Antibiotic resistance determinants in the interplay between food and gut microbiota
Open accessAbstract
A complex and heterogeneous microflora performs sugar and lactic acid fermentations in food products. Depending on the fermentable food matrix (dairy, meat, vegetable etc.) as well as on the species composition of the microbiota, specific combinations of molecules are produced that confer unique flavor, texture, and taste to each product. Bacterial populations within such "fermented food microbiota" are often of environmental origin, they persist alive in foods ready for consumption, eventually reaching the gastro-intestinal tract where they can interact with the resident gut microbiota of the host. Although this interaction is mostly of transient nature, it can greatly contribute to human health, as several species within the food microbiota also display probiotic properties. Such an interplay between food and gut microbiota underlines the importance of the microbiological quality of fermented foods, as the crowded environment of the gut is also an ideal site for genetic exchanges among bacteria. Selection and spreading of antibiotic resistance genes in foodborne bacteria has gained increasing interest in the past decade, especially in light of the potential transferability of antibiotic resistance determinants to opportunistic pathogens, natural inhabitants of the human gut but capable of acquiring virulence in immunocompromised individuals. This review aims at describing major findings and future prospects in the field, especially after the use of antibiotics as growth promoters was totally banned in Europe, with special emphasis on the application of genomic technologies to improve quality and safety of fermented foods.
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Resistance due to mutation of chromosomal genes is considered to pose a low risk of horizontal spread.
“However, resistance due to mutation of chromosomal genes is considered to pose a low risk of horizontal spread [128,129].”
From Current Concepts in Probiotic Safety and Efficacy (2026) · cites this paper as [129]
The ‘Genetic transferability of AbR in fermented food microbiota’ section says mobile elements are key to horizontal spread and that their association with resistance genes appears essential for transferability. It does not specifically assess resistance caused by mutations of chromosomal genes or classify its horizontal-spread risk as low. Page numbers are unavailable in our copy. (LLM, conf=0.76)
Experimental — accuracy not yet measuredIntrinsic antimicrobial resistance is generally regarded as having a low potential of horizontal spread.
“Although gene exchange among viable microorganisms is expected to occur in open ecosystems such as the gastrointestinal tract, intrinsic antimicrobial resistance is generally regarded as having a low potential of horizontal spread, whereas acquired resistance encoded by additional genes is considered to carry a substantially higher risk of lateral transfer [128,129].”
From Current Concepts in Probiotic Safety and Efficacy (2026) · cites this paper as [129]
Table 1 in “Origin and spread of antibiotic resistance in foodborne bacteria” distinguishes intrinsic from acquired vancomycin resistance. “Genetic transferability of AbR in fermented food microbiota” says mobile elements facilitate horizontal spread, but the paper does not explicitly say that intrinsic resistance generally has a low potential to spread horizontally. (LLM, conf=0.72)
Experimental — accuracy not yet measuredAcquired resistance encoded by additional genes is considered to carry a substantially higher risk of lateral transfer.
“Although gene exchange among viable microorganisms is expected to occur in open ecosystems such as the gastrointestinal tract, intrinsic antimicrobial resistance is generally regarded as having a low potential of horizontal spread, whereas acquired resistance encoded by additional genes is considered to carry a substantially higher risk of lateral transfer [128,129].”
From Current Concepts in Probiotic Safety and Efficacy (2026) · cites this paper as [129]
The “Genetic transferability of AbR in fermented food microbiota” section (page unavailable) says mobile elements enable horizontal spread of resistance genes and gives examples of gene transfer. It does not establish that acquired resistance genes generally carry a substantially higher transfer risk than intrinsic resistance; it says transferability also depends on genomic context. (LLM, conf=0.83)
Experimental — accuracy not yet measuredGene exchange among viable microorganisms is expected to occur in open ecosystems such as the gastrointestinal tract.
“Although gene exchange among viable microorganisms is expected to occur in open ecosystems such as the gastrointestinal tract, intrinsic antimicrobial resistance is generally regarded as having a low potential of horizontal spread, whereas acquired resistance encoded by additional genes is considered to carry a substantially higher risk of lateral transfer [128,129].”
From Current Concepts in Probiotic Safety and Efficacy (2026) · cites this paper as [129]
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References 91 · Cited by 105
- Authors
- Devirgiliis, C., Barile, S., & Perozzi, G.
- Affiliations
- Istituto Nazionale di Ricerca per gli Alimenti e la Nutrizione (IT)
- Corresponding author
- Perozzi, Giuditta
- Venue
- Genes & Nutrition
- Published
- 2011-04-28
- Volume
- 6
- Issue
- 3
- Pages
- 275-284
- ISSN
- 1555-8932 (ISSN-L)
- 1865-3499
- PMC
- PMC3145056
- OpenAlex
- W1997989258
- Cited by
- 105
- References
- 91
- Citations by year
- 2026: 2 · 2025: 6 · 2024: 3 · 2023: 6 · 2022: 8 · 2021: 8 · 2020: 7 · 2019: 4 · 2018: 9 · 2017: 10 · 2016: 6 · 2015: 9 · 2014: 17 · 2013: 4 · 2012: 6
- FWCI
- 3.94
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Genes & Nutrition (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Ministère de l’Agriculture, de l’Agroalimentaire et de la Forêt
- Ministero delle Politiche Agricole Alimentari e Forestali (DM 3688/7303/08)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- antibiotic resistance determinants, fermented foods, gut microbiota, food microbiome, probiotics, foodborne bacteria, horizontal gene transfer, antibiotic growth promoters, food safety, opportunistic pathogens, genomic technologies
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