Nanopore-Targeted Sequencing Improves the Diagnosis and Treatment of Patients with Serious Infections

Zhang, Yi; Lu, Xuan; Tang, Liang; Xia, Linghui; Hu, Yu

doi:10.1128/mbio.03055-22

Cited by 15 publications

(8 citation statements)

References 35 publications

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“…With the advance of rapid NGS analyzing techniques (ie, nanopore-targeted sequencing), the turn-around time for NGS was greatly reduced from around 24 hours 48 to theoretically 6 hours. 49 Based on our model, a specified testing panel can be developed for detecting high-risk type γ patients. The microbes in the model should be further evaluated for their role and their functional contribution in host–microbe interaction.…”

Section: Discussionmentioning

confidence: 99%

Phenotypes and Lung Microbiota Signatures of Immunocompromised Patients with Pneumonia-Related Acute Respiratory Distress Syndrome

Hu,

Shen,

et al. 2024

JIR

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We aim to identify the clinical phenotypes of immunocompromised patients with pneumonia-related ARDS, to investigate the lung microbiota signatures and the outcomes of different phenotypes, and finally, to develop a machine learning classifier for a specified phenotype. Methods: This prospective study included immunocompromised patients with pneumonia-related ARDS. We identified phenotypes using hierarchical clustering to analyze clinical variables and serum cytokine levels. We then compared outcomes and lung microbiota signatures between phenotypes. Based on lung microbiota markers, we developed a random forest classifier for a specified phenotype with worse outcomes. Results: This study included 92 patients, who were divided into three phenotypes, namely "type α" (N = 33), "type β" (N = 12), and "type γ" (N = 47). Compared to type α or type β, patients with type γ had no obvious inflammatory presentation and had significantly lower IL-6 levels and more severe oxygenation failure. Type γ was also related to higher 30-day mortality and lower ventilator free days. The microbiota signatures of type γ were characterized by lower alpha diversity and distinct compositions than those of other patients. We developed a lung microbiota-derived random forest model to differentiate patients with type γ from other phenotypes. Conclusion:Immunocompromised patients with pneumonia-related ARDS can be clustered into three clinical phenotypes, namely type α, type β, and type γ. Phenotypes were distinguished from each other with different outcomes and lung microbiota signatures. Type γ, which was characterized by insufficient inflammation response and worse outcomes, can be detected with a random forest model based on lung microbiota markers.

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Section: Discussionmentioning

confidence: 99%

Phenotypes and Lung Microbiota Signatures of Immunocompromised Patients with Pneumonia-Related Acute Respiratory Distress Syndrome

Hu,

Shen,

et al. 2024

JIR

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“…GVHD is a serious complication that can occur after transplantation, where the donor's immune cells attack the recipient's tissues. A recent study by Zhang et al utilised nanopore sequencing to perform transcriptome analysis of immune cells involved in GVHD [ 67 ]. They identified gene expression patterns associated with the development and severity of GVHD, providing valuable insights into the underlying molecular mechanisms.…”

Section: Clinical Applicationsmentioning

confidence: 99%

The application of long-read sequencing in clinical settings

Oehler,

Wright,

Stark

et al. 2023

Hum Genomics

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Long-read DNA sequencing technologies have been rapidly evolving in recent years, and their ability to assess large and complex regions of the genome makes them ideal for clinical applications in molecular diagnosis and therapy selection, thereby providing a valuable tool for precision medicine. In the third-generation sequencing duopoly, Oxford Nanopore Technologies and Pacific Biosciences work towards increasing the accuracy, throughput, and portability of long-read sequencing methods while trying to keep costs low. These trades have made long-read sequencing an attractive tool for use in research and clinical settings. This article provides an overview of current clinical applications and limitations of long-read sequencing and explores its potential for point-of-care testing and health care in remote settings.

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“…In microbial identification, tNGS is particularly valuable for distinguishing bacterial species using the 16S ribosomal RNA (rRNA) gene or fungal species through the internal transcribed spacer 1/2 (ITS-1/2) regions. This approach enables precise taxonomic classification and can be applied to various environmental samples, clinical specimens, and food safety assessments [53][54][55]. However, one substantial challenge in tNGS is the meticulous selection of target regions.…”

Section: Targeted Sequencingmentioning

confidence: 99%

Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology

Bianconi,

Aschbacher,

Pagani

2023

Antibiotics

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Recent advancements in sequencing technology and data analytics have led to a transformative era in pathogen detection and typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming the standard for pathogen analysis and control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into pathogen epidemiology and the emergence of antimicrobial-resistant strains. Antimicrobial resistance (AMR) is a pressing global public health issue. While clinical laboratories have traditionally relied on culture-based antimicrobial susceptibility testing, the integration of genomic data into AMR analysis holds immense promise. Genomic-based AMR data can furnish swift, consistent, and highly accurate predictions of resistance phenotypes for specific strains or populations, all while contributing invaluable insights for surveillance. Moreover, genome sequencing assumes a pivotal role in the investigation of hospital outbreaks. It aids in the identification of infection sources, unveils genetic connections among isolates, and informs strategies for infection control. The One Health initiative, with its focus on the intricate interconnectedness of humans, animals, and the environment, seeks to develop comprehensive approaches for disease surveillance, control, and prevention. When integrated with epidemiological data from surveillance systems, genomic data can forecast the expansion of bacterial populations and species transmissions. Consequently, this provides profound insights into the evolution and genetic relationships of AMR in pathogens, hosts, and the environment.

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Nanopore-Targeted Sequencing Improves the Diagnosis and Treatment of Patients with Serious Infections

Abstract: We introduce the application of NTS in blood samples of patients with serious infections and expound the efficiency and accuracy of NTS in detecting pathogenic microorganisms. Our work builds on the considerable interest of the scientific community in the management of serious infection.

Cited by 15 publications

References 35 publications

Phenotypes and Lung Microbiota Signatures of Immunocompromised Patients with Pneumonia-Related Acute Respiratory Distress Syndrome

Phenotypes and Lung Microbiota Signatures of Immunocompromised Patients with Pneumonia-Related Acute Respiratory Distress Syndrome

The application of long-read sequencing in clinical settings

Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology

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