Poultry farm resistome: from genes to ecosystems



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Abstract

The intensive application of antimicrobial agents in industrial poultry farming contributes to the formation and maintenance of an extensive resistome – the collection of antibiotic resistance genes within microbial communities. This review synthesizes current data on the structure, diversity, and circulation of antibiotic resistance genes in poultry production systems within the context of the “One Health” concept. It offers a unique, systemic perspective, viewing a poultry farm as an integrated ecosystem for the circulation of resistance genes.

Metagenomic studies have revealed over 600 types of resistance genes in the poultry microbiome, conferring resistance to 25 classes of antibiotics. The most prevalent genes confer resistance to tetracyclines (tetA, tetB, tetM), β-lactams (blaTEM, blaCTX-M, blaCMY-2), macrolides (ermB, ermA), fluoroquinolones (qnrS, qnrB), and aminoglycosides. Of particular concern is the detection of carbapenemase genes (blaNDM, blaOXA-48) and genes conferring resistance to last-resort drugs such as tigecycline (tetX4) and colistin (mcr-1). The concentration of resistance genes in poultry litter can reach 10¹⁶ copies per gram, exceeding levels found in other types of livestock waste.

The review details key ecological reservoirs, including the gut microbiome, hatcheries, biofilms in water systems, litter, and production surfaces. The primary dissemination mechanisms encompass vertical transmission via hatcheries, horizontal gene transfer mediated by plasmids and transposons, and large-scale dispersion through litter into agro-ecosystems. The role of co-selection with heavy metal and biocide resistance genes in maintaining the resistome in the absence of antibiotic pressure is highlighted.

This review emphasizes the necessity for an integrated approach to resistome control. This includes optimizing antimicrobial use, enhancing biosecurity measures, developing alternative prophylactic strategies, and implementing effective waste management protocols to mitigate environmental and epidemiological risks.

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About the authors

Olga S. Chemisova

Don State Technical University

Email: chemisova@inbox.ru
ORCID iD: 0000-0002-4059-2878
SPIN-code: 1129-7436

Cand. Sci. (Biol.), Head of the laboratory "Collection of pathogenic microorganisms"

Russian Federation, building 6, 1 Gagarina Square, 344003, Rostov-on-Don, Russia

Darya A. Sedova

Don State Technical University

Email: dased0va@yandex.ru
ORCID iD: 0000-0003-1194-7251
SPIN-code: 6197-7220

Senior Lecturer, Department of Bioengineering

Russian Federation, building 6, 1 Gagarina Square, 344003, Rostov-on-Don, Russia

Alina A. Sereda

Don State Technical University

Author for correspondence.
Email: alina.sereda2001@mail.ru
ORCID iD: 0009-0007-2130-0175
SPIN-code: 2638-2848

Graduate Student, Faculty of Bioengineering and Veterinary Medicine

Russian Federation, building 6, 1 Gagarina Square, 344003, Rostov-on-Don, Russia

Yuliia P. Gordeeva

Don State Technical University

Email: GordeevaYP@yandex.ru
ORCID iD: 0009-0003-0888-2861
SPIN-code: 1440-6753

Graduate Student, Faculty of Bioengineering and Veterinary Medicine

Russian Federation, building 6, 1 Gagarina Square, 344003, Rostov-on-Don, Russia

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