High‐Throughput Metagenomics for Identification of Pathogens in the Clinical Settings

Small Methods, Год журнала: 2020, Номер 5(1)

Опубликована: Дек. 13, 2020

Abstract The application of sequencing technology is shifting from research to clinical laboratories owing rapid technological developments and substantially reduced costs. However, although thousands microorganisms are known infect humans, identification the etiological agents for many diseases remains challenging as only a small proportion pathogens identifiable by current diagnostic methods. These challenges compounded emergence new pathogens. Hence, metagenomic next‐generation (mNGS), an agnostic, unbiased, comprehensive method detection, taxonomic characterization microorganisms, has become attractive strategy. Although studies, cases reports, have confirmed success mNGS in improving diagnosis, treatment, tracking infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners clinicians understand both benefits limitations when applying it practice. Interestingly, emerging third‐generation technologies may partially offset disadvantages mNGS. In this review, mainly: a) history technology; b) various NGS technologies, common platforms, workflows applications; c) pathogen identification; d) global expert consensus on NGS‐related methods e) associated with metagenomics described.

Язык: Английский

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Emerging contaminants: A One Health perspective

The Innovation, Год журнала: 2024, Номер 5(4), С. 100612 - 100612

Опубликована: Март 13, 2024

Язык: Английский

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Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections

Journal of Advanced Research, Год журнала: 2021, Номер 38, С. 201 - 212

Опубликована: Сен. 29, 2021

Metagenomic next-generation sequencing (mNGS) has changed the diagnosis landscape of lower respiratory tract infections (LRIs). With development newer assays, it is now possible to assess all microorganisms in a sample using single mNGS analysis. The applications for LRIs span wide range areas including LRI diagnosis, airway microbiome analyses, human host response and prediction drug resistance. currently an exciting transitional period; however, before implementation clinical setting, there are several barriers overcome, such as depletion nucleic acid, discrimination between colonization infection, high costs, so on. Aim Review: In this review, we summarize potential challenges promote integration into management patients with setting. Key Scientific Concepts Once its analytical validation, validation utility been demonstrated, will become important tool field infectious disease diagnosis.

Язык: Английский

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MBPD: A multiple bacterial pathogen detection pipeline for One Health practices

iMeta, Год журнала: 2023, Номер 2(1)

Опубликована: Янв. 31, 2023

Bacterial pathogens are one of the major threats to biosafety and environmental health, advanced assessment is a prerequisite combating bacterial pathogens. Currently, 16S rRNA gene sequencing efficient in open-view detection However, taxonomic resolution applicability this method limited by domain-specific pathogen database, profiling method, target variable regions. Here, we present pipeline multiple (MBPD) identify animal, plant, zoonotic MBPD based on large, curated database full-length genes 1986 reported species covering 72,685 sequences. In silico comparison allowed provide appropriate similarity threshold for both variable-region platforms, while subregion V3-V4 (mean: 88.37%, accuracy rate compared V1-V9) outperformed other regions identification sequencing. Benchmarking real data sets suggested superiority broader range detections with methods, including 16SPIP MIP. Beyond detecting known causal agent human, plant diseases, capable identifying cocontaminating from biological samples. Overall, agricultural, veterinary, medical, monitoring achieve One Health.

Язык: Английский

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Application of next-generation sequencing to identify different pathogens

Frontiers in Microbiology, Год журнала: 2024, Номер 14

Опубликована: Янв. 29, 2024

Early and precise detection identification of various pathogens are essential for epidemiological monitoring, disease management, reducing the prevalence clinical infectious diseases. Traditional pathogen techniques, which include mass spectrometry, biochemical tests, molecular testing, culture-based methods, limited in application time-consuming. Next generation sequencing (NGS) has emerged as an technology identifying pathogens. NGS is a cutting-edge method with high throughput that can create massive volumes sequences broad prospects field diagnosis. In this review, we introduce detail, summarizes different pathogens, including bacteria, fungi, viruses, analyze challenges outlook using to identify Thus, work provides theoretical basis studies evidence support distinguishing

Язык: Английский

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Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections

Nature Medicine, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 12, 2024

Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) is an agnostic method for broad-based diagnosis central nervous system (CNS) infections. Here we analyzed the 7-year performance clinical CSF mNGS testing 4,828 samples from June 2016 to April 2023 performed by University California, San Francisco (UCSF) microbiology laboratory. Overall, detected 797 organisms 697 (14.4%) samples, consisting 363 (45.5%) DNA viruses, 211 (26.4%) RNA 132 (16.6%) bacteria, 68 (8.5%) fungi and 23 (2.9%) parasites. We also extracted laboratory metadata a subset (n = 1,164) 1,053 UCSF patients. Among 220 infectious diagnoses in this subset, 48 (21.8%) were identified alone. The sensitivity, specificity accuracy CNS infections 63.1%, 99.6% 92.9%, respectively. exhibited higher sensitivity (63.1%) than indirect serologic (28.8%) direct detection both (45.9%) non-CSF (15.0%) (P < 0.001 all three comparisons). When only considering made testing, increased 86%. These results justify routine use diagnostic hospitalized patients with suspected infection.

Язык: Английский

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Liquid biopsy for infectious diseases: a focus on microbial cell-free DNA sequencing

Theranostics, Год журнала: 2020, Номер 10(12), С. 5501 - 5513

Опубликована: Янв. 1, 2020

Metagenomic next-generation sequencing (mNGS) of microbial cell-free DNA (mcfDNA sequencing) is becoming an attractive diagnostic modality for infectious diseases, allowing broad-range pathogen detection, noninvasive sampling, and rapid diagnosis. At this key juncture in the translation metagenomics into clinical practice, integrative perspective needed to understand significance emerging mcfDNA technology. In review, we summarized actual performance tests recently used health care settings diagnosis a variety diseases further focused on practice considerations (challenges solutions) improving accuracy relevance results produced by evolving technique. Such knowledge will be helpful physicians, microbiologists researchers what going quickly progressing field non-invasive promote routine implementation technique disease.

Язык: Английский

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The Diagnostic Value of Metagenomic Next–Generation Sequencing in Lower Respiratory Tract Infection

Frontiers in Cellular and Infection Microbiology, Год журнала: 2021, Номер 11

Опубликована: Сен. 9, 2021

Lower respiratory tract infections are associated with high morbidity and mortality significant clinical harm. Due to the limited ability of traditional pathogen detection methods, anti-infective therapy is mostly empirical. Therefore, it difficult adopt targeted drug therapy. In recent years, metagenomic next-generation sequencing (mNGS) technology has provided a promising means for pathogen-specific diagnosis updated diagnostic strategy lower infections. This article reviews value mNGS infections, impact different sampling methods on efficiency mNGS, current technical difficulties in application mNGS.

Язык: Английский

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Metagenomic next-generation sequencing for accurate diagnosis and management of lower respiratory tract infections

International Journal of Infectious Diseases, Год журнала: 2022, Номер 122, С. 921 - 929

Опубликована: Июль 28, 2022

This study aimed to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in patients with suspected lower respiratory tract infections.This retrospective reviewed infections at Wuhan Union Hospital. Data including demographic, laboratory, and radiological profiles; treatment; outcomes were recorded analyzed.mNGS identified pathogenic microbes 100/140 (71.4%) patients, although 135 (96.4%) had received empiric antibiotic treatment before mNGS tests. Single bacterial infection (35/100, 35%) was most common type positive results, followed by single fungal (14/100, 14%), bacterial-viral coinfection viral (12/100, 12%), bacterial-fungal (9/100, 9%), fungal-viral bacterial-fungal-viral (7/100, 7%). Moreover, compared culture test, showed higher sensitivity (63/85, 74.1% vs 22/85, 25.9% P = 0.001) processing time (24 hours 48 hours). Antibiotic adjusted or confirmed based on results 123 (87.9%) five (3.6%), 33 (23.6%), 85 (60.7%) whom downgraded, upgraded, unchanged, respectively. Almost all regardless escalation, de-escalation, no change treatment, significant improvement symptoms inflammatory indicators. In addition, 17 (12.1%) referred Pulmonary Hospital for further because tuberculosis.mNGS could be a promising technique microbiological diagnosis management, potentially improving patients.

Язык: Английский

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High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance

Computational and Structural Biotechnology Journal, Год журнала: 2022, Номер 20, С. 5378 - 5392

Опубликована: Янв. 1, 2022

Increasing globalization, agricultural intensification, urbanization, and climatic changes have resulted in a significant recent increase emerging infectious zoonotic diseases. Zoonotic diseases are becoming more common, so innovative, effective, integrative research is required to better understand their transmission, ecological implications, dynamics at wildlife-human interfaces. High-throughput sequencing (HTS) methodologies enormous potential for unraveling these contingencies improving our understanding, but they only now beginning be realized livestock research. This study investigates the current state of use technologies detection pathogens such as bovine, dogs (Canis lupus familiaris), sheep (Ovis aries), pigs (Sus scrofa), horses (Equus caballus), chicken (Gallus gallus domesticus), ducks (Anatidae) well how it can improve monitoring infections. We also described several high-throughput approaches improved known, unknown, agents, resulting disease diagnosis, surveillance In coming years, continued advancement will hasten development various new genomic technological studies on farm animals.

Язык: Английский

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