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Nanopore DNA Sequencing for Metagenomic Soil Analysis
Published on: December 14, 2017
Diagnosis and treatment of refractory infectious diseases using nanopore sequencing technology: Three case reports
Qing-Mei Deng1,2,3, Jian Zhang3, Yi-Yong Zhang3
1Science Island Branch, Graduate School of University of Science and Technology of China, Hefei 230031, Anhui Province, China.
Background:
Infectious diseases are still one of the greatest threats to human health, and the etiology of 20% of cases of clinical fever is unknown; therefore, rapid identification of pathogens is highly important. Traditional culture methods are only able to detect a limited number of pathogens and are time-consuming; serologic detection has window periods, false-positive and false-negative problems; and nucleic acid molecular detection methods can detect several known pathogens only once. Three-generation nanopore sequencing technology provides new options for identifying pathogens.
Case Summary:
Case 1: The patient was admitted to the hospital with abdominal pain for three days and cessation of defecation for five days, accompanied by cough and sputum. Nanopore sequencing of the drainage fluid revealed the presence of oral-like bacteria, leading to a clinical diagnosis of bronchopleural fistula. Cefoperazone sodium sulbactam treatment was effective. Case 2: The patient was admitted to the hospital with fever and headache, and CT revealed lung inflammation. Antibiotic treatment for Streptococcus pneumoniae, identified through nanopore sequencing of cerebrospinal fluid, was effective. Case 3: The patient was admitted to our hospital with intermittent fever and an enlarged neck mass that had persisted for more than six months. Despite antibacterial treatment, her symptoms worsened. The nanopore sequencing results indicate that voriconazole treatment is effective for Aspergillus brookii. The patient was diagnosed with mixed cell type classical Hodgkin's lymphoma with infection.
Conclusion:
Three-generation nanopore sequencing technology allows for rapid and accurate detection of pathogens in human infectious diseases.
Insights
Rapid pathogen identification is crucial for treating infectious diseases. Three-generation nanopore sequencing offers a fast and accurate method for detecting various pathogens, improving patient outcomes.
Area of Science:
- Microbiology
- Genomics
- Medical Diagnostics
Background:
- Infectious diseases remain a significant global health threat, with unknown causes in 20% of fever cases.
- Traditional diagnostic methods are limited by time, scope, and accuracy issues like window periods and false results.
- Advanced nucleic acid detection methods can identify known pathogens but lack comprehensive coverage.
Observation:
- Case 1: Nanopore sequencing identified oral-like bacteria in a patient with bronchopleural fistula, leading to effective antibiotic treatment.
- Case 2: Cerebrospinal fluid sequencing detected *Streptococcus pneumoniae* in a patient with meningitis, enabling targeted antibiotic therapy.
- Case 3: Nanopore sequencing identified *Aspergillus brookii* in a patient with Hodgkin's lymphoma and infection, guiding effective antifungal treatment.
Findings:
- Three-generation nanopore sequencing technology enables rapid and precise pathogen identification.
- This advanced sequencing approach accurately detects a wide range of microbial agents.
- Clinical case studies demonstrate the successful application of nanopore sequencing in diagnosing and guiding treatment for diverse infections.
Implications:
- Nanopore sequencing offers a powerful new tool for infectious disease diagnostics.
- Accelerated pathogen detection can significantly improve clinical decision-making and patient management.
- This technology has the potential to revolutionize the approach to diagnosing and treating complex infectious diseases.
