Frontiers in microbiology · 2026
Genomic characterization of vancomycin-resistant Enterococcus faecium and van-carrying mobile genetic elements in a tertiary hospital in northeastern China.
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Yao Han, Wang Jiaxin, Dong Rongrong, Yi Wenjing, Zhang Meng, Zhu Ning, Jia Shanshan, Wu Ruihong, Guo Xiaohan, Dong Tingting, Peng Zhihan, Jiang Lili, Li Wei, Yang Chun, Yuan Mengyao, Guan Qingtian, Xu Jiancheng
Аннотация
BACKGROUND: Vancomycin resistant Enterococcus faecium (VREfm) poses a significant healthcare challenge due to its multidrug resistance and genomic plasticity. Vancomycin resistance is commonly mediated by van gene clusters located on transposons, which are often associated with plasmids.
METHODS: 19 VREfm isolates were collected from different departments of the First Hospital of Jilin University between 2019 and 2024. Whole-genome sequencing (WGS) was performed on the strains for comprehensive genomic analysis. Multilocus sequence typing (MLST) was used to determine the sequence types of the strains. Plasmids were grouped based on Mash distance, and plasmid content was analyzed using the MOB-suite tool. Genome-wide comparisons and average nucleotide identity (ANI) analysis were conducted using FastANI. The TnCentral database was used to analyze resistance-associated transposons. The objective was to characterize the genomic diversity of VREfm isolates and the genetic contexts of van-carrying plasmids and transposons.
RESULTS: Among the 19 VREfm isolates, vanA was detected in 16 isolates, while vanM was identified in 3 isolates. MLST analysis revealed five sequence types (ST17, ST68, ST78, ST80, and ST547) with distinct temporal distributions. ST17 and ST68 were more frequently observed among isolates collected between 2019 and 2022, whereas ST78 was more common among isolates collected in 2023-2024 and was associated with multiple plasmid types. These observations suggest differences in lineage composition and plasmid backgrounds across the sampling period. Plasmidome analysis identified 19 plasmid groups, with resistance genes mainly concentrated in four major groups, some of which were shared across different sequence types. Notably, several resistance plasmids lacked functional replicons, suggesting plasmid fragmentation events. Transposon analysis revealed substantial structural diversity among Tn1546 variants, including insertions, deletions, and rearrangements, highlighting the complexity of vanA- and vanM-associated mobile genetic elements across different plasmid and clonal backgrounds.
CONCLUSION: This study provides genomic insights into the diversity and relatedness of VREfm isolates in a tertiary hospital over a 5-year period. The findings describe the diversity of sequence types, plasmid backbones, and van-associated mobile genetic elements within this hospital collection.
METHODS: 19 VREfm isolates were collected from different departments of the First Hospital of Jilin University between 2019 and 2024. Whole-genome sequencing (WGS) was performed on the strains for comprehensive genomic analysis. Multilocus sequence typing (MLST) was used to determine the sequence types of the strains. Plasmids were grouped based on Mash distance, and plasmid content was analyzed using the MOB-suite tool. Genome-wide comparisons and average nucleotide identity (ANI) analysis were conducted using FastANI. The TnCentral database was used to analyze resistance-associated transposons. The objective was to characterize the genomic diversity of VREfm isolates and the genetic contexts of van-carrying plasmids and transposons.
RESULTS: Among the 19 VREfm isolates, vanA was detected in 16 isolates, while vanM was identified in 3 isolates. MLST analysis revealed five sequence types (ST17, ST68, ST78, ST80, and ST547) with distinct temporal distributions. ST17 and ST68 were more frequently observed among isolates collected between 2019 and 2022, whereas ST78 was more common among isolates collected in 2023-2024 and was associated with multiple plasmid types. These observations suggest differences in lineage composition and plasmid backgrounds across the sampling period. Plasmidome analysis identified 19 plasmid groups, with resistance genes mainly concentrated in four major groups, some of which were shared across different sequence types. Notably, several resistance plasmids lacked functional replicons, suggesting plasmid fragmentation events. Transposon analysis revealed substantial structural diversity among Tn1546 variants, including insertions, deletions, and rearrangements, highlighting the complexity of vanA- and vanM-associated mobile genetic elements across different plasmid and clonal backgrounds.
CONCLUSION: This study provides genomic insights into the diversity and relatedness of VREfm isolates in a tertiary hospital over a 5-year period. The findings describe the diversity of sequence types, plasmid backbones, and van-associated mobile genetic elements within this hospital collection.