When metagenomic next-generation sequencing detects Nocardia: from clinical interpretation to immune-based clinical management

Background Metagenomic next-generation sequencing (mNGS) increasingly detects Nocardia , but interpreting positive results remains challenging. We aimed to identify host factors and read thresholds that distinguish nocardiosis (ND) from colonization/contamination, and to characterize clinical features linked to immune status. Methods A retrospective analysis from 74 patients at Qilu Hospital of Shandong University from April 2022 to October 2025 was conducted. We assessed mNGS for distinguishing Nocardia infection from colonization or contamination, identified risk factors for nocardiosis, and compared patients’ clinical features, imaging findings, and antimicrobial adjustments. Results A total of 56 patients with ND and 18 non-ND patients were included. Multivariate logistic regression identified farming exposure, bronchiectasis, and immunocompromised status were significantly associated with ND. An estimated read per million (RPM) thresholds of 56 could distinguish Nocardia infection from colonization/contamination (AUC 0.774; 95% CI, 0.654 – 0.895), with a higher sensitivity than traditional tests ( P  P  = 0.03), lymphadenopathy (62.50% vs. 40.63%, P = 0.046) and fungal co-infections (54.17% vs. 18.75%, P  = 0.006), while bronchial wall thickening was more common in immunocompetent patients (ICPs) (31.25% vs. 4.17%, P  = 0.019). Nocardia was the sole pathogen in 42.9% of true infection cases, and mNGS led to a change in anti- Nocardia management in 87.5% of patients. Conclusion Our study indicated mNGS is a useful tool for distinguishing Nocardia infection from colonization/contamination, and immune-based phenotyping may guide individualized management strategies for patients with nocardiosis.