Many different bacteria can kill the chicks in the shell.  The shell is a very porous membrane, it is full of small holes that allow moisture as well as bacteria to pass through.  It is through this porous membrane that the embryo exchanges gasses and aquires needed moisture.  Nutritional  substances are stored in the egg as it develops in the hen.  Your dead- in- shell, can be caused by a number of different problems. Determining the point in development at which death occurred can be very helpful in establishing the cause.

Periodic candling of the eggs will help you determine when in the  incubation process death is occurring.  The blood vessels that are  visible from about the 3-4 day should  slowly increase in density .  You  should then be able to see the small embryo slowly increasing in size.  The egg will darken as the chick takes up more and more of the  available space.   The air sac should stay about the same size, with only  a small increase in size during the last third of incubation.  A large increase in the air sac size or a change in shell color to dull gray suggests a dead embryo.  A stop in the increasing opacity of the developing egg or cloudiness suggests  embryo death.

When you have a dead in shell, carefully open the egg on the end that  has the air cell.  A small membrane separates the embryo from the air cell.  If this membrane has not been broken, the death is most likely caused by the egg being chilled early in the incubation process.  The first trimester is the most critical period.  An egg chilled during this time  will often continue to develop, but will fail to break into the air cell and will die without hatching, (late death) . Chilling in the third trimester often does not affect hatch.

If the air cell membrane has been broken, carefully examine the chick.  If the problem is insufficient humidity, the chick will appear to be stuck to the side of  the egg.  When there is too little  moisture, the chick becomes glued to the shell and is unable to rotate and chip his way out of the egg.  He becomes trapped in the egg and dies, ( failure to hatch).  The chick will appear fully developed but the liquid around him often has a thick, sticky appearance.

Most bacterial and viral deaths will occur in the first half of incubation.  Bacterial problems resulting in embryo death are uncommon in dry nests with clean eggs.