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

Study Overview
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Brief Summary
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The aim of this quality control study is to compare two different techniques to determine ESBL-producing E.coli transmission.

Detailed Description
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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.

Official Title
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Comparison of Pulsed-field Gel Electrophoresis and Whole Genome Sequencing to Determine Transmission Rate of ESBL-producing E.Coli

Conditions
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Analysis Transmission Rate

Intervention / Treatment
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* Diagnostic Test: Pulsed-field gel electrophoresis and whole genome sequencing
* Other: Data collection


Participation Criteria
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Eligibility Criteria
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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.
Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| ESBL E.coli strains from 24 contact-index patients<br>48 ESBL-E. coli strains from 24 contact-index patients | Diagnostic Test: Pulsed-field gel electrophoresis and whole genome sequencing<br>* Comparison of the two different techniques<br>Other: Data collection<br>* 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<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| 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. | January 2012- December 2020 |