The expansion of NGS implementation in clinical and public health practice accelerated drastically during the SARS-CoV-2 pandemic, where NGS has been playing a vital role in tracking dangerous strains of the virus. NGS applications not only influenced public health decision-making but also have been crossing into the clinical field with individual patients’ results being potentially available to the physicians. Hence, the topic of implementation of NGS methods in clinical and public health microbiology, its challenges and special considerations, is as timely as ever.

The use of Next Generation Sequencing (NGS) in clinical and public health microbiology laboratories has been steadily expanding in the past decade. However, this progress has been held back by multiple logistical challenges, like the absence of regulatory compliance framework, lack of clear quality guidelines, the need for standardization and interoperability between laboratories, as well as cost and turn-around-time limitations.

Authors are invited to submit their manuscripts as either Original Research, Review, Mini-review, Perspective, or Opinion articles that focus on the specifics of the use of NGS in the clinical and public health microbiology laboratories, addressing topics like:

• Integration of NGS technology (wet lab and bioinformatics) into traditional clinical microbiological workflows: challenges, feasibility studies, strategies for implementation
• NGS assay development and technical validation for clinical & public health use. These include but are not limited to the development of standardized wet laboratory approaches and reference genomic materials for validation and quality assurance
• Approaches to regulatory compliance (CLIA, CAP, ISO) and quality assurance for NGS assays used in clinical settings
• Interpretation, reporting, and communication of NGS results. Developing systems for reporting actionable and unambiguous NGS results to the stakeholders, clinicians and epidemiologists, providing clinically significant patient results and improving public health response
• Creating standardized, portable, and reproducible bioinformatics workflows that fit clinical and public health needs while complying with the laboratory quality assurance systems and data safety regulations
• Solutions for NGS Data management and sharing that comply with patient data privacy and security requirements while ensuring the potential for diseases surveillance
• Resources and support needed for implementing NGS program for genomic surveillance
• Use of NGS for public health decision making and strategic planning to enhance public health preparedness, including development of genomic epidemiology approaches to investigation and control for current and future emerging infectious diseases
• Multi-disciplinary collaboration in the best practice of NGS for clinical and public health microbiology
• Determination of appropriate training and qualifications of analytical personnel (wet lab, bioinformatics) for NGS work in clinical and public health laboratories, including but not limited to the need to provide additional training for existing personnel and challenges in talent recruitment.

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Frontiers in Public Health

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