When metagenomic next-generation sequencing detects Nocardia: from clinical interpretation to immune-based clinical management
In brief
A 56-reads-per-million threshold helped distinguish Nocardia infection
In this retrospective study of 74 patients, metagenomic sequencing at a threshold of 56 reads per million helped distinguish Nocardia infection from colonization or contamination, with higher sensitivity than traditional tests. Sequencing prompted a change in anti-Nocardia management for 87.5% of patients, but the single-center findings need validation before the threshold can guide decisions broadly.
- Journal
- Frontiers in cellular and infection microbiology (Q1)
- Published
- 18 September 2026
- Study design
- Cohort / observational study
- Evidence level
- Level 3, Low (CEBM 3b)
- Authors
- Ping Li, Xiao Yang, Yuxia Chen, Lili Wang, Qiqi Cui, Zhihong Wu, et al.
- PMID
- 42827663
- DOI
- 10.3389/fcimb.2026.1911562
Why clinicians should know about it
- Picked for Microbiology (medical) (paper of the day, 5 October 2026): Defines mNGS thresholds for Nocardia infection
Abstract
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 < 0.001). In ND group, immunosuppressed patients (ISPs) (42.9%) had more pulmonary interstitial fibrosis (29.17% vs. 6.25%, 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.
Abstract as published, via PubMed.
For healthcare professionals. The summary is generated by AI from the published abstract, and the evidence level is assigned automatically from the study design on the Oxford CEBM hierarchy. Neither is medical advice. Read the full paper before changing practice.