# Characterization of Enterococcus faecium Based on Multi-Omics Approaches: Genomic, Transcriptomic, and Phenotypic Analyses

## TL;DR

This study characterizes an Enterococcus faecium strain from yak feces, revealing its genetic and pathogenic similarities to human strains and its potential public health risks.

## Contribution

The study provides a comprehensive multi-omics analysis of an animal-derived E. faecium strain, elucidating its pathogenic mechanisms and cross-host transmission potential.

## Key findings

- The yak-derived E. faecium strain is closely related to human clinical isolates, indicating a risk of cross-host transmission.
- The strain exhibits resistance to multiple antibiotics and harbors key virulence genes.
- Transcriptomic analysis reveals a 'Recognition–Response–Damage' signaling pathway activated during infection.

## Abstract

Enterococcus faecium has emerged as a critical pathogen in hospital-acquired infections worldwide. This bacterium not only exhibits inherent resilience but also possesses a remarkable capacity to acquire antimicrobial resistance genes, posing a serious challenge to public health. Beyond clinical settings, E. faecium is widely distributed in animals and natural environments, serving as a reservoir for antimicrobial resistance genes and virulence factors, thereby contributing to persistent risks of cross-species transmission. In this study, a bacterial strain was isolated from yak feces collected on the Qinghai–Tibet Plateau and was characterized as E. faecium. We aim to systematically investigate its phylogenetic relationship with human-derived strains, its antimicrobial resistance phenotypes and genetic determinants, and its virulence potential through an integrated multi-omics approach encompassing genomics, transcriptomics, and phenotypic assays. Furthermore, we seek to fully elucidate the pathogenic signaling pathway from host recognition to tissue injury. Our findings provide critical evidence for assessing the public health risks associated with animal-derived E. faecium and offer novel theoretical insights into its pathogenic mechanisms.

Animal-derived E. faecium poses a public health risk due to its capacity to acquire antimicrobial resistance (AMR) and virulence genes. However, the pathogenicity and cross-host transmission potential of strains originating from unique environments, such as the Qinghai–Tibet Plateau, remain poorly understood. In this study, a strain of E. faecium was isolated from yak feces. We constructed a phylogenetic tree and identified AMR and virulence genes via whole-genome sequencing. Antimicrobial susceptibility testing was performed to determine its resistance phenotype. An in vivo mouse infection model was established to assess pathogenicity, and transcriptomic analysis was utilized to investigate the host’s molecular response mechanisms in infected intestinal tissue. The results indicated that this yak-derived strain is closely related to human clinical isolates, suggesting a risk of cross-host transmission. The strain harbored the AMR genes AAC(6′)-Ii, msrC, and eatAv and exhibited resistance to penicillin, kanamycin, erythromycin, and clindamycin. The strain harbored key virulence genes, such as bopD, Acm, and ClpP. Infection with this strain caused characteristic inflammatory damage in mouse intestinal tissue, as revealed by histopathological examination, including epithelial necrosis, vascular congestion, and inflammatory cell infiltration. Transcriptomics further delineated a complete “Recognition–Response–Damage” signaling axis: pathogen recognition through Toll-like receptors and NOD-like receptors activates the NF-κB and MAPK signaling pathways. This activation is accompanied by significant upregulation of various inflammatory factors and recruits immune cells via chemokine signaling, ultimately leading to tissue damage. Our findings provide insights into the pathogenic pathway of this strain from genetic determinants to phenotypic manifestations, providing a theoretical foundation for assessing the public health risk posed by animal-derived E. faecium and for developing targeted intervention strategies.