Organic Poultry Production in the US: Health Issues

Organic Poultry Production in the United States was published by ATTRA in 2008. It discusses organic husbandry including living conditions, health, genetics and origin, feed and processing as specified under the livestock requirements of the US Department of Agriculture National Organic Program (NOP). This article covers issues regarding health and hygiene, including a comparison of NOP standards with those in other countries.
calendar icon 3 February 2009
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General Aspects of Health

Proactive health management is used in organic production. A working relationship with an avian veterinarian is an integral part of health management and an animal health plan is often part of the Organic System Plan.

Provide adequate housing and space, ventilation and good nutrition to reduce stress and maintain the immune system. Prevent the introduction of disease with the use of vaccines and biosecurity practices. Use natural treatments if needed.

Vaccines are allowed in organic production to prevent disease. Interestingly, vaccines may be genetically engineered, a practice that is otherwise not permitted in organic production. This information appears in section 205.104(e) of the NOP Final Rule. Poultry vaccines are commonly used in the United States to prevent Marek's disease, Newcastle, infectious bronchitis and coccidiosis.

Probiotics are often used in organic poultry production, particularly to replace antibiotic growth promoters, which are not permitted. Probiotics are beneficial microbes, fed to birds to establish beneficial gut microflora, reducing colonisation by pathogenic organisms such as Salmonella and E. coli. This mechanism is called competitive exclusion because beneficial microorganisms are competing with pathogenic ones for nutrients and attachment areas in the gut. Other natural products include prebiotics, which are non-digestible food ingredients that benefit the host by selectively stimulating the growth of bacterial species present in the gut. An example is lactose, which is used by beneficial lactic acid bacteria in the gut but cannot be digested by chickens. Other prebiotics include fructo-oligosaccharides, inulin and lactulose, which alter the microbial balance in favor of beneficial bacteria (Novak and Troche, 2006). Manno-oligasaccharides appear to have a different mechanism that prevents pathogenic bacteria from adhering to the gut lining.

The NOP emphasises that drugs, growth promotants and synthetic parasiticides are not permitted, but natural materials can be used. However, no materials in violation of the Federal Food, Drug and Cosmetic Act should be used. Examples of natural treatments include enzymes, antioxidants, pyrethrum for controlling mites and botanicals such as garlic and oregano.

Antibiotics and other medical treatment must not be withheld if needed, and these birds should be diverted to nonorganic markets. Mortality may be higher in large-scale organic production than conventional production because medications are not permitted. Necrotic enteritis is a common health problem in large organic broiler flocks. In fact, broiler mortality may be 5 to 10 per cent in organic production. Organic layer flocks may have 3- to 5-per cent mortality rate.

Good biosecurity and sanitation practices should be followed on the farm, including limiting visitor access to the bird area. Sunlight and dry conditions help reduce pathogens in outdoor areas and foot baths with approved disinfectants, such as iodine, can be used at the entrance to houses, as well as disposable booties or dedicated footwear. The use of 'all-in, all-out' management (completely harvesting a flock before starting a new one) results in the reduction of pathogens, many of which die during the downtime. Mixing ages in a flock is a risk because older birds may be carriers of disease for younger birds. Likewise, mixing species can result in some species carrying diseases to other species. See the sections below on biosecurity and sanitation.

External parasites such as mites should be managed by allowing birds to dust-bathe. Many producers also add diatomaceous earth to dust baths. If mite treatment is needed, pyrethrum is a natural product that is permitted in organic production. For roost mites that do not actually live on birds themselves, the roosts, cracks and crevices in the house should also be treated. Natural oils, such as linseed oil, are often used on roosts.

Incidence of internal parasites – such as roundworms, caecal worms and capillary worms – can be a problem in organic poultry production and has been the focus of scientific studies (Permin et al., 1999 and Thamsborg et al., 1999). Rotating access to different outdoor areas is key in reducing incidence of internal parasites. Anticoccidial medications are not permitted for control of the protozoan parasite coccidiosis; therefore many producers focus on management or the use of a vaccine. See ATTRA's Parasite Management for Natural and Organic Poultry Production: Coccidiosis for more information.

"Preventing disease starts with clean birds. If you purchase birds or eggs, make sure they are from breeding fl ocks approved by the USDA National Poultry Improvement Program, which certifies flocks are free of certain diseases."

Moulting is a natural process that birds undergo annually to renew their feathers. Molting can help replenish the reproductive systems and bones of layers. Moult usually takes several weeks and egg production declines or ceases. A flock of the same age and origin will molt about the same time, although there may be some variation among individuals in the length of moult. Force-moulting is a way to induce the layers in a flock to moult at a particular time and at a faster rate. Moult can be forced by reducing the nutrient density of the diet and reducing the light period.

In conventional layer operations, layers are destroyed or processed at about 70 weeks of age or they are force-moulted and then, after laying begins again, kept until about 105 weeks of age. If producers force-moult, they should provide a moult diet and should provide a light period of at least eight hours.

The NOP does not have specific standards on forced moulting, but generally certifiers do not permit it due to stress to the bird. Organic producers usually destroy or process the flock at about 70 weeks, although small producers may let birds moult naturally.

Natural moulting is not as efficient as forced moulting, but it maintains bird welfare and extends the productive life of the layer (fewer layers are needed over time). Ideally, layers should be allowed to moult naturally and kept for at least two to three years.

Although the welfare of the bird is a cornerstone of organic poultry production, welfare assurance programmes, such as Humane Farm Animal Care (HFAC) and American Humane Association (AHA), have measurable standards and can document that birds have adequate access to feed and water, have good litter and air quality, that caretakers are trained, handling and euthanasia methods are humane and more. Birds are particularly stressed during catching, transport and processing.

Food safety in organic poultry production is an area of interest. Some studies have shown that food-borne diseases are more prevalent in organic livestock production than conventional. In a Danish study, campylobacter was found in all 22 organic broiler flocks compared to only one-third of conventional broiler flocks (Heuer et al., 2001). Organic birds are generally kept longer than conventional and have more opportunity to encounter pathogens. In contrast, Lunangtongkum et al. (2006) found that campylobacter bacteria developed resistance to fluoroquinolones, a group of antibiotics important in human health, in 46 per cent of conventionally raised chickens and 67 per cent of conventional turkeys, but only 2 per cent of the organically raised chickens and turkeys.


Sanitation between flocks is particularly important and a downtime of two to three weeks will help control pathogens that need a host to survive.

Cleaning is the first step because organic matter must be removed in order for a disinfectant to work. First sweep or air-blow the house from top to bottom to remove organic matter, and then spray the house with a high-pressure sprayer and detergent. Rinse and allow to dry, and then apply disinfectant.

Approved materials that are used for disinfection and sanitation of premises and equipment include chlorine materials, iodine, hydrogen peroxide, peracetic acid, phosphoric acid and organic acids. Hydrogen peroxide is particularly corrosive to metal and should be rinsed well. Iodine may stain surfaces. Alcohol is also a disinfectant but not very effective. Propane-fuelled heat tools are also used to disinfect.

In addition, water lines need regular care. Water lines can be flushed with organic acids, such as citric acid or vinegar, to loosen debris, and then sanitized with iodine or hydrogen peroxide between flocks. Chlorine is also used for routine sanitation of water lines when birds are in the house. Chlorine level should not be more than 4 ppm.


Good biosecurity is important in any poultry operation and particularly in organic operations. Since wild birds, particularly waterfowl, can carry diseases that harm domestic poultry, it is important to exclude wild waterfowl from the free-range poultry area. Outdoor feeders should not attract wild birds. For example, a self-feeder dispenses feed to poultry on demand. See the Solway Feeders for examples of self-feed dispensers. If necessary, netting can be placed over outdoor yards.

The USDA's Biosecurity for the Birds has information on biosecurity. Although highly pathogenic H5N1 avian influenza is not currently in the United States, there is concern that wild waterfowl may carry various types of avian influenza to free-range flocks. See ATTRA's Avian Influenza in Free-Range and Organic Poultry Production for more information.

Physical Interventions

Physical alterations are allowed if they are essential for animal welfare and done in a manner that minimizes pain. However, physical alterations should not be done on a routine basis.

Beak trimming in particular is a controversial practice performed on layers to reduce feather pecking. Feather pecking is a concern in cage-free and organic poultry production because of large group sizes. Feather pecking is an indicator of stress in the perpetrator and the victim and can lead to cannibalism. Beak-trimming is only permitted if other methods of prevention fail. Most welfare programmes require that beak trimming be done before 10 days of age with a humane method such as a hot blade or infra-red. No more than 50 per cent of the beak should be trimmed, as measured from beak tip to nostril (Kuenzel, 2007).

Ideally, animals should be able to breed without human intervention, but artificial insemination is allowed by the NOP.

Preventing Feather Pecking

Prevention of feather pecking begins early, when rearing the pullets. In a Dutch study, researchers Monique Bestman and Jan-Paul Wagenaar (2006) found pullets that feather peck during rearing will continue to feather peck as layers. However, pullets that do not feather peck during rearing will not later. Pullets need to be raised on litter (not in cages), have perches and a low stocking density. Flocks that feather pecked were at a density of 35 chicks per square metre (3.2 chicks per square foot), while flocks that did not feather peck were at only 22 chicks per square metre (two chicks per square foot) during the first four weeks of life.

Other risk factors that led to feather pecking included the use of slat flooring during the first weeks of life (no litter), absence of perches and no grain scattered for a pecking incentive. Bestman and Wagenaar quoted the 1955 work of German scientist Dr Erich Bäumer, who said, "During the first weeks of life, a pullet learns to eat. They will peck at everything in order to find out what is edible and what not. If their environment consists mainly of flock mates, the chance is big they start pecking at their flock-mates' plumage."

Hanging roughage or providing it in baskets also helps reduce feather pecking and birds learn to peck at different levels. If pullets are reared by an organic pullet specialist, the producer should ensure these practices have been followed so that the layers producers buy are less likely to feather peck.

Table 1. Comparison of highlights of poultry requirements regarding health issues of selected organic programmes
USDA NOP European Union Soil Association (UK) Canada National Bio-Gro (New Zealand) IFOAM 2002
Health Downtime between flocks required Downtime between flocks required Goal is to eliminate need for vaccines; no GMO vaccines
Antibiotics Not permitted Antibiotics permitted as last resort; withdrawal is double Emphasizes that vaccinations before 2 days cannot have antibiotics Not clear Antibiotics can be used as last resort if withdrawal is double
Beak trimming Permitted as last resort Permitted as last resort Not permitted; nor is wing clipping Permitted as a last resort Not permitted Not permitted
Artificial insemination Not specified, generally permitted Permitted Permitted Permitted Permitted
Forced moulting Expressly prohibited
Caponization Permitted for traditional product Expressly prohibited


Bestman, M. and J.P. Wagenaar. 2006. Feather pecking in organic rearing hens. Joint Organic Congress, Odense, Denmark, May 30-31, 2006.
Heuer, O.E., K. Pederson, J.S. Anderson and M. Madsen. 2001. Prevalence and antimicrobial susceptibility of thermophilic Campylobacter in organic and conventional broiler flocks. Letters in Applied Microbiology 33:269-74.
Lunangtongkum, T., T.Y. Morishita, A.J. Ison, S. Huang, P.F. McDermott and Q. Zhang. 2006. Effect of conventional and organic production practices on the prevalence and antimicrobial resistance of Campylobacter spp. in poultry. Pp. 113-120. Proceedings of the 1st IFOAM International Conference on Animals in Organic Production, St. Paul, MN, Aug. 23-25, 2006.
Novak, C. and C. Troche. 2006. Use of Bio-Mos® to Control Salmonella and Campylobacter in Organic Poultry. Accessed Dec. 2007.
Permin, A., M. Bisgaard, F. Frandsen, M. Pearman, J. Kold and P. Nansen. 1999. Prevalence of gastrointestinal helminths in different poultry production systems. British Poultry Science 40(4): 439-443.
Thamsborg, S.M., A. Roepstorff and M. Larsen. 1999. Integrated and biological control of parasites in organic and conventional production systems. Veterinary Parasitology 84(3/4): 169-186.

Further Reading

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January 2009
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