Stem rot on tomatoes is usually caused by a species of bacteria called Pectobacterium carotovorum or by Erwinia carotovora subsp. carotovora. It is most often found on staked/trellised tomatoes due to stems being damaged by rubbing on ties or stakes. It is also found in tomatoes that have been pruned.
How It Spreads
The bacteria usually only infects plants that have been damaged as it enters the system through cuts and abrasions.
Bacterial stem rot affects mostly nightshade vegetables. A fungal disease also called stem rot, affects a wide variety of edible and ornamental plants.
The initial symptom, wilting of the whole plant, is usually noticed when the first lot of fruit is ripe and ready for harvest. The wilting is caused by the pith (centre of the stem) disintegrating. This disease is similar to pith necrosis in that respect. Unlike pith necrosis however, the outside of the stem will also become wet and slimy if a tomato plant is infected with stem rot. Sometimes, in severe cases, plant extremities may also turn black and drop off.
An effective treatment has not yet been identified. If you catch it early however, you may be able to prune off affected areas to prevent spread to the rest of the plant. If you do this, disinfect the cut with an infusion of garlic or chives in water. The success of this method is variable.
The best way to prevent this disease is to tie plants loosely to stakes with soft ties that won't rub on the stems. I would also recommend not pruning your tomato plants.
If you must prune plants (those gardening in very humid climates who grow very bushy tomatoes may need to do some light pruning to improve air circulation but in almost all cases, if plants are adequately spaced, pruning is unnecessary) always disinfect your secateurs in between each cut and, in particular, in between plants. A dilute bleach solution is suitable as is a solution of (or even straight) eucalyptus oil. Always make sure your plants are healthy as well. If plants are suffering from nutrient or water deficiencies (or too much water) then they will be much more likely to succumb to disease if you prune them or they become damaged as a result of being staked or trellised.