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Yolk Sac Infection

Other Names: Navel-ill, Mushy Chick Disease, Omphalitis

Omphalitis, also known as yolk sac infection, is a common cause of death of newly hatched chicks. It is most commonly caused by infection with Escherichia coli bacteria (approximately 70% of cases), however Staphylococcus aureus, Salmonella spp, Streptococcus spp, Enterobacter hafniae, Klebsiella spp. , Pseudomonas spp, and Aspergillus fumigatus are also frequent causes. Chicks can become infected during incubation, while hatching, or when in the brooder.
  • Incubation: For bacteria to enter incubating eggshells, it must be either already present in the incubator or introduced into it. This occurs as a result of improper or lack of disinfecting the incubator and/or associated equipment (egg turning device, thermometers), setting dirty eggs in the incubator, or by candling eggs with dirty, especially, moist or wet, hands. If infertile or dead embryos are left in the incubator these also have the potential to contaminate the incubator with bacteria, especially if they explode. This emphasizes the importance of candling to eliminate eggs that are not fertile or embryos that have died while in the incubator.
  • Hatching: Chicks can become infected during the hatching phase if exposed to bacteria from old contaminated sponges used to help increase humidity levels, or if old shelf liners are used that are not clean.
  • Post-hatch: Just before a chick hatches from an egg, it 'absorbs' the yolk sac through the navel. Once the yolk sac is fully absorbed, the navel immediately begins to heal and dries out. However, if chicks are unable to fully absorb the yolk sac prior to hatching (or are helped out of the egg before they were meant to hatch), they will have an attached mass apparent on the outside of their bodies, which is the unabsorbed yolk sac. Chicks with unabsorbed yolk sacs are at a great disadvantage. The yolk of the egg is a source of vital nutrients and protective antibodies for the chick. When chicks are unable to absorb all of the nutrients, they will not be as strong and have a weakened immune system. In addition, unabsorbed yolk sacs are essentially an unhealed naval or open lesion, which makes the chick more susceptible to bacteria infection. When yolk sacs become infected, they are often described as yellowish-brown to green to yellowish red in color.
Most chicks with a yolk sac infection die within 24 hours of hatching, peaking at 5 to 7 days. Chicks that make it to day 2 or 3 are often much smaller than the other birds. Any chicks that recover will have a poor immune system, making them more susceptible to infection with other opportunistic pathogens and developing chronic respiratory diseases.

Clinical Signs

Soft and distended abdomen
Wet or open navel
Unabsorbed, enlarged yolk sack
Discoloration of navel
Foul (rotten egg) odor
Droopy head
Huddling near heat source


  • History
  • Clinical signs
  • Bacterial isolation
  • Necropsy


Supportive careApply 1% iodine solution to the umbilici of any chicks which were assisted hatches. 
AntibioticsAmikacin or tobramycin for 72 hours.
ProbioticsFor the first 2 weeks of life.
ElectrolytesGiven orally for the first 24-48 hours.



  • Follow strict egg and incubator hygiene. Disinfect the incubator and any equipment and hatching materials used prior to incubation
  • Remove infertile eggs and eggs with dead embryos from the incubator promptly
  • Disinfect all surfaces that may come into contact with hatchlings during the first few days after hatching
  • Keep dust down in incubator and hatching area
  • Handle chicks under optimal climatic conditions from the moment of pulling from incubator until their placement in the brooder to avoid chilling or overheating, as either will be detrimental to the chicks’ immune status and yolk sac resorption.
  • Delay feeding and watering of newly hatched chicks, to allow them to better absorb their yolk sac.


Poor, most affected chicks die within 3 days of hatching.

Scientific References

Age Range

Incubated eggs and recently hatched chicks are at risk.

Risk Factors

  • Incubation of dirty eggs or eggs with eggshell defects
  • Collection of dirty and clean eggs at the same time that are intended for breeding
  • Lack of hygiene in laying nests
  • Not disinfecting or fumigating the incubator or brooding area prior to putting eggs in
  • Assisting chicks out of their shells.
  • Fluctuating environmental temperature
  • Chicks with large yolk sacs
  • Poor fertile egg storage conditions
  • High humidity levels during incubation