Tuesday, November 27, 2012

Getting a Patient's Perspective

Note: I suggest not reading this post if you are eating, or have recently done so. Not that I'm trying to gross anyone out, but this is a medical blog after all, and some medical stuff is, well ... you know.

Self-diagnosis: It's a common phenomenon, one in which a little knowledge is a dangerous thing. When you take Psych 101 in college, for example, suddenly having a bad day or two makes you think you are schizophrenic or bipolar. And when you are a pre-med, every cough, sneeze, or tickle sends you to Google, which inevitably yields the most rare and horrible diseases as its search results.

Then again, sometimes The Google Doc is right.

It was in my case last week, when, ironically, I wound up with one of the very bacterial infections I wrote about in my recent post "The Kinky World of Bacterial Sex."

It all started with some vertigo and nausea. When that didn't go away after a few days, I headed for a local urgent care center, where the doctor there diagnosed me with a sinus infection and gave me a prescription for amoxicillan. I'm still not clear on whether that diagnosis was correct, because I didn't really have any sinus symptoms ... but then again, I'm not a doctor. I started taking the antibiotic. Almost immediately, I started having diarrhea. But I was out of town visiting a friend, so I shrugged it off as related to a temporary change in my diet. After a couple of days, though, when my body was wracked with horrible abdominal pain, I admitted something was not right and called the urgent care center. The doc there (a different one than I had seen before) told me to stop taking the amoxicillan. But the pain and diarrhea only got worse, so I went back to urgent care when I got home from my trip. Blood work and abdominal CT (to rule out appendicitis) were normal. But a stool culture revealed exactly what Google had suggested when I first looked up the keywords "amoxicillan" and "diarrhea": Clostridium difficile, or C. diff.

When that showed up as a possible diagnosis during a Google search on my iPhone, I attempted to be rational and dismissed it as the worst-case scenario. My symptoms could also have been side effects from the amoxicillan itself, and in my attempt to not self-diagnose, I believed that's what they were. But it appears that my worst-case scenario came true.

Well, not exactly. My association with C. diff from writing my recent blog post was that it's a nasty superbug, one that is resistant to antibiotics and very difficult to treat. That is true, in some cases. But certainly not always. Usually, you can treat it with the antibiotic Flagyl, or if that doesn't work, Vancomycin. In some cases, C. diff infections require hospitalization and IV antibiotics. But that's unlikely in my case, especially since I have not recently been in an environment (such as a long-term care facility or a hospital) where the superbug strains of C. diff tend to thrive.

The irony of contracting a C. diff infection after writing about it on this blog certainly does not escape me. Neither does the irony of switching roles from confident pre-medical student to sick, scared patient.

Before I received a definitive diagnosis yesterday, I was frustrated and scared. I didn't know what was wrong with me. I was in a lot of pain. I couldn't keep food down. My normally active and productive lifestyle had been reduced to a cycle of sleep - drink Gatorade - go to the bathroom - repeat. A friend suggested I change my perspective and try to look at the experience as a learning one, one in which I could gain a better understanding of what it is like to be a patient. Because one day, I will be treating patients, and if I have a good understanding of what it is like to be one, hopefully I will be a better and more compassionate physician. So I started paying attention to how the practitioners were treating me, trying to figure out, from my own reactions to their behaviors, what kind of doctor I wanted as my own doctor. And hence, what kind of doctor I wanted to be to others. I learned a great deal from both doctors and their support staff.

I remember the first physician I saw at the urgent care center. While she was nice enough (I guess), her demeanor and body language suggested that she was in a hurry and that she was just trying to get through our visit. She didn't explain anything about my diagnosis, or the medication I was to take. I understand that physicians these days have a huge patient load and are very busy. But I think there are ways to take just a minute or two to help assure a patient that he or she isn't an inconvenience, which is how I felt. The second doctor I saw at the urgent care center was much better. She was more thorough in terms of her interview with me, and she acted like she cared about my well-being. She had concern and compassion that I could see, hear, and feel. I could tell she was busy, too, but she made sure to tell my why she was ordering an abdominal CT, why she wasn't giving me any medications right then and there, and what might help me feel better until I had a diagnosis and course of treatment. She also made a point of asking me multiple times if I had any questions.

But obviously, it's not just the physicians who comprise a treatment team. There are nurses, techs, receptionists, and other support staff. I tried to learn from them as well. The tech who took my vitals and drew my blood on my second visit to urgent care was amazing. I'm not always good with names, but I remember hers - Melissa. She made me feel at ease, in part by being calm herself, in part through humor. I was somewhat dehydrated (from the diarrhea), so my veins were difficult to find when she was trying to draw blood for a CBC. Melissa was very patient, and rather than hurry and stick me multiple times, kept palpating my arm until one popped out. I was very grateful for that.

And then there was the radiology support services lady at the hospital where I went for my abdominal CT scan. She was amazing. I had never had an abdominal CT before, so had not had the pleasure of the lovely barium contrast drink they give you (and they give you a LOT of it). I was already feeling sick, and the bitter-off taste of the clear liquid wasn't helping. The woman at the front desk walked through the waiting area and asked how the drink was going down. I told her not so well, and she asked whether it would help if I had some juice to help wash it down. When I said "yes," she replied, "Well, I'll go see if I can scrounge some up for you." Her kindness - and the apple juice she found - made all the difference in the world.

Sometimes you can't cure someone, but you can bring them a little bit of comfort. That's the kind of doctor I want to be.

Sunday, November 4, 2012

Elemental, My Dear Watson

As I was studying for the MCAT yesterday (General Chemistry), doing the Examkrackers practice problems, I kept having to refer back to the periodic table at the beginning of the book. Now, I know quite a bit of the periodic table information - the molar masses of oxygen (~16), carbon (~12), and nitrogen (~14), for example. But if a problem comes up about nickel, I'm gonna be in a pickle.

Thankfully, I discovered today, we DO get a periodic table on the MCAT, which includes atomic numbers and atomic weights (whew!). Otherwise, I thought I was going to have to memorize this song ...

It's All Coming Back To Me Now

Finally, after some hemming and hawing, I have begun studying for the MCAT. "M"-Day for me is March 23, 2013. So I've got a bit of time. But given that I took Physics, General Biology, and General Chemistry two years ago (2010-2011), and Organic Chem one year ago (2011-2012), I feel the need to do some hard-core review. That, and the fact that the average MD/PhD matriculant's MCAT score is a 35 puts a bit of pressure on.

To put that score in perspective, the mean MCAT score for 2011, according to the American Association of Medical Colleges, was a 25.1. That's out of a best-possible 45. Not a single person got a 45 in 2011. The highest score was a 42. To get a 35, I would have to be in the 94th percentile. Yikes. (See the full score report from the AAMC here.)

My strategy is to use the Examkrackers review books series, both the subject matter review books and the "1,001" questions books. I have started Gen Chem, Orgo, and Gen Bio. Today I will venture into the world of Physics. I am making flashcards on Quizlet, which I can study anywhere using their iPhone app. With all of these resources, along with taking (and re-taking) the available AAMC practice tests, I believe I will be as prepared as I can be.

That said, I was a bit worried, when I first opened the review books, that I would have forgotten ... EVERYTHING. Not so. And thus, the song "It's All Coming Back To Me Now" has been cycling through my head. And of course, like most songs that play in my head over and over again, I had forgotten most of the lyrics. Solution: YouTube. So here, I present Glee performing this song, in celebration of the fact that my science knowledge is ... all coming back to me now.

Saturday, November 3, 2012

Stupid Google! (and some HTML resources)

Dear Google:

Your Dynamic layout series is wonderful, in many respects. It is interactive, reader-friendly, and attractive. However, there is one major problem: The inability to change the HTML coding stifles creativity, and seems to go against the philosophy of Google itself. I hope you will fix this problem. In the meantime, I am sadly restricted to one of your lesser templates, simply because it affords me the ability to customize my pages. Were it not for my followers (however few they may be), I would consider changing blogging platforms. For now, though, I will hold out hope for your listening to the many complaints online about this omission in your template design.


Lorien Menhennett
For those of you who may have visited my blog in the last few days, you may have noticed that it has been a revolving door of layouts and templates. For this, I apologize. I realize this can be disorienting and confusing to readers ... I know it is to the author.

The reason for this is as follows: I found a very wonderful template, called the Dynamic series. However, I wanted to customize it by changing the HTML coding. After about an hour of frustration on both my blog and other blogs dedicated to helping bloggers blog, I discovered that this template series does not allow you to edit the HTML code. It is fixed, so to speak. I find this very frustrating. Hence my faux open letter to Google in my faux version of The New York Times (at right).

I find it humorous that this was a problem for me (at 5 a.m. on a Saturday, especially). I never would have dreamed that I would be editing HTML code. But I have learned bits and pieces of it, through different Web sites and others' blogs. This post is a shout-out to those of you who are experts at this foreign language, which I am slowly learning. This post is also a complaint to Google for not making it possible to speak this language in the Dynamic template series, which aside from this issue is pretty darn cool.

With that said, here are two sites I have found helpful in learning HTML code. Just in case, ya know, you want to try it out too ...

This site is great. It offers tons of code HTML code resources. One of my favorite things about this site is that it has "code generators." I know, I know ... the purists will call me lazy, but I really like that I can just specify the number of columns, rows, background color, etc. in a table and have the site churn out the whole table's code for me, which I can then copy and paste into my blog. (Here is the specific table generator link: http://www.quackit.com/html/html_table_generator.cfm.)

There are blogs about everything. Including blogs about blogging. This is a great one if you need tips on technical things (I have found it quite useful).

IFLS Helps Make Facebook Worth the Trouble

IFLS: The Facts

Founder: Elise Andrew (employed by LabX Media Group, which owns LabWrench and publishes Lab Manager Magazine and The Scientist)

Description: A community built for the posting and sharing of scientific updates, quotes, cartoons, jokes and photographs. We're dedicated to bringing the amazing world of science straight to your newsfeed in an amusing and accessible way. Tell us what makes you say "wow!"

Facebook Page "Likes": 1.6 million

Alternate site: If our name bothers you, please see our mirror page here: 

Source: IFLS FB page
Like many people, I have mixed feelings about Facebook. There are definitely pros and cons associated with this social networking site.

But, like hundreds of millions of other people in the world, I have decided it's worth the trouble. I love keeping up with old friends, yes, espeically the ones who live far away and now have little kiddos I never get to see. But also in great part because of one single FB page: I f***ing Love Science, aka "IFLS." (Note: There most definitely is an expletive in that title, which I have asterisked out. Not that doing so hides it very well ... )

With so many FB pages out there, so many people posting photos and status updates, why do I care about this particular one? Because it appeals to the scientist in me. In so many ways.

IFLS posts are sometimes hilarious, sometimes poignant, sometimes thought-provoking, sometimes informational, sometimes ridiculous (or a mix thereof).

I don't pay heed to every single post from IFLS - there are quite a few every day - but I make sure to at least glance through them when I'm taking a study break and in need of a hearty laugh or some inspiration.

In this blog post, I present a few recent photos posted by IFLS. Happy viewing ...

Friday, November 2, 2012

The Kinky World of Bacterial "Sex" (and why we should care)

An image of Clostridium difficile,
a potentially deadly bacteria.
C. diff. It's a name that may not mean much to the layperson, but to any health care worker, it causes shuddering and trembling.

Just ask my mom, who is a hospice nurse. She has a patient who has been afflicted with this nasty (and sometimes deadly) bacterial infection for weeks now. It can be resistant to most antibiotics, and is also quite resistant to destruction. Killing it requires bleach; soap and water or alcohol-based hand rub don't do a thing. C. diff is also very infectious, so my mom's patient has unfortunately had to be under isolation precautions this whole time. Which for anyone would be awful, but if you are in your last days of life, being isolated from the world - and having anyone who entered your world have to gown up and wear gloves - would be terrible. (At least I think so.)

So what exactly is C. diff, and what makes it so evil (to us at least)? Here is a bit about this robust bacteria, from the Mayo Clinic's Web site:

"Clostridium difficile (klos-TRID-e-uhm dif-uh-SEEL), often called C. difficile or C. diff, is a bacterium that can cause symptoms ranging from diarrhea to life-threatening inflammation of the colon. Illness from C. difficile most commonly affects older adults in hospitals or in long term care facilities and typically occurs after use of antibiotic medications." (Source: Mayo Clinic)

Bacteria can be beautiful -
and also dangerous.
That all said, bacteria are fascinating little buggers. (Not to mention beautiful under the microscope, as you can see from the picture at left.) And they are not all bad. There are bacteria in our bodies that are quite helpful to us, in fact. Bacteria can also be highly adaptive, which makes them all the more interesting - and potentially dangerous, when it comes to certain species.

One of the major issues facing health care today is MDROs - Multi-Drug Resistant Organisms. This includes several kinds of bacteria (such as Vancomycin-Resistant Enterococci, or VRE; and Methicillin-Resistant Staphylococcus aureus, or MRSA; as well as C. diff). As you can probably tell from the names, these organisms are resistant to specific drug treatments - the antibiotics vancomycin and methicillin, respectively, in the cases of VRE and MRSA.

But let's step back for a moment. How do antibiotics work? Or rather, how are they supposed to work? Antibiotics are separated into different classes depending on how they affect bacteria. For example, antibiotics can target a bacteria's:
1. Cell wall
2. Cell membrane
3. Essential enzymes

Antibiotics, when they work, cause destruction of the bacteria via one of these targeting mechanisms. Which is how they make us well again.

As I said, though, bacteria are highly adaptive. They can undergo "evolution" - favorable DNA changes - very rapidly, enabling them to resist an antibiotic's targeting mechanism. Examples of these rapid adaptations include:

1. No longer relying on a glycoprotein cell wall
2. Enzymatic deactivation of antibiotics
3. Decreased cell wall permeability to antibiotics
4. Altered target sites of antibiotic
5. Efflux mechanisms to remove antibiotics
6. Increased mutation rate as a stress response

(Thank you, Wikipedia, for the very succinct list above.)

Anyone who has read much about evolution, though, knows that this process is usually a very slow one: favorable DNA mutations gradually accumulate over time via reproduction and the passage of these favorable mutations down to offspring.

But bacteria are a little, well, different in terms of their DNA-transferring and reproductive capabilities. And these differences are what enable them to rapidly exchange DNA mutations in an expedited manner. How does this work? Well, let me explain.

Bacteria have not one, not two, but THREE methods for sharing DNA. This is in addition to an extremely rapid method of asexual reproduction called binary fission. I will explore each of these in detail (with pictures, of course).

Enter the world of bacterial "sex" ...

1. Conjugation. (See images, and explanation, below.)

Diagram of bacterial conjugation.
Bacterial Conjugation:
An image of the sex pilus
Conjugation is the closest that bacteria get to mating (i.e., sex). What happens is that one bacterial cell, termed the "donor," produces a cellular protrusion called a sex pilus. The sex pilus attaches to the "recipient" cell, and brings the two cells together. DNA is then replicated and transferred across the cell membranes, from the donor to the recipient. (Note: the donor possesses what is called an "F factor" - this is what enables it to transfer its DNA to the recipient. This F factor can also be transmitted, allowing both cells to then be donors.) This method of gene transfer can transmit antibiotic resistance from one bacterial cell to another. 

2. Transformation. This is the process by which a bacterial cell basically absorbs DNA from the environment through its membrane, incorporates the exogenous (outside) DNA into its own, and then expresses those new genes. The new DNA can either be incorporated into the bacteria's circular chromosome, or as a separate circular piece of DNA called a "plasmid." (See the diagram below.)

Diagram of bacterial transformation.

An electron micrograph, and a diagram, of a bacteriophage.
This is called a T4 bacteriophage.
3. Transduction. This process is a bit more complicated to explain, as it involves not only bacteria, but bacteriophages (aka "phages"). Phages are little viruses that infect bacteria. (Yes, bacteria are subject to infection, too.) What happens is that these bacteriophages attach to the bacteria, inject their phage DNA, and the phage DNA takes over the cellular machinery of the bacterial cell. Rather than meet its own needs (i.e., produce bacterial proteins), the bacterial cell begins to express the phage genes, producing new bacteriophage components. These phage components are assembled, again with the help of the bacteria's cellular machinery. Eventually, the bacteria lyses (breaks open), releasing the little viruses. Those new viruses can then go infect other bacterial cells. Sometimes, a piece of bacterial DNA gets "stuck" in a baby bacteriophage. So that when that bacteriophage goes on to infect another bacterial cell, the previous (and now lysed) bacteria's DNA gets injected and incorporated into the new bacterial cell. To complicate matters, there are two different cycles of bacteriophage infection: lytic and lysogenic. In the lytic cycle, the bacterial cell is immediately destroyed (lysed) and the new baby phages are released. In the lysogenic cycle, the phage DNA is incorporated into the bacteria and remains dormant until activated by certain environmental or stress conditions. So in order for a bacterial cell to share its newly incorporated DNA (from the phage infection), it must be in the lysogenic cycle. (For a graphic explanation of transduction, see the diagram below. Note that in Step 5, this is a second bacterial cell which is being infected.)
Diagram of bacterial transduction.

E. coli cells, some of which
are undergoing binary fission.
4. Binary Fission. So let's assume a bacterial cell has gotten a piece of DNA that gives it antibiotic resistance. It could transmit that DNA via one of the mechanisms above, to one bacteria at a time. But bacteria also reproduce, albeit asexually. And they are quite efficient at it. In a very simplified explanation, a bacterial cell replicates its DNA (which is in the form of one circular chromosome), the two chromosomes move toward opposite "poles" of the cell, and then the cell splits in half, forming two new cells. These divisions are measured in "generation times," which can be quite rapid. For example, under optimal conditions, E. coli's generation time is about 17 minutes. For Staphylococcus aureus, it's about 27-30 minutes. For S. aureus, that means that in 30 minutes, you go from 1 to 2 cells. After an hour, you have 4, then 8, 16, 32, and so on. It doesn't take long, then, to develop a sizeable colony. (Source: Online Textbook of Bacteriology)

So what does this mean? In essence, once one bacteria (or a few) accumulate DNA mutations that confer antibiotic resistance, there are myriad ways - conjugation, transformation, and transduction - to spread that DNA around. And then those bacterial cells "reproduce" (asexually) via binary fission and a whole host of nasty, antibiotic-resistant bacteria results. So when someone is given an antibiotic, the bacteria that are NOT resistant will die, but those that ARE resistant will live, and continue to reproduce. Not good. (At least, not for us. Good for the bacteria, obviously!)

The misure and overuse of antibiotics contribute to this problem by helping antibiotic-resistant bacteria survive, proliferate, and then spread to other people. This is especially an issue in hospitals and other health care facilities, such as nursing homes, where people are in close contact with each other (or contaminated objects come into contact with people) and patients are often immune compromised to begin with. 

Unfortunately, many of these so-called "superbugs" are resistant to multiple drugs, and are very virulent (infectious and harmful). And while there was a time several decades ago that saw wild discovery and development of new antibiotics, that has trailed off in recent years. In part because antibiotics are not seen as the "cash cows" that other drugs may be, and in part because the low fruit of antibiotic development has been plucked, it seems.

There is now an effort (at least of some sorts) to search for new sources of antibiotics, both natural and synthetic, as well as to curtail unnecessary use of antibiotics. But the "superbugs" are here to stay. For a good while, at least. And it's all thanks to the kinky world of bacterial "sex."