Genomic insights into vanA- and vanM-positive Enterococcus faecium.
- 1Department of Laboratory Medicine, Children's Hospital, National Clinical Research Center for Children and Adolescents' Health and Diseases, Zhejiang University School of Medicine, No. 3333 Binsheng road, Hangzhou, Zhejiang Province, China.
- 2Department of Laboratory Medicine, Children's Hospital, National Clinical Research Center for Children and Adolescents' Health and Diseases, Zhejiang University School of Medicine, No. 3333 Binsheng road, Hangzhou, Zhejiang Province, China. [email protected].
- 3Department of Laboratory Medicine, Children's Hospital, National Clinical Research Center for Children and Adolescents' Health and Diseases, Zhejiang University School of Medicine, No. 3333 Binsheng road, Hangzhou, Zhejiang Province, China. [email protected].
Abstract
Background
Enterococcus faecium (E. faecium) co-harboring the vanA and vanM genes is an emerging multidrug-resistant pathogen mediating high-level vancomycin resistance, yet its epidemiological and genomic characteristics remain poorly understood, creating critical knowledge gaps for clinical infection control and the management of high-risk patient populations. Using a clinical isolate from a pediatric patient and publicly available genomes from the National Center for Biotechnology Information (NCBI) database, this study aimed to elucidate the genomic features, phylogenetic relationships, and genetic context of the resistance gene clusters in vanA- and vanM-positive E. faecium.Methods
Complete genome sequencing was performed on 24VR2004. Comparative analysis included 97 NCBI-sourced vanA- and vanM-positive genomes. Resistance/virulence genes were analyzed via CARD/VFDB databases; phylogenetic analysis and resistance gene cluster genetic context analysis were conducted.Results
24VR2004 (ST80, CC17) had vancomycin MIC > 256 µg/mL, 23 resistance genes, 15 virulence genes. Its vanA (intact, Tn1546-M97297.1) and vanM (vanX-in-vanM-cl-deleted, flanked by IS1216E/ISEfa4) were on different plasmids. Among the total 98 isolates analyzed (our clinical isolate 24VR2004 and 97 NCBI-derived genomes), all originated from Asia, with 60.2% recovered from urine samples. ST555 was the predominant sequence type, accounting for 56.1% of the cohort, and strain 24VR2004 was phylogenetically closely related to two ST80 isolates from Guangdong, China. Three complete genomes had plasmid-borne vanA and vanM: two (24VR2004, GCA_053011635.1) on separate plasmids, one (GCA_023658035.1) on one plasmid. vanA clusters in all three were within Tn1546-like transposons (intact in 24VR2004's p24VR2004_P3 and GCA_053011635.1's CP172562.1), while CP058893.1's vanA clusters lacked vanY_in_vanA_cl and vanZ_in_vanA_cl but had a duplicated vanX_in_vanA_cl downstream. All vanM clusters lacked vanX_in_vanM_cl; p24VR2004_P2's vanM clusters had IS1216E upstream and ISEfa4 downstream, others only IS1216E upstream.Conclusion
All vanA- and vanM-positive E. faecium isolates included in this study are geographically restricted to Asia, with ST555 as the predominant sequence type. Plasmid-borne dual resistance clusters, mediated by Tn1546-like transposons and IS1216E, drive their dissemination. This study provides preliminary genomic evidence regarding the dissemination and genetic context of vanA- and vanM-positive E. faecium and may support future surveillance and infection control efforts for high-risk populations.
Related
- High Prevalence of vanA‐Positive Vancomycin‐Resistant Enterococcus faecalis and Enterococcus faecium: Antibiotic Resistance, Biofilm Formation, and Virulence Profiles
- Limited, outbreak-biased and unevenly reported: genomic insights into vancomycin-resistant Enterococcus faecium in Germany as reported between 2015 and 2025
- Recombination and accessory genome turnover shaped the rise and decline of vanA Enterococcus faecium ST80 in Denmark.
- Genomic insight into Enterococcus faecium biofilm formation isolated from catheter associated urinary tract infection
- Risk Factors and Outcomes of Vancomycin-Resistant Enterococcus faecium Bloodstream Infection in Hematologic Malignancies and Stem Cell Transplant Recipients: A Case-Control Study
BibTeX
@article{fang2026genomic,
title = {{Genomic insights into vanA- and vanM-positive Enterococcus faecium.}},
author = {Chao Fang and Zheng Zhou and Xiucai Zhang and Jintao Xia and Shixing Liu and Yining Zhao and Shiqiang Shang and Mingming Zhou},
journal = {BMC microbiology},
year = {2026},
month = aug,
doi = {10.1186/s12866-026-05483-w},
url = {https://europepmc.org/article/MED/42958470},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Genomic insights into vanA- and vanM-positive Enterococcus faecium.
AU - Chao Fang
AU - Zheng Zhou
AU - Xiucai Zhang
AU - Jintao Xia
AU - Shixing Liu
AU - Yining Zhao
AU - Shiqiang Shang
AU - Mingming Zhou
PY - 2026
DA - 2026/08/01
JO - BMC microbiology
DO - 10.1186/s12866-026-05483-w
UR - https://europepmc.org/article/MED/42958470
AB - Background Enterococcus faecium (E. faecium) co-harboring the vanA and vanM genes is an emerging multidrug-resistant pathogen mediating high-level vancomycin resistance, yet its epidemiological and genomic characteristics remain poorly understood, creating critical knowledge gaps for clinical infection control and the management of high-risk patient populations. Using a clinical isolate from a pediatric patient and publicly available genomes from the National Center for Biotechnology Information (NCBI) database, this study aimed to elucidate the genomic features, phylogenetic relationships, and genetic context of the resistance gene clusters in vanA- and vanM-positive E. faecium.Methods Complete genome sequencing was performed on 24VR2004. Comparative analysis included 97 NCBI-sourced vanA- and vanM-positive genomes. Resistance/virulence genes were analyzed via CARD/VFDB databases; phylogenetic analysis and resistance gene cluster genetic context analysis were conducted.Results 24VR2004 (ST80, CC17) had vancomycin MIC > 256 µg/mL, 23 resistance genes, 15 virulence genes. Its vanA (intact, Tn1546-M97297.1) and vanM (vanX-in-vanM-cl-deleted, flanked by IS1216E/ISEfa4) were on different plasmids. Among the total 98 isolates analyzed (our clinical isolate 24VR2004 and 97 NCBI-derived genomes), all originated from Asia, with 60.2% recovered from urine samples. ST555 was the predominant sequence type, accounting for 56.1% of the cohort, and strain 24VR2004 was phylogenetically closely related to two ST80 isolates from Guangdong, China. Three complete genomes had plasmid-borne vanA and vanM: two (24VR2004, GCA_053011635.1) on separate plasmids, one (GCA_023658035.1) on one plasmid. vanA clusters in all three were within Tn1546-like transposons (intact in 24VR2004's p24VR2004_P3 and GCA_053011635.1's CP172562.1), while CP058893.1's vanA clusters lacked vanY_in_vanA_cl and vanZ_in_vanA_cl but had a duplicated vanX_in_vanA_cl downstream. All vanM clusters lacked vanX_in_vanM_cl; p24VR2004_P2's vanM clusters had IS1216E upstream and ISEfa4 downstream, others only IS1216E upstream.Conclusion All vanA- and vanM-positive E. faecium isolates included in this study are geographically restricted to Asia, with ST555 as the predominant sequence type. Plasmid-borne dual resistance clusters, mediated by Tn1546-like transposons and IS1216E, drive their dissemination. This study provides preliminary genomic evidence regarding the dissemination and genetic context of vanA- and vanM-positive E. faecium and may support future surveillance and infection control efforts for high-risk populations.
SN - 1471-2180
ER -