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. 2025 May 9:15:1584214.
doi: 10.3389/fcimb.2025.1584214. eCollection 2025.

A comprehensive evaluation of plasma metagenomics sequencing for the diagnosis of suspected infection in pediatric patients with hematologic diseases

Shihai Zhang #  1 , Qiang Guo #  1 , Wei Gai #  2 , Yuxin Guo  2 , Yafeng Zheng  2
Affiliations

A comprehensive evaluation of plasma metagenomics sequencing for the diagnosis of suspected infection in pediatric patients with hematologic diseases

Shihai Zhang et al. Front Cell Infect Microbiol. .

Abstract

Background: As a non-invasive technology, plasma cell-free DNA (cfDNA) next-generation sequencing (mNGS) has been widely used for clinical detection of a variety of infectious diseases. Infections are a major cause of poor prognosis in children with hematologic diseases. So far, there has been limited research on the use of plasma cfDNA mNGS in children with hematological disorders at high risk of infection.

Methods: We retrospectively analyzed the clinical data of 73 children with hematological disorders suspected of early infection admitted to Anhui Children's Hospital between September 2023 and February 2024. The diagnostic performance and clinical implications of mNGS versus conventional microbiological testing (CMT) were evaluated.

Results: The positive rate of mNGS was significantly higher than that of CMT (69.86% vs 31.51%, P < 0.001). When compared with the final clinical diagnosis, the sensitivity of mNGS was significantly higher than that of CMT (71.88% vs 35.94%, P < 0.001). There is a high degree of agreement between the positive results of the two assays (78.95%). A total of 46 pathogens were identified in children with hematologic diseases, of which 41 pathogens were detected by mNGS and only 12 pathogens were detected by CMT. In these patients, the most common bacteria detected were Klebsiella pneumoniae and Mycoplasma pneumoniae. Human betaherpesvirus 5 (CMV) was the most commonly detected virus. All fungi were detected only by mNGS. Overall, mNGS had a positive effect on the clinical treatment for 65.75% of patients in this study. Positive results are more likely to be obtained with mNGS when white blood cell counts, neutrophil counts, and lymphocyte counts are low.

Conclusions: Early plasma cfDNA mNGS improved the performance of pathogen detection in children with hematological diseases. Rapid identification of the pathogen followed by precise targeted antimicrobial therapy improves the prognosis of patients.

Keywords: cell-free DNA; hematologic diseases; infection; metagenomic next-generation sequencing; pediatric.

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Conflict of interest statement

WG, YZ and YG are employed by WillingMed Technology Beijing Co., Ltd. The remaining 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
Comparison of the performance of plasma mNGS with blood culture (BC) and conventional microbial tests (CMT). (A) Positivity rates of different tests in total patients, as well as in infected and non-infected groups, where red indicates a positive proportion and green indicates a negative proportion; (B) Comparison of assay performance, including sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and total coincidence rate (TCR); (C) ROC curves of mNGS and CMT assays in detecting clinical infections; (D) Concordance analysis of mNGS and CMT results. **P<0.01, ***P<0.001.
Figure 2
Figure 2
Distribution of pathogens detected by mNGS and CMT in infected patients. (A) Venn diagram showing the number of pathogens detected by mNGS and CMT, where red represents the pathogens detected by mNGS and blue represents those detected by CMT; (B) Types of pathogens detected by mNGS and CMT; (C) Pathogen spectrum for mNGS and CMT detection.
Figure 3
Figure 3
Differences in laboratory indices (routine blood indices synchronized with plasma mNGS or 48-hour detection) between patients in the mNGS-positive and mNGS-negative groups.
See this image and copyright information in PMC

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