Poultry Litter: The Hidden Microbial Reactor

 

Dr. Majed Hamid Al-Sayegh

17/ 12/ 2025

The Most Dangerous Reservoir of Pathogens and Resistance Genes in Chicken Farms

First: Introduction: From “Waste” to a Critical Control Point. Traditionally, poultry litter is treated as “waste” to be disposed of at the end of the cycle. However, recent evidence from microbiome and resistance gene studies shows that litter is the central biological reactor in chicken farms, the largest reservoir of pathogens and antibiotic resistance genes, and a crucial link between bird health, air quality, soil and water safety, and human health within the One Health framework.

 

Litter is not simply sawdust or straw, but a dynamic mixture of feces, uric acid, feed residues, feathers, and water leaking from drinkers and cooling systems. This warm, carbon- and nitrogen-rich environment, with variable humidity and potentially less-than-ideal ventilation, creates an ideal environment for the growth of bacteria, viruses, parasites, and fungi, and for the exchange of resistance genes among them.

 

Second: The Microbiome and Resistance Gene Reservoir in Poultry Litter

The use of metagenomics and large-scale sequencing techniques has revealed that poultry litter hosts a highly complex microbial community consisting of: Enterobacteriaceae (such as Escherichia coli and Salmonella), Clostridium, Enterococcus, and saprophytic fungi such as Aspergillus and Penicillium. In addition to this microbiome, studies show that litter contains a large and diverse reservoir of antibiotic resistance genes (ARGs), including resistance to tetracyclines, sulfonamides, macrolides, beta-lactams, and others. A significant portion of these genes are carried on plasmids and mobile genetic elements that facilitate horizontal transfer between bacterial species, making litter an active platform for the evolution and spread of resistance within the farm.

A recent study on agricultural soil fertilized with poultry litter showed that repeated litter use can enrich the soil with diverse resistance genes and alter the microbiome composition and relative concentrations of these genes compared to untreated soil.

Third: Major Pathogens in Litter: Bacteria, Viruses, and Fungi

Enteric bacteria such as Salmonella, Campylobacter, and pathogenic E. coli (APEC) are capable of surviving for extended periods in litter, especially at medium to high humidity. Tracing infection chains in some studies has shown concordance between isolates from bird intestines, litter samples, and air and surface samples within the poultry house, confirming the central role of litter as a circulating reservoir for infection and its recycling between chickens and the environment.
Fungi, including azole-resistant species, have been documented in poultry environments; dust, litter, and air form overlapping pathways for the dispersal of fungal spores within the poultry houses and to workers. A 2025 study indicated that poultry facilities can be reservoirs for fungi resistant to azole treatments, with poultry litter and dust turbid playing a clear role.

Viruses, such as Newcastle disease viruses, infectious bronchitis virus (IBV), bursal infection virus (IBDV), and, most importantly, highly pathogenic avian influenza viruses (HPAI), are shed in large quantities in feces and settle on litter surfaces. Recent avian influenza simulations have shown that the virus can survive on litter surfaces for several days at moderate temperatures and is carried on fine dust particles (1–5 microns) that escape from poultry houses and travel potentially long distances depending on wind direction and ventilation conditions.

 

Fourth: Litter and Air: Dust and Bioaerosols as a Bridge of Infection.

Litter and air within a chicken house are interconnected systems. Every movement of the birds, every step taken by the workers, and every fan operation stirs up fine litter particles laden with bacteria, viruses, fungi, free DNA, and resistance genes. Studies conducted in 2024–2025 detected high levels of fine particulate matter (PM10 and PM2.5) and bacterial loads in the air of broiler houses during both summer and winter, with concentrations varying according to bird age, litter condition, and ventilation rate.

A study on the microbiome and resistance genes in the indoor air of poultry houses showed that bacteria carrying resistance genes can become part of bioaerosols and travel within and between houses, creating a double threat to the health of both birds and workers. This means that controlling air quality is fundamentally dependent on controlling litter quality; they are two sides of the same coin: what multiplies in the litter becomes inhaled air, and what is released from the air returns to the litter, carrying with it a new mix of microbes and resistance genes.

 

Fifth: Intestinal Parasites and Coccidia: Poultry Litter as a Life Cycle Stage

Coccidiosis (Eimeria spp.) is the clearest example of a parasite’s life cycle being linked to litter. The osteostat is excreted unspored in the feces, then transforms into an infectious spore form in warm, moist litter within hours to days, and is subsequently ingested again with the litter, feed, or water. Recent reviews on coccidiosis have confirmed that the level of infection pressure in the poultry house is directly related to litter moisture, the number of litter cycles, and the degree of litter accumulation around drinkers and feeders.

An Egyptian trial on the effectiveness of certain chemical additives to poultry litter demonstrated that modifying litter properties (such as lowering pH or improving drying) can reduce the survival of pathogenic bacteria and inhibit the sporulation of coccidia osteostats, reinforcing the idea that litter is not a passive environment but rather a crucial point of intervention in coccidiosis control programs. Reviews of phytochemicals have shown that some compounds, such as artemisinin, can reduce the ability of osteophytes to sporulate and survive in litter, opening the door to integrated strategies combining litter management, nutrition, and vaccination.

 

Sixth: Litter as a vector for resistance genes to the soil and farming system.

When litter is removed from poultry houses, it is often used as a rich source of organic fertilizer. However, this pathway directly links the farm’s reservoir of resistance microbes to the soil, water, and plants. A 2025 study on soil treated with poultry litter showed that repeated litter fertilization increases the diversity and density of antibiotic resistance genes in the soil compared to untreated fields, with the potential for some of these genes to be transferred to soil bacteria or the root-associated microbiome.

Other studies on the dynamics of resistance gene transfer have shown that the overuse of antibiotics in the poultry industry, coupled with poor waste management, contributes to the contamination of various ecosystems (soil, water, and plants) with resistance genes that can subsequently be detected in bacteria isolated from food, the environment, or even human patients. In contrast, several experiments have demonstrated that controlled thermal composting of litter/manure can significantly reduce the concentrations of resistance genes, residual antibiotics, and pathogenic bacteria, compared to raw stockpiling or long-term cold storage. A combination of good aeration, an appropriate carbon-to-nitrogen ratio, and sufficient composting time (8–10 weeks) has been shown to reduce resistance genes and bacterial loads in the final compost products.

 

Seventh: Modern Control Strategies: From the Poultry Level to the Policy Level.

1- At the Farm Level
Litter Moisture and Ventilation Management:
• Maintain moisture within the “dry-fried” range to minimize dust, odors, and coccidiosis.

• Repair drinker leaks immediately and adjust misting and cooling systems to prevent litter saturation.

Conscious Litter Reuse Policy:
• Reduce the number of cycles on the same litter on farms with a complex disease history (salmonella, coccidiosis, necrotizing enteritis).

• When reusing litter, apply treatments between cycles (drying, turning, improving materials such as aluminum compounds or gypsum) according to local guidelines.

Reducing the Selective Pressure of Antibiotics: • Review antibiotic use protocols with your veterinarian. Shifting to effective vaccination programs and alternative feed additives (organic acids, probiotics, phytochemicals) to reduce reliance on antibiotics, in line with the recommendations of the latest reviews on antibiotic resistance in the poultry sector.

• Regular litter monitoring
• Incorporating litter sampling for microbiome analysis or detection of specific pathogens (Salmonella, resistant E. coli, coccidia) into internal quality programs at advanced farms.

2- At the level of waste and compost management: 

• Adopting mandatory thermal composting protocols before using litter as fertilizer in high-risk fields (fresh vegetables, farms near residential areas).
• Aligning litter and compost piles so they are located sufficiently far from houses and waterways, while preventing surface runoff of contaminated leachate.

3- At the level of legislation and policies. The 2025 reviews on poultry farm environments and resistance genes underscore the need for countries to have regulatory frameworks that consider:

• Incorporating qualitative litter indicators into licensing requirements and Good Practice (GAP) principles.

• Recognizing litter management as a clear component of National Antimicrobial Resistance Action Plans (NAPs) within the One Health framework.

• Encouraging applied research into litter and compost microbiome modification to reduce pathogens and resistance genes before they reach the agricultural environment.

 

Eighth: Conclusion: Whoever controls the litter controls the narrative of health on the farm.

The picture painted by recent evidence is clear: poultry litter is the microbial and epidemiological heart of the broiler farm. What happens in it impacts flock health, poultry dust and air quality, soil, water, and plants, and ultimately, human health at the end of the food chain. Litter is not a peripheral issue, but a critical control point that must be brought to the forefront of veterinary, administrative, and legislative attention. Investing in understanding and managing litter—moisture, aeration, reuse, composting, and fertilization—is not a minor technical detail, but a strategic step toward reducing disease, curbing antibiotic resistance, minimizing public complaints, and protecting the environment in the Middle East, North Africa, and globally.