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

Ádám Kerek1,2, Nikolett Palkovicsné Pézsa1,2, Eszter Kaszab2,3,4

  • 1Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary.

Frontiers in Veterinary Science
|October 20, 2025
PubMed
Abstract

Insights

Probiotic bacteria used in animal and human health can carry antimicrobial resistance genes (ARGs). This study found resistance to key antibiotics in several probiotic strains, emphasizing the need for careful safety assessments.

Area of Science:

  • Microbiology
  • Genomics
  • Public Health

Background:

  • Antimicrobial resistance (AMR) is a growing global health threat.
  • Probiotic microorganisms in veterinary and human medicine may harbor AMR.

Purpose of the Study:

  • To characterize phenotypic and genotypic antimicrobial resistance profiles of industrial probiotic strains.
  • To identify antimicrobial resistance genes (ARGs) in these probiotics.

Main Methods:

  • Phenotypic resistance assessed using Minimum Inhibitory Concentration (MIC) testing.
  • Genotypic analysis performed via whole-genome sequencing.
  • Five probiotic strains analyzed: *Enterococcus faecium, Bacillus licheniformis, Bacillus subtilis, Lactobacillus rhamnosus*, and *Pediococcus acidilactici*.

Main Results:

  • Multiple strains showed resistance to clinically relevant antibiotics (gentamicin, amoxicillin, tylosin, florfenicol).
  • Whole-genome sequencing detected 27 distinct ARGs, mainly related to efflux pumps and target modification.
  • *Bacillus licheniformis* exhibited the most diverse ARG profile; *Pediococcus acidilactici* had no detectable ARGs.

Conclusions:

  • Probiotic strains can possess significant antimicrobial resistance.
  • Combined phenotypic and genotypic analysis is crucial for ensuring the safety of probiotics.
  • This research informs the safe application of probiotics in animal and human healthcare.
Keywords:
ARGBacillusEnterococcusLactobacillusPediococcusantimicrobial resistancenext-generation sequencingprobiotics

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