Targeted Next-Generation Sequencing (tNGS) for Pathogenic Microorganisms: A Comprehensive Review

Targeted Next-Generation Sequencing (tNGS) for Pathogenic Microorganisms: A Comprehensive Review

Abstract:

Targeted Next-Generation Sequencing (tNGS) has emerged as a powerful tool for the rapid and accurate identification and characterization of pathogenic microorganisms. This review provides an extensive overview of the application of tNGS in the field of pathogen detection and genomics. We discuss the principles and methodologies of tNGS, as well as its advantages and limitations. Furthermore, we highlight various applications of tNGS, including the identification of known and emerging pathogens, antimicrobial resistance profiling, epidemiological investigations, and outbreak surveillance. Additionally, we discuss the challenges and future prospects of tNGS in clinical diagnostics and public health. Overall, this review showcases the immense potential of tNGS in improving our understanding of pathogenic microorganisms and enhancing our ability to respond to infectious disease threats.

Keywords: Targeted Next-Generation Sequencing, tNGS, pathogenic microorganisms, genomics, diagnostics, antimicrobial resistance, epidemiology, outbreak surveillance, pathogen detection, clinical diagnostics, public health

1. Introduction

1.1 Overview of pathogenic microorganisms 1.2 Traditional methods for pathogen detection and identification 1.3 Introduction to Next-Generation Sequencing (NGS) 1.4 Principles and methodologies of targeted NGS

2. Advantages and Limitations of targeted NGS

2.1 Increased sensitivity and specificity 2.2 Cost and time efficiency 2.3 Limitations and challenges of targeted NGS

3. Applications of targeted NGS in pathogen detection and genomics

3.1 Identification of known pathogens 3.2 Discovery of emerging pathogens 3.3 Antimicrobial resistance profiling 3.4 Epidemiological investigations 3.5 Outbreak surveillance

4. Case studies and examples of targeted NGS applications

4.1 Case study 1: Identification of bacterial pathogens 4.2 Case study 2: Viral detection and genotyping 4.3 Case study 3: Fungal pathogen identification 4.4 Case study 4: Antimicrobial resistance profiling 4.5 Case study 5: Epidemiological investigations

5. Challenges and future prospects of targeted NGS

5.1 Data management and analysis 5.2 Standardization and quality control 5.3 Ethical and legal considerations 5.4 Integration of targeted NGS into routine diagnostics 5.5 Future directions and potential advancements

6. Conclusion

References: (Please note that the following references are only for illustrative purposes and need to be replaced with relevant and recent literature)

1. Smith J, et al. (2020). Targeted next-generation sequencing for pathogen detection: challenges and opportunities in clinical diagnostics. Clin Microbiol Rev, 33(3), e00119-19.
2. Johnson R, et al. (2019). Applications of targeted next-generation sequencing for infectious disease research and diagnostics. Genome Med, 11(1), 80.
3. Li M, et al. (2018). Targeted next-generation sequencing for the detection of ciprofloxacin resistance in Neisseria gonorrhoeae. Antimicrob Agents Chemother, 62(9), e00595-18.
4. Wang J, et al. (2017). Genomic characterization of Salmonella enterica serovar Typhimurium DT104 isolates from food and human samples by next-generation sequencing. Front Microbiol, 8, 1549.
5. Kohl TA, et al. (2018). Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach. J Clin Microbiol, 56(7), e01847-17.