I'm so sorry to hear about your foal . I am somewhat puzzled as to why your vet seems to think that this condition is somehow related to foals that are closely bred.
The following is pretty common knowledge regarding the diagnosis of Rhodocuccus equi and may be of help.
Rhodococcus equi, (previously known as Corynebacterium equi) causes a persistent bacterial pneumonia in foals, and may become established as an endemic disease on some breeding farms. It may result in considerable losses through costs of diagnosis and treatment, and in some cases, through death. A better understanding of the disease may reduce its significance. There appears to be an increase in the importance of this bacterial disease, with the increased concentration of foals on a smaller number of breeding farms.
A recent survey at the Ontario Veterinary College showed that Rhodococcus equi infection accounted for 10% of all foals sent for post mortem examination and 45% of all foals with pneumonia. These numbers, however, may not reflect the true incidence of the disease in Ontario. While the infection does not seem to be a problem on many breeding farms, on farms with endemic disease, all the foals may become sufficiently ill to require treatment.
Ecology of the Organism
Rhodococcus equi is a robust soil organism widespread in the environment. It has simple nutritional requirements, which are perfectly met by materials in the manure of animals, whether from horses, cattle, pigs, or even chickens. The organism will potentially multiply wherever there is horse manure. Temperature also plays a major role in the growth of Rhodococcus equi, with optimum growth at 30ºC. In Ontario’s hot summer of 1988, death of foals was not restricted to those born to mares on breeding farms, under ideal temperatures, one organism may multiply 10,000 times in a few days in an area contaminated by horse manure.
There seems to be a direct relationship between the number of Rhodococcus equi in the environment of young foals and the number of cases of pneumonia. Because the organism reaches the lung by inhalation, dusty manure-contaminated environments (such as are commonly found in loafing paddocks on horse breeding farms in the summer) are potentially lethal sources of infection. The equivalent of one tablespoon of dusty soil kicked up by a mare, perhaps into the face of her sleeping foal, can contain a million of these bacteria. To prevent Rhodococcus equi infections, foals should thus ideally be born in January (when the organism remains frozen in the ground).
Rhodococcus equi can also multiply to dangerous levels in the intestine of a young foal. Foals establish a normal intestinal flora of bacteria from birth to 12 weeks. In this period, they seem to be susceptible to being infected by abnormally high levels of Rhodococcus equi. Levels of up to 10,000 organisms per gram of manure are sometimes shed from infected foals. After 12 weeks, the bacteria rapidly decline in number and no longer multiply in the intestine. The ability of the organism to multiply in foals, but not in adult horses is likely another reason why horse breeding farms may become progressively infected with Rhodococcus equi. Any of the bacteria then found in the intestine result from acquisition of grass.
These facts help to explain why some farms become heavily infected with the bacteria and develop problems each year with foal pneumonia. Little is known about the susceptibility of this robust organism to disinfectants. However, because many horse breeding farms do not use concrete, disinfection procedures are often difficult to carry out in the stalls and impossible in the loafing paddocks. In the areas where the foals are kept, regular disposal of manure and dust control have proven effective in reducing the levels of bacteria.
