Abstract
Distinguishing lower respiratory tract infection (LRTI) from incidental pathogen carriage (IPC) is clinically challenging. The immunologic and microbial factors defining the states of LRTI and IPC are poorly understood. Here, we perform host-microbe metatranscriptomic profiling of tracheal aspirates from 326 mechanically ventilated children with clinically adjudicated LRTI (n = 207), IPC (n = 70), or non-infectious respiratory failure (n = 49). In the airway microbiome, LRTI shows reduced alpha diversity and taxonomic richness, while IPC displays greater bacterial abundance, enrichment in respiratory anaerobes, and increased metabolic activity. At the host level, patients with LRTI exhibit a distinct lower airway transcriptional signature of innate and adaptive immune activation compared to those with IPC, who have similar transcriptional profiles to uninfected controls. Mediation analyses suggest the airway microbiome influences the host response to pathogens. An integrated host-microbe metatranscriptomic classifier accurately discriminates LRTI from IPC and controls (AUC = 0.89, 95% confidence interval (CI) 0.85–0.92). The single gene FABP4, encoding a macrophage-associated lipid chaperone and recently described pneumonia biomarker, performs similarly when combined with alpha diversity; FABP4 protein alone achieves an AUC = 0.88 (95% CI 0.82–0.93). Together, our findings reveal distinct ecological and immunologic archetypes defining LRTI and IPC, and support data-driven, biology-informed LRTI diagnostics incorporating host and microbial features.
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Data availability
FASTQ files containing the microbial sequencing reads following subtraction of reads aligning to the human genome have been deposited in the NCBI Sequence Read Archive under BioProject accession PRJNA748764. Processed host gene counts, microbial taxon counts, and deidentified clinical metadata are available in the GitHub repository associated with this work: https://github.com/infectiousdisease-langelier-lab/Incidental_pathogen_carriage (https://doi.org/10.5281/zenodo.19078486)87. Source data for each of the figures is provided in the Supplementary information. Source data are provided with this paper.
Code availability
The code used for data processing, statistical analyses, and figure generation is publicly available at: https://github.com/infectiousdisease-langelier-lab/Incidental_pathogen_carriage (https://doi.org/10.5281/zenodo.19078486)87.
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Acknowledgements
We thank all patients and their families for participating in this study. We acknowledge the contributions of the principal investigators, coinvestigators, and research coordinators at each of the study sites where patients were enrolled. This study was supported by the Collaborative Pediatric Critical Care Research Network, the Eunice Kennedy Shriver National Institute of Child Health and Human Development, the National Heart, Lung and Blood Institute UG1HD083171 (P.M.M.), 1R01HL124103 (P.M.M.), R01AI182308 (P.M.M. and C.R.L.), 5R01HL155418 (C.R.L.), and the Chan Zuckerberg Biohub (C.R.L.). The study sponsors were not involved in study design, in the collection, analysis, or interpretation of data, in writing of the manuscript, or in the decision to submit the manuscript for publication.
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E.C.L., P.D., A.G. and C.R.L. conceived and designed the study. C.R.L. and P.M.M. supervised the study. C.R.L., P.M.M., C.M.M., M.K.L. and L.A. enrolled the cohort. C.R.L., P.M.M., C.M.M. and M.K.L. performed clinical adjudications. P.D., A.G., H.V.P., E.M. and B.D.W. generated the data. E.C.L., P.D. and A.G. analyzed the data and generated the figures. E.C.L. and C.R.L. wrote the manuscript. E.C.L., P.D., A.G., H.V.P., C.M.M., M.K.L., J.A., E.M., B.D.W., J.L.D., L.A., P.M.M. and C.R.L. edited the manuscript. C.R.L. and P.M.M. acquired funding.
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E.C.L., H.V.P., C.R.L., and P.M.M. are listed as inventors on a provisional patent application titled “Diagnostic & prognostic immune markers for critical infections” filed by the University of California San Francisco and currently pending. All other authors declare no competing interests.
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Lydon, E.C., Deosthale, P., Glascock, A. et al. Host–microbiome archetypes differentiate infection from pathogen carriage in the human lower airway. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71863-5
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DOI: https://doi.org/10.1038/s41467-026-71863-5
