Phenotypic and Molecular Characterization of Clinical Isolates of Vancomycin-Resistant Enterococcus faecium in the Health District of Bolzano (Italy) During 2021–2023

TL;DR

This study analyzed 44 vancomycin-resistant Enterococcus faecium isolates from Italy to understand their antibiotic resistance and genetic makeup.

Contribution

The study provides a detailed genomic and phenotypic characterization of VREfm isolates in a specific Italian health district.

Findings

Most isolates had the VanA phenotype and vanHAX genotype, with high resistance to multiple antibiotics.

Two isolates showed linezolid resistance due to genetic mutations or transferable resistance genes.

Genomic analysis revealed that most ST80 isolates clustered closely, indicating potential clonal spread.

Abstract

Vancomycin-resistant Enterococcus faecium (VREfm) is an emerging pathogen responsible for healthcare-associated infections. For this reason, 44 VREfm isolates collected during 2021–2023 were characterized using phenotypic and genomic approaches. VREfm isolates were identified by MALDI-TOF and antimicrobial susceptibility tests were performed with Vitek 2, Sensititre, or E-test. Sequence type (ST), antibiotic resistance genes, virulence factors and genetic relatedness were determined using Next Generation Sequencing. Forty-three isolates had a VanA phenotype and vanHAX genotype and one had a VanB phenotype and vanHBX genotype. Isolates showed high antibiotic resistance to various antibiotics, but generally remained susceptible to quinupristin/dalfopristin, tigecycline and eravacycline. Two isolates were resistant to linezolid, showing the chromosomal mutation G2576T in domain V of the 23S rRNA gene in one isolate, and the transferable linezolid resistance genes cfr(D) and optrA in the other. Thirty-eight isolates belonged to ST80, one to ST17 (ST80 and ST17 are included in CC17) and one to ST697. Genomic analysis of the ST80 isolates showed that nearly all of them belonged to a single cluster. To prevent further spread of VREfm in the nosocomial environment, in addition to the application of up-to-date infection control strategies and antibiotic stewardship programs, the implementation of genomic surveillance is recommended.

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