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Application of metagenomic next-generation sequencing in children with pneumonia of unknown etiology.

Haixia Huang·Yueqiang Fu·Enmei Liu·Ke Bai·Jing Li·Chengjun Liu·Yu Deng·Feng Xu
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Abstract

OBJECTIVE: To investigate the pathogen spectrum and clinical application value of metagenomic next-generation sequencing (mNGS) in lower respiratory tract specimens from children with pneumonia of unknown etiology. METHODS: A retrospective analysis was conducted on children hospitalized in the intensive care unit (ICU) and respiratory department ward of Children's Hospital of Chongqing Medical University from January 2025 to December 2025. All enrolled cases presented negative results for conventional respiratory pathogen tests and received mNGS testing of lower respiratory tract specimens for etiological identification. The mNGS findings and clinical data of the included children were analyzed. RESULTS: A total of 92 children were enrolled, including 54 males and 38 females, with ages ranging from 2 months to 13 years and 8 months. Causative pathogens were detected in 77 cases (83.7%). The clinically adjudicated etiological diagnosis rates of bacteria, viruses, fungi and atypical pathogens were 75.0% (69/92), 37.0% (34/92), 13.0% (12/92) and 5.4% (5/92), respectively. Thirty-eight cases were complicated with polymicrobial infection, among which bacterial-viral infection was predominant, accounting for 23.1% (24/92). Children with immunocompromised conditions exhibited higher incidences of clinically adjudicated bacterial, fungal and polymicrobial infection than immunocompetent patients. The most common clinically confirmed causative pathogens in immunocompromised children were Streptococcus pneumoniae, human cytomegalovirus, Haemophilus influenzae, Stenotrophomonas maltophilia and Enterococcus faecalis. Treatment regimens were adjusted in 58 cases (63.0%) based on mNGS findings, switching to pathogen-targeted anti-infective therapy. CONCLUSION: For pediatric pneumonia with negative conventional etiological tests, mNGS of lower respiratory tract specimens significantly enhances pathogen detection rates, effectively identifies polymicrobial infection and opportunistic pathogens. Immune status serves as a critical stratification factor influencing pathogen spectrum and infection patterns, with immunocompromised children being more susceptible to opportunistic infections. Adjustment of anti-infective regimens based on mNGS results can effectively facilitate personalized anti-infective therapy.

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HumansFemaleMaleChild, PreschoolHigh-Throughput Nucleotide SequencingInfantMetagenomicsRetrospective StudiesChildAdolescentPneumoniaBacteriaCoinfectionImmunocompromised HostViruseschildrenlower respiratory tract specimensmetagenomic next-generation sequencingpneumoniaunknown etiologyJournal Article

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Haixia Huang, Yueqiang Fu, Enmei Liu, Ke Bai, Jing Li, Chengjun Liu, Yu Deng, Feng Xu. 2026-09-01. Application of metagenomic next-generation sequencing in children with pneumonia of unknown etiology.. https://doi.org/10.3389/fcimb.2026.1922924

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