Clinical metagenomics

Chiu, Charles Y.; Miller, Steven A.

doi:10.1038/s41576-019-0113-7

Cited by 1,023 publications

(905 citation statements)

References 147 publications

Supporting

Mentioning

822

Contrasting

Unclassified

Order By: Relevance

“…Despite its longer turnaround time and higher cost, mNGS demonstrated a satisfying level of sensitivity when compared to PCR assays in our study. Moreover, the nature of unbiased sequencing offers higher tolerance for genetic drift in the target pathogens, whereas certain changes in sequence can result in critical impact on the assay efficiency 21,22 . Along with targeted assays, mNGS should serve as an indispensable tool for sensitive and close monitoring of the molecular evolution for SARS-COV-2.…”

Section: Discussionmentioning

confidence: 99%

Optimizing diagnostic strategy for novel coronavirus pneumonia, a multi-center study in Eastern China

Zhang

Teng

et al. 2020

Preprint

View full text Add to dashboard Cite

COVID-19 caused by a novel coronavirus SARS-CoV-2 emerged in Wuhan, Hubei province since December 2019, and caused a rapid outbreak throughout China and globally. Cities outside Hubei are also facing great challenge and require implementing of effective and feasible strategy in precision diagnosing novel coronavirus pneumonia (NCP).We described a multicenter prospective study on diagnostic strategy of suspected NCP patients from January 22 nd to February 9 th , 2020 in Eastern China cities. Nasopharyngeal swabs were collected from the patients. The epidemiological characteristics, clinical symptoms, laboratory assessments, and computed tomographic (CT) scans were obtained. Pathogen screen were performed including RT-PCR, multiplex PCR, rapid flu antigen tests and mNGS.We enrolled 53 suspected NCP patients, among whom 20 were laboratory-confirmed. Fourteen (70%) and 3 (15%) patients were positive for the first and second SARS-CoV-2 RT-PCR test, respectively. All NCP patients were positive for mNGS. Chest CT images and the symptoms of early stage NCP patients were similar to other viral pneumonia patients. We identified 11 of 20 co-infections in NCP cases, including regular respiratory virus, fungi and bacteria synchronously. Genomic analysis showed that 8 of 10 cases had no mutation in virus genome, while 2 cases had only one single mutation in N gene.Our study discovered that a combination of chest CT, SARS-CoV-2 RT-PCR and multi-plex PCR is recommended in regions outside Hubei province. Co-infection of other pathogens with SARS-CoV-2 exists and should be acknowledged. Repeated sampling, change of specimen type or metagenomics sequencing could further facilitate during critical clinical cases.

show abstract

Section: Discussionmentioning

confidence: 99%

Optimizing diagnostic strategy for novel coronavirus pneumonia, a multi-center study in Eastern China

Zhang

Teng

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Since that time, several laboratories, including the laboratory who co-authored that initial case study, have validated metagenomic analyses of next-generation sequencing data directly from a variety of clinical sample types. A detailed description of next-generation sequencing and metagenomics methods is provided in the following references (62,63). It is important to highlight that each laboratory has highly lab-and sample-type specific methods from sample preparation, library preparation, sequencing platform and depth, to bioinformatic analysis and interpretation.…”

Section: Next-generation Sequencing and Clinical Metagenomicsmentioning

confidence: 99%

Appropriate Use and Future Directions of Molecular Diagnostic Testing

Graf

Pancholi

2020

Curr Infect Dis Rep

View full text Add to dashboard Cite

Purpose of Review Major technologic advances in two main areas of molecular infectious disease diagnostics have resulted in accelerated adoption or ordering, outpacing implementation, and clinical utility studies. Physicians must understand the limitations to and appropriate utilization of these technologies in order to provide cost-effective and well-informed care for their patients. Recent Findings Rapid molecular testing and, to a lesser degree, clinical metagenomics are now being routinely used in clinical practice. While these tests allow for a breadth of interrogation not possible with conventional microbiology, they pose new challenges for diagnostic and antimicrobial stewardship programs. This review will summarize the most recent literature on these two categories of technologic advances and discuss the few studies that have looked at utilization and stewardship approaches. This review also highlights the future directions for both of these technologies. Summary The appropriate utilization of rapid molecular testing and clinical metagenomics has not been well established. More studies are needed to assess their prospective impacts on patient management and antimicrobial stewardship efforts as the future state of infectious disease diagnostics will see continued expansion of these technologic advances.

show abstract

“…Metagenomic next-generation sequencing (mNGS) is a promising candidate approach for broad-spectrum pathogen identification in clinical samples, as nearly all potential pathogens (viruses, bacteria, fungi and parasites) can be detected by uniquely identifying DNA and/or RNA shotgun sequences 6,7 . This method has been successfully applied for the clinical diagnosis of infectious diseases 8,9 , outbreak surveillance 10,11 and pathogen discovery 12 .…”

mentioning

confidence: 99%

“…Viral genome sequencing is essential for outbreak management, as it enables origin determination and monitoring of viral transmission patterns 10 . In general, target enrichment of NGS libraries is required to obtain sufficient viral genome coverage for phylogenetic and molecular clock analyses 6 . The enrichment of libraries using multiplex PCR of tiled amplicons (tiling multiplex PCR) and/or capture probe enrichment has been successfully used for the genomic surveillance of EBOV 18,19 , ZIKV [20][21][22] and yellow fever virus (YFV) outbreaks 23 .…”

mentioning

confidence: 99%