Non-invasive molecular surveillance of drug-resistant bacterial and fungal pathogens in severe ICU pneumonia: a comparative study of nasopharyngeal swabs and BALF

Background Drug-resistant bacterial and fungal infections represent a major cause of morbidity and mortality among critically ill and immunocompromised patients with severe pneumonia. Molecular diagnostics using bronchoalveolar lavage fluid (BALF) are considered the reference standard for pathogen identification but are invasive and often contraindicated in unstable intensive care unit (ICU) patients. Safer non-invasive sampling strategies that maintain diagnostic reliabilityfor clinically relevant and potentially drug-resistant pathogens are therefore urgently needed. Methods In this prospective cohort study conducted between January 1 and July 30, 2024, paired nasopharyngeal swabs (NPS) and BALF samples were collected from 105 ICU patients with severe pneumonia. Pathogen detection was performed using targeted next-generation sequencing (tNGS) with a focus on clinically significant bacterial, viral, and fungal pathogens commonly associated with antimicrobial resistance. Concordance between NPS and BALF was evaluated using positive percent agreement (PPA) and negative percent agreement (NPA), with BALF serving as the reference standard. Longitudinal two-phase sampling was performed in 74 patients to assess the capacity of NPS to monitor temporal changes in pathogen profiles. Results Compared with BALF, NPS demonstrated high concordance for major bacterial pathogens frequently associated with drug resistance, including Acinetobacter baumannii , Staphylococcus aureus , and Escherichia coli , with PPA ≥ 80.0% and overall detection rates ≥90.0%. NPA exceeded 95.0% for most pathogens, indicating a low false-positive rate. Viral detection showed moderate sensitivity (PPA ≤ 80.0%), while fungal concordance was variable, ranging from 0.0% for Aspergillus flavus to 50.0% for Pneumocystis jirovecii . Longitudinal analyses revealed limited utility of NPS for monitoring dynamic pathogen changes over time, with higher agreement observed only for Staphylococcus aureus (72.7%), Acinetobacter baumannii (62.5%), and fungal pathogens (75.0%). Conclusion Nasopharyngeal swab–based tNGS represents a feasible and less invasive approach for the early molecular identification of common bacterial pathogens, including those frequently implicated in drug-resistant infections, in patients with severe ICU pneumonia. While NPS may support early antimicrobial decision-making when BALF is not immediately available, its reduced sensitivity for fungal and viral pathogens and limited performance in longitudinal surveillance underscore the continued necessity of BALF for comprehensive infection assessment, particularly in immunocompromised and high-risk ICU populations.