Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation
ABSTRACT Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are causing nosocomial infections and outbreaks. Bacterial typing methods are used to assist in outbreak investigations. Most of them, especially genotypic methods like multi-locus sequence typing (MLST), whole genome se...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2023-10-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.00984-23 |
| _version_ | 1797658209750614016 |
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| author | T. C. Scheier J. Franz M. Boumasmoud F. Andreoni B. Chakrakodi B. Duvnjak A. Egli W. Zingg A. Ramette A. Wolfensberger R. D. Kouyos S. D. Brugger |
| author_facet | T. C. Scheier J. Franz M. Boumasmoud F. Andreoni B. Chakrakodi B. Duvnjak A. Egli W. Zingg A. Ramette A. Wolfensberger R. D. Kouyos S. D. Brugger |
| author_sort | T. C. Scheier |
| collection | DOAJ |
| description | ABSTRACT Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are causing nosocomial infections and outbreaks. Bacterial typing methods are used to assist in outbreak investigations. Most of them, especially genotypic methods like multi-locus sequence typing (MLST), whole genome sequencing (WGS), or pulsed-field gel electrophoresis, are quite expensive and time-consuming. Fourier-transform infrared (FT-IR) spectroscopy assesses the biochemical composition of bacteria, such as carboxyl groups in polysaccharides. It is an affordable technique and has a faster turnaround time. Thus, the aim of this study was to evaluate FT-IR spectroscopy for VREfm outbreak investigations. Basic performance requirements like reproducibility and the effects of incubation time were assessed in distinct sample sets. After determining a FT-IR spectroscopy cut-off range, the clustering agreement between FT-IR and WGS within a retrospective (n: 92 isolates) and a prospective outbreak (n: 15 isolates) was investigated. For WGS an average nucleotide identity (ANI) cut-off score of 0.999 was used. Basic performance analysis showed reproducible results. Moreover, FT-IR spectroscopy readouts showed a high agreement with WGS-ANI analysis in clinical outbreak investigations (V-measure 0.772 for the retrospective and 1.000 for the prospective outbreak). FT-IR spectroscopy had a higher discriminatory power than MLST in the outbreak investigations. After determining cut-off values to achieve optimal resolution, FT-IR spectroscopy is a promising technique to assist in outbreak investigation as an affordable, easy-to-use tool with a turnaround time of less than one day. IMPORTANCE Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are a frequent cause of nosocomial outbreaks. Several bacterial typing methods are used to track transmissions and investigate outbreaks, whereby genome-based techniques are used as a gold standard. Current methods are either expensive, time-consuming, or both. Additionally, often, specifically trained staff needs to be available. This study provides insight into the use of Fourier-transform infrared (FT-IR) spectroscopy, an affordable, easy-to-use tool with a short turnaround time as a typing method for VREfm. By assessing clinical samples, this work demonstrates promising results for species discrimination and reproducibility. FT-IR spectrosopy shows a high level of agreement in the analysis of VREfm outbreaks in comparison with whole genome sequencing-based methods. |
| first_indexed | 2024-03-11T17:55:54Z |
| format | Article |
| id | doaj.art-3953d3b0973945979da921a515ae3568 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-03-11T17:55:54Z |
| publishDate | 2023-10-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-3953d3b0973945979da921a515ae35682023-10-17T13:04:35ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972023-10-0111510.1128/spectrum.00984-23Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigationT. C. Scheier0J. Franz1M. Boumasmoud2F. Andreoni3B. Chakrakodi4B. Duvnjak5A. Egli6W. Zingg7A. Ramette8A. Wolfensberger9R. D. Kouyos10S. D. Brugger11Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich , Zurich, SwitzerlandDepartment of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich , Zurich, SwitzerlandDepartment of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich , Zurich, SwitzerlandDepartment of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich , Zurich, SwitzerlandDepartment of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich , Zurich, SwitzerlandDepartment of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich , Zurich, SwitzerlandInstitute of Medical Microbiology, University of Zurich , Zurich, SwitzerlandDepartment of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich , Zurich, SwitzerlandInstitute for Infectious Diseases, University of Bern , Bern, SwitzerlandDepartment of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich , Zurich, SwitzerlandDepartment of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich , Zurich, SwitzerlandDepartment of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich , Zurich, SwitzerlandABSTRACT Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are causing nosocomial infections and outbreaks. Bacterial typing methods are used to assist in outbreak investigations. Most of them, especially genotypic methods like multi-locus sequence typing (MLST), whole genome sequencing (WGS), or pulsed-field gel electrophoresis, are quite expensive and time-consuming. Fourier-transform infrared (FT-IR) spectroscopy assesses the biochemical composition of bacteria, such as carboxyl groups in polysaccharides. It is an affordable technique and has a faster turnaround time. Thus, the aim of this study was to evaluate FT-IR spectroscopy for VREfm outbreak investigations. Basic performance requirements like reproducibility and the effects of incubation time were assessed in distinct sample sets. After determining a FT-IR spectroscopy cut-off range, the clustering agreement between FT-IR and WGS within a retrospective (n: 92 isolates) and a prospective outbreak (n: 15 isolates) was investigated. For WGS an average nucleotide identity (ANI) cut-off score of 0.999 was used. Basic performance analysis showed reproducible results. Moreover, FT-IR spectroscopy readouts showed a high agreement with WGS-ANI analysis in clinical outbreak investigations (V-measure 0.772 for the retrospective and 1.000 for the prospective outbreak). FT-IR spectroscopy had a higher discriminatory power than MLST in the outbreak investigations. After determining cut-off values to achieve optimal resolution, FT-IR spectroscopy is a promising technique to assist in outbreak investigation as an affordable, easy-to-use tool with a turnaround time of less than one day. IMPORTANCE Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are a frequent cause of nosocomial outbreaks. Several bacterial typing methods are used to track transmissions and investigate outbreaks, whereby genome-based techniques are used as a gold standard. Current methods are either expensive, time-consuming, or both. Additionally, often, specifically trained staff needs to be available. This study provides insight into the use of Fourier-transform infrared (FT-IR) spectroscopy, an affordable, easy-to-use tool with a short turnaround time as a typing method for VREfm. By assessing clinical samples, this work demonstrates promising results for species discrimination and reproducibility. FT-IR spectrosopy shows a high level of agreement in the analysis of VREfm outbreaks in comparison with whole genome sequencing-based methods.https://journals.asm.org/doi/10.1128/spectrum.00984-23FT-IR spectroscopyIR Biotypervancomycin-resistant enterococcioutbreak investigation |
| spellingShingle | T. C. Scheier J. Franz M. Boumasmoud F. Andreoni B. Chakrakodi B. Duvnjak A. Egli W. Zingg A. Ramette A. Wolfensberger R. D. Kouyos S. D. Brugger Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation Microbiology Spectrum FT-IR spectroscopy IR Biotyper vancomycin-resistant enterococci outbreak investigation |
| title | Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation |
| title_full | Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation |
| title_fullStr | Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation |
| title_full_unstemmed | Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation |
| title_short | Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation |
| title_sort | fourier transform infrared spectroscopy for typing of vancomycin resistant enterococcus faecium performance analysis and outbreak investigation |
| topic | FT-IR spectroscopy IR Biotyper vancomycin-resistant enterococci outbreak investigation |
| url | https://journals.asm.org/doi/10.1128/spectrum.00984-23 |
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