Diagnostic accuracy of metagenomic next-generation sequencing in diagnosing infectious diseases: a meta-analysis

Liu, Jian; Zhang, Qiao; Dong, Yongquan; Yin, Jie; Qiu, Yunqing

doi:10.1038/s41598-022-25314-y

Cited by 22 publications

(10 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As clinical and academic teams came together through the unifying pandemic imperative [10], the translational research timeline for pathogen sequencing shortened. Diagnostic accuracy studies are beginning to demonstrate satisfactory performance with pathogen detection [11 ▪ ,12 ▪ ] and there are innovative approaches to detecting AMR elements using nanopore sequencing with cas9 enrichment [13 ▪ ] or predicting AMR using machine learning [14]. There is also increasing focus on clinical laboratory quality requirements including validation, reproducibility, setting limits of detection, and producing positive and negative internal controls and externally distributed reference materials for quality assurance [15].…”

Section: The Respiratory Metagenomics Propositionmentioning

confidence: 99%

Respiratory metagenomics: route to routine service

Edgeworth

2023

Current Opinion in Infectious Diseases

View full text Add to dashboard Cite

Purpose of reviewThe coronavirus disease 2019 pandemic demonstrated broad utility of pathogen sequencing with rapid methodological progress alongside global distribution of sequencing infrastructure. This review considers implications for now moving clinical metagenomics into routine service, with respiratory metagenomics as the exemplar use-case.Recent findingsRespiratory metagenomic workflows have completed proof-of-concept, providing organism identification and many genotypic antimicrobial resistance determinants from clinical samples in <6 h. This enables rapid escalation or de-escalation of empiric therapy for patient benefit and reducing selection of antimicrobial resistance, with genomic-typing available in the same time-frame. Attention is now focussed on demonstrating clinical, health-economic, accreditation, and regulatory requirements. More fundamentally, pathogen sequencing challenges the traditional culture-orientated time frame of microbiology laboratories, which through automation and centralisation risks becoming increasingly separated from the clinical setting. It presents an alternative future where infection experts are brought together around a single genetic output in an acute timeframe, aligning the microbiology target operating model with the wider human genomic and digital strategy.SummaryPathogen sequencing is a transformational proposition for microbiology laboratories and their infectious diseases, infection control, and public health partners. Healthcare systems that link output from routine clinical metagenomic sequencing, with pandemic and antimicrobial resistance surveillance, will create valuable tools for protecting their population against future infectious diseases threats.

show abstract

Section: The Respiratory Metagenomics Propositionmentioning

confidence: 99%

Respiratory metagenomics: route to routine service

Edgeworth

2023

Current Opinion in Infectious Diseases

View full text Add to dashboard Cite

show abstract

“…Current investigations combine more than one omics approach to image a highresolution picture of the gut microbiota dynamics [41]. Genomics is concerned with identifying the genetic composition of a single bacterium, but metagenomics is concerned with identifying the genetic composition of an entire community of bacterial communities (for instance, the entire gut microbiome of humans) [42]. Metagenomics consists of several culture-independent techniques (i.e., experimental and bioinformatic approaches) to analyze extracted DNA directly from biological samples, such as saliva, stool, and sputum [43].…”

Section: Gut Dysbiosis In Hepatic Encephalopathymentioning

confidence: 99%

Gut Dysbiosis and Blood-Brain Barrier Alteration in Hepatic Encephalopathy: From Gut to Brain

et al. 2023

View full text Add to dashboard Cite

A common neuropsychiatric complication of advanced liver disease, hepatic encephalopathy (HE), impacts the quality of life and length of hospital stays. There is new evidence that gut microbiota plays a significant role in brain development and cerebral homeostasis. Microbiota metabolites are providing a new avenue of therapeutic options for several neurological-related disorders. For instance, the gut microbiota composition and blood-brain barrier (BBB) integrity are altered in HE in a variety of clinical and experimental studies. Furthermore, probiotics, prebiotics, antibiotics, and fecal microbiota transplantation have been shown to positively affect BBB integrity in disease models that are potentially extendable to HE by targeting gut microbiota. However, the mechanisms that underlie microbiota dysbiosis and its effects on the BBB are still unclear in HE. To this end, the aim of this review was to summarize the clinical and experimental evidence of gut dysbiosis and BBB disruption in HE and a possible mechanism.

show abstract

“…Pathogens can be identified from clinical and environmental samples using metagenomic sequencing—deep sequencing to recover pathogen genomic sequences [ 3 , 4 ]. The information generated from rapid pathogen identification is critical for guiding rapid response policies [ 4 , 5 , 6 , 7 ]. For example, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first characterised using metagenomic sequencing when unknown cases of pneumonia began appearing in Wuhan, China (see Section 4 .…”

Section: Introductionmentioning

confidence: 99%

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Quek,

2024

Pathogens

View full text Add to dashboard Cite

High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens—bacteria, fungi, parasites and viruses—including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.

show abstract

Diagnostic accuracy of metagenomic next-generation sequencing in diagnosing infectious diseases: a meta-analysis

Cited by 22 publications

References 46 publications

Respiratory metagenomics: route to routine service

Respiratory metagenomics: route to routine service

Gut Dysbiosis and Blood-Brain Barrier Alteration in Hepatic Encephalopathy: From Gut to Brain

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Contact Info

Product

Resources

About