Metagenomics-enabled microbial surveillance

Nature Microbiology, Год журнала: 2022, Номер 7(4), С. 486 - 496

Опубликована: Апрель 1, 2022

Язык: Английский

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Microfluidic space coding for multiplexed nucleic acid detection via CRISPR-Cas12a and recombinase polymerase amplification

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Окт. 29, 2022

Abstract Fast, inexpensive, and multiplexed detection of multiple nucleic acids is great importance to human health, yet it still represents a significant challenge. Herein, we propose acid testing platform, named MiCaR, which couples mi crofluidic device with CRISPR- C as12a nd multiplex r ecombinase polymerase amplification. With only one fluorescence probe, MiCaR can simultaneously test up 30 targets through microfluidic space coding. The limit achieves 0.26 attomole, the assay takes 40 min. We demonstrate utility by efficiently detecting nine HPV subtypes targeted 9-valent vaccine, showing sensitivity 97.8% specificity 98.1% in 100 patient samples at risk for infection. Additionally, also show generalizability our approach successfully eight most clinically relevant respiratory viruses. anticipate this effective, undecorated versatile platform be widely used detection.

Язык: Английский

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Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases

Genes, Год журнала: 2022, Номер 13(9), С. 1566 - 1566

Опубликована: Авг. 31, 2022

Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these laboratory: whole genome (WGS), targeted metagenomics and shotgun sequencing. These being utilized initial identification pathogenic organisms, detection antimicrobial resistance mechanisms epidemiologic tracking organisms within outside hospital systems. In this review, we analyze provide a comprehensive summary how currently used public health, basic research, laboratory environments. health arena, WGS is to identify epidemiologically track food borne outbreaks disease surveillance. systems, multi-drug-resistant nosocomial infections transmission organisms. addition, examine approaches (targeted shotgun) circumvent traditional biased culture methods potential pathogens directly from specimens. We also expand on important factors consider when implementing technologies, what possible infectious diagnosis next 5 years.

Язык: Английский

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Metagenomic Sequencing for Microbial DNA in Human Samples: Emerging Technological Advances

International Journal of Molecular Sciences, Год журнала: 2022, Номер 23(4), С. 2181 - 2181

Опубликована: Фев. 16, 2022

Whole genome metagenomic sequencing is a powerful platform enabling the simultaneous identification of all genes from entirely different kingdoms organisms in complex sample. This technology has revolutionised multiple areas microbiome research to clinical diagnoses. However, one major challenges study overwhelming non-microbial DNA present most host-derived specimens, which can inundate microbial signals and reduce sensitivity microorganism detection. Various host depletion methods facilitate have been developed received considerable attention this context. In review, we an overview current approaches along with explanations their underlying principles, advantages disadvantages. We also discuss applications laboratory diagnoses and, finally, envisage direction further perfection samples overabundant DNA.

Язык: Английский

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Genomics in the long-read sequencing era

Trends in Genetics, Год журнала: 2023, Номер 39(9), С. 649 - 671

Опубликована: Май 23, 2023

Язык: Английский

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Liquid Biopsy Based on Cell-Free DNA and RNA

Annual Review of Biomedical Engineering, Год журнала: 2024, Номер 26(1), С. 169 - 195

Опубликована: Фев. 12, 2024

This review delves into the rapidly evolving landscape of liquid biopsy technologies based on cell-free DNA (cfDNA) and RNA (cfRNA) their increasingly prominent role in precision medicine. With advent high-throughput sequencing, use cfDNA cfRNA has revolutionized noninvasive clinical testing. Here, we explore physical characteristics cfRNA, present an overview essential engineering tools used by field, highlight applications, including prenatal testing, cancer organ transplantation surveillance, infectious disease Finally, discuss emerging broadening scope biopsies to new areas diagnostic

Язык: Английский

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Status check: next-generation sequencing for infectious-disease diagnostics

Journal of Clinical Investigation, Год журнала: 2024, Номер 134(4)

Опубликована: Фев. 14, 2024

Next-generation sequencing (NGS) applications for the diagnostics of infectious diseases has demonstrated great potential with three distinct approaches: whole-genome (WGS), targeted NGS (tNGS), and metagenomic (mNGS, also known as clinical metagenomics). These approaches provide several advantages over traditional microbiologic methods, though challenges still exist.

Язык: Английский

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Enhancing lower respiratory tract infection diagnosis: implementation and clinical assessment of multiplex PCR-based and hybrid capture-based targeted next-generation sequencing

EBioMedicine, Год журнала: 2024, Номер 107, С. 105307 - 105307

Опубликована: Сен. 1, 2024

Язык: Английский

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Open-set deep learning–enabled single-cell Raman spectroscopy for rapid identification of airborne pathogens in real-world environments

Science Advances, Год журнала: 2025, Номер 11(2)

Опубликована: Янв. 8, 2025

Pathogenic bioaerosols are critical for outbreaks of airborne disease; however, rapidly and accurately identifying pathogens directly from complex air environments remains highly challenging. We present an advanced method that combines open-set deep learning (OSDL) with single-cell Raman spectroscopy to identify in real-world containing diverse unknown indigenous bacteria cannot be fully included training sets. To test further enhance identification, we constructed the datasets aerosolized bacteria. Through optimizing OSDL algorithms strategies, Raman-OSDL achieves 93% accuracy five target pathogens, 84% untrained bacteria, 36% reduction false positive rates compared conventional close-set algorithms. It offers a high detection sensitivity down 1:1000. When applied real >4600 bacterial species, our identifies single or multiple simultaneously within hour. This tool advances surveilling prevent infection transmission.

Язык: Английский

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Comparison of mNGS with conventional methods for diagnosis of cryptococcal meningitis: a retrospective study

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Янв. 29, 2025

The application of metagenomic next-generation sequencing (mNGS) in the diagnosis cryptococcal meningitis is relatively under characterized. Here, we retrospectively evaluated data from patients who were tested using mNGS and/or routine testing, including fungal culture, India ink staining, and antigen (CrAg) testing. performance was then assessed. Initial cerebrospinal fluid (CSF) samples collected 65 with suspected central nervous system (CNS) infection conventional tests mNGS. offers a culture-independent approach, facilitating rapid unbiased detection broad spectrum pathogens. Patients bacterial tuberculous or viral used as mNGS-positive controls one autoimmune encephalitis patient an mNGS-negative control. In 45 diagnosed meningitis, sensitivity, specificity, positive predictive value, negative concordance rate 92%, 100%, 90.9%, 95.6%, respectively. Compared to methods, sensitivity slightly lower than CrAg (96.7%) but higher (79.5%) culturing (63.4%). Of two cases (2/25, 8.0%), by while other only A combination methods enhanced 100%. Our study demonstrates that both offer excellent diagnostic accuracy for utilizing can enhance clinical assessment management.

Язык: Английский

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