5b0c93d304e1ef3b9898f81a54f31034  opeforinf_a2025m12v12n12pofa718.pdf
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7dda1e4257c15c9c07a45f71a21037cb35eb6d2939fc95efcd054c8f2e244008  opeforinf_a2025m12v12n12pofa718.pdf

Title:           Rapid Detection of VREfm Clusters: FTIR Spectroscopy as a Practical Alternative to Whole-Genome Sequencing
Subject:         DOI: 10.1093/ofid/ofaf718; Open Forum Infectious Diseases, 12, 12, 2025-11-24.; Abstract: Vancomycin-resistant Enterococcus faecium (VREfm) has become a significant nosocomial pathogen due to its potential to cause outbreaks. Whole-genome sequencing (WGS) is considered the reference method for determining genomic relatedness among outbreak strains, but its routine use in clinical microbiology laboratories remains challenging. Consequently, faster and simpler typing methods are needed. Fourier transform infrared spectroscopy (FTIR) captures the unique infrared fingerprint of each isolate, enabling the comparison of spectral profiles to infer genomic relatedness. In this study, we evaluated the performance of FTIR for identifying genomic clusters of VREfm in a tertiary hospital, in comparison with three WGS-based methods: core-genome multilocus sequence typing (cgMLST), core-genome single nucleotide polymorphism analysis (cgSNP), and split k-mer analysis (SKA). A total of 87 VREfm isolates, collected between April 2020 and October 2023, were typed using both FTIR and WGS. Among these, 56 were associated with three outbreaks in the surgery, nephrology, and oncohematology units, according to conventional epidemiology. Concordance between typing methods was assessed using the Adjusted Rand index (AR) and Adjusted Wallace coefficient (AW). All three WGS-based methods yielded similar clustering results and revealed one monoclonal and two polyclonal outbreaks. Using cgMLST as the reference, an optimal FTIR cutoff range of 0.210–0.227 was determined. FTIR clustering results showed strong concordance with WGS-based methods; however, concordance with SKA was slightly lower. These findings suggest that FTIR provides clustering information comparable to WGS-based methods, providing a rapid and practical alternative to support timely infection control measures during VREfm outbreaks.
Keywords:        cgSNP; FTIR; outbreak; SKA; vancomycin-resistant enterococcus faecium
Author:          Jun Hao Wang-Wang
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      Title: Rapid Detection of VREfm Clusters: FTIR Spectroscopy as a Practical Alternative to Whole-Genome Sequencing
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        Title: MATERIAL AND METHODS
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          Title: Study Design and Setting
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          Title: Routine Microbiological Diagnostics and Antimicrobial Susceptibility Testing
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          Title: Concordance Between Clustering Methodologies
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        Title: RESULTS
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          Title: Emergence of VREfm
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          Title: cgMLST and cgSNP Analysis
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          Title: SKA Clustering Reveals Little Subdivision Within cgMLST Clusters
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          Title: FTIR Largely Captures WGS Clusters and Reflects Epidemiological Outbreaks
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    Title: Rapid Detection of VREfm Clusters: FTIR Spectroscopy as a Practical Alternative to Whole-Genome Sequencing
    Author: Jun Hao Wang-Wang
    Subject: DOI: 10.1093/ofid/ofaf718; Open Forum Infectious Diseases, 12, 12, 2025-11-24.; Abstract: Vancomycin-resistant Enterococcus faecium (VREfm) has become a significant nosocomial pathogen due to its potential to cause outbreaks. Whole-genome sequencing (WGS) is considered the reference method for determining genomic relatedness among outbreak strains, but its routine use in clinical microbiology laboratories remains challenging. Consequently, faster and simpler typing methods are needed. Fourier transform infrared spectroscopy (FTIR) captures the unique infrared fingerprint of each isolate, enabling the comparison of spectral profiles to infer genomic relatedness. In this study, we evaluated the performance of FTIR for identifying genomic clusters of VREfm in a tertiary hospital, in comparison with three WGS-based methods: core-genome multilocus sequence typing (cgMLST), core-genome single nucleotide polymorphism analysis (cgSNP), and split k-mer analysis (SKA). A total of 87 VREfm isolates, collected between April 2020 and October 2023, were typed using both FTIR and WGS. Among these, 56 were associated with three outbreaks in the surgery, nephrology, and oncohematology units, according to conventional epidemiology. Concordance between typing methods was assessed using the Adjusted Rand index (AR) and Adjusted Wallace coefficient (AW). All three WGS-based methods yielded similar clustering results and revealed one monoclonal and two polyclonal outbreaks. Using cgMLST as the reference, an optimal FTIR cutoff range of 0.210 0.227 was determined. FTIR clustering results showed strong concordance with WGS-based methods; however, concordance with SKA was slightly lower. These findings suggest that FTIR provides clustering information comparable to WGS-based methods, providing a rapid and practical alternative to support timely infection control measures during VREfm outbreaks.
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  Checksum: d6f842a0
   Type: CRC32
  Checksum: 5b0c93d304e1ef3b9898f81a54f31034
   Type: MD5
  Checksum: 47ad0c4d56ae07b5a72983257a0ed641b188116b
   Type: SHA-1
  Checksum: 7dda1e4257c15c9c07a45f71a21037cb35eb6d2939fc95efcd054c8f2e244008
   Type: SHA-256