Research Topic

Application of Next Generation Sequencing (NGS) and CRISPR-Cas Systems in The Diagnosis of Infectious Diseases

About this Research Topic

Infectious diseases are caused by pathogens, including bacteria, fungi, viruses, parasites, protozoa, and other microorganisms. Effective control and treatment of infectious diseases require early and rapid pathogen detection. Novel pathogen diagnostic technologies such as next-generation sequencing (NGS) and the CRISPR-Cas systems have shown great potential to transform the landscape of laboratory diagnosis of infectious disease.

NGS allows for high throughput sequencing of genomic materials from all microorganisms in various clinical samples without prior knowledge. NGS has been applied to pathogen identification and discovery, phylogenetic inference, drug resistance genotyping, and virulent gene mapping in infections of the central nervous system, respiratory system, gastrointestinal system, and urinary system. Particularly, it is advantageous to detect and identify unknown and atypical pathogens or coinfections. Notably, metagenomic RNA sequencing discovered novel SARS-CoV-2 virus that causes COVID-19 illness.

CRISPR technology has been widely used in genome editing and genetic engineering in the past several years. It also shows excellent potential in pathogen detection with high sensitivity. Different types of CRISPR-Cas systems have been applied to detect bacteria, DNA, and RNA virus. Although its clinical application warrants further research, diagnostic tests using Cas12 and Cas13 enzymes showed promising results in detecting the emerging SARS-CoV-2 virus.

NGS and CRISPR technologies show great potential in improving accuracy, sensitivity, and turnaround time of pathogen detection in infectious diseases. However, several problems need to be addressed before its full application in the clinic. These include technical challenges such as sample preparation and storage for low biomass clinical samples, human contamination removal for NGS technology, off-target phenomenon, and multiplexing capability for CRISPR based diagnostic technology. Besides, bioinformatic analysis, clinical interpretation of the diagnostic report, cost need to be further addressed. In this research topic, we aim to provide an overview of recent progress in NGS and CRISPR-Cas system applications in the diagnosis of infectious disease and seek innovative solutions to resolve existing challenges.

We welcome submissions of Reviews, Mini-Reviews, Original Research, Clinical Trials, Case Reports, and Commentaries that cover, but are not limited to, the following topics:
1. Applications of NGS or CRISPR-Cas system in pathogen detection
2. Applications of NGS or CRISPR-Cas system in resistance genotyping of pathogens
3. Applications of NGS or CRISPR-Cas system in emerging infectious diseases
4. Methodologies development for NGS or CRISPR-Cas system application in diagnosis of Infectious Disease


Keywords: Sequencing, Infectious Diseases, CRISPR-Cas Systems, Pathogen Detection, Diagnosis


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.

Infectious diseases are caused by pathogens, including bacteria, fungi, viruses, parasites, protozoa, and other microorganisms. Effective control and treatment of infectious diseases require early and rapid pathogen detection. Novel pathogen diagnostic technologies such as next-generation sequencing (NGS) and the CRISPR-Cas systems have shown great potential to transform the landscape of laboratory diagnosis of infectious disease.

NGS allows for high throughput sequencing of genomic materials from all microorganisms in various clinical samples without prior knowledge. NGS has been applied to pathogen identification and discovery, phylogenetic inference, drug resistance genotyping, and virulent gene mapping in infections of the central nervous system, respiratory system, gastrointestinal system, and urinary system. Particularly, it is advantageous to detect and identify unknown and atypical pathogens or coinfections. Notably, metagenomic RNA sequencing discovered novel SARS-CoV-2 virus that causes COVID-19 illness.

CRISPR technology has been widely used in genome editing and genetic engineering in the past several years. It also shows excellent potential in pathogen detection with high sensitivity. Different types of CRISPR-Cas systems have been applied to detect bacteria, DNA, and RNA virus. Although its clinical application warrants further research, diagnostic tests using Cas12 and Cas13 enzymes showed promising results in detecting the emerging SARS-CoV-2 virus.

NGS and CRISPR technologies show great potential in improving accuracy, sensitivity, and turnaround time of pathogen detection in infectious diseases. However, several problems need to be addressed before its full application in the clinic. These include technical challenges such as sample preparation and storage for low biomass clinical samples, human contamination removal for NGS technology, off-target phenomenon, and multiplexing capability for CRISPR based diagnostic technology. Besides, bioinformatic analysis, clinical interpretation of the diagnostic report, cost need to be further addressed. In this research topic, we aim to provide an overview of recent progress in NGS and CRISPR-Cas system applications in the diagnosis of infectious disease and seek innovative solutions to resolve existing challenges.

We welcome submissions of Reviews, Mini-Reviews, Original Research, Clinical Trials, Case Reports, and Commentaries that cover, but are not limited to, the following topics:
1. Applications of NGS or CRISPR-Cas system in pathogen detection
2. Applications of NGS or CRISPR-Cas system in resistance genotyping of pathogens
3. Applications of NGS or CRISPR-Cas system in emerging infectious diseases
4. Methodologies development for NGS or CRISPR-Cas system application in diagnosis of Infectious Disease


Keywords: Sequencing, Infectious Diseases, CRISPR-Cas Systems, Pathogen Detection, Diagnosis


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.

About Frontiers Research Topics

With their unique mixes of varied contributions from Original Research to Review Articles, Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author.

Topic Editors

Loading..

Submission Deadlines

13 December 2020 Abstract
12 April 2021 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

Loading..

Topic Editors

Loading..

Submission Deadlines

13 December 2020 Abstract
12 April 2021 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

Loading..
Loading..

total views article views article downloads topic views

}
 
Top countries
Top referring sites
Loading..