Nanopore Sequencing in Ophthalmology

Nanopore Sequencing in Ophthalmology - a Paradigm Shift in Pathogen Determination?

In this pilot study, the feasibility of the Oxford Nanopore MinION to identify pathogens from vitrectomy samples in eyes with endophthalmitis shall be assessed. The MinION is a low cost commercially available device for DNA/ RNA analysis that, in studies, has been used for pathogen determination in various infectious diseases as well as for the genetic characterization of hematologic tumors.

Study Overview

• Status: Recruiting
• Conditions: Endophthalmitis

Detailed Description

Vitreous samples and anterior chamber taps from eyes with endophthalmitis are taken during routine vitrectomy. The gathered samples are divided in half to undergo routine culture for microbial growth and nanopore sequencing with the MinION Mk1b, a commercially available device for DNA/RNA sequencing. Base reads from Nanopore sequencing are then compared with available libraries for pathogen identification. The Nanopore sequencing results for pathogens are compared versus the results of the microbiological culture of the same eye as the gold standard. Clinical features and visual function before and after vitrectomy are gathered from patient charts. Treatment is not altered due to results of the Nanopore sequencing.

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

Contacts and Locations

• Study Contact: Name: Michael Sommer, MD; Phone Number: 004331638531033; Email: michael.sommer@medunigraz.at
• Study Contact Backup: Name: Gerald Seidel, MD, PhD; Phone Number: 004331638580714; Email: gerald.seidel@medunigraz.at

Study Locations

• Austria
  • Styria
    • Graz, Styria, Austria, 8036
      • Recruiting
      • Universitäts Augenklinik Graz
      • Contact: Michael Sommer, MD; Phone Number: 004331638531033; Email: michael.sommer@medunigraz.at
      • Contact: Gerald Seidel, MD, PhD; Phone Number: 004331638580714; Email: gerald.seidel@medunigraz.at

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 18 years to 99 years (Adult, Older Adult)
• Accepts Healthy Volunteers: N/A

• Sampling Method: Non-Probability Sample

Study Population

Eyes of adult patients with endophthalmitis

Description

Inclusion Criteria:

• Eyes of patients with endophthalmitis

Exclusion Criteria:

• No informed consent possible
• Participation in other studies

Study Plan

How is the study designed?

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Pathogen detection	Pathogens detected by Nanopore sequencing versus microbiologic culture	In vitro analysis after vitrectomy for endophthalmitis. Start of analysis: Within the next working day after sample acquisition. Time for Nanopore sequencing: Approximately up to 10 hours. Time for culture: 24 hours up to 14 days.

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Time to pathogen detection	Time in days from gathering of the sample until arrival of results	Time measured from start of analysis until arrival of results. Time for Nanopore sequencing: Approximately up to 10 hours. Time for culture: 24 hours up to 14 days.
Visual acuity	Visual acuity measured with Snellen charts	Gathered from patient charts two months after vitrectomy.

Collaborators and Investigators

• Sponsor: Medical University of Graz

Study record dates

Study Major Dates

• Study Start (Actual): April 22, 2022
• Primary Completion (Estimated): December 1, 2024
• Study Completion (Estimated): December 1, 2024

Study Registration Dates

• First Submitted: April 22, 2022
• First Submitted That Met QC Criteria: May 12, 2022
• First Posted (Actual): May 13, 2022

Study Record Updates

• Last Update Posted (Estimated): December 5, 2023
• Last Update Submitted That Met QC Criteria: December 4, 2023
• Last Verified: December 1, 2023

More Information

Terms related to this study

• Keywords: Next Generation Sequencing; Nanopore sequencing; Endophthalmitis
• Additional Relevant MeSH Terms: Infections; Eye Diseases; Eye Infections; Endophthalmitis
• Other Study ID Numbers: NSIO

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