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Effects of Hygiene Methods on the Microbiome and Resistome of Poultry Litter Cover

Effects of Hygiene Methods on the Microbiome and Resistome of Poultry Litter

Annals of Animal Science
Volume 26 (2026): Issue 3 (August 2026)
By: ,  ,  ,  ,  ,  ,   and    
Open Access
|Sep 2026
Figures & tables

Figures & Tables

Long description: The diagram illustrates the process of poultry litter management from commercial farm operations through in-house prevention and used-litter sanitation to farmland application. It shows risk factors including antibiotic therapy, metaphylaxis, antibiotic contaminants, microbial hazards, and contamination with ARBs and ARGs. Preventive methods used in the presence of birds include biological treatments, such as biopreparations and Yucca schidigera extract, and chemical methods, such as humic additives and aluminosilicates. Used-litter sanitation includes chemical methods based on calcium compounds and acidifying additives; biological methods such as storage, anaerobic digestion, and aerobic composting; and physical methods such as UV radiation and pasteurisation. The final risk relates to the transfer of antibiotic residues, ARBs, and ARGs to soil, water, crops, humans, and animals.
Figure 1.

Schematic representation of preventive methods for bacterial transmission and antibiotic resistance genes in poultry litter.

Table 1.

Properties of chemical and biological additives utilised in the sanitation of poultry litter

Method typeExamplePropertiesReferences
ChemicalHumic substances (humic acids, peat)

  • Acidify the litter and absorb moisture

  • Adsorb antibiotic residues

  • Strong interaction with fluoroquinolones, less intense with sulphonamides

  • Affect bacterial communities (e.g. reduce E. coli counts)

  • Inhibit the spread of ARGs

  • More effective when combined with other methods (e.g. composting)

Xie et al. (2021), Kulikova et al. (2022), Dančová et al. (2025)
Bentonite

  • Adsorbs antibiotic residues

  • Affects bacterial communities (e.g. reduces Campylobacter counts)

  • May reduce potential ARG proliferation, especially regarding sulphonamides

Prasai et al. (2016), Qiu et al. (2022), Peng et al. (2018)
Zeolites

  • Retain organic compounds, increase sludge porosity

  • High efficiency in antibiotic adsorption and degradation

  • Affect bacterial communities (e.g. reduce Enterobacteriaceae without disrupting beneficial bacteria)

  • Improve ARG removal during composting

  • More effective when combined with other methods (e.g. composting)

Prasai et al. (2017)
Superphosphate

  • Acidifies the litter, absorbs moisture, reduces ammonia emissions

  • Shows antibacterial effects

  • Inhibits the spread of ARGs

Peng et al. (2018)
Activated carbon, biochar

  • Stabilisation of organic matter

  • Regulates the growth of microorganisms in litter

  • Highly effective in the adsorption and degradation of antibiotics

Feng et al. (2022), Karamova et al. (2022)
BiologicalProbiotics (Bacillus spp., Lactobacillus spp.)

  • Compete with pathogens in the gut for space and nutrients, inhibiting their growth

  • Effective in litter sanitation

  • Moderate effect on bacterial communities (pathogens)

Tian et al. (2021), Juricova et al. (2022)
Yucca schidigera extract

  • Reduces odours

  • Antagonistic properties against pathogens: E. coli, Salmonella, Enterococcus faecalis

Matusiak et al. (2016)
Table 2.

Properties of chemical, biological and physical methods utilised in the processing and sanitation of chicken manure.

Method typeExamplePropertiesInvestment/Operating cost*References
12345
ChemicalCaO (quicklime), Ca(OH)2 (hydrated lime)

  • Alkalisation of litter environment, pH > 12, protein denaturation, enzyme inactivation.

  • May raise litter temperature and increase ammonia emissions.

  • High effectiveness in antibiotic residue inactivation, pathogen and ARG elimination.

Medium / mediumMaguire et al. (2006), Więckol-Ryk et al. (2023)
NaHSO4 (sodium bisulphate)

  • pH reduction, microorganism deactivation.

  • Lower effectiveness in antibiotic residue and ARG inactivation compared to alkaline method.

Low / lowRothrock et al. (2008)
Al2(SO4)3·14H2O (alum)

  • pH reduction, phosphate binding, ammonia emission reduction.

  • Moderate effectiveness in antibiotic residue and ARG inactivation.

Low / lowChoi et al. (2008), Gandhapudi et al. (2006)
Nanotechnology (e.g. nano-Ag)

  • Biocidal action, bacterial cell wall damage.

  • High toxicity.

  • High effectiveness in antibiotic residue, pathogen and ARG elimination.

High / mediumCzyż et al. (2023), Mohammed et al. (2022)
BiologicalStorage (manure storage)

  • Temporary microbial inactivation.

  • Low impact on antibiotic residues and ARG.

  • Moderate impact on bacterial communities (pathogens).

Low / lowFerguson et al. (2004)
Aerobic composting

  • Aerobic decomposition of poultry litter or chicken manure.

  • Economical and environmentally friendly approach.

  • Requires temperature and moisture control.

  • High effectiveness in antibiotic residue inactivation.

  • Very high effectiveness in pathogen elimination.

  • High ARG elimination (tet, ermB, qnr, bla) only in thermophilic phase (>80°C).

Medium / mediumQiu et al. (2021), Esperon et al. (2020)
Aerobic composting with mineral additives (e.g. bentonite)

  • Adsorption of active substances, stabilisation of organic matter, odour reduction.

  • High effectiveness in inactivating antibiotic residues.

  • Very high effectiveness in eliminating pathogens.

  • High effectiveness in eliminating ARG to tetracyclines, sulphonamides and macrolides (tet, ermB, sul).

Medium / mediumQiu et al. (2022)
Aerobic composting with carbon additives (biochar, bamboo charcoal)

  • Adsorption of pollutants, stabilisation of organic matter, increased nitrogen retention.

  • Very high effectiveness in inactivating antibiotic residues.

  • Very high effectiveness in eliminating pathogens and ARG to tetracyclines, sulphonamides and phenicols (tet, sul floR, cfr).

Medium–high / mediumCui et al. (2016), Li et al. (2017)
Aerobic composting with biochar and Bacillus subtilis inoculation

  • Sorption of pollutants, stabilisation of organic matter, increased nitrogen retention.

  • Highly effective in inactivating antibiotic residues.

  • Very highly effective in eliminating pathogens and ARG to tetracyclines and macrolides (tet, ermB).

Medium–high / mediumWu et al. (2024)
Aerobic composting with semi-permeable membrane technology (SMHC)

  • Very high effectiveness in inactivating antibiotic residues.

  • Very high effectiveness in eliminating pathogens.

  • Very high effectiveness in eliminating ARG on beta-lactams and colistin (blaNDM-1 and mcr-1).

High / medium–highXing et al. (2021), Cui et al. (2020)
Anaerobic digestion (methane fermentation)

  • Anaerobic decomposition of biowaste, biogas production, post-fermentation acidification, odour reduction.

  • Highly effective in inactivating antibiotic residues after thermophilic fermentation only.

  • Moderate effectiveness in eliminating pathogens (47–72%) under thermophilic conditions.

  • Moderate effectiveness in eliminating ARG (possibility of increasing the number of tet, sul, ermA genes).

High / highTian et al. (2016), Jang et al. (2018), Sun et al. (2022)
Anaerobic digestion with thermal pretreatment (TPT)

  • Pre-treatment carried out before Anaerobic digestion (AD) at 70–180°C.

  • Intensification of the AD process.

  • Very high effectiveness in inactivating antibiotic residues (tetracycline, macrolides, lincosamides).

  • Very high effectiveness in eliminating pathogens.

Very high / highPourrostami Niavol et al. (2024)
Anaerobic digestion with hydrothermal pretreatment (HTP)

  • Pre-treatment carried out before AD at 120–200°C under high-pressure conditions.

  • Very high effectiveness in inactivating antibiotic residues (e.g. tylosin).

  • Very high effectiveness in eliminating pathogens.

  • Very high effectiveness in eliminating ARG to beta-lactams and macrolides.

  • sulphonamides, quinolones and tetracyclines (blaTEM, ermB, sul, qnr, tet).

Very high / highParanhos et al. (2023)
Anaerobic digestion with alkaline and ultrasonic microwave-acid pretreatment (MW-H)

  • Raising pH, protein denaturation.

  • High effectiveness in eliminating pathogens and ARB before AD.

  • Moderate effectiveness in eliminating ARG (possible increase in ARG in post-fermentation).

Medium / mediumWang et al. (2019), Tong et al. (2016)
Anaerobic digestion with ultrasonic pretreatment and biochar

  • Sonication breaks down structures; biochar adsorbs antibiotics and stabilises microflora.

  • Highly effective in eliminating ARG (possible increase in ARG in post-fermentation).

High / mediumZhang et al. (2019 a)
PhysicalUV radiation

  • Enzymatic inactivation, damage to pathogens, DNA/RNA and ARG.

  • Effective only on a thin layer of chicken manure.

  • Highly effective in eliminating pathogens.

  • Moderately effective in eliminating ARG.

Medium / mediumEl-Maghawry et al. (2024)
Pasteurisation (thermal heating)

  • Protein denaturation, damage to microbial DNA/RNA.

  • Highly effective in eliminating pathogens (70°C) and bacterial spores (>90°C).

  • Moderately effective in eliminating ARG.

Medium–high / mediumMartens and Böhm (2009)

[i] The investment and operating costs were estimated based on the report by Flotats et al. (2011).

DOI: https://doi.org/10.2478/aoas-2025-0116 | Journal eISSN: 2300-8733 (formerly 1642-3402) | Journal ISSN: 1642-3402
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Language: English
Page range: 1313 - 1332
Submitted on: Apr 9, 2025
Accepted on: Oct 9, 2025
Published on: Sep 6, 2026
Published by: National Research Institute of Animal Production
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year
Keywords:
poultry litter treatment,
antibiotics,
resistance,
MDR,
HGT
Related subjects:
Medicine,
Veterinary medicine

© 2026 Przemysław Racewicz, Sebastian Nowaczewski, Marcin Hejdysz, Piotr Ślósarz, Sebastian Kaczmarek, Piotr Pawlak, Zofia E. Madeja, Magdalena Szyndler-Nędza, published by National Research Institute of Animal Production
This work is licensed under the Creative Commons Attribution 4.0 License.

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