Abstract
Background To improve the quality of nucleic acid detection reagents, we provided a new strategy, Shine, to explore specific, sensitive and conserved biomarkers from massive microbial genomic data within intrapopulations in order to improve detection sensitivity and accuracy. It is obvious that the more comprehensive genomic data are, the more effective the detection biomarkers.
Results We demonstrated that our method could detect undiscovered multicopy conserved species-specific or even subspecies-specific target fragments, according to several clinical projects. In particular, this approach was effective for any pathogenic microorganism even in incompletely assembled motifs. Based on our strategy, the detection device designed with quantitative PCR primers and probes for systematic and automated detection of pathogenic microorganisms in biological samples may cover all pathogenic microorganisms without limits based on genome annotation. On the website https://bioinfo.liferiver.com.cn, users may select different configuration parameters depending on the purpose of the project to realize routine clinical detection practices.
Conclusions It is recommended that our strategy is suitable to identify shared universal phylogenetic markers with few false positive or false negative errors and to automate the design of minimal primers and probes to detect pathogenic communities with cost-effective predictive power.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Abstract has been divided into three different parts; Result has been divided into four different parts and related text updated; Table2 and Supplemental Table1-8 updated; Abbreviations updated; Ethical Approval and Consent to participate updated; Consent for publication updated; Availability of data and materials updated; Competing interests updated; Funding updated; Authors' contributions updated; Author information updated.
Abbreviations
- PCR
- Polymerase Chain Reaction
- LDT
- Laboratory-developed Test
- DNA
- Deoxyribo Nucleic Acid
- RNA
- Ribonucleic Acid
- 16S rRNA
- 16S Ribosomal RNA
- MEGA
- Molecular Evolutionary Genetics Analysis
- PAML
- Phylogenetic Analysis by Maximum Likelihood
- NCBI
- National Center for Biotechnology Information
- GISAID
- Global Initiative on Sharing All Influenza Data
- EzBioCloud
- ChunLab’s public data and analytics portal
- EuPathDB
- Eukaryotic Pathogen Database Project
- GiardiaDB
- Giardia Genomics Resources
- TrichDB
- Trichomonas Informatics Resources
- FungiDB
- Fungal & Oomycete Informatics Resources
- HKU1
- Human coronavirus HKU1
- OC43
- Human coronavirus OC43
- NL63
- Human coronavirus NL63
- 229E
- Human coronavirus 229E
- MERS
- Middle East respiratory syndrome-related coronavirus
- SARS-CoV
- Severe acute respiratory syndrome coronavirus
- SARS-CoV-2
- Severe acute respiratory syndrome coronavirus 2
- MTBC
- Mycobacterium tuberculosis complex
- BP
- Bordetella pertussis
- BPP
- Bordetella parapertussis
- CAP
- community-acquired pneumonia
- HIV
- human immunodeficiency virus
- CRISPR
- Clustered Regularly Interspaced Short Palindromic Repeats
- CRISPR-Cas
- CRISPR-associated (Cas) genes
- SHERLOCK
- specific high-sensitivity enzymatic reporter unlocking
- STOP
- SHERLOCK testing in one pot
- SGs
- study groups