The development of secondary bacterial infections after having flu is a very important complication for horses, both in terms of the degree and longevity of the illness and the financial implications to the owner. For non-sports horses it is probably the most important part of the whole flu syndrome.
Secondary infection may occur if the horse has a compromised immune system, either due to age, stress or illness or because the lining of the respiratory tract has not fully recovered and the horse is over exercised.
Typical signs include a thick yellow/green nasal discharge (shown below), and a wet, often productive cough. The horse may develop a high temperature and be dull and off its food. These signs will usually last for much longer than they would with infection of flu alone. Horses who are very compromised may develop particularly severe infections, leading to pneumonia or even death.
Call your vet if you are concerned that your horse may have a bacterial infection.