Application of next-generation sequencing to identify different pathogens

Aljuboori M Nafea; Yuer Wang; Duanyang Wang; Ahmed M Salama; Manal A Aziz; Shan Xu; Yigang Tong

doi:10.3389/fmicb.2023.1329330

Application of next-generation sequencing to identify different pathogens

Front Microbiol. 2024 Jan 29:14:1329330. doi: 10.3389/fmicb.2023.1329330. eCollection 2023.

Authors

Aljuboori M Nafea^#^{1

2}, Yuer Wang^#¹, Duanyang Wang¹, Ahmed M Salama^{3

4}, Manal A Aziz², Shan Xu¹, Yigang Tong¹

Affiliations

¹ College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
² College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq.
³ State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China.
⁴ Medical Laboratory at Sharkia Health Directorate, Ministry of Health, Sharkia, Egypt.

^# Contributed equally.

Abstract

Early and precise detection and identification of various pathogens are essential for epidemiological monitoring, disease management, and reducing the prevalence of clinical infectious diseases. Traditional pathogen detection techniques, which include mass spectrometry, biochemical tests, molecular testing, and culture-based methods, are limited in application and are time-consuming. Next generation sequencing (NGS) has emerged as an essential technology for identifying pathogens. NGS is a cutting-edge sequencing method with high throughput that can create massive volumes of sequences with a broad application prospects in the field of pathogen identification and diagnosis. In this review, we introduce NGS technology in detail, summarizes the application of NGS in that identification of different pathogens, including bacteria, fungi, and viruses, and analyze the challenges and outlook for using NGS to identify clinical pathogens. Thus, this work provides a theoretical basis for NGS studies and provides evidence to support the application of NGS in distinguishing various clinical pathogens.

Keywords: Sanger; bacteria; fungi; next generation sequencing; pathogens.

Publication types

Review

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by the Fundamental Research Funds for the Central Universities (buctrc202230), National Natural Science Foundation of China (32100940, 82151224), and National Key Research and Development Program of China (2021YFC0863400).