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Kate Peffer, District Veterinarian Central Tablelands LLS

Posted Flock & Herd September 2016


Omphalitis, colloquially known as yolk sac infection, is the main infectious cause of chicken mortality in the first week post-hatching and accounts for large economic losses to the poultry industry (Amare et al., 2013). During incubation, extraembryonic membranes encircle the yolk substance and constitute the yolk sac, which attaches to the gut of the chicken by a yolk stalk. Just before hatching, the yolk sac is pulled from the egg cavity to the abdomen of the chick as an extension of the intestines. When the temperature and humidity during incubation and hatching are incorrect, the yolk sac is not properly resorbed and chicks hatch with improperly open, unhealed navels. As the yolk sac contains high levels of fat and water it provides a favorable source of nutrients for bacteria and, in combination with unhealed navels, presents a ready portal of entry for bacteria into the abdomen of the chicken (Khan et al., 2004).


On July the 6th, 2016, a 186,000 hen commercial layer farm in the Central Tablelands reported losing 140 of their 14,000 recently purchased three day old chickens. The chickens had arrived at the property two days prior and had begun dying on arrival. While this was only a 0.01% mortality, at this stage of rearing the property had usually only lost 12-20 chickens. Along with the losses, the producer reported approximately 5% of the remaining chickens appeared lethargic to semi-comatose, inappetant and huddled. The property consistently purchased chickens from the same parent flock and had managed their chicken shed in the same way with respect to disinfecting, heating, lighting, feed and water source as they had done for all previous batches.

Clinical findings

On arrival at the property it was clear that at least 5% of the remaining chickens were huddled, lethargic to semicomatose and showed no interest in the feed available.

Image of young chick
Figure 1. Lethargic chicken


Five recently dead chickens were provided for post-mortem. All chickens had a black semi-opened scab formed around the umbilicus. Three of the five chickens had red-black necrotic lesions on the serosa, particularly around the entry of the umbilicus to the abdomen. The abdomens of the chickens appeared distended and felt soft to touch. On opening the abdomen there was a putrefactive and offensive odour and increased amounts of serous fluid. The livers varied from mottled red to tan in colour. Intestines were thickened and enlarged and showed evidence of increased liquid faeces. The yolk sac of each chicken was enlarged and full of viscoid yellow-green to watery yellow-brown material and the peripheral vessels around the sac were enlarged.

A diagnosis of yolk sac infection was made on post-mortem.

Image of chick post-mortem
Figure 2. Enlarged black umbilicus connecting to an enlarged yolk sac containing green to yellow foul-smelling contents. There is also congestion of the vessels throughout the yolk sac.
Image of chick post-mortem
Figure 3. Enlarged yolk sac with discoloured contents, inflamed intestine and yellow-red mottled liver.
Image of chick post-mortem
Figure 4. Enlarged yolk sac

Laboratory results

Four chickens displaying the above clinical signs were packaged and sent to the laboratory for post-mortem and bacterial culture of the yolk sac. However, due to transport error, the chickens were in transit for four days and, on arrival at the laboratory, were decomposing and unsuitable for examination.


Omphalitis is considered to be a hatchery problem influenced primarily by poor temperature and humidity control in combination with faecal contamination on the eggs or incubator. Fluctuating temperatures during incubation, and particularly hatching, increase the incidence of unabsorbed yolk sac and unhealed navels. Inadequate incubation humidity results in excessive water retention in the egg and slow healing navels. Birds with slow healing or incompletely healed navels are then highly susceptible to bacterial infection when contamination with faeces occurs in the incubator or transportation boxes.

Different types of bacterial agents have been known to cause yolk sac infection including Proteus spp., Enterobacter spp., Pseudomonas spp., Klebsiella spp., Staphylococcus spp., Streptococcus spp., Clostridium spp., Bacillus cereus and Enterococcus spp. A study by Amare et al., 2013, found that 59.37% of samples from chicks with omphalitis contain mixed bacterial species, with Escherichia coli the most predominate isolate followed by Staphylococcus aureus. Mortality rates were consistently found to be highest when E.coli isolates were identified.

While mortality rates associated with omphalitis are estimated to be around 5-15% in chickens, loss can be much greater and up to 50% can be expected in turkeys (reference). Mortality usually begins at hatching and continues up until 10-14 days of age, peaking at day 4-5 (Pattison et al., 2008). While there is no specific treatment, antibiotics based on the prevalence and type of bacteria involved may be of some benefit in the acute stage. Despite antibiotic use, satisfactory outcomes are rarely attained as severely affected chicks die and unaffected birds are unlikely to benefit from antibiotic treatment (Pattison et al., 2008). Ensuring correct humidity, temperature and sanitary conditions during incubation, hatching and transport are the most important methods of prevention.


  1. Amare A, Amin A, Shiferaw A, Nazir S, Negussie H. Yolk Sac Infection (Omphalitis) in Kombolcha Poultry Farm, Ethiopia. American-Eurasian Journal of Scientific Research 2013; 8:10-14
  2. Khan K, Khan S, Aslam A, Rabbani M, Tipu M. Factors Contributing to Yolk Retention in Poultry: A Review. Pakistan Vet. J. 2004;24:46-51
  3. Pattison M, McMullin P, Bradbury J, Alexander D. Poultry Diseases, 6th Ed, 2008. Elsevier. Edinburgh


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