Atypical bacteria are bacteria that do not color with gram-staining but rather remain colorless: they are neither Gram-positive nor Gram-negative. These include the Chlamydiaceae and the Mycoplasmataceae (including mycoplasma and ureaplasma); the Rickettsiaceae are also often considered atypical.
Gram-positive bacteria have a thick peptidoglycan layer in their cell wall, which retains the crystal violet during Gram staining, resulting in a purple color. Gram-negative bacteria have a thin peptidoglycan layer which does not retain the crystal violet, so when safranin is added during the process, they stain red.
The Chlamydiaceae and Mycoplasmataceae lack a peptidoglycan layer so do not retain crystal violet or safranin, resulting in no color. Ricketsiaceae are technically Gram-negative, but are too small to stain well, so are often considered atypical.
Peptidoglycans are the site of action of beta-lactam antibiotics such as penicillins and cephalosporins, so chlamydia and mycoplasma are naturally resistant to these drugs, which in this sense also makes them “atypical” in the treatment of their infections. Macrolides such as erythromycin however, are usually effective.
Finally, some of these bacteria can cause a specific type of pneumonia referred to as atypical pneumonia. That is not to say that atypical pneumonia is strictly caused by atypical bacteria, for this disease can also have a fungal, protozoan or viral cause.