Next-Generation Sequencing in Infectious Disease Management: Integrative Fungal and Bacterial Diagnostics from Innovation to Clinical Practice

Next-generation sequencing (NGS) is advancing infectious disease diagnostics by enabling comprehensive, culture-independent detection and characterization of both fungal and bacterial pathogens. This Research Topic aims to showcase cutting-edge advances in applying NGS technologies to uncover complex microbial, microbiome, and mycobiome interactions, as well as to identify causative agents of infection with high sensitivity and specificity. By leveraging innovative bioinformatics tools, targeted and metagenomic sequencing panels, and powerful automation, researchers and clinicians can map functional profiles, metabolic pathways, resistance genes, and epidemiological patterns of pathogens. This collection will bridge fundamental research and clinical practice, highlighting the transformative role of NGS in predictive diagnostics, antimicrobial stewardship, and global health surveillance.

We welcome contributions that focus on the integration of NGS into fungal and bacterial infection diagnostics, covering basic science, translational research, and clinical implementation. The scope of this Research Topic spans metagenomic sequencing, CRISPR-based pathogen detection, AI-assisted data interpretation, and NGS data analysis, reflecting the technological innovation in the field and the implications to infection diagnostics.

Manuscripts within the scope of this Research Topic include, but are not limited to:

o Comparative studies of NGS-based diagnostics versus traditional culture and PCR approaches for fungal and bacterial infections

o Development, validation, and clinical application of targeted and metagenomic NGS panels for pathogen, microbiome, and mycobiome identification

o Technological and computational advancements—including AI-driven analytics—for detecting, profiling, and surveilling mixed microbial communities and resistance determinants

o Characterization of fungal networks and their roles in the human microbiome in health and disease, using NGS methodologies

o Implementation of automated bioinformatics pipelines and solutions for accurate, efficient interpretation of NGS data in bacterial and fungal diagnostics

o Reviews and highlighting limitations, opportunities, and future directions for NGS in integrated bacterial and fungal diagnostics

Topic Editor, Dr. Arryn Craney, is the founder of Petrified Bugs LLC. All Topic Editors declare no competing interests with regard to the Research Topic subject.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Classification
• Clinical Trial
• Community Case Study
• Curriculum, Instruction, and Pedagogy
• Data Report
• Editorial
• FAIR² Data
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Classification
• Clinical Trial
• Community Case Study
• Curriculum, Instruction, and Pedagogy
• Data Report
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Policy and Practice Reviews
• Policy Brief
• Review
• Study Protocol
• Systematic Review
• Technology and Code

Keywords: AI-driven analytics, Automated bioinformatics pipelines, Bioinformatics tools, Diagnostic, Infectious disease diagnostics, Metagenomics, Microbiome, Mycobiome, Next-generation sequencing (NGS), NGS data analysis, Pathogen identification

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.