Mobile antimicrobial resistance genes in probiotics
Open accessAbstract
Even though people around the world tend to consume probiotic products for their beneficial health effects on a daily basis, recently, concerns were outlined regarding the uptake and potential intestinal colonisation of the bacteria that they transfer. These bacteria are capable of executing horizontal gene transfer (HGT) which facilitates the movement of various genes, including antimicrobial resistance genes (ARGs), among the donor and recipient bacterial populations. Within our study, 47 shotgun sequencing datasets deriving from various probiotic samples (isolated strains and metagenomes) were bioinformatically analysed. We detected more than 70 ARGs, out of which rpoB mutants conferring resistance to rifampicin, tet(W/N/W) and potentially extended-spectrum beta-lactamase (ESBL) coding TEM-116 were the most common. Numerous ARGs were associated with integrated mobile genetic elements, plasmids or phages promoting the HGT. Our findings raise clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.
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Risk categories for probiotics are associated with four interrelated factors: acquired antimicrobial resistance genes, virulence factors, translocation, and mobile or unstable genomic elements that allow horizontal gene transfer.
“Risk categories for probiotics are associated with four interrelated factors: acquired antimicrobial resistance genes, virulence factors, translocation, and mobile or unstable genomic elements that allow horizontal gene transfer [43,44].”
From Current Concepts in Probiotic Safety and Efficacy (2026) · cites this paper as [43]
The Introduction (page not available) explains that probiotic bacteria can carry antimicrobial resistance genes and that plasmids and prophages increase their potential for horizontal transfer. The paper does not present the claimed four-factor risk categories or identify virulence factors and probiotic translocation as factors in such a framework. Its use of “translocate” refers to a plasmid moving between bacteria during conjugation. (LLM, conf=0.88)
Experimental — accuracy not yet measuredCommercial probiotic products may contain ARGs or transferable resistance determinants, although the level of risk varies substantially among product types, bacterial taxa and analytical pipelines.
“Previous studies have shown that commercial probiotic products may contain ARGs or transferable resistance determinants, although the level of risk varies substantially among product types, bacterial taxa and analytical pipelines [15,16,17,18,19,20].”
From Integrated Phenotypic and Sequencing-Based Resistome Assessment of Antimicrobial Resistance Determinants in a Sample of Commercial Farm-Animal Probiotic Products (2026) · cites this paper as [16]
The Discussion reports ARGs in probiotic samples, including genes that may be mobile, and shows differences between metagenomic samples, isolates and bacterial taxa. The Introduction notes that earlier studies used diverse methodologies, but our copy does not establish that the level of risk varies substantially by analytical pipeline. (LLM, conf=0.85)
Experimental — accuracy not yet measuredMobility, ecological opportunity and recipient compatibility determine whether an ARG becomes a clinically relevant hazard.
“This framework is consistent with the broader horizontal gene transfer (HGT) literature, which emphasizes that mobility, ecological opportunity and recipient compatibility determine whether an ARG becomes a clinically relevant hazard [11,12,16,17].”
From Integrated Phenotypic and Sequencing-Based Resistome Assessment of Antimicrobial Resistance Determinants in a Sample of Commercial Farm-Animal Probiotic Products (2026) · cites this paper as [16]
The Introduction (page unavailable) links ARG mobility to transfer in the intestinal tract and says that transfer to pathogenic bacteria may reduce antibiotic-treatment efficacy. It also describes cell-to-cell contact as an opportunity for conjugation. The paper does not identify recipient compatibility as a factor determining clinical hazard, so it supports only part of the three-factor claim. (LLM, conf=0.84)
Experimental — accuracy not yet measuredThe present farm-animal dataset appears less concerning than several reports on broader probiotic or food-associated bacterial collections, where ARGs were frequently detected together with plasmid or iMGE signals.
“the present farm-animal dataset appears less concerning than several reports on broader probiotic or food-associated bacterial collections, where ARGs were frequently detected together with plasmid or iMGE signals [16,17].”
Probiotic products and probiotic-associated taxa may carry detectable ARGs, but public-health relevance depends on taxon identity, gene function, genomic context and mobility potential rather than on ARG counts alone.
“previous studies have shown that probiotic products and probiotic-associated taxa may carry detectable ARGs, but that public-health relevance depends on taxon identity, gene function, genomic context and mobility potential rather than on ARG counts alone [15,16,17,18,22,23].”
An earlier shotgun-based analysis of probiotic samples detected more than 70 ARGs and numerous ARGs associated with plasmids, phages or iMGEs.
“It also appears less alarming than the earlier shotgun-based analysis of probiotic samples that detected more than 70 ARGs and numerous ARGs associated with plasmids, phages or iMGEs [16].”
ARGs carried by probiotic candidates may be transferred to intestinal bacteria through horizontal gene transfer, potentially reducing the effectiveness of antibiotic therapy when acquired by pathogenic bacteria.
“This issue is particularly relevant because ARGs carried by probiotic candidates may be transferred to intestinal bacteria through horizontal gene transfer, potentially reducing the effectiveness of antibiotic therapy when acquired by pathogenic bacteria. 43”
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Two Faces of Fermented Foods—The Benefits and Threats of Its Consumption
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Self-citationAccounting for the health risk of probiotics
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Positive biofilms to guide surface microbial ecology in livestock buildings
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“Risk categories for probiotics are associated with four interrelated factors: acquired antimicrobial resistance genes, virulence factors, translocation, and mobile or unstable genomic elements that allow horizontal gene transfer [43,44].”
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Antimicrobial resistance gene lack in tick-borne pathogenic bacteria
Papp, M., Tóth, A. G., Valcz, G., Makrai, L., Nagy, S. Á., Farkas, R., & Solymosi, N. (2023) · Scientific Reports · doi:10.1038/s41598-023-35356-5 · Cited by 13 · see citing works
Self-citationNpmC – a novel A1408 16S rRNA methyltransferase in the gut of humans and animals
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Effects of Postbiotic Administration on Canine Health: A Systematic Review and Meta-Analysis
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Modulation of the Human Microbiome: Probiotics, Prebiotics, and Microbial Transplants
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Harnessing Probiotics to Combat Candidiasis: Mechanisms, Evidence, and Future Directions
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Can Postbiotics Represent a New Strategy for NEC?
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“It also appears less alarming than the earlier shotgun-based analysis of probiotic samples that detected more than 70 ARGs and numerous ARGs associated with plasmids, phages or iMGEs [16].”
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Antipathogenic and probiotic potential of enterococci found in the entrails of the palmetto bug
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Az új generációs genomszekvenálás lehetséges helye a kutyaharapások kezelésében
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- Authors
- Tóth, A. G., Csabai, I., Judge, M. F., Maróti, G., Becsei, Á., Spisák, S., & Solymosi, N.
- Affiliations
- Semmelweis University (HU)
- Eötvös Loránd University (HU)
- University of Veterinary Medicine (HU)
- Ludovika University of Public Service (HU)
- Corresponding author
- Solymosi, Norbert
- Venue
- Antibiotics
- Publisher
- openRxiv
- Published
- 2021-05-04
- Volume
- 10
- Issue
- 11
- Pages
- 1287-1287
- ISSN
- 2079-6382 (ISSN-L)
- PMC
- PMC8614787
- OpenAlex
- W3205359199
- Cited by
- 97
- References
- 99
- Citations by year
- 2026: 26 · 2025: 25 · 2024: 26 · 2023: 13 · 2022: 6 · 2021: 1
- FWCI
- 3.65
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Antibiotics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Repository of the Academy's Library (Library of the Hungarian Academy of Sciences) (acceptedVersion)
- Közszolgálati Tudásportál (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- ELTE Digital Institutional Repository (EDIT) (Eötvös Loránd University) (submittedVersion, cc-by)
- Funders
- European Commission (874735, TKP2020, HORIZON2020, 2020–4.1.1-TKP2020, 2020-4.1.1)
- Semmelweis Egyetem (2020-4.1.1.-TKP2020, TKP2020)
- Magyar Tudományos Akadémia (2020-4.1.1, LP2020-5/2020, Lendület Programme LP2020-5/2020)
- Horizon 2020 Framework Programme (874735 (VEO), 874735)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Physical Sciences › Environmental Science › Pollution › Pharmaceutical and Antibiotic Environmental Impacts
- Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Antibiotic Use and Resistance
- Keywords
- antimicrobial resistance genes, probiotics, horizontal gene transfer, mobile genetic elements, plasmids, bacteriophages, rpoB mutations, rifampicin resistance, intestinal colonization, probiotic safety
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