Comparison of Pulsed-field Gel Electrophoresis and Whole Genome Sequencing to Determine Transmission Rate of ESBL-producing E.Coli (PFGE-WGS)

June 6, 2023 updated by: University Hospital, Basel, Switzerland
The aim of this quality control study is to compare two different techniques to determine ESBL-producing E.coli transmission.

Study Overview

Status

Enrolling by invitation

Conditions

Intervention / Treatment

Detailed Description

Pulse-field gel electrophoresis (PFGE) was considered the reference standard to determine transmission events of extended-spectrum Beta-Lactamase (ESBL) producing E.coli . However, this technique lacks the resolution to differentiate closely related strains, which is needed to identify ESBL-transmission. Furthermore, PFGE is not able to distinguish mobile genetic elements. In contrast, whole genome sequencing (WGS) allows the identification of single-nucleotide polymorphisms (SNPs) that differentiate bacterial strains and mobile genetic elements, such as plasmids at the highest possible resolution, therefore enabling investigation of their relatedness by phylogenetic analyses and ultimately detailed exploration of transmission pathways. As WGS is now readily available and affordable, the investigators aim to reinvestigate transmission events in the 24 index-contact patient-pairs identified after cessation of contact precautions by reassessing the genetic relatedness of both strains and mobile genetic elements by sequencing all 48 recovered ESBL- E.coli strains.

The investigators hypothesize that the number of transmission events as defined by transmission of ESBL-producing E. coli strains may have been overestimated by PFGE as compared to WGS, as PFGE lacks the resolution to differentiate closely related strains. However, transmission of mobile genetic elements may have been missed by PFGE as this technology is not able to identify the genetic relatedness of plasmids, genes and other mobile genetic elements. Thus WGS may reveal additional transmission events defined as the transmission of mobile genetic elements.

Different sequencing approaches may yield different results in terms of detection of transmission events.

The investigators hypothesize that short-read sequencing may suffice to reliably detect relatedness of strains but that additional long-read sequencing approaches are needed to detect transmission of mobile genetic elements.

Study Type

Observational

Enrollment (Estimated)

48

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Locations

  • Switzerland
      • Basel, Switzerland, 4031
        • University Hospital Basel, Division of Infectious Diseases and Hospital Epidemiology

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Ages Eligible for Study

  • Child
  • Adult
  • Older Adult

Accepts Healthy Volunteers

No

Sampling Method

Probability Sample

Study Population

The patient population is defined as the 24 contact-index patient pairs identified during screening of contact patients after cessation of contact precautions during June 2012 to December 2013 at the University Hospital Basel and from January 2012 to December 2013 at the FELIX PLATTER-Hospital.

Description

Inclusion Criteria:

  • The patient population is defined as the 24 contact-index patient pairs identified during screening of contact patients after cessation of contact precautions as part of a quality control, performed from June 2012 to December 2013 at the University Hospital Basel and from January 2012 to December 2013 at the FELIX PLATTER-Hospital.

Exclusion Criteria:

  • Patients not meeting the above mentioned inclusion criteria.

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

Cohorts and Interventions

Group / Cohort
Intervention / Treatment
ESBL E.coli strains from 24 contact-index patients
48 ESBL-E. coli strains from 24 contact-index patients
Diagnostic test: Pulsed-field gel electrophoresis and whole genome sequencing
Comparison of the two different techniques
Other: Data collection
Demographic data (age, gender, hospital admission and discharge date, rooms and wards with dates of admission and discharge, hospitalization prior to current hospital stay, discharge destination, outcome, cause of death, travel history, recent hospitalization in an ESBL-high burden region, admission from another healthcare facility, admission from a long-term care facility, occupational or household contact to animals) Clinical data (date of diagnosis of ESBL-producing E. coli carriage, type of infection/colonization with ESBL- producing E. coli, comorbidities, Charlson Comorbidity Index, infectious diseases after detection of ESBL-PE, active open wounds, indwelling vascular devices, urinary catheterization) Treatment data (Immunosuppression, antibiotic therapy, concomitant medication and surgical therapy prior to and during hospital stay) Microbiological data

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Number of transmission events as determined by WGS
Time Frame: January 2012- December 2020
Transmission events will be categorized into transmission of strains and transmission of mobile genetic elements. The number of transmission events as determined by WGS will be compared to the number of transmission events as determined by PFGE. Patient-related characteristics and exposures will be compared between patients with and without transmission events.
January 2012- December 2020

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

University Hospital, Basel, Switzerland

Investigators

  • Principal Investigator: Sarah Tschudin Sutter, Prof. Dr. MD, University Hospital, Basel, Switzerland

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (Actual)

March 6, 2020

Primary Completion (Estimated)

December 31, 2024

Study Completion (Estimated)

December 31, 2024

Study Registration Dates

First Submitted

March 24, 2020

First Submitted That Met QC Criteria

March 24, 2020

First Posted (Actual)

March 26, 2020

Study Record Updates

Last Update Posted (Actual)

June 7, 2023

Last Update Submitted That Met QC Criteria

June 6, 2023

Last Verified

June 1, 2023

More Information

Terms related to this study

Other Study ID Numbers

  • 2020-00188

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

No

Studies a U.S. FDA-regulated device product

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

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