Metagenomic Next-Generation Sequencing (mNGS) for Detecting Pathogens and Antimicrobial Resistance Genes (ARGs), and Guiding Antimicrobial Therapy in Cancer Patients from Southwest China.

Authors

Zhao Qian, Wan Qian, Wang Si-Wei, Zhao Pei, Li Yi, Xu Shan-Ling, Chen Chen

Published in

Journal of global antimicrobial resistance. Aug 06, 2026. Epub Aug 06, 2026.

Abstract

Cancer patients often face etiological diagnosis challenges due to repeated hospitalizations, antibiotic exposure, and conventional microbiology tests (CMTs) limitations (low positivity, long turnaround). Metagenomic next-generation sequencing (mNGS) enables rapid and accurate pathogen detection, however, its clinical utility in cancer patients requires further investigation.
Two years of mNGS results and clinical data of cancer patients in Sichuan Cancer Hospital were collected. The pathogens and antimicrobial resistance genes (ARGs) were analyzed. The diagnostic performance was evaluated via sensitivity, specificity, accuracy, positive and negative predictive value. The clinical significance in guiding antimicrobial therapy was assessed by comparing outcomes between mNGS-guided and empirical therapy groups. Multivariable logistic regression analysis was performed to explore risk factors for multidrug-resistant organisms (MDROs) and opportunistic pathogens infections in cancer population.
The study included 340 mNGS results from 267 cancer patients. Streptococcus pneumoniae, Pseudomonas aeruginosa, Candida albicans and Epstein-Barr virus were the most common Gram-positive and Gram-negative bacteria, fungus and virus, respectively. The main ARGs were ESBLs and aminoglycoside resistance genes. mNGS showed high pathogen diagnostic sensitivity (97.50%) and moderate ARGs diagnostic sensitivity (64.29%). The mNGS-guided group had lower mortality (29.5% vs. 34.1%, p=0.65) and shorter duration of mechanical ventilation (39.34 ± 81.15 vs. 42.30 ±102.39 hours, p= 0.88). Age (p=0.028) and prior 90-day antibiotic use (p=0.047) independently predicted MDROs infections; immunodeficiency predicted Pneumocystis jirovecii (p=0.005) and Aspergillus spp. (p=0.010) infections.
mNGS was reliable for pathogen diagnosis in cancer patients. However, its clinical significance on guiding antimicrobial therapy requires more prospective multicenter studies to confirm.

PMID:
42562314
Bibliographic data and abstract were imported from PubMed on 07 Aug 2026.

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