Diagnostic efficacy of targeted next-generation sequencing in suspected lower respiratory tract infections of patients with cancer - a retrospective study

Sep 30, 2026

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Lower respiratory tract infections (LRTIs) pose a major risk to cancer prognosis, while conventional microbial culture often misses pathogens, delaying effective treatment and driving inappropriate antibiotic use. This retrospective study evaluates targeted next-generation sequencing (tNGS) for diagnosing LRTIs in malignant patients. Among 190 suspected cases, tNGS was performed on sputum and bronchoalveolar lavage fluid alongside conventional culture, yielding 58 pathogens versus 16 by culture and higher detection and sensitivity. tNGS also guided antibiotic changes in 41 patients.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages11

Reading Time28 min

AccessFree to download

Study Overview

Clinical Need and Background

Diagnostic Approach (tNGS and CMC)

Study Design and Comparison Results

Clinical Implications

[www. nature.com/scientificreports](www. nature.com/scientificreports) OPEN Diagnostic efficacy of targeted next-generation sequencing in suspected lower respiratory tract infections of patients with cancer: a retrospective study Xiaoqing Fan1,5, Yue Liang1,5, Xinmiao Liu2,5, Liping Meng1,5, Xinfei Zhao3, Yajun Huang3, Yan Sun1, Yulin Sun2 & Hongjun Gao1,2,4􀀍 Lower respiratory tract infections (LRTIs) significantly threaten the prognosis of cancer. Conventional microbial culture (CMC) often fails to identify pathogens, leading to inappropriate antibiotic use and delayed treatment. This study assesses the effectiveness of targeted next-generation sequencing (tNGS) for diagnosing LRTIs in malignant patients, including those with lung cancer and extrapulmonary malignancies. A retrospective study was conducted on 190 patients diagnosed with malignant tumours and suspected LRTI. Sputum and bronchoalveolar lavage fluid (BALF) samples were analysed using both tNGS and CMC concurrently. tNGS involves DNA/RNA extraction, PCR amplification, and sequencing, followed by clinical interpretation of the results. tNGS identified 58 pathogens compared with the 16 identified by CMC, with detection rates of 91.6% versus 24.2%, respectively. The sensitivity oftNGS was significantly greater (96.1%) than that ofCMC (33.3%) . Notably, 67.4% of patients tested positive exclusively via tNGS, highlighting its superior ability to detect pathogens, especially in mixed infections. Moreover, antibiotic therapy was modified for 41 patients on the basis of the findings from tNGS, resulting in escalations, de-escalations, or maintenance strategies. tNGS is an efficient diagnostic tool for LRTIs in cancer patients. Its rapid results can improve clinical decision-making and antibiotic optimization, potentially enhancing patient outcomes, especially in the diagnosis and treatment of special infection cases. Keywords Lung cancer, Extrapulmonary malignancies, Lower respiratory tract infections, Targeted nextgeneration sequencing, Conventional microbial culture Lower respiratory tract infections (LRTIs) are an inclusive term that covers a range of conditions, including acute bronchitis, pneumonia, and acute flare-ups of chronic respiratory diseases such as chronic obstructive pulmonary disease or bronchiectasis1. LRTIs are the most common infections in humans, particularly among vulnerable populations such as patients with malignant tumours. It is estimated that 2.74 million deaths worldwide occur each year because of LRTIs2. The process for diagnosing lower respiratory tract infections in cancer patients in clinical practice involves clinicians formulating a differential diagnosis based on an assessment of the patient’s clinical symptoms, physical signs, imaging abnormalities, and microbiological laboratory results. Additionally, in practical clinical settings, it frequently becomes necessary to initiate empirical antibiotic therapy because of the patient’s clinical condition, even prior to the availability of laboratory results. However, 1Department of Clinical Laboratory, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China. 2Department of Clinical Laboratory, State Key Laboratory of Molecular Oncology, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences, Peking Union Medical College, Chaoyang District, Beijing, China. 3Taiyuan Kingmed Center for Clinical Laboratory Co., Ltd, Taiyuan, China. 4The Medical Laboratory Center, The Affiliated Hospital of Inner Mongolia Minzu University, Tongliao 028005, China. 5These authors contributed equally: Xiaoqing Fan,Yue Liang, Xinmiao Liu and Liping Meng. 􀀍 email: [gaohongjun@cicams.ac.cn](gaohongjun@cicams.ac.cn) [www. nature.com/scientificreports/](www. nature.com/scientificreports/) the clinica

FAQs

Why is targeted next-generation sequencing used for suspected LRTIs in cancer patients?

Conventional microbial culture often fails to identify pathogens reliably, leading to inappropriate antibiotic choices and delayed treatment. tNGS provides more comprehensive pathogen detection to support faster and more accurate clinical decisions.

How does the study compare tNGS with conventional microbial culture?

The study analyzed sputum and bronchoalveolar lavage fluid samples using both tNGS and conventional microbial culture concurrently. It then compared pathogen counts, detection rates, and sensitivity between the two methods.

What clinical impact did tNGS have on antibiotic therapy?

Antibiotic therapy was modified for 41 patients based on tNGS findings, including escalation, de-escalation, or maintenance strategies, indicating its role in optimizing treatment selection.

Sep 30, 2026

Uploaded by Asher