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Metagenomic Sequencing in Clinical Infectious Diseases

Completed
Conditions
Bacterial Infections and Mycoses
Registration Number
NCT05353634
Lead Sponsor
Liaocheng People's Hospital
Brief Summary

Progress in the diagnosis of infectious pathogens depends on the development of effective methods and the discovery of suitable biomarkers. There are several kinds of methods that have been used in diagnosis of various pathogens, such as microscopic examination, culture, serologic diagnosis or molecular approaches, etc. However, these methods have similar limitations, that is, the single detection of reagents. More importantly, physicians seldom consider infections with rare pathogens. Recently developed metagenomic next-generation sequencing (mNGS) has the capability to overcome limitations of traditional diagnostic tests. This new technology could identify all pathogens directly from sample with a single run in a hypothesis-free and culture-independent manner. Studies have shown that mNGS is more sensitive than traditional culture method in clinical conditions such as blood stream, respiratory and general infections. More importantly, due to unbiased sampling, mNGS is theoretically able to identify not only known but also unexpected pathogens or even discovery novel organisms. It should be noted that mNGS also has some limitations such as human genome contamination and possibly environmental microbial contamination. The vast majority of reads in mNGS are derived from human host. This would impede the overall analytical sensitivity of mNGS for pathogen detection. Host depletion methods or targeted sequencing may help to partially mitigate this disadvantage. As mNGS could not, by itself, define whether the detected microbe is the causative pathogen or environmental microorganism, a multidisciplinary discussion by clinicians, microbiologists as well as the lab technicians is required to interpret the result.

Detailed Description

Not available

Recruitment & Eligibility

Status
COMPLETED
Sex
All
Target Recruitment
2022097
Inclusion Criteria
  • All the patients have received mNGS testing in clinical practice.
Exclusion Criteria
  • Interruption of patient treatment process and incomplete information

Study & Design

Study Type
OBSERVATIONAL
Study Design
Not specified
Primary Outcome Measures
NameTimeMethod
Receiver operating characteristic (ROC) curves evaluate the performance of mNGS and traditional microbiological testingFrom admission to discharge, 3 weeks

Receiver operating characteristic (ROC) curves were used to evaluate the performance of the logarithm of reads per kilobase per million mapped reads \[lg(RPKM)\], genomic coverage, and relative abundance of the organism in predicting the true-positive pathogenic bacteria. Clinical data were rigorously evaluated and summarized to identify promising clinical indices and limitations of the mNGS-based test.

Secondary Outcome Measures
NameTimeMethod

Trial Locations

Locations (1)

Liaocheng People's Hospital

🇨🇳

Liaocheng, Shandong, China

Liaocheng People's Hospital
🇨🇳Liaocheng, Shandong, China

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