One cool thing about microbiology is getting a sideways glance at the epidemiology of a lot of diseases, both in seeing what specimens get handled and in observing trends over time.
One example comes from my being at the "downtown" hospital this month. With a much more indigent population, the AFB bench is a lot busier because of all the tuberculosis patients. However, the hospital only runs fungal cultures once a week, whereas my program's "main" hospital does it every day. Why? If I remember the explanation correctly, the main hospital does a lot of fungal cultures on immunosuppresed patients, mostly transplant recipients. The downtown hospital doesn't do transplants, though. They have a whole lot of HIV patients, but the regular blood culture bench is sufficient to look for most fungal infections that they might have.
Even more interesting is a story the main hospital's lab director has told us once or twice. A few years ago, Klebsiella Pneumoniae Carbapenemase started popping up. These are Klebsiella pneumoniae bacteria that are resistant to one of the most powerful categories of antibiotics. One particular strain, KPC 2, first showed up in New York. The very first KPC strain our lab saw was KPC 2, in a patient visiting from New York. After he arrived, a bunch more examples showed up. The patient returned to NY, and the incidence of KPC 2 died down. Of course, KPC 3 started showing up and got a stronger foothold in the area. A few weeks ago, another KPC 2 specimen registered in the lab, and yep, the patient was from New York. The clinical approach would be the same in all these cases, but it's fun to keep tabs on this sort of stuff.
Saturday, August 16, 2008
Sunday, August 10, 2008
learning pathology
One challenge facing pathology interns is, well, we have no idea what we're doing. Medical school prepares you to be a clinician -- a general practitioner or a surgeon. Sure, I took a pathology class my second year, but that was more than two years ago, and compared to what a pathologist actually needs to know, that would be like saying an arithmetic class prepared me for upper-level calculus.
(Note: My fellow interns feel the same way; i.e., they possess very little actual pathology knowledge and have a ton to learn. There are certainly some well-prepared interns out there, but they are the exception more than the rule.)
Fortunately, our residency program is cognizant of our neophyte status and has many things in place to get us up to speed:
* We all observed an autopsy our first week here. While that doesn't mean I'm ready to do one myself, it was good to have a general idea of how to approach them.
* Once a week for the first month, we have a "grossing conference" where one of the upper-level residents shows us how to prepare a surgical specimen for microscopic examination. For example, we were shown how to take a kidney, examine it outside the body, cut it into pieces, take appropriate specimens (cancer, margins, etc.), and submit them to be placed on slides.
* Also once a week, there are "normal histology" sessions where we relearn what normal tissue looks like. We learned that first year, which is even more toward the back of my brain, and you can't diagnose the abnormal without recognizing the normal.
* We have occasional lectures on how to survive CP call. This is especially important for those of us who haven't had blood bank/transfusion, since the majority of calls the CP resident receives deals with those issues.
* Every week, there are unknowns that the attendings go over with the residents. As first years, our goal is to describe what the lesions look like. We aren't expected to offer a differential diagnosis until second year, which is good, because I still can't even describe the things properly.
* There are study sets of surgical pathology slides for us to look over. This is mostly interesting cases, but I think some bread-and-butter diagnoses are mixed in as well. In the microbiology lab, there are plenty of study sets, which is about the only way to actually observe the more rare bugs. Other CP rotations probably do something similar to this as well.
* Once a month, we get a test over a particular topic (mediastinal masses, for example), where we have an hour to offer diagnoses on slides and answer fill-in-the-blank questions. All the residents participate in this. It's both comforting and unsettling to see that, while the PGY-1s averaged about a 30 on the one we just took, the PGY-4s averaged about a 70 on the exact same test.
If that sounds like a lot, it is! I feel overwhelmed, not just with how much I need to know to be a great pathologist, but with how much I need to know just not to feel like an idiot at the microscope. It's gonna be a long four years ...
(Note: My fellow interns feel the same way; i.e., they possess very little actual pathology knowledge and have a ton to learn. There are certainly some well-prepared interns out there, but they are the exception more than the rule.)
Fortunately, our residency program is cognizant of our neophyte status and has many things in place to get us up to speed:
* We all observed an autopsy our first week here. While that doesn't mean I'm ready to do one myself, it was good to have a general idea of how to approach them.
* Once a week for the first month, we have a "grossing conference" where one of the upper-level residents shows us how to prepare a surgical specimen for microscopic examination. For example, we were shown how to take a kidney, examine it outside the body, cut it into pieces, take appropriate specimens (cancer, margins, etc.), and submit them to be placed on slides.
* Also once a week, there are "normal histology" sessions where we relearn what normal tissue looks like. We learned that first year, which is even more toward the back of my brain, and you can't diagnose the abnormal without recognizing the normal.
* We have occasional lectures on how to survive CP call. This is especially important for those of us who haven't had blood bank/transfusion, since the majority of calls the CP resident receives deals with those issues.
* Every week, there are unknowns that the attendings go over with the residents. As first years, our goal is to describe what the lesions look like. We aren't expected to offer a differential diagnosis until second year, which is good, because I still can't even describe the things properly.
* There are study sets of surgical pathology slides for us to look over. This is mostly interesting cases, but I think some bread-and-butter diagnoses are mixed in as well. In the microbiology lab, there are plenty of study sets, which is about the only way to actually observe the more rare bugs. Other CP rotations probably do something similar to this as well.
* Once a month, we get a test over a particular topic (mediastinal masses, for example), where we have an hour to offer diagnoses on slides and answer fill-in-the-blank questions. All the residents participate in this. It's both comforting and unsettling to see that, while the PGY-1s averaged about a 30 on the one we just took, the PGY-4s averaged about a 70 on the exact same test.
If that sounds like a lot, it is! I feel overwhelmed, not just with how much I need to know to be a great pathologist, but with how much I need to know just not to feel like an idiot at the microscope. It's gonna be a long four years ...
Friday, August 1, 2008
so ... what do pathologists do, anyway?
One of the reasons I started this blog is that most people don't really know what pathologists do. When I was a medical student, patients would ask me what field I wanted to enter, and my answer usually gave them a puzzled look. A few people replied, "So you're just going to work with dead people?"
A lot of physicians also don't seem to understand what pathologists do, or at least aren't aware of their full range of skills and limitations. So, here is a quick rundown. If this is too long to read, just know that anytime something gets sent to "the lab," a pathologist is responsible for the results that are returned.
ANATOMIC PATHOLOGY
There are actually two halves to pathology: anatomic and clinical. AP is the branch that most people are more familiar with, and that medical students study during second year. The three main "sub-categories" are surgical pathology, cytopathology, and autopsy.
Surgical pathology is the preparation and evaluation of patient tissue. This includes both surgical specimens (a gallbladder removed during surgery, for example, or a breast cancer mass) and biopsies (a mole removed at the dermatologist's, or a polyp plucked out during a colonoscopy). These tissues are sent to pathology, where they are "grossed," or cut into and prepared. They are then stained with colorful dyes, and a pathologist looks at them under the microscope and determines what exactly is going on.
This is a topic for another post, but I do want to mention that this is rarely cut and dry. Medical students may learn that basal cell carcinoma of the skin looks one way, but a pathologist knows that it can have many different appearances. Furthermore, many diseases exist along a spectrum, and determining where exactly something sits on the spectrum can be as difficult as looking at one spot on a spectrum of 1,000 colors and identifying the corresponding crayon. Fortunately, there are ways of getting answers, usually through staining the tissue with dyes that only stick to certain entities.
Autopsy is what everyone associates with pathologists. There's not much to say here, except that there is a lot more to the field than just this. Some pathologists gain additional training in forensics and do these all the time, but some just cover them occasionally for their hospital or practice, and others probably manage to avoid them altogether. Autopsies are also performed less frequently than in the past, for a few reasons.
Cytology is similar to surgical pathology, except that the specimen being looked at under the microscope is a cluster of cells instead of a firm piece of tissue. Pap smears are a good example of this. Cytology also offers pathologists patient contact, as they perform fine needle aspirations (FNAs) to suck out the cells that are going to be examined.
CLINICAL PATHOLOGY
This covers such a wide variety of fields that I'm pretty sure I don't know everything that's involved. Pathologists oversee or consult on labs running tests on bodily fluids. This includes microbiology labs, clinical chemistry labs (where routine blood tests get sent), and many more. Disciplines such as transfusion medicine and hematopathology also fall within CP.
Some of this is just oversight and troubleshooting. Techs do the day-to-day work in the lab, but when a weird test result pops up, a machine is clearly producing bad results, or a clinician has a question to ask, the pathologist steps up to the plate.
Pathologists also oversee the blood bank and approve giving out blood products. As a good example, my institution is really, really short on a particular blood type right now, so we have to be stingy with it. A surgeon may call and ask for twenty units, and the pathologist on call will approve five (sounds bad if you are that patient, but not if you're the car-crash victim coming in ten minutes from now).
This aspect of pathology is poorly communicated to most medical students (we had one guy come in for an hour and mumble about a bunch of tests the lab ran; if you'd asked me then, I wouldn't have been able to identify him as a pathologist). Most nonmedical people probably aren't aware that doctors oversee all the labs, either, since on the surface it doesn't seem like you'd need a doctor down there.
That's everything in a nutshell. I'm only one month into my four-year residency. Maybe 47 months from now, I will write this essay again in light of what I've learned and what I think is important to emphasize.
A lot of physicians also don't seem to understand what pathologists do, or at least aren't aware of their full range of skills and limitations. So, here is a quick rundown. If this is too long to read, just know that anytime something gets sent to "the lab," a pathologist is responsible for the results that are returned.
ANATOMIC PATHOLOGY
There are actually two halves to pathology: anatomic and clinical. AP is the branch that most people are more familiar with, and that medical students study during second year. The three main "sub-categories" are surgical pathology, cytopathology, and autopsy.
Surgical pathology is the preparation and evaluation of patient tissue. This includes both surgical specimens (a gallbladder removed during surgery, for example, or a breast cancer mass) and biopsies (a mole removed at the dermatologist's, or a polyp plucked out during a colonoscopy). These tissues are sent to pathology, where they are "grossed," or cut into and prepared. They are then stained with colorful dyes, and a pathologist looks at them under the microscope and determines what exactly is going on.
This is a topic for another post, but I do want to mention that this is rarely cut and dry. Medical students may learn that basal cell carcinoma of the skin looks one way, but a pathologist knows that it can have many different appearances. Furthermore, many diseases exist along a spectrum, and determining where exactly something sits on the spectrum can be as difficult as looking at one spot on a spectrum of 1,000 colors and identifying the corresponding crayon. Fortunately, there are ways of getting answers, usually through staining the tissue with dyes that only stick to certain entities.
Autopsy is what everyone associates with pathologists. There's not much to say here, except that there is a lot more to the field than just this. Some pathologists gain additional training in forensics and do these all the time, but some just cover them occasionally for their hospital or practice, and others probably manage to avoid them altogether. Autopsies are also performed less frequently than in the past, for a few reasons.
Cytology is similar to surgical pathology, except that the specimen being looked at under the microscope is a cluster of cells instead of a firm piece of tissue. Pap smears are a good example of this. Cytology also offers pathologists patient contact, as they perform fine needle aspirations (FNAs) to suck out the cells that are going to be examined.
CLINICAL PATHOLOGY
This covers such a wide variety of fields that I'm pretty sure I don't know everything that's involved. Pathologists oversee or consult on labs running tests on bodily fluids. This includes microbiology labs, clinical chemistry labs (where routine blood tests get sent), and many more. Disciplines such as transfusion medicine and hematopathology also fall within CP.
Some of this is just oversight and troubleshooting. Techs do the day-to-day work in the lab, but when a weird test result pops up, a machine is clearly producing bad results, or a clinician has a question to ask, the pathologist steps up to the plate.
Pathologists also oversee the blood bank and approve giving out blood products. As a good example, my institution is really, really short on a particular blood type right now, so we have to be stingy with it. A surgeon may call and ask for twenty units, and the pathologist on call will approve five (sounds bad if you are that patient, but not if you're the car-crash victim coming in ten minutes from now).
This aspect of pathology is poorly communicated to most medical students (we had one guy come in for an hour and mumble about a bunch of tests the lab ran; if you'd asked me then, I wouldn't have been able to identify him as a pathologist). Most nonmedical people probably aren't aware that doctors oversee all the labs, either, since on the surface it doesn't seem like you'd need a doctor down there.
That's everything in a nutshell. I'm only one month into my four-year residency. Maybe 47 months from now, I will write this essay again in light of what I've learned and what I think is important to emphasize.
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