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A smelly problem

Ana Alcaraz Published on 20 November 2013

A postmortem examination is a unique experience because it utilizes the full spectrum of all five senses in order to decipher a case. Upon entering the postmortem room, I hone in on the clues that stimulate my senses.

I see changes in various tissue types; I touch the different consistencies, and I hear the contrast between bone and cartilage. Although these senses are essential in solving a case, the sense of smell is another important sense actively used during a postmortem examination.



And by this I do not mean that you are working in a smelly room – a distinct smell of a specific pathology. The smell could be so strong you could “taste” the diagnosis.

Getting the postmortem specimens as soon as possible is critical to a successful investigation, so postmortem changes such as autolysis are minimized.

For example, if a specimen was left out in the sun for a couple of hours, the aroma of rotting flesh is overwhelming – and postmortem changes can be severe.

In these conditions, it may be difficult to determine the disease process that the animal succumbed to. This situation provides a good example of how smell could be one of those pieces of information that can be helpful or deceiving.

The smell of a carcass may be helpful when you recognize a distinct smell attributed to a specific disease process, but it can be leading you in the wrong diagnostic direction if you misinterpret the smell.


A few years back, I had a case of some heifers where the smell helped us, and it was actually a vital piece of information for the resolution of the case. The animal was a big heifer with a story of diarrhea and sudden death.

The pathology residents working with me on the case were eager to try and unravel the mystery of the cause of death of this animal. The three cavities were open: thorax, heart and abdomen.

We knew we had a dog and a cat coming in that afternoon, but they were due to arrive later in the day, so we decided to start working on the dead heifer. Two residents and three students divided up the examination and the sampling of the organs in order to finish early.

One resident was in charge of the thoracic cavity with the help of one student. The other resident took over the abdominal cavity with the help of two other students. She organized the students and followed standard protocol.

First, the abdominal cavity and the gastrointestinal tract were examined. In cows the gastrointestinal tract is composed of rumen, reticulum, omasum and abomasum followed by the small intestine and large intestine.

Following the gastrointestinal tract, we examined the abdominal organs: liver, adrenals, kidneys, urinary bladder, uterus and so on.


When we got to the intestines, we ran into “the smell.” The whole room smelled like a septic tank. The odor is unmistakable – if you have smelled it, you know what I am talking about. One of the students told us that her prior job was cleaning septic tanks, and that she recognized the smell from that experience.

There is a diverse array of smells in this world, and different people react differently to them, which makes it challenging to use them in pathology. Explaining a particular smell is a problem in itself.

For example, how would you describe the smell of an orange to someone who has never smelled one? You first need to identify and distinguish the smell, but then how are you going to put into words what the actual smell of an orange is? An orange smells like an orange, just like a septic tank would smell like a septic tank.

When you conduct necropsies regularly, you start identifying certain patterns that help you in the resolution of future cases. One of these patterns is that in cases of salmonellosis, the intestinal content often smells like a septic tank.

Salmonella is one of the most debilitating intestinal diseases. It is an important disease for dairy farmers because it weakens the animal and leads to significant drops in milk production and may lead to death.

Additionally, salmonellosis also presents an important public health concern because it is a zoonotic disease, which means that it can be transmitted from animals to humans.

In fact, salmonellosis affects many different species, including snakes and turtles, which can also become a source of salmonella in humans.

Back to our case. When we opened the smelly intestine, we found multiple small ulcerated areas in the intestinal mucosa covered by some soft, pale, whitish material.

Such changes are characteristic of what you expect to find in salmonella cases. The rest of the organs were macroscopically normal.

We took samples of each tissue to send out for microscopic analysis; those pieces needed to be no thicker than your pinky to be properly fixed and processed to the point when they can be studied under the microscope.

We also collected tissues for submission to the diagnostic lab for the isolation of the infectious cause. Needless to say, the diagnostic lab isolated salmonella a week later. The samples submitted to virology were negative, thus no virus was found in this case.

Salmonella is a powerful bacterium that will cause a severe disease just by itself. These tests just confirmed our tentative diagnosis, but the clue that gave it away was its distinct, “malodorous” smell.

An example of another disease with a definitive smell, similar to what happens in salmonellosis, is parvovirus in puppies.

The diarrhea and the intestinal content have characteristic smells in affected puppies. There are also examples of non-infectious smells of use in pathology investigations, as cases of arsenic intoxication smell like garlic.

To be a good pathologist you need to use all your senses … Well, almost all, because it is not recommended to use taste. PD

Ana Alcaraz is a veterinarian who trained as a pathologist at Cornell University. She has led hundreds of postmortem livestock investigations. She enjoys challenging cases and thought-provoking discussion.


Ana Alcaraz
Associate Professor of Anatomic Pathology
Western University of Health Sciences