Detection of Pathogen and Antibiotic Resistance Genes by Targeted Next-Generation Sequencing in ICU Patients.

Detection of Pathogen and Antibiotic Resistance Genes by Targeted Next-Generation Sequencing Compared With Metagenomic Next-Generation Sequencing in ICU Patients.

It is difficult to determine the pathogens in the early stage of infection in critically ill patients, and empirical use of broad-spectrum antibiotics for a long time is often necessary, leading to antibiotics drug resistance. Targeted next generation sequencing (tNGS) can provide faster results for pathogen and related antibiotic resistant diagnosis. But it lacks sufficient clinical evidence. Evidence regarding the clinical diagnostic accuracy and drug resistance is needed to comprehensively evaluate targeted next generation sequencing (tNGS) for diagnosis of patients in ICU who and will be critical to inform national policy.

Study Overview

• Status: Not yet recruiting
• Conditions: Infections; Critical Illness; Diagnosis
• Intervention / Treatment: Diagnostic test: targeted next-generation sequencing (tNGS)

Detailed Description

Infectious diseases are one of the highest mortality and morbidity diseases in humans. Due to the difficulty in identifying the pathogen in the early stage of infection, patients with severe infections often need to empirically use broad-spectrum antimicrobials for a long time. The traditional gold standard of etiological detection - etiological culture, even in sepsis patients, only about 60% of the results are positive. Therefore, the accurate identification and rapid classification of pathogenic microorganisms is very important for the patient's precise diagnosis and timely treatment.

Metagenomic next generation sequencing (mNGS), which has emerged in recent years, have been shown to provide early diagnosis and targeted medication guidance for bloodstream infections and respiratory infections, but it is expensive and not able to provide related drug resistant genes. Therefore, targeted next generation sequencing (tNGS) has been derived, which is characterized by rapid sequencing and genetic testing for drug resistance.

The purpose of this study is to evaluate the efficacy of etiological diagnosis and provide patients with more accurate treatment.

• Study Type: Observational
• Enrollment (Estimated): 20

Contacts and Locations

• Study Contact: Name: Ting Li; Phone Number: 011-86-15608657562; Email: 3423580562@qq.com
• Study Contact Backup: Name: Fangyi Li; Phone Number: 011-86-15603056533; Email: Lify8@mailsysu.edu.cn

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Adult; Older Adult
• Accepts Healthy Volunteers: No

• Sampling Method: Non-Probability Sample

Study Population

Patients in ICU truly have infected disease and non-infected disease diagnosed by two ICU physicians determining whether the patient have an infectious etiology and identifying the pathogen through existing clinical guidelines, clinical features, laboratory tests, microbiological tests, chest imaging, and treatment response.

Description

Inclusion Criteria:

• The presence of an infection or clearly excluded the presence of infection.
• Etiological culture and/or metagenomic next-generation sequencing detection of specimens sent for testing.

Exclusion Criteria:

• Suspected infection.
• Participation in other clinical trials in the past 2 months.

Study Plan

How is the study designed?

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
Non-Infection group; Participants received traditional etiological culture of suspected site of infection.	Diagnostic test: targeted next-generation sequencing (tNGS); To provide rapid etiological diagnosis of patients by means of targeted next-generation sequencing.
Infection group; Participants received traditional etiological culture, metagenomic next-generation sequencing of infectious sites.	Diagnostic test: targeted next-generation sequencing (tNGS); To provide rapid etiological diagnosis of patients by means of targeted next-generation sequencing.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Sensitivity	The probability of being positive in clinical composite diagnosis, the probability that etiological culture, mNGS, and tNGS tests are also positive, which is also known as the true positive rate.	1 year
Specificity	It refers to the probability that cultures, mNGS, and tNGS tests are also negative in the presence of non-infection confirmed by the gold standard.	1 year

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
False-positive rate	It refers to the probability that the gold-standard confirmed absence of infection is also positive for etiological culture, mNGS, and tNGS tests.	1 year
False-negative rate	It refers to the probability of being positive in the clinical composite diagnosis, and the probability that etiological cultures, mNGS, and tNGS tests will also be negative.	1 year
Positive predictive value	Positive predictive value is the probability that subjects with a positive test truly have the disease.	1 year
Negative predictive value	Negative predictive value is the probability that subjects with a negative screening test truly don't have the disease.	1 year
Kappa values	Kappa values are used to measure the agreement between two raters. The range of possible values of kappa is from -1 to 1, though it usually falls between 0 and 1. Unity represents perfect agreement, indicating that the raters agree in their classification of every case. Kappa values of 0.41~0.60 are moderately consistent, 0.61~0.80 are basically consistent, and 0.81~1.00 is almost identical.	1 year
Drug resistant gene by targeted next-generation sequencing	It refers to the distribution of drug resistance by targeted next-generation sequencing using the Comprehensive Antibiotic Resistance Database.	1 year

Collaborators and Investigators

• Sponsor: Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University
• Investigators: Study Director: Zhijie He, Sun Yat-sen Memorial Hospital,Sun Yat-sen University

Publications and helpful links

General Publications

• Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet. 2019 Jun;20(6):341-355. doi: 10.1038/s41576-019-0113-7.
• Diao Z, Han D, Zhang R, Li J. Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections. J Adv Res. 2021 Sep 29;38:201-212. doi: 10.1016/j.jare.2021.09.012. eCollection 2022 May.
• Miao Q, Ma Y, Wang Q, Pan J, Zhang Y, Jin W, Yao Y, Su Y, Huang Y, Wang M, Li B, Li H, Zhou C, Li C, Ye M, Xu X, Li Y, Hu B. Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice. Clin Infect Dis. 2018 Nov 13;67(suppl_2):S231-S240. doi: 10.1093/cid/ciy693.
• Pei XM, Yeung MHY, Wong ANN, Tsang HF, Yu ACS, Yim AKY, Wong SCC. Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases. Cells. 2023 Feb 2;12(3):493. doi: 10.3390/cells12030493.
• Li S, Tong J, Liu Y, Shen W, Hu P. Targeted next generation sequencing is comparable with metagenomic next generation sequencing in adults with pneumonia for pathogenic microorganism detection. J Infect. 2022 Nov;85(5):e127-e129. doi: 10.1016/j.jinf.2022.08.022. Epub 2022 Aug 26. No abstract available.
• Gaston DC, Miller HB, Fissel JA, Jacobs E, Gough E, Wu J, Klein EY, Carroll KC, Simner PJ. Evaluation of Metagenomic and Targeted Next-Generation Sequencing Workflows for Detection of Respiratory Pathogens from Bronchoalveolar Lavage Fluid Specimens. J Clin Microbiol. 2022 Jul 20;60(7):e0052622. doi: 10.1128/jcm.00526-22. Epub 2022 Jun 13.

Study record dates

Study Major Dates

• Study Start (Estimated): December 20, 2023
• Primary Completion (Estimated): August 10, 2024
• Study Completion (Estimated): August 10, 2024

Study Registration Dates

• First Submitted: October 19, 2023
• First Submitted That Met QC Criteria: November 27, 2023
• First Posted (Estimated): December 5, 2023

Study Record Updates

• Last Update Posted (Estimated): December 5, 2023
• Last Update Submitted That Met QC Criteria: November 27, 2023
• Last Verified: November 1, 2023

More Information

Terms related to this study

• Keywords: ICU; infections; Next-generation sequencing; Targeted Next-generation sequencing
• Additional Relevant MeSH Terms: Pathologic Processes; Disease Attributes; Critical Illness
• Other Study ID Numbers: SYSKY-2023-667-03

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: NO

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No