Comparative Evaluation of mNGS and Traditional Culture Methods in Pathogen Detection for Pulmonary Infections

Sep 28, 2026

Retrospective cohort study evaluated metagenomic next-generation sequencing (mNGS) for pulmonary infections by directly comparing diagnostic accuracy and clinical applicability with traditional culture methods in a Traditional Chinese Medicine (TCM) hospital. Sixty-seven consecutive patients with radiologically and clinically confirmed pulmonary infections were enrolled between December 2022 and September 2024. Results showed mNGS identified pathogens in 89.55% versus 20.90% for culture, detected viral co-infections in 44.78%, and revealed fastidious or non-culturable pathogens. Findings support targeted antimicrobial therapy and potential reduction of antibiotic resistance.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages8

Reading Time20 min

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Purpose

Methods

Results

Conclusion

Introduction

Infection and Drug Resistance Open Access Full Text Article ORIGINAL RESEARCH Comparative Evaluation of mNGS and Traditional Culture Methods in Pathogen Detection for Pulmonary Infections Weijun Chen 1 , *, Ruijie Liu 1 , *, Qiyong Qi 1 , Lingen Xu2 , Guiqin Sun 3 1Laboratory Department, Xinchang Hospital of Traditional Chinese Medicine, Shaoxing, Zhejiang, People’s Republic of China; 2Intensive Care Unit, Xinchang Hospital of Traditional Chinese Medicine, Shaoxing, Zhejiang, People’s Republic of China; 3School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China *These authors contributed equally to this work Correspondence: Guiqin Sun, School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, 548 Binwen Road, Binjiang District, Hangzhou, Zhejiang, People’s Republic of China, 310053, Tel +86 13868118601, Fax +86 0571-86633307, Email [sunguiqin2001@163.com](sunguiqin2001@163.com); Lingen Xu, Intensive Care Unit, Xinchang Hospital of Traditional Chinese Medicine, No. 188, Shijiu Feng Road, Qixing Street, Shaoxing, Zhejiang, People’s Republic of China, 312500, Tel +86 13857514222, Fax +86 0575-86502818, [Email xlger@163.com](Email xlger@163.com) | Purpose: This study aimed to evaluate the diagnostic accuracy and clinical applicability of metagenomic next-generation sequencing (mNGS) in pulmonary infections by comparing it with traditional culture methods in a Traditional Chinese Medicine (TCM) hospital setting.
Methods: This retrospective cohort study enrolled 67 consecutively admitted patients with radiologically and clinically confirmed pulmonary infections from the Department of Respiratory Infectious Diseases at Xinchang Hospital of Traditional Chinese Medicine between December 2022 and September 2024. Clinical specimens included blood, bronchoalveolar lavage fluid (BALF), sputum, hydrothorax and cerebrospinal fluid (CSF) . mNGS and conventional culture were performed to compare detection rates and microbial community profiles.
Results: Among 67 cases, mNGS identified pathogens in 89.55%(60/67), compared to 20.90%(14/67) by traditional culture. Of 14 dual-positive cases, only 1 (1/14, 7.14%) showed complete concordance, while most exhibited discordance or partial genus-level overlap. mNGS further detected viral co-infections in 44.78%(30/67) and identified fastidious/non-culturable pathogens such as enterovirus, human herpesvirus type 1, and Mycobacterium tuberculosis. Patients with chronic diseases were more susceptible to EB virus infections.
Conclusion: mNGS significantly enhances pathogen detection in pulmonary infections, supports targeted antimicrobial therapy, and holds potential for contributing to clinical outcomes and reducing antibiotic resistance.
Keywords: mNGS, pulmonary infection, pathogens, antibiotic resistance, detection | | --- | | Introduction
Pneumonia is frequently observed in clinical settings and is typically caused by pathogens such as influenza A and B viruses, coronaviruses including SARS-CoV, MERS-CoV, and SARS-CoV-2, Klebsiella pneumoniae, Candida albicans, Pseudomonas aeruginosa, and Mycobacterium tuberculosis.1–3 These pathogens can cause varying degrees of damage to lung tissue. If anti-infective treatments are ineffective, there is a risk of severe decline in lung function or even respiratory failure, which can be life-threatening.4 The reference standard for diagnosing pulmonary infections primarily relies on the isolation and culture of pathogens, complemented by antimicrobial susceptibility testing to guide therapy.5,6 However, this culture-based approach has several critical limitations. First, the turnaround time is lengthy, typically requiring 48–72 hours, which delays diagnosis.7 Second, it has limited sensitivity for detecting fungal pathogens such as Aspergillus spp. and Cryptococcus spp., making the early diagnosis of fungal pneumoni

FAQs

What is the purpose of this study on mNGS and traditional culture?

To evaluate diagnostic accuracy and clinical applicability of mNGS for pulmonary infections by comparing it with traditional culture methods in a TCM hospital setting.

How was the study conducted and who were the participants?

A retrospective cohort enrolled 67 consecutively admitted patients with radiologically and clinically confirmed pulmonary infections between December 2022 and September 2024.

What were the main findings comparing mNGS with culture?

mNGS detected pathogens in 89.55% of cases versus 20.90% by traditional culture, identified viral co-infections in 44.78%, and detected fastidious/non-culturable pathogens.

Sep 28, 2026

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