Changes, and A Tale of Cow Conjunctivitis and Pneumonia

Things have been grim this year. Pandemic. No toilet paper in the stores. Being afraid to even go in said stores. Losing my little old Mimi. 

I've decided to take the blog in a new direction. A bit of an experiment, just to see how it works. This is nothing new--CircusK9 has evolved more than once since I started it lo these dozen years ago. 

I want to talk more about my job. I love my job. Despite the inherent ick factor that some people might have about the subject, my job provides me with an endless stream of absurd and interesting tales.

Like this one. I have developed a good working relationship with a clinic in SW Arkansas. This three-vet practice sees all species, and they send most of their necropsy cases to the lab. Because of the distance from their clinic to Little Rock, and because they are not on the route of one of our regular couriers, the vets often conduct field necropsies of production animals and send us a "box of parts" instead of the entire cow. Cheaper and faster.

One of the vets has been working with a beef cow-calf operation for some weeks that is having a big problem with conjunctivitis in the herd. The usual bacteria responsible for this is Moraxella bovis. That's the one you learn about in vet school. But that's not what they got back from swab samples. They got a species of Mycoplasma. They started to treat the conjunctivitis but some of the cows began dying from respiratory disease.

Cows are prey animals and have an amazing capacity for hiding respiratory disease until things become pretty disastrous in there. I've opened up cows to find 80% or more of their lungs full of pus and bacteria, and heart and lungs stuck to each other and the body wall with expansive fibrin adhesions. This is not good. Most vets who work with these animals, including me, suspect that cows harbor subclinical bacterial pneumonias pretty much all the time, and are just waiting for some stressor--transportation, parturition, change in weather, change in feed--to cross that line into severe respiratory disease.

So my friend sent me two boxes of parts from two cows from the conjunctivitis herd. He also sent some horrifying pictures of the conjunctivitis--I will spare you. I never really got anything definitive from the parts other than confirming that it was a bacterial pneumonia. He kept calling me to talk about this Mycoplasma they had isolated from the eyes, not Moraxella. It was a species I had not heard of, and I initially thought I just wasn't understanding him clearly. He often calls me when he's in a windy field standing over a dead cow so there is lots of background noise. 

See, Mycoplasma bovis is a common culprit in bovine respiratory disease. Mycoplasmas are special bacteria--they don't have cell walls. They like to form microabscesses which are very difficult to treat. In fact, cows with Mycoplasma pneumonia are often not treated (they are culled). The lungs my vet friend sent to me did not look like Mycoplasma lungs. They looked like Mannheimia or Pasteurella lungs. But we failed to culture those bacteria. And you can't really culture Mycoplasma. We rely on PCR tests to identify that one. But I didn't initially request a Mycoplasma PCR because, well, the lungs didn't look like Mycoplasma lungs.

It's weird how distinctive these different bacterial infections can be. And after you see dozens of gnarly cow lungs, you get a feel for how the different bacterial pneumonias present grossly. My pathologist agreed--the tissue damage we saw on the microscope slides of the lungs was most consistent with Mannhemia. How come we didn't culture it? Sometimes that happens. Failure to culture doesn't mean it wasn't there.

But my vet friend kept going on about this "bovoculi"--and I finally put it together. 

Mycoplasma bovoculi--get it? bov = cow, oculi = eye--is a Mycoplasma implicated (link will open a PDF) in the past few years in a particularly nasty cow conjunctivitis. I found out that it likes to hang out with its friend Mycoplasma bovis. Which we found in the lungs of these cows when I had the PCR test run.

Some vet school adages really prove to be true, over and over. Common diseases commonly present uncommonly. I missed the Mycoplasma connection in this case, but I guarantee it won't happen again.

Sweet Mimi

Yesterday, Mimi's burdens became too heavy, and I had to pick them up and help her take the last steps of her journey. 

Little old girl, you can now run fast, run far, and take long naps in the sun.

You were with me for 15 years--it will never be long enough. 

Quicksilver Let's Play House 9/5/2005-11/11/2020

Well Hello, Little Frie....Oh Fucking Fuck

As I was walking to my car yesterday morning to leave for work, I noticed ...something... in my far peripheral vision.

 

 

Yeah. I had passed within a couple of feet from her.

She was a real beauty, as you can see. But I'm afraid I'm not willing to share my property with poisonous snakes, so I had to dispatch her.

I calmly put my bags in the car, and opened the garage door. I went in and put on my knee-high work boots, grabbed a shovel and a hatchet, and did the deed.

I briefly considered taking her body to work to take a look at (I have the PPE, the tools, and a way to properly dispose of her). But then decided that was probably taking things just a wee bit too far.

Tales From The Necropsy Floor: "My eyes! My eyes!"

A couple of weeks ago, on a Monday, I was doing a necropsy of a cow that I had taken in over the weekend. She had been in our cooler for at least 36 hours but had been dead for at least a day or so when we put her in there. That's a long way of saying she was definitely dead and bloated.

When I was reaching across her to remove the muscles and fat of the abdominal wall to expose the abdomen, I accidentally nicked her enormous, gas-distended rumen with my scalpel. The blast of gas and aerosolized rumen liquid shot up my face and right into my eyes.

Uh-oh. 

I had an N95 mask on so my mouth and nose were protected. But not my eyes. I wear glasses but have not yet found safety goggles that don't damage my extremely expensive and utterly necessary eyeglasses. A face shield would have been useless. I stopped to wash my face but the inoculation had already occurred.

Sure enough, 48 hours later, I woke up with red, painful, gunky eyes. This progressed to a piercing headache that I couldn't tamp down with ibuprofen, and quite a bit of pain when I had to move my eyes. 

I finally gave up the following Monday, called in sick to work, and hauled myself to an urgent care clinic. I was diagnosed with conjunctivitis, of course, but also something called epi-scleritis, which meant the muscles and other tissues around my eye were involved too. 

Better living through the standard pharmacopia, however: antibacterial eye ointment (oily, gross) and diclofenac, a stronger NSAID than anything I could get OTC. I even got a steroid shot in my butt at the clinic. I started feeling better in just a few hours. 

While this sort of thing is a fairly typical hazard of my profession, and I was not exposed to anything really nasty, it will certainly change my behavior in the future. For starters, I think I will decompress those rumens first thing!

Tales From The Necropsy Floor

At the lab, we see a colorful array of species and their endlessly variable disease presentations. There is a seasonality to some of our cases--more kittens in the spring, more cows in the fall, more cow abortions in March through May. But that doesn't mean we don't see kittens in winter, cows in summer, and abortions any time of the year. 

Backyard poultry cases always liven up the necropsy floor. They usually have interesting parasites, internal and external. And when it's an older laying hen, it almost always has cancer. Invariably, those older hens come wrapped in scented trash bags. I am not sure exactly why so many backyard bird owners submit their birds wrapped in scented trash bags. Maybe there's an instruction manual that I haven't come across yet. 

My colleague and I divide the week's necropsy cases up between us, mainly so I can get admin work done and be free for meetings and such. And even though I have my days on the floor, and X has his days, we often end up working necropsy cases at the same time. While it can get kind of chaotic for the tech who has to bounce back and forth between us, it's a great opportunity for us to learn from each other. We look over each other's shoulder, poking and prodding and asking questions, and we argue about differentials and diagnostics.In fact, we argue about these things all the time, but when we have the animal remains in front of us, there is an extra dimension to the discussions. To be clear, I don't use "argue" with a combative connotation. It may get heated but it's always professional.

My colleague X and I have radically different styles when doing necropsies, and although we usually arrive at the same list of differentials for any given case, we get there by separate routes. That doesn't mean our conclusions are not sound or supported by gross findings, but it does highlight how many different ways that diseases can present themselves. 

Performing a necropsy requires a systematic approach to ensure that you don't miss anything, and my colleague and I use the same basic approach for all cases. But there are stylistic differences. For the gross pathology component, I tend to lay all tissues out and examine them as a group while he examines each tissue and organ as he goes, but the end result is the same. Swabs get taken and sometimes fresh tissues are set aside for other tests. For the histopathology part, selected tissue samples are placed in formalin. We use formalin as a fixative to firm up tissues so we can cut very thin slices and put them onto microscope slides.

The biggest difference in our styles is how we select tissues for histopathology. I have a very parsimonious style, so, for example, if the spleen is normal, I'll place a small piece of it in the formalin jar and discard the rest. My colleague thinks big. Very big. It's not unusual for him to place entire cat heads (he was interested in one of the eyes) and the complete bodies and all viscera from small chickens in the formalin jar. This has become a bit of a running joke back in the histo lab because when my cases are laid out for trimming, there is a neat little pile of tissues, easy to sort and select. When his cases are laid out for trimming, there are enormous, macabre mounds of organs and appendages.

Yesterday, I picked up a backyard bird case from him in order to even out our case load for this week. But I didn't tell the technician that I was taking the bird. She thought my colleague was doing all three cases that afternoon, and she set out equipment at each station with him in mind. 

The chick was about 4 weeks old, not even as long as my palm. But the technician had a three-liter formalin jar all ready to go. Three liters, nearly a gallon of formalin, for tissues from an animal that didn't even weigh 50 g. As I tossed my tiny little pile of tissue samples into this massive jar, I glanced over at my colleague who was working nearby on a cat and I loudly said to the technician, "Well, it's obvious that you expected X to be doing this necropsy instead of me!" He looked up, blinked a couple of times over his mask, and all three of us cracked up.

I am grateful that I work with a colleague like X who can take a bit of good-natured teasing and not alter his style one tiny bit.

"Dr. A Never Met An E. coli That She Didn't Like"

For the great majority of our necropsy cases, we can identify the cause of death right away. There might be a few specifics to sort out, like confirming the specific kind of cancer. But we can usually get most of the diagnosis while on the necropsy floor. 

There are always exceptions. I mentioned in a previous post the handful of cases we were seeing of young dogs with bloody parvo guts that never tested positive for parvovirus. Cultures of tissues from these cases did result in scant to moderate growth of E. coli. Usually, that alone isn't enough to provide a diagnosis.

We culture E. coli and its friends in many of our cases. But not all E. coli are the same. E. coli is everywhere, inside you and outside. It can be considered an environmental contaminant. Animals poop it out, it can live in the soil--you can't get rid of it. But we use sterile techniques to acquire our culture swab samples. So when I get any growth of E. coli, especially from poultry cases, I lean heavily to that as a possible cause of death. 

We've recently had a run of necrotic, hemorrhagic pneumonias in companion animals. Some of them had scant growth of E. coli from lung swabs. But your generic environmental contaminant strain of E. coli doesn't cause that kind of tissue damage. You need a hemolytic strain for this. Our bacteriology group had not been mentioning anything about hemolytic behavior in their reports.

Well. I asked the bacteriology supervisor about this, and it turns out her techs had failed to report the culture results correctly, and the bacteria they cultured were in fact hemolytic. 

I was able to correct the couple of cases that we still had open, but there were half a dozen other cases that were likely hemolytic E. coli infections. But because I've "never met an E. coli that [I] didn't like," according to our pathologist, I had fortunately included a diagnosis of "colibacillosis, suspected" on those cases. 

One of the important aspects of getting a diagnosis is integration. Clinical history, what you see during necropsy, results of tests for viruses and cultures of bacteria, what you see through the microscope when you look at the stained tissue slides, what you learn by reading published literature--all of these disparate types of data get rolled up into a narrative of pathology for each case.

There is one more component of that integration that is much harder to describe. It is a combination of the pathologist's experience, bias, application of the rule that "common diseases present uncommonly" (which means don't go looking for uncommon diseases right off the bat), and a type of gestalt that can develop when you see several similar cases cluster in time (there is definitely a seasonality to some diseases, and some diseases are more common in some species than others). 

The title of this post has complicated subtexts. It is an acknowledgement that I was right in proposing colibacillosis diagnoses for those cases. But it also contains a warning about jumping to diagnostic conclusions without considering all of the differentials. It isn't always E. coli's fault. 

Except when it is.

Lessons From The Past

Early on in the pandemic, I found myself most strongly affected by empty shelves at the grocery store. It was stressful enough to be leaving for work throughout March and April and May when all my neighbors were staying at home. It was stressful to insist back in March that my team at work wear masks when nobody else at the lab was doing so. But seeing large gaps and entire aisles with nothing but stray scraps of paper and dust on the shelves made me the most anxious. Increased my heart rate. I hated going to the store. I stopped my normal weekly trips and stretched out my visits to once every three weeks. 

The weird mass hysteria over toilet paper and paper goods also affected me in an unexpected way. I found myself looking at a paper towel and thinking, well, I've only used this corner of it. I can use it again. And I would carefully set it aside for that purpose.

My grandparents lived through the depression. They are long gone now, but as a kid, I would see them hoard bits of wire and string, re-use a kleenex all day, save tag-ends of soap and cooking grease to accumulate in jars and cans. I distinctly remember thinking at the time that this was odd behavior, but I never really made the connection until now. It's not odd at all when you see those empty store shelves.

I was already thinking a lot about this when I encountered an example of how this pandemic has changed our behavior at work too. 

We use a particular kind of disinfectant to clean the necropsy area at the lab. There are many cleaners that will effectively kill the biological agents that we know are present, but lots of those cleaners are corrosive. We use disinfectant in our boot wash and apply disinfectant solution to many different types of metal, plastic, and ceramic surfaces and tools, and we are ourselves exposed to it. We prefer to use neutral types of disinfectants. 

When we started running low on our stock, we placed an order like we always have. And weeks passed. It wasn't available from that vendor. This vendor might have it, but delivery would be in October or later. Another vendor said, yes, we have it, then the next day said, oops, sorry, no we don't. I started evaluating our options. We could use commercial grade bleach but it really was a choice of last resort. Bleach wasn't available from any vendor either but our bacteriology section had some bottles we could have borrowed. Then our Safety Coordinator came up with a bottle of a very concentrated phenol cleaner that nobody else at the lab wanted to use. Just mixing this stuff up into a solution required full PPE to protect the user. I said, I'll take it! We wear full PPE in necropsy anyway. We could make it work. It wouldn't corrode our boots or our metal tools. If things became dire, we could switch to bleach.

Just a few days later, our shipment of neutral disinfectant arrived. After a brief celebration, I told my team to prepare a purchase requisition for more. The new normal is that we need to order supplies and equipment many weeks in advance. We can no longer wait until we actually need something.

Remember how we started: the pandemic has affected us in subtle ways. I decided that we will reserve our precious neutral disinfectant for important things like tables and equipment. And the phenol cleaner will be used for the boot wash bucket, which is mixed and emptied daily. I told my two technicians, both in their late 20s/early 30s, about my grandparents and the Great Depression, but I am sure they didn't understand how that related to using phenol cleaner for the boot wash.

Hoarding. Choosing less desirable items to preserve things we have decided are more desirable. Using less. Not odd behavior at all.