Incubation Problems due to Breeders’ Microbial & Fungal Infections.




 Responsible microorganism






Mycoplasma gallisepticum

Mycoplasma meleagridis

Mycoplasma synoviae

Mycoplasma anatum




General view:

Embryo Mortality after day 15th of incubation.

Mortality of embryos immediately after eggshell piping.


Infection spreading:

 Infection is transmitted inside the breeder hen by close contact of the infected air sacs of the breeder bird with the follicles of its ovary. Mycoplasma infection is transmitted to the yolk shack of the egg thus the embryo is infected.

Additional spreading of the disease happens inside incubators and chick transport boxes.



By post mortem examination of the embryo immediately after piping the eggshell

We find a foamy yellowish exudate inside the thoracic air sacks of the embryo. This post mortem examination should be performed to at least 20 samples and repeated three times for three consecutive incubation cycles.


The veterinarian must always correlate these findings to possible clinical signs of the disease on the breeding flock.











Salmonella Gallinarum








General view:

 Some fertile eggs are not developed at all. Another part of the batch of these embryos dies during incubation and hatching time. Some embryos stay alive and become carriers of the disease.


Infection spreading:

The gonads of the breeders (ovary and testicles) are infected. The infected hens lay infected eggs. A healthy hen may even give infected eggs if it is mated by an infected rooster.

 The percentage of infected eggs may be between 1-50%.


Diagnosis and prevention:

 Some of the eggs examined do not have developed blastoderm.

 Routine disinfection of the eggs before placement inside the incubator







 Salmonella Typhimurium




Many other Salmonella









General view:

 Dead embryos. If the embryos do not die they infect healthy chicks of the same batch.


Infection spreading:

 Paratyphoid is a breeders’ food borne disease. The flock is infected by consuming feed contaminated by S. Typhimurium. Then it transmits the microbe by the feces. The egg is infected when passing through the cloaca. Thus S. Typhimurium is already present on the egg shells.

Salmonella Typhimurium find its way through the pores of the egg shell during the first week of incubation.

 Infected chicks that survive infect the healthy ones by the hatcher dust and egg shell contact.

Another way of spreading of the disease is by chick sexing procedure, transfer boxes and brooding spaces.


Diagnosis and prevention

Regular microbiological examination of the breeder feed.

Routine disinfection of the eggs before placement inside the incubator








Escherichia Coli


 Together with:


Staphylococcus Aureus


Streptococcus Faecalis




General view:


Dead embryos. If the embryos do not die they infect healthy chicks of the same batch. The chicks that survive usually develop omphalitis (yolk sack infection). If Staphylococcus Aureus is complicated the chick dies at the first 3 days after hatching. If Streptococcus Faecalis is complicated the chicks die by septicemia at the age of 10-20 days.


Infection spreading:


Pathogenic strains of Escherichia coli infect the intestine of the breeders. Then the uterus is infected through hen’s cloaca from which the eggs are infected.

Inside the hatchers the infection of the chick’s lungs and air sacks is air borne.


Diagnosis and prevention:


Routine disinfection of the eggs before placement inside the incubator






Aspergillus Fumigatus



General view:


Some embryos die during incubation. Most of them Survive.


Infection spreading:


The eggs are contaminated from the environment of by the nest material. Washed eggs or eggs dipped in antibiotic solutions are more susceptible to infection by Aspergillus Fumigatus. The infection is done through the pores of their eggshell.

Inside the hatchers the infection is transmitted   by air.


Diagnosis and prevention:


Sometimes we can detect Aspergillosis by candling of the eggs. The Aspergillosis infection lesions are present inside the egg’s air cell.

Careful disinfection of the incubators and the eggs before placement. Disinfection of the hatchers. Regular cleaning of the nests.




Source: Poultry Clinical Pathology by Efstratios B. Artopoios, 1st Edition in Greek language.1980, Editor: Thessaloniki Veterinary School

Comparative Effectiveness of Various Methods of Disinfection of Hatching Eggs.


The incubator environment that is kept at high temperature and humidity is an excellent place for the microbes to multiply.

A very good indicator of how much an egg is infected externally is a scientific term known as Total Bacterial Count.

Almost everyone who incubates poultry eggs knows that before incubating, the eggs they must be sanitized.


Disinfecting reduces the population of the microbes on the surface of the egg.

This prevents fatal infections of the embryo that may kill it inside the egg. Egg sanitation also prevents in most cases the disease transmission from the breeders to the newly hatched chicks.

But which method of disinfection we should follow?

Since formaldehyde fumigation (the classical method) is not a convenient method for the back yard poultry breeder for a series of reasons, other alternatives should be taken into consideration. Some of them, as you will easily understand from  the diagram are more environment friendly, more effective and a lot more easier to apply.

This  paper states that chemical disinfectants have undesirable effects on developing chick embryos such as retarded growth reflected by malformed limbs and beaks and also muscle weakness  in a few hatched chicks.

Here is an easily understood graphic presentation of the effectiveness of various methods and compounds used for disinfecting the eggs before placing them to the incubator.

Source: This short article is based on this excellent paper.

Not all treatments may be safe, check out the source for more information on which of these should be avoided.


Michael J. Mavridis D.V.M
CEO / Founder of Mavridis Zootechniki Ltd.

Incubation Problems due to Breeders’ Micro Mineral Deficiences



The problems of embryo mortality during incubation are not allways incubator
oriented.  The table below discusses when and how micro mineral deficiencies of the
breeder flock affect the survival possibilities of the chicken embryo in ovo.




Deficiency Signs






Peak deaths prior to emergence. Chondrodystrophy, dwarfism, long bone shortening, head malformations, edema, and abnormal feathering are prominent.





Deaths prior to emergence and the appearance of rumplessness, depletion of vertebral column, eyes underdeveloped, and missing limbs.





Deaths at early blood stage with no malformations





Prolongation of hatching time, reduced thyroid size

and incomplete abdominal closure





Low hematocrit; low blood hemoglobin; poor extra-embryonic circulation in candled eggs.






High incidence of dead embryos early in incubation


Source:Nutrient Requirements of Poultry: Ninth Revised Edition,1994

Incubation Problems due to Breeders’ Vitamin Deficiences


The problems of embryo mortality during incubation are not allways incubator
oriented. The table below discusses when and how vitamin deficiencies of the
breeder flock affect the survival possibilities of the chicken embryo in ovo.



Deficiency Signs



Vitamin A




Death at about 48 hours of incubation from failure to develop the circulatory system; abnormalities of kidneys, eyes, and skeleton.
Vitamin D  

Death at about 18 or 19 days of incubation, with malpositions, soft bones, and with a defective upper mandible prominent.


Vitamin E  

Early death at about 84 to 96 hours of incubation, with hemorrhaging and circulatory failure (implicated with selenium).




Vitamin K


No physical deformities from a simple deficiency, nor can they be provoked by antivitamins, but mortality occurs between 18 days and hatching, with variable hemorrhaging



High embryonic mortality during emergence but no obvious symptoms other than polyneuritis in those that survive



Mortality peaks at 60 hours, 14 days, and 20 days of incubation, with peaks prominent early as deficiency becomes severe. Altered limb and mandible development, dwarfism, and clubbing of down are defects expressed by embryo.



Embryo readily synthesizes sufficient niacin from tryptophan. Various bone and beak malformations occur when certain antagonists are administered during incubation






High death rate at 19 to 21 days of incubation, and embryos have parrot beak, chondrodystrophy, several skeletal deformities, and webbing between the toes.


 Pantothenic  acid  

Deaths appear around 14 days of incubation, although marginal levels may delay problems until emergence. Variable subcutaneous hemorrhaging and edema; wirey down in poults.






Early embryonic mortality based on antivitamin use


Folic acid  

Mortality at about 20 days of incubation. The dead generally appear normal, but many have bent tibiotarsus, syndactyly, and mandible malformations. In poults, mortality at 26 to 28 days of incubation with abnormalities of extremities and circulatory system.


Vitamin B12  

Mortality at about 20 days of incubation, with atrophy of legs, edema, hemorrhaging, fatty organs, and head between thighs malposition


Nutrient Requirements of Poultry: Ninth Revised Edition,1994


Michael J. Mavridis D.V.M
CEO / Founder of Mavridis Zootechniki Ltd.

Free 50 hens Poultry coop e-book




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Michael J. Mavridis D.V.M
CEO / Founder of Mavridis Zootechniki Ltd.