Analysis Transmission RatePFGE-WGSNCT04323553
Comparison of Pulsed-field Gel Electrophoresis and Whole Genome Sequencing to Determine Transmission Rate of ESBL-producing E.Coli
An observational study of Analysis Transmission Rate, run by University Hospital, Basel, Switzerland at 1 site in Switzerland.
Trial summary
The aim of this quality control study is to compare two different techniques to determine ESBL-producing E.coli transmission. Read more about this study
- Who is it for?
- Any age
- Conditions the study is for
- Analysis Transmission Rate
- What is being tested?
- Pulsed-field gel electrophoresis and whole genome sequencing and Data collection
- How many people
- 43 participants
- Where
- 1 siteSwitzerland
- Study dates
- 6 Mar 2020to 7 Jan 2025
- Phase
- Observational
- Are there results?
- None posted in the registry
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages Any age
- All sexes
- No healthy volunteers
- Child, Adult, Older adult
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.
Who may be able to join
- 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.
Who cannot join
- Patients not meeting the above mentioned inclusion criteria.
Trial locations and contacts
1 site in 1 country.
Switzerland1 site
University Hospital Basel, Division of Infectious Diseases and Hospital Epidemiology
Basel, 4031
About this study
The aim of this quality control study is to compare two different techniques to determine ESBL-producing E.coli transmission.
Read the 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.
- Conditions
- Analysis Transmission Rate
- Being tested
- Pulsed-field gel electrophoresis and whole genome sequencing, Data collection
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
Pulsed-field gel electrophoresis and whole genome sequencingDiagnostic test
Comparison of the two different techniques
Data collectionOther
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
| Study group | Role | What they receive |
|---|---|---|
| ESBL E.coli strains from 24 contact-index patients | 48 ESBL-E. coli strains from 24 contact-index patients Receives: Diagnostic Test: Pulsed-field gel electrophoresis and whole genome sequencing; Other: Data collection |
What is being measured
The primary outcome is the main question the study is designed to answer.
Number of transmission events as determined by WGS
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.
Measured: January 2012- December 2020
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted26 Mar 2020
- Study start6 Mar 2020
- Primary completion7 Jan 2025
- Study completion7 Jan 2025
Why it stopped: This study is no longer of interested as one of the technology used is already outdated.
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Other trials for Analysis Transmission RateStudies of the same condition, open and under way.
- More trials run by University Hospital, Basel, SwitzerlandThe sponsor's other registered studies.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Observational
- Observational model
- Other
- Time perspective
- Retrospective
- Enrolment
- 43 participants (actual)
Sponsor and investigators
- Lead sponsor
- University Hospital, Basel, Switzerland
- Sponsor type
- University, hospital or other
- Responsible party
- Sponsor
- Investigators
- Sarah Tschudin Sutter, Prof. Dr. MD, Principal investigator, University Hospital, Basel, Switzerland
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT04323553
- Sponsor's protocol ID
- 2020-00188
- Acronym
- PFGE-WGS
- Status last verified
- Jan 2025
- First submitted
- 24 Mar 2020
- Last updated
- 15 Jan 2025
- Results posted
- No
- Data monitoring committee
- No
- FDA-regulated drug
- No
- FDA-regulated device
- No
Study at a glance
From the registry record, last updated by the sponsor on 15 Jan 2025. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Comparison of Pulsed-field Gel Electrophoresis and Whole Genome Sequencing to Determine Transmission Rate of ESBL-producing E.Coli
- ClinicalTrials.gov ID
- NCT04323553
- Acronym / sponsor ID
- PFGE-WGS / 2020-00188
- Conditions
- Analysis Transmission Rate
- Study type
- Observational
- Recruitment status
- TerminatedReason stopped: This study is no longer of interested as one of the technology used is already outdated.
- Enrolment
- 43 participants (actual)
- Lead sponsor
- University Hospital, Basel, SwitzerlandUniversity, hospital or other
- Study start
- 6 Mar 2020 (actual)
- Primary completion
- 7 Jan 2025 (actual)
- Study completion
- 7 Jan 2025 (actual)
- First posted
- 26 Mar 2020 (actual)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
The aim of this quality control study is to compare two different techniques to determine ESBL-producing E.coli transmission.
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 design
- Observational model
- Other
- Time perspective
- Retrospective
- Number of arms
- 1
| Arm | Type | Receives |
|---|---|---|
| ESBL E.coli strains from 24 contact-index patients | – | Diagnostic Test: Pulsed-field gel electrophoresis and whole genome sequencing, Other: Data collection48 ESBL-E. coli strains from 24 contact-index patients |
Who may qualify
- Sex
- All
- Healthy volunteers
- Not accepted
- Age groups
- Child, Adult, Older adult
- 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.
Key inclusion criteria (1 listed)
- 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.
Key exclusion criteria (1 listed)
- Patients not meeting the above mentioned inclusion criteria.
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Interventions
| Intervention | Type | Arms |
|---|---|---|
| Pulsed-field gel electrophoresis and whole genome sequencingComparison of the two different techniques | Diagnostic test | ESBL E.coli strains from 24 contact-index patients |
| Data collectionDemographic 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 | Other | ESBL E.coli strains from 24 contact-index patients |
Primary outcome
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.
Results and safety
The study was stopped early (reason given: This study is no longer of interested as one of the technology used is already outdated.). Results are not available in the source record.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 15 Jan 2025.
Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part. This study is not recruiting at the moment.
Sarah Tschudin Sutter, Prof. Dr. MD principal investigator
University Hospital, Basel, Switzerland
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
An observational study of Analysis Transmission Rate, run by University Hospital, Basel, Switzerland at 1 site in Switzerland.
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
The sponsor lists 1 inclusion and 1 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: stopped early, as of the sponsor's last update on 15 Jan 2025. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 1 site in Switzerland. Whether a site is taking part right now should be confirmed with that site. See every site.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
Are results available for this study?
The study was stopped early (reason given: This study is no longer of interested as one of the technology used is already outdated.). Results are not available in the source record.
How can a doctor refer a patient or contact the research team?
The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Number of transmission events as determined by WGS (time frame: January 2012- December 2020). It is what the study was designed to measure, not a finding.
Where can I read the original study information?
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 15 Jan 2025.