Molecular Diagnostics of Bacterial Infections and Antibiotic Resistance in Blood Samples and Rectal Swabs Using Advanced NGS Sequencing Methods (ARES_NGS)

This is an experimental study without drug and device, non-profit, on biological samples stored at the Tropica Biobank of the DITM. The aim of the project is to verify the performance of NGS-based assays, which can be used in the field of microbiology. The clinical evaluation investigations of NGS technology will be conducted on an adequate number of clinical blood samples and rectal swabs. The analyzes will be compared with the standard microbiology methods used in the DITM diagnostic routine.

Study Overview

• Status: Recruiting
• Conditions: Resistance Bacterial
• Intervention / Treatment: Diagnostic test: NGS Analysis

• Study Type: Interventional
• Enrollment (Estimated): 100
• Phase: Not Applicable

Contacts and Locations

Study Locations

• Italy
  • Verona
    • Negrar, Verona, Italy, 37024
      • Recruiting
      • IRCCS Sacro Cuore Don Calabria hospital
      • Contact: Elena Pomari; Phone Number: +390456013111; Email: elena.pomari@sacrocuore.it
      • Principal Investigator: Elena Pomari
      • Sub-Investigator: Pierantonio Orza
      • Sub-Investigator: Francesca Perandin

Participation Criteria

Eligibility Criteria

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

Description

Inclusion criteria:

• Samples of patients for whom blood culture and Multi Drug Resistant (MDR) surveillance tests were carried out in rectal swabs at the IRCCS Sacro Cuore Don Calabria Hospital
• Samples for which the Information and consent to the conservation of biological samples for research purposes has been signed at the Tropica Biobank or
• Samples for which, after all reasonable efforts, it was not possible to obtain the signature of the Information and consent to the conservation of biological samples for research purposes at the Tropica Biobank (e.g. patients in intensive care, immobilized patients unable to sign or with serious alterations of consciousness).

Exclusion criteria:

• Absence of data relating to positivity or negativity to the germs of interest
• Absence of stored residual material

Study Plan

How is the study designed?

Design Details

• Primary Purpose: Diagnostic
• Allocation: N/A
• Interventional Model: Single Group Assignment
• Masking: None (Open Label)

Number of Arms

1

Arms and Interventions

Participant Group / Arm

Intervention / Treatment

Other: NGS analysis; Residual anonymized samples stored at -80°C at the Tropica Biobank of the DITM and for which diagnostic analysis for germ infection has previously been carried out at the DITM by blood culture and MDR surveillance in routine diagnostic rectal swab will be used. DNA extraction will be carried out on these residual samples (with subsequent quality and quantification analysis of the nucleic acid) for subsequent NGS analyses.

Diagnostic test: NGS Analysis; An analytical pipeline with NGS technology developed in the GENRES study will be used for the identification of infecting microorganisms and the drug resistance they carry. For this purpose, a sequencing method will be identified and adopted that can obtain gene sequences of approximately 75 bp in length and on the Illumina MiSeq platform. Furthermore, IT software and bioinformatics analyzes with specific quality control parameters (pre- and post-alignment of reads) will be identified and adopted in order to develop an IVD system that includes a complete package of sequencing kits and software.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Microorganism presence (positive/negative)	Microorganism presence identified by NGS technology.	Baseline
Microorganism identification	Microorganism identification obtained using NGS technology.	Baseline

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Identification of Gene mutations that convey resistance to antibiotics (resistant/susceptible)	Results (resistant/susceptible) obtained using NGS technology in the identification of gene mutations that convey resistance to antibiotics.	Baseline

Collaborators and Investigators

• Sponsor: IRCCS Sacro Cuore Don Calabria di Negrar

Study record dates

Study Major Dates

• Study Start (Actual): June 28, 2022
• Primary Completion (Estimated): December 1, 2024
• Study Completion (Estimated): December 1, 2024

Study Registration Dates

• First Submitted: March 6, 2024
• First Submitted That Met QC Criteria: March 13, 2024
• First Posted (Actual): March 20, 2024

Study Record Updates

• Last Update Posted (Actual): March 20, 2024
• Last Update Submitted That Met QC Criteria: March 13, 2024
• Last Verified: March 1, 2024

More Information

Terms related to this study

• Additional Relevant MeSH Terms: Infections; Bacterial Infections and Mycoses; Bacterial Infections
• Other Study ID Numbers: 2022-13

Drug and device information, study documents

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