Genomic insights into vanA- and vanM-positive Enterococcus faecium

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.

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.

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.

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.