Targeted Next Generation Sequencing (tNGS) for Pathogen Detection
In the realm of infectious diseases, accurate identification of pathogens plays a pivotal role in determining the most effective treatment and management strategies. The complexity of pathogenic microorganisms, coupled with the limitations of traditional clinical methods such as low throughput and time-consuming culture techniques, often result in the challenge of diagnosing pathogens in approximately 50% of infected patients. Enter the realm of innovation: the application of high-throughput sequencing technology, also known as Next Generation Sequencing (NGS), is revolutionizing pathogen detection.
Limitations in Traditional Pathogens Testing
- Limited Sensitivity: The effectiveness of traditional testing approaches, such as smear testing and immunological assays, is hampered by various factors such as sampling inconsistencies, variations in bacterial excretion, the window period of infection, technological constraints, and other variables. Consequently, these tests often yield unsatisfactory levels of sensitivity, leading to a significant likelihood of false-negative outcomes.
- Incomplete Primary Screening: Traditional detection techniques exhibit a restricted pathogen spectrum, leaving room for the issues of both overlooked infections and the inability to detect the full range of pathogens. This limitation highlights the need for a broader and more comprehensive screening approach.
- Challenges in Detecting Drug-Resistant Bacteria: The rise of drug-resistant bacterial infections poses a substantial threat to effective patient treatment. While the judicious utilization of antibiotics remains pivotal in addressing this concern, the identification of drug-resistant bacteria through conventional detection technologies proves to be arduous. This challenge hampers timely and accurate intervention strategies.
- Elevated Costs: The emergence of metagenomic next-generation sequencing (mNGS) as a prominent pathogenicity testing methodology has shown remarkable potential in enhancing the identification of pathogenic microorganisms. Nonetheless, the relatively high cost associated with mNGS testing contributes to a significant economic burden on patients. Consequently, the adoption of this advanced approach in clinical settings remains constrained due to financial considerations.
Enhancing Precision Anti-Infection Strategies Through tNGS Technology
Based on targeted NGS (tNGS) technology, Our Pathogen Targeted NGS Products harness the power of cutting-edge sequencing technologies to address these challenges. This sophisticated technique enriches dozens to hundreds of known pathogenic microorganisms, along with their virulence and resistance genes, using ultra-multiplex PCR amplification or hybridization capture technology. Subsequently, high-throughput multi-pathogen parallel testing, grounded in NGS, is performed.
CD Genomics tNGS Technology
Multiple research endeavors have consistently showcased the superior cost-effectiveness of targeted Next-Generation Sequencing (tNGS) over prevailing pathogen detection methods. tNGS exhibits heightened sensitivity, significantly minimizing the occurrences of both "false-positive" and "false-negative" outcomes in contrast to the established "gold standard" in pathogen diagnosis, as underscored by the influential Flurin study. Notably, the Flurin study distinctly revealed that tNGS outcomes outperformed the conventional culture-based test, exhibiting heightened sensitivity and a marked reduction in the incidence of false-positive and false-negative results.
Results of both tests in the periprosthetic joint infection group. (Flurin et al., 2021)
Workflow of Multiplex PCR Amplification
- Ultra-Multiplex PCR: We start by extracting DNA/RNA directly from your samples. This genetic material is then subjected to ultra-multiplex PCR primer amplification —specially designed to capture the specific pathogens of interest.
- Library Construction: The enriched genetic material is processed to construct a sequencing library, a crucial step that prepares the samples for the upcoming high-throughput sequencing.
- High-Throughput Sequencing: Using advanced sequencing technologies, we decode the genetic material, generating a vast amount of data ready for analysis.
- Data Processing and Analysis: Our bioinformatics experts take over, employing sophisticated tools to process and analyze the sequencing data. This is where the magic happens—pathogens are identified, and species-specific resistance genes are scrutinized.
Workflow of Hybridization Capture Technology
- Step 01: DNA/RNA Extraction
We kick-start the process with DNA/RNA extraction, a pivotal step that lays the foundation for accurate analysis.
- Step 02: NGS Library Preparation
The journey continues with NGS library preparation. This involves cDNA synthesis and NGS Prep, collectively enhancing the genetic material for subsequent analysis. Our optimized methods reduce the preparation time to approximately 5 hours, ensuring a swift transition to the next stage.
- Step 03: Target Enrichment
Here, we delve into the heart of precision—target enrichment. Using cutting-edge hybridization capture techniques, we focus on amplifying the specific genetic regions of interest. While competitors often take up to 16 hours for this step, our streamlined approach slashes this time to around 4 hours. Portions covered through the Complete Kit are conveniently highlighted in red, keeping you informed at every stage.
Sequencing is where the magic happens. We harness the power of Illumina Sequencers, ensuring compatibility across platforms. The duration of this step depends on the read length, allowing for flexibility in achieving your desired results.
Completing the workflow, our dedicated team of experts engages in meticulous data analysis. In approximately 3 hours, we generate a comprehensive Virus Data Report—a valuable resource that distills complex data into actionable insights.
Benefits
- Comprehensive Coverage: Our service encompasses over 95% of current clinical pathogens, both DNA and RNA-based.
- Host Background Independence: Unlike some traditional methods, our detection isn't influenced by the host background, ensuring precise results.
- Enhanced Specificity: Through our target capture strategy, we achieve higher specificity in pathogen detection.
- Cost-Effectiveness: Our service minimizes costs while maximizing the depth and breadth of pathogen identification.
Empowering Our Clients Across Varied Applications
Our Pathogen Targeted NGS Service has demonstrated its prowess, proving to be a catalyst for progress, innovation, and effective solutions.
- Epidemiological Studies: Unveiling the intricate dynamics of pathogen spread and evolution is pivotal in understanding disease propagation. Our advanced sequencing service has proven invaluable in investigating outbreaks, pinpointing sources of infection, and meticulously tracking the emergence of drug-resistant strains.
- Antibiotic Resistance Monitoring: In a landscape shadowed by the emergence of antibiotic-resistant pathogens, the need for identifying resistance genes has never been more pressing. Our service stands as a sentinel, not only detecting pathogens but also meticulously evaluating the presence of specific resistance genes. This critical information guides antibiotic selection and empowers informed treatment strategies.
- Transplant Medicine: In the realm of transplant medicine, where vulnerability is heightened, infections pose unique challenges. Our service swiftly identifies pathogens in transplant recipients, fostering early interventions and personalized treatment pathways.
- Research and Surveillance: Embarking on an expedition to explore the intricacies of microbial diversity is no small feat. Our service has emboldened researchers to delve into a multitude of environments—be it hospital settings or the vast expanse of natural ecosystems. This endeavor illuminates the mysterious tapestry of microbial communities, unraveling insights that resonate with human and environmental health.
- Infection Control: The urgency of rapid pathogen detection in healthcare facilities cannot be overstated. Our service operates as a beacon of swiftness, instantly revealing the culprits behind outbreaks. This knowledge empowers healthcare professionals with the precision to enact targeted containment strategies.
- Veterinary Medicine: Our service's reach extends beyond human pathogens, venturing into the realm of veterinary medicine. In the diagnosis and management of infectious diseases in animals, our sequencing service proves to be an invaluable asset.
- Pharmaceutical Development: For enterprises dedicated to developing antimicrobial drugs and vaccines, our service offers a vantage point. By providing insights into the prevalence and diversity of pathogens, we actively contribute to the crafting and validation of novel interventions.
- Public Health Surveillance: Government agencies are entrusted with safeguarding public health, and our service stands as a stalwart ally. Its integration into ongoing pathogen surveillance equips these agencies with the foresight to detect potential threats early, facilitating well-informed decisions in the realm of public health policies.
- Global Health Initiatives: The impact of our service resonates globally, transcending resource limitations. Its cost-effectiveness and expansive coverage are a lifeline in resource-scarce settings, fortifying disease control and management on an international scale.
Reference:
- Flurin, Laure, et al. "Targeted next generation sequencing for elbow periprosthetic joint infection diagnosis." Diagnostic Microbiology and Infectious Disease 101.2 (2021): 115448.
