| Summary: |
Early detection of high-risk Escherichia coli clones producing extended-spectrum β-lactamase (ESBL) and/or
carbapenemase in hospitals is key for preventing extended transmission chains and poor clinical outcomes.
Whole genome sequencing (WGS) is the reference method to support infection control, but still not suitable
for real-time analysis of multidrug resistant (MDR) bacteria in many settings. Fourier transform infrared (FTIR)
spectroscopy has proven potential to support outbreak detection and interruption of transmission chains
due to its fast and reliable accuracy for strain typing in several clinically relevant pathogens, but only a small
number of E. coli isolates have been tested. We aim to develop and validate an accurate and reproducible
workflow for real-time screening and identification of MDR E. coli high-risk clones based on FT-IR
spectroscopy, using WGS as reference.
Supported by a network of experts in E. coli, strain typing and FT-IR spectroscopy (PT, DE, NO, SP), and
previous knowledge and experience with K. pneumoniae, we will use representative and well-characterized
collections of E. coli outbreak and non-outbreak isolates from reference public health institutes in Europe
(n=600, 2015-2022) to train and validate a machine-learning classification model for real-time screening and
identification of MDR E. coli high-risk clones based on FT-IR spectroscopy, including an inter-institutional
comparison. For that, a correlation will be established between FT-IR spectra from different instruments,
core genome multi-locus sequence typing (cgMLST)/in silico serotyping and epidemiological data to support
guidance, recommendations and protocols for the use of the technology to support outbreak detection and
infection control and improve surveillance of MDR E. coli in Europe. All partners will be involved in a training
workshop in FT-IR analysis and all data will be made available to the scientific community. This will
strengthen fu  |
Summary
Early detection of high-risk Escherichia coli clones producing extended-spectrum β-lactamase (ESBL) and/or
carbapenemase in hospitals is key for preventing extended transmission chains and poor clinical outcomes.
Whole genome sequencing (WGS) is the reference method to support infection control, but still not suitable
for real-time analysis of multidrug resistant (MDR) bacteria in many settings. Fourier transform infrared (FTIR)
spectroscopy has proven potential to support outbreak detection and interruption of transmission chains
due to its fast and reliable accuracy for strain typing in several clinically relevant pathogens, but only a small
number of E. coli isolates have been tested. We aim to develop and validate an accurate and reproducible
workflow for real-time screening and identification of MDR E. coli high-risk clones based on FT-IR
spectroscopy, using WGS as reference.
Supported by a network of experts in E. coli, strain typing and FT-IR spectroscopy (PT, DE, NO, SP), and
previous knowledge and experience with K. pneumoniae, we will use representative and well-characterized
collections of E. coli outbreak and non-outbreak isolates from reference public health institutes in Europe
(n=600, 2015-2022) to train and validate a machine-learning classification model for real-time screening and
identification of MDR E. coli high-risk clones based on FT-IR spectroscopy, including an inter-institutional
comparison. For that, a correlation will be established between FT-IR spectra from different instruments,
core genome multi-locus sequence typing (cgMLST)/in silico serotyping and epidemiological data to support
guidance, recommendations and protocols for the use of the technology to support outbreak detection and
infection control and improve surveillance of MDR E. coli in Europe. All partners will be involved in a training
workshop in FT-IR analysis and all data will be made available to the scientific community. This will
strengthen fundamental and applied knowledge on FT-IR spectroscopy and set the scene for an expert
network within and beyond ESGEM/ESGMD-ESCMID to support innovation and large-scale/cross-country
FT-IR applications in Europe. Funding is requested for exchange of test strains, FT-IR experiments and onsite
visits. |