Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pneumonia in Patients With Cancer.

BACKGROUND

With the development of new sequencing technologies, metagenomic next-generation sequencing (mNGS) has become a diagnostic tool for respiratory tract infections. Patients with cancer may develop pneumonia caused by infections or antitumor therapy. Therefore, pneumonia in patients with cancer is more complex than that in healthy individuals. Currently, few reports are available on the use of mNGS for diagnosing pneumonia in patients with cancer.

METHODS

In this retrospective study, 14 patients with cancer diagnosed with pneumonia in March 2023 were enrolled from the Emergency Department of the Chinese Academy of Medical Sciences Cancer Hospital. Sputum samples from the patients were examined using conventional tests and mNGS to identify pathogens. The mNGS and conventional test results were compared to assess the diagnostic yield in patients with cancer.

RESULTS

The overall pathogen detection rate of mNGS was 64.29% (9/14), with corresponding diagnostic sensitivity, specificity, false-negative rate and false-positive rate of 90.00%, 25.00%, 10.00% and 75.00%, respectively. Among 13 paired sputum specimens, mNGS exhibited a numerically higher pathogen detection rate (61.54%, 8/13) than conventional diagnostic assays (38.46%, 5/13). McNemar's paired chi-square test demonstrated no statistically significant difference between the two detection methods (p = 0.37), and Kappa concordance analysis generated a coefficient of 0.27 (p = 0.23), suggesting poor inter-method consistency. Compared with conventional tests, mNGS detected additional pathogens in 8 specimens and identified a greater number of pathogens in 9/14 (64%) samples. Moreover, mNGS results led to diagnostic revisions and subsequent antimicrobial therapy adjustments in 64% (9/14) of enrolled patients. Additionally, mNGS detected antibiotic resistance genes in five patients, which provided guidance for antibiotic selection.

CONCLUSIONS

Metagenomic next-generation sequencing (mNGS) showed potential value in pathogen detection, as it appeared to identify pathogens more rapidly and comprehensively than conventional methods. It may provide auxiliary support for the diagnosis and treatment of pneumonia in this vulnerable population.