Audie & all,
This is gonna be fairly lengthy, so put your reading glasses on - or get ready scroll past it.
I do those diagnostic workups on aborted/stillborn calves all the time - and as a beef producer and former food-animal practitioner, they used to frustrate me. A lot. We arrive at a definitive answer as to the cause of abortion/death in less than 25% of the cases. Lots of those 'inconclusive' reports.
After doing them for the last 20 years, though, I've justified it with myself that an awful lot of the ones we see are NOT due to infectious or contagious causes. We have no problem identifying those IBR, BVD, Lepto, Neospora, and nitrate-toxicity abortions - and I've come to the point that I'm mainly doing these to rule in/out the infectious problems that the producer and veterinarian can actually do something about.
Most of the abortion/stillbirth cases I see are just a sporadic single animal, with no history of others in the herd aborting. I can count on one hand(and have some fingers left over) the number of true 'abortion storms' I've been involved with in nearly 30 years of veterinary medicine and diagnostics - but if you read the textbooks, you'd think an abortion storm was just around every corner.
Many times, the diagnosticians at the lab are 'working with their hands tied behind their back' in a way.
We often get the aborted or stillborn calf, but rarely get placenta(afterbirth) to examine. I know, I know - sometimes it's not available: the dogs/coyotes or the cow already ate it, or it's still in the cow as she disappears over the top of the next hill, or the farmhand pitched it in the manure pit, etc.
But in close to 50% of the cases where I get placenta to look at, I find a lesion or isolate a specific pathogen - from the placenta; but there's NOTHING - zero, zip, nada - abnormal in the calf or any of its tissues. Unfortunately, I only receive placenta in *maybe* 10% of the cases I work up. I tell my veterinary clients and producers - If you can only send the calf or the placenta, send me the placenta! I'm more likely to find the answer there than in the calf.
Paired serum samples from the dam - one at the time of the abortion, one 2-3 weeks later - can also help tremendously in ruling in/out infectious causes - antibody titers to IBR, Lepto, etc., will be rising or decreasing between the initial and convalescent samples, depending upon whath agent may have caused the abortion. But we rarely get serum samples, and even more rarely do we get that important 'convalescent' sample so we can see if antibody levels are going up, down, or are unchanged. A single sample doesn't tell us much, other than that the cow has been exposed to a specific agent at one point in time - could be natural exposure, or could be due to vaccination.
We know that a lot of human miscarriages are due to women having an 'incompetent cervix' - their cervix won't or can't stay closed, causing premature delivery or allowing bacterial from the vagina to gain access to the fetus and placenta. While cows don't walk upright on their hind legs like people do, I wonder how many cows might have an incompetent cervix, which allows the normal bacteria from the vagina to get through and infect the placenta.
Additionally, there is some degree of immunosuppression at the maternal-placental interface; if not, the cow's immune system would reject that 'foreign object'. I can't help but think that this immunosuppression at that level also inhibits the cow's ability to fight off local infections of the placenta that can cause abortion.
For the most part, we don't know how many of these aborted/stillborn calves have potentially lethal genetic defects - whether they are a heritable defect or just an 'accident'. About 20 years ago, researchers at U.of Saskatchewan undertook a study to look at this aspect. They took third-trimester fetuses that had been aborted, but not autolyzed, and cultured fibroblasts(connective tissue cells) from the pericardial sac, then karyotyped them, like they do with cells taken by amniocentesis or chorionic villus sampling in women looking for Down's Syndrome, etc., in human fetuses. In about 11% of those bovine fetuses sampled, there were genetic abnormalities that *might* have contributed to fetal death and abortion. Since this study was done on nice, fresh, third-trimester fetuses, I have to wonder how many of those earlier ones, or the ones that are retained in utero and are sorta rotten by the time the cow expels them might be genetically abnormal. It seems that in some cases, abortion is Mother Nature's way of getting rid of an unfit or unsurvivable fetus.
Then, there are always the stillbirth/neonatal death cases - full-term calves that the owner finds dead. Some of those have swollen tongues/heads, and you KNOW that they had a prolonged difficult delivery, and may have been dead or so weak and hypoxic by the time the cow got 'em out that they just didn't make it. Then there are those that make me think they were probably a posterior presentation(backwards) and the calf 'drowned' after his umbilical cord got crimped off in the pelvic canal and before the cow managed to get him all the way out. And then, you also have to consider prevailing weather conditions as a contributing factor, especially if the calf was born to a heifer - some of 'em just don't know what to do with that calf to get him cleaned up, dried off, and on his feet nursing.
Hope this gives you a new perspective on why results from your diagnostic lab may be 'Inconclusive' - and hopefully will also give you some tips on what samples to make sure are collected and submitted for examination so that our chances are improved in being able to tell you why that calf was aborted.