS, mNGS, and culture methods. (D) A pie chart illustrating the consistency of results between mNGS and tNGS, with double positive results further categorized into completely matches, more microbes detected by mNGS, and more microbes detected by tNGS. (E) The variability in the distribution of pathogens across different age groups when utilizing tNGS. (F) The variability in the distribution of pathogens across different age groups when utilizing mNGS.
Figure 2
Figure 2
Evaluation of Clinical Diagnostic Efficacy of mNGS and tNGS Methods. (A) Box plot showing the log10(reads) in the true positive (TP) group compared with that in the false positive (FP) group. (B) Pipe chart revealing the improvement of 55 patients adjusted the anti-infective treatment. (C) Comparison of turnaround time between mNGS and tNGS.
See this image and copyright information in PMC

References

    1. Aguilar Y. A., Rueda Z. V., Maya M. A., Vera C., Rodiño J., Muskus C., et al. (2021). Is it possible to differentiate pneumocystis jirovecii pneumonia and colonization in the immunocompromised patients with pneumonia? J. Fungi (Basel). 7, 1036. doi: 10.3390/jof7121036 - DOI - PMC - PubMed
    1. Cassini A., Högberg L. D., Plachouras D., Quattrocchi A., Hoxha A., Simonsen G. S., et al. (2019). Attributab le deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis. Lancet Infect. Dis. 19, 56–66. doi: 10.1016/S1473-3099(18)30605-4 - DOI - PMC - PubMed
    1. Chen T., Chen X., Zhang S., Zhu J., Tang B., Wang A., et al. (2021). The genome sequence archive family: toward explosive data growth and diverse data types. Genomics Proteomics Bioinf. 19, 578–583. doi: 10.1016/j.gpb.2021.08.001 - DOI - PMC - PubMed
    1. Chen S., Zhou Y., Chen Y., Gu J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890. doi: 10.1093/bioinformatics/bty560 - DOI - PMC - PubMed
    1. Chiu C. Y., Miller S. A. (2019). Clinical metagenomics. Nat. Rev. Genet. 20, 341–355. doi: 10.1038/s41576-019-0113-7 - DOI - PMC - PubMed

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