About this Research Topic
Timely and accurate pathogen diagnosis is critical for effective treatment, outbreak prevention and precise antibiotics administration of infectious diseases, which remains a challenge in clinical practice. Metagenomic next generation sequencing (mNGS) allows researchers and laboratory specialists to analyze the mixed collection of sequencing reads in human clinical samples, including sequences from bacteria, viruses, fungi and parasites besides the host. This new technology shows great potential in pathogen diagnosis. The sensitivity and faster turnaround time are higher than conventional clinical microbiology tests, especially for fastidious and atypical pathogens. However, current mNGS based pathogen detection and diagnosis are facing challenges from both technical and practical aspects. First, sequencing noise can be introduced from different steps such as samples preparation, sequencing, data analysis and reporting algorithm. Also, the interpretation of the results such as detection limits and detection rates are not straightforward to clinicians, compared with traditional culture-based technologies. Such challenges and considerations should be fully addressed before the wild application of mNGS as a pathogen detection tool. Further, these clarifications might help to properly find the best clinical application scenarios, refine the medical treatments, and improve the clinical effectiveness of mNGS in complex infectious diseases.
This Research Topic is focused on the application of mNGS for infectious diseases diagnosis and treatment, including experiment process and clinical usage. Its purpose is to level up the clarification of NGS process, to support the development of efficient experiment methods, data interpretation algorithms and to report good examples of related clinical applications. We hope this Research Topic could facilitate the discovery of novel methods and help NGS specialists and clinicians to know mutual concerns and work together to improve the clinical effectiveness of mNGS.
We welcome submissions of Original Research, Reviews, Mini Reviews and Clinical Trials, focusing on but not limited to the following topics：
• Novel methodologies development for mNGS.
• Assessment of pathogen detection sensitivity/specificity by using mNGS.
• Effects of mNGS on clinical treatment pathway.
• Assessment of patient’s clinical outcomes by using mNGS.
• Deep analysis of sequences generated by using mNGS
Please note: All genomes (excluding human genomes) must be uploaded into the public genomic database for validation. And sample metadata should be clear and consistent, including sample name, sample type, sequencing instruments, sequencing strategy, data size, and number of human genomes. For case reports, authors should focus on the confidence level of mNGS.
This Research Topic is focused on the application of mNGS for infectious diseases diagnosis and treatment, including experiment process and clinical usage. Its purpose is to level up the clarification of NGS process, to support the development of efficient experiment methods, data interpretation algorithms and to report good examples of related clinical applications. We hope this Research Topic could facilitate the discovery of novel methods and help NGS specialists and clinicians to know mutual concerns and work together to improve the clinical effectiveness of mNGS.
We welcome submissions of Original Research, Reviews, Mini Reviews and Clinical Trials, focusing on but not limited to the following topics：
• Novel methodologies development for mNGS.
• Assessment of pathogen detection sensitivity/specificity by using mNGS.
• Effects of mNGS on clinical treatment pathway.
• Assessment of patient’s clinical outcomes by using mNGS.
• Deep analysis of sequences generated by using mNGS
Please note: All genomes (excluding human genomes) must be uploaded into the public genomic database for validation. And sample metadata should be clear and consistent, including sample name, sample type, sequencing instruments, sequencing strategy, data size, and number of human genomes. For case reports, authors should focus on the confidence level of mNGS.
Keywords: metagenomics; next-generation sequencing; infection disease; clinical diagnosis and treatment; clinical effectiveness, #CollectionSeries
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.
