Phenotypic and genotypic characterization of probiotic strains in the context of antimicrobial resistance

Ádám Kerek; Nikolett Palkovicsné Pézsa; Eszter Kaszab; Ákos Jerzsele; Orsolya Farkas

doi:10.3389/fvets.2025.1684650

Phenotypic and genotypic characterization of probiotic strains in the context of antimicrobial resistance

Front Vet Sci. 2025 Oct 3:12:1684650. doi: 10.3389/fvets.2025.1684650. eCollection 2025.

Authors

Ádám Kerek^{1

2}, Nikolett Palkovicsné Pézsa^{1

2}, Eszter Kaszab^{2

3

4}, Ákos Jerzsele^{1

2}, Orsolya Farkas^{1

2}

Affiliations

¹ Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary.
² National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, Budapest, Hungary.
³ Faculty of Health Sciences, One Health Institute, University of Debrecen, Debrecen, Hungary.
⁴ Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary.

Abstract

Introduction: Antimicrobial resistance (AMR) has emerged as a critical global public health concern, particularly with regard to microorganisms used as probiotics in both veterinary and human healthcare. The aim of this study was to characterize the phenotypic and genotypic resistance profiles of several industrially applied probiotic bacterial strains, with special emphasis on the presence of antimicrobial resistance genes (ARGs).

Methods: Five strains, Enterococcus faecium, Bacillus licheniformis, Bacillus subtilis, Lactobacillus rhamnosus, and Pediococcus acidilactici were analyzed. Minimum inhibitory concentration (MIC) testing revealed resistance in multiple strains to clinically relevant antibiotics such as gentamicin, amoxicillin, tylosin, and florfenicol.

Results: Whole-genome sequencing identified 27 distinct ARGs, primarily associated with efflux pumps and target protection or modification mechanisms. The Bacillus licheniformis strain harbored the most diverse ARG profile, whereas no resistance genes were detected in Pediococcus acidilactici.

Discussion: These findings highlight the necessity of integrating phenotypic and genotypic assessments for the safe application of probiotic strains in animals and potentially human use.

Keywords: ARG; Bacillus; Enterococcus; Lactobacillus; Pediococcus; antimicrobial resistance; next-generation sequencing; probiotics.