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1. Distinctive circulating microbial metagenomic signatures in the plasma of patients with lung cancer and their potential value as molecular biomarkers

Author

Huijuan Chen, XueNa Yao, Chunyan Yang, Yiran Zhang, Henan Dong, Jincheng Zhai, Dongjie Fan, and Qiming Zhou

Subjects
Lung cancer, Plasma, Whole genome sequencing, Circulating microbial nucleic acids, Biomarkers, Medicine
Abstract

Abstract Lung cancer (LC) remains the leading cause of cancer death globally. Recent reports have suggested that circulating microbial nucleic acids have potential as promising biomarkers for cancer liquid biopsies. However, circulating microbial profiles and their potential clinical value in LC patients remained unexplored. In this study, plasma samples from 76 LC patients, 9 liver cancer patients, 11 pancreatic cancer patients, and 53 healthy controls (HCs) were collected and underwent metagenomic analyses by whole genome sequencing. The composition and relative abundance of the microbial profiles were significantly different between the LC patients and HCs. A distinct plasma-based microbial profile was observed in LC patients. By differential analysis using MaAslin, 40 significant species between LC patients and HCs were identified. Five species were selected as optimal circulating microbial biomarkers for LC. The constructed classifier based on these five species showed an AUC of 0.9592, 0.9131, and 0.8077 in the discovery, validation, and additional validation cohorts, respectively. Furthermore, metagenomic profiles of 25 lung tumor tissue and plasma paired samples were analyzed and compared. The microbial diversity was significantly increased in plasma compared with the tumor tissue. Among the 13 shared core microbial species, 10 had no difference between the tumor tissue and paired plasma. In conclusion, circulating microbial nucleic acids in the plasma have potential as biomarkers for LC liquid biopsies. The microbiome in the tumor tissue was one of the possible sources of circulating microbial nucleic acids.

Published
2025
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2. Profile of Bacteria with ARGs Among Real-World Samples from ICU Admission Patients with Pulmonary Infection Revealed by Metagenomic NGS

Author

Huijuan Chen, Xuena Yao, Wenxuan Liu, Yang Gao, Xinhua Bai, and Jing Wang

Subjects
Pharmacology, medicine.medical_specialty, biology, intensive care units, business.industry, antibiotic resistant bacteria, pulmonary infection, Pulmonary infection, biology.organism_classification, Icu admission, antibiotic resistance genes, Infectious Diseases, Infection and Drug Resistance, Metagenomics, Internal medicine, medicine, Pharmacology (medical), business, Bacteria, Original Research
Abstract

Huijuan Chen,1 Xinhua Bai,2 Yang Gao,2 Wenxuan Liu,2 Xuena Yao,2 Jing Wang2 1Department of Biomedical Engineering, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, People’s Republic of China; 2Department of Clinical Laboratory, Beijing Capitalbio Medlab, Beijing, People’s Republic of ChinaCorrespondence: Huijuan Chen Tel +86-10-8722-9999Email m13810539097@163.comBackground: Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by antibiotic resistance pathogens. A thorough and up-to-date knowledge of the local spectrum of antibiotic resistant bacteria can improve the antibiotic treatment efficiency. In this study, we aimed to reveal the profile of bacteria with antibiotic resistance genes (ARGs) in real-world samples from ICU admission patients with pulmonary infection in Mainland, China, by metagenomic next-generation sequencing (mNGS).Methods: A total of 504 different types of clinical samples from 452 ICU admission patients with pulmonary infection were detected by mNGS analysis.Results: A total of 485 samples from 434 patients got successful mNGS results. Among 434 patients, one or more bacteria with ARGs were detected in 192 patients (44.24%, 192/434), and ≥ 2 bacteria with ARGs were detected in 85 (19.59%, 85/434) patients. The predominant detected bacteria were Corynebacterium striatum (C. striatum) (11.76%, 51/434), Acinetobacter baumannii (A. baumannii) (11.52%, 50/434) and Enterococcus faecium (E. faecium) (8.99%, 39/434). ermX conferred resistance to MSLB and cmx to phenicol were the only two ARGs detected in C. striatum; in A. baumannii, most of ARGs were resistance-nodulation-division (RND)-type efflux pumps genes, which conferred resistance to multi-drug; ermB conferred resistance to MSLB and efmA to multi-drug were the predominant ARGs in E. faecium. Bacteria with ARGs were detected in 50% (140/280) bronchoalveolar lavage fluid (BALF) and 50.5% (48/95) sputum samples, which were significantly higher than in blood and cerebrospinal fluid (CSF) samples.Conclusion: High level of bacteria with ARGs was observed in clinical samples, especially BALF and sputum samples from ICU admission patients with pulmonary infection in Mainland, China. And C. striatum resistant to MSLB and/or phenicol, multi-drug resistance A. baumannii and E. faecium were the lead bacteria.Keywords: intensive care units, pulmonary infection, antibiotic resistant bacteria, antibiotic resistance genes

Published
2021
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