Tag Archives: microbiology

World Tuberculosis Day

24 Mar

Today is World Tuberculosis Day, a day dedicated to raising awareness to one of the world’s deadliest diseases, because no holiday is complete if it doesn’t involve celebrating the misery of millions of people.
That’s why Christmas is so popular.

Tuberculosis is a disease caused by the bacteria Mycobacterium tuberculosis, which is one of those bacteria that is really awesome to talk about and really annoying to work with.
Really, really, really annoying.
Seriously, you have no idea.
It sucks.

The Disease

Despite how charming Doc Holiday made tuberculosis look, the disease is just as annoying as the bacterium. If you catch tuberculosis, treatment can take anywhere from 6 months to 2 or 3 years, depending on it’s drug resistance. Oh yeah, it’s highly drug resistant. And we only really have 8 types of drugs to treat it with (2 first line and 6 second line drugs) . Mutli-drug resistant TB (MDR-TB) is resistant to rifampicin and isoniazid, the first line of drug defense doctors use. Extensively drug-resistant TB (XDR-TB) is also resistant to three or more of the six classes of second-line drugs. Totally resistant TB was first reported in 2003, and was pretty rare. At first. Now it’s a bit more widespread.
Because it’s an annoying bastard.

Also, if the drug resistance and multi-year treatment isn’t bad enough, in the United States, you have no choice on whether or not you get treated. You HAVE to get treated, because the disease is such a danger to public health. Part of the drug resistance is due to people no continuing their treatment, which can be rigorous. And while there is a vaccine, it’s has varying degrees of effectiveness against pulmonary tuberculosis.

On top of everything else, many cultures have a huge social stigma against those who have it, even after they’ve been cured. During the treatment, they may be completely ostracized from their village and even their families who fear the disease. You can’t blame the people for wanting to protect themselves, but it also leaves the patient , leaving them with no emotional support structure and facing the shame of disease. They will often find themselves alone, and become very depressed and stop taking their treatment. It’s a problem Doctor’s Without Borders has to face every day, and has done their best to bring public attention to the multiple issues surrounding the disease with their adorably named project “TB And Me”.

Most people think that TB is a “third world problem.” But in reality, it’s everywhere. There are parts of London which have rates nearly as high as Chinese provinces. Alaska is facing a tuberculosis epidemic among their homeless and do random sweeps every few weeks. Even my father caught tuberculosis as a boy living in Colorado. It is highly contagious: a person with active TB can infect 10 to 15 people a year. It killed 1.7 million people in 2009. Over 2 billion people are infected, though not all of these cased are active. Of these 2 billion, 10% will develop an active infection during their lifetime.

The Bitchy Diva

It’s a Class III organism, which means you have to use a bunch of annoying precautions when working with it. Not only do you have to process the specimens under a biohood, you have to do it in a special room completely dedicated to working with tuberculosis, and only tuberculosis. This room separated from the rest of the lab by a series of doors and negative air pressure. You also have to wear a special mask so you don’t accidentally inhale it, since the infective dose of M. tuberculosis is fewer than 10 bacterium. And before you work with it, you have to spread bleach-soaked paper towels everywhere, so that if by chance even one bacterium falls onto the counter, it will immediately die a horrible, bleachy death.

We don’t mess around with tuberculosis. It’s not a fun and cute bacteria like E.coli. It’s a high maintenance bitchy little diva that will slowly and violently murder your lungs if it gets a chance.

Science Stuffs

Mycobacterium are a genus of Actinobacteria. There are over 70 species of Mycobacteria, but most people are familiar with M. tuberculosis and M. leprae, the causative agent of leprosy. While most clinically significant bacteria grow within 18-48 hours, Mycobacteria takes it’s time. Some species will form colonies within 7 days (termed “rapid growers,” because microbiologists have a skewed perception of time), while other may take 6 weeks or longer to grow. Maybe they like to take their time growing because they don’t want to come across as desperate. Or maybe they’re just stubborn and will grow when they’re damn well good and ready.
Either way, it’s really annoying.

One of the most significant characteristics of Mycobacterium is their cell wall, which is thicker than most other bacteria and completely stuffed with mycolic acids that give it a waxy appearance. The cell wall consists of the hydrophobic mycolate layer and a peptidoglycan layer held together by the polysaccharide arabinogalactan, which is one of those words I love watching drunk people try to pronounce.

M. tuberculosis is a bacillus and may be considered Gram-positive, but this is actually a huge misnomer. Due to the high lipid content of their unique cell wall and general stubbornness, they do not retain any portion of the Gram stain, and thus are neither truly Gram positive  or Gram negative. While they don’t truly retain crystal violet, upon staining they can appear to be weakly Gram positive, because it likes to laugh in the face of logic. Or they won’t stain at all and be referred to as “ghosts.” Again, either way, it’s really really annoying.

If only they were this cute.

A much more useful stain for this species is the Ziehl–Neelsen stain, commonly referred to as the acid-fast stain.
M. tuberculosis is acid-fast, meaning they are resistant to decolorization by acids during staining.  This is due the the lack of an outer cell membrane. It decided somewhere along the way that outer cell membranes were too mainstream, and never bothered getting one.


 M. tuberculosis is nonphotochromogenic, meaning it won’t produce a pigment in the presence or absence of light. Their colonies are buff-colored, dry, rough, and honestly rather ugly. They look like demented warts.


If growth conditions are optimal in broth cultures, M. tuberculosis will actually grow in long, rope-like strands, which we called “cording,” which is actually pretty cool. M. tuberculosis is strictly aerobic, requiring high amounts of oxygen, which is why it loves to invade your lungs.. They are nonmotile, and lack spores and capsules. In terms of biochemical identification, they are negative for catalase, including the 68 degrees Celsius catalase test which is commonly performed on Mycobacteria species. They are positive for niacin and nitrate.

M. tuberculosis was first described on 24 March 1882 by Robert Koch, a guy every biologist should recognize, if not for all his grand achievements in the field of microbiology, then at least for his dapper style.

 Note the fine beard and bow tie, which can both be used to clean microscopes. He received a Nobel Prize in 1905 for his discovery. In 1998 we sequenced it’s annoying little genome.

Doctors Without Borders have made several awesome infographic posters to help educate about TB rates:
TB-infographic-treatment
TB-effects-infographic2-final

Stop TB - In My Lifetime, World TB Day, March 24. http://www.cdc.gov/tb/events/WorldTBDay/default.htm

Click here to learn more about World TB Day!
Click here to learn more about Tuberculosis and it’s growing drug resistance.

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Job Hunt, Part II

22 Mar

A few days ago, I was contacted with a job offer.
It wasn’t the job I had originally applied and interviewed for, but a similar starting position in a different department.
Microbiology.

I was very torn.
The job seemed almost too good to be true, at least for a new grad entering the field. The benefits, perks, and staff are amazing. The college is famous for it’s well-funded science programs. However, it’s in a city where I know few, if any, people. It gets dark and extremely cold during the winter (-40F or colder), and the contract is for 3 years, which is longer than I anticipated. I would literally be facing my biggest weakness in the lab (microbiology), my biggest medical fear (depression), as well as my biggest fear in life (loneliness).
This is simultaniously exciting and terrifying.

I received a lot of mixed messages from friends when I told them of the offer.
Many supported it.
Others told me to keep looking.
Some reminded me of my dreams of traveling and helping in developing countries. Some pointed out that I was really looking for a job that provided blood banking experience, while others countered that there are very few blood banking jobs in this state. (Most of the available jobs are in general chemistry.)

There are also very few microbiology jobs. Clinical microbiology relies heavily on logical thinking, which I love. But also requires you to maintain a sizable amount of knowledge, which I suck at. That is why I both love it and fear it. It can be overwhelming. It’s much harder to start in the main lab and move to microbiology; If you don’t use that information every day, you quickly lose it.

It is also true that I do have aspirations of working abroad.
It’s one of the main reasons I went into this field. But in order to do the kind of work I want to do, you need either power, money, or experience. I have none.
I can’t do Peace Corps right away, as they don’t offer lab positions, (but would be an excellent choice if and when I decide to move into public health).
Doctors Without Borders takes people in my field, but only with experience.
Global Volunteer Network would take me, but it’s a trip I can’t currently afford.


Some reminded me of the risk.
Depression is a very serious condition that runs in my family. I am fortunate that I am not as prone to depression as others in my family. While some members of my family struggle with it every day, mine is very rare, typically mild, and always situational. However, the constant winter darkness does affect me, a condition known as SAD (Seasonal Affective Disorder).

But the simple truth is that, no matter where I go, there will be risks.
Physical, emotional, and psychological risks.
If I take this job, I risk depression, extreme cold, and loneliness. If I were to take of tomorrow to work in Sudan, I risk malaria, sleeping sickness, and witnessing genocide. If I go to Arizona, I risk controversial politics, sunburn, and skin cancer, which I am incredibly predisposed to.
(Seriously. My skin is basically a big game of “Find The Cancerous Freckle.”)


Ships are safe in harbors, my friends, but we all know that’s not what ships are for.

So I accepted the job.

Life is full of risk, and to spend your entire life trying to play it safe isn’t wise, nor really all that possible. The key is to identify the risks, and weigh them against the benefits. When I weigh the risks of this opportunity against it’s benefits, I realize that I have a lot to gain, and relatively little to lose.
To start my career in microbiology is an incredible opportunity that I hadn’t dared dream about. That’s why I stuck to searching for general chemistry and blood banking jobs. The fact that I could have most of my extensive student loans paid off in 3 years is another possibility I hadn’t dared dream about. That would provide me with financial freedom to pursue other interests, such as travel, grad school, or volunteering abroad.
With a microbiology background, I would also have a better chance of going being accepted in a public health program, which I would love.


SAD lamps, exercise, medication, and working in a lab with freaking windows (I still can’t get over that) can help me manage through the winter blues. Honestly, working in a positive environment doing what I love goes a long way in contributing towards my happiness.

And here’s a confession: These past few months have been some of the worse in my life. I have never been more depressed then these past few months while I was unemployed. I love working in a lab so much that not being in a lab was literally devastating. The process of searching for jobs, filling out applications, getting your hopes up, going to interviews, is emotionally and psychologically exhausting. On top of everything, there is the knowledge that despite the improving job market in the United States, unemployment rates for my generation are over 16%, and those who do get jobs are often underpaid. Many experts agree that my generation was one of the hardest groups hit by the global recession. There were days I physically could not get out of bed. I felt overwhelmed and helpless. While I’ve seen friends go through that level of depression, I myself had never experienced it before.

And as soon as I received this offer, my situation completely reversed. I was waking up, happily, at 7:30 every morning. I was getting dressed. I was eating balanced meals. I was smiling again, even when I was by myself. Just the idea of working in a lab again lifted my spirits.

For me, such a drastic improvement is well worth the risks.

Job Hunt, Part I

21 Mar

Yesterday I woke up, settled in with a delicious cup of pressed Ethiopian yirgacheffe (my absolute favorite coffee),  and knocked out three job applications before noon (like a boss!). Literally five seconds after submitting my third application, I received a phone call from the hospital I interviewed at last week. They said that I didn’t get the job  I had applied and interviewed for, but they did want to offer me another job:
Day shift in the microbiology department.

I was completely stunned. I was completely speechless as the cheerful human resources lady rattled off the benefits of the job, which were far greater than I had ever hoped for in a first job. Of course,  there were a few downsides. I told her I would need a couple of days to consider the offer before deciding.

So here is the good, the okay, and the bad:

The Good:

  • A lab with windows!!!! This is rare for hospital labs, especially in this state.
  •  $20,000 loan forgiveness, paid in $6,000 increments over 3 years. The money actually doesn’t have to go towards student loans. They don’t require a receipt, so it’s actually more of a bonus. It will be going towards my loans though.
  •  Full health benefits from a very reputable company
  • Paid time off, of which I can accumulate 23 days in a year, and use up to 20 of those days at a time.
  • $26/hour
  • The microbiology department manager seems incredibly intelligent and kind, and would make a good mentor. This is something I really, really want, more than anything else, in a first job. I don’t want to be stuck in a lab where everyone does their job and goes home. I want a lab where the coworkers aren’t afraid to teach, challenge, and nurture me. This may sound needy, but this is a field where there are only 2 people entering the field for every 6 retiring out of it, and has a huge generation gap (workers are either over 50, or under 30. There are very few in between). I believe that it is imperative that mentorships be formed, so that the knowledge of those 40+ years of experience can be passed on to the upcoming generation, who lacks such experience.  I seemed to impress the microbiology manager when I mentioned  Richard Lenski’s experiment with E.coli evolution, which caused one strain to utilize citrate.
  • The city is home to a university with a very impressive science program, so I can expand my education.

The Okay:

  • The shift is a day shift, which would make taking the university’s science classes rather difficult, unless I could eventually  a few weekdays off. There are very few evening science classes at this university. I may take a few evening art classes first, so I can meet people, and then after a semester or two, ask for a few days off to take daytime classes.
  • Microbiology department: I have a love-hate relationship with clinical microbiology. I absolutely love microbiology. The day-to-day of clinical microbiology can be frustrating at times. I am very inexperienced with it, and don’t catch on with it as quickly as I did bloodbanking. The perk is that it would allow me to specialize at the very beginning of my career. The risk is that I may struggle in the beginning. Also, as one microbiologist pointed out, it is much easier to transition out of micro into the general lab, than transition into micro from the general lab. There is an overwhelming amount of information you have to know at all times in the micro department, which is easily forgotten if you’re in the general lab and not using it. It’s easier to start in microbiology than trying to move into it after years of not doing it. This opportunity in microbiology, though challenging, would also make me a better candidate for Doctors Without Borders, who prefer medical laboratory scientists with a microbiology background.

The Bad:

  •  This is a 3 year contract.
  •  The city has extremely cold winters (-50F)
  • Even worse than the cold, is the darkness.  I am already prone to SAD (Seasonal Affective Disorder) and depression runs in the family. However, a few of my friends who have lived there assure me the darkness isn’t that much longer than the winter darkness of my current location.
  • I wouldn’t be in blood banking, which is one of my biggest passions. (I do have a passion for microbiology as well)
  • I will be in a city where I know nobody, and loneliness is my biggest fear. I sometimes have trouble making friends, as I can be shy at times (unless I’ve consumed enough coffee). Also, many people initially don’t know what to think about a woman who thinks E.coli and blood cells are cute. Apparently it’s not a common sentiment.


I’ve asked friends their opinion of my offer. The feedback has been enormous, and mixed. Most people in  my current location loathe the city where the job is located, because of its severe winters. Many are encouraging me to go. Others are jealous of the benefits, as well as a new grad getting a day shift (rather unusual in my field).  Some think that I should focus more on my life-long dreams of working abroad. Some think I should pursue blood banking, though others are quick to point out that blood banking jobs in my state are currently rather rare. So are micro jobs, and for me to have one like this is incredible. Some pointed out that having 3 years of experience on a resume will be impressive, especially in microbiology. They’re right. If I stick with this for at least three years, it will open up a lot of doors, especially if I want to pursue a masters degree in epidemiology.

Plastic-Eating Fungi

11 Mar

Plastic-Eating Fungi Found In The Amazon May Solve World’s Waste Problem

By Emma Hutchings

A group of students and professors from Yale University have found a fungi in the Amazon rainforest that can degrade and utilize the common plastic polyurethane (PUR). As part of the university’s Rainforest Expedition and Laboratory educational program, designed to engage undergraduate students in discovery-based research, the group searched for plants and cultured the micro-organisms within their tissue.

Several active organisms were identified, including two distinct isolates of Pestalotiopsis microspora with the ability to efficiently degrade and utilize PUR as the sole carbon source when grown anaerobically, a unique observation among reported PUR biodegradation activities.

Polyurethane is a big part of our mounting waste problem and this is a new possible solution for managing it. The fungi can survive on polyurethane alone and is uniquely able to do so in an oxygen-free environment. The Yale University team has published their findings in the article ‘Biodegradation of Polyester Polyurethane by Endophytic Fungi’ for the Applied and Environmental Microbiology journal.

 

Iditarod and Diphtheria

3 Mar

Today is the ceremonial start of the Iditarod! Which, if you live in Alaska, is kind of a big deal. And if you live elsewhere, it’s just another Friday.
Either way, today is a good day.

The Iditarod is a 1,000ish mile race (though this year it’s only 975 miles) commemorating the infamous diptheria epidemic and celebrated every year with a grand ceremonial start and Alaskans bickering which dog, Balto or Togo, deserves more credit for the original race.

The original run was actually a huge deal. Alaska is huge state with very few roads. Hell, even our capitol city cannot be reached by road. There weren’t, and still aren’t, any roads to Nome. So when the diphtheria epidemic hit Nome in 1925, people panicked. The nearest antitoxin supply was in Anchorage, about 1000 miles away. It was the middle of winter, and winter storms produced strong gales of -85 degrees F. Nearly every Alaskan can recite this story in their sleep.

So today, while most of Anchorage is crammed downtown to celebrate the ceremonial start of the Iditarod, I am curled up with  warm cup of coffee and celebrating the Iditarod in my own way: With good ol’ fashioned science.
(Plus it’s really, really snowy out today, and my poor little car still doesn’t have snow tires.)

Today’s topic: Corynebacterium diphtheriae!

(Yay!)

 C. diphtheriae is the adorable little bugger responsible for diphtheria, and has some odd little quirks that are fun to explore.
First, the basics: It’s a Gram-positive, highly pleomorphic bacilli, belonging to a peculiar group of bacterium called Actinobacteria. It is non-motile and aerobic. It often arranges itself in peculiar ways that microbiologists refer to as “Chinese letters.” (Unless you’re a Chinese microbiologist, in which case you would probably refer to them as Korean letters or something.) The less racist/more politically correct microbiologists refer to the morphology as a “picket fence” or “palisades” referring to how they lay next to one another. Its very distinct, instantly recognizable, and always makes me want to build kick-ass purple picket fence around my home.

(Because white picket fences are sooooo 6 decades ago.)

As for agars, C. diphtheriae is typically grown on Loeffler medium or tellurite agar. CTBA agar, which contains postassium tellurite, cystine, bovine serum, and sheep’s blood, is a common one found in labs due to the fact C. diphtheriae will form black colonies with characteristic brown halos, which differentiate it from most other Corynebacterium species.

(Be warned though, that C. ulcerans and C. pseudotuberculosis will also cause brown halos).

C. diphtheriae is also metachromatic, which means that a single stain will result in two or more different colors. This is due to the granules found at the polar ends of the bacterium, known as Babes Ernst Granules, which will stain a different color and are responsible for the notable club-shape of the bacterium. Ponder’s and Alberts’s stains can be used to demonstrate this phenomenon.

 Which looks pretty freaking groovy.

C. diptheriae produces a particularly nasty toxin which is responsible for Diptheria. Medical microbiologists must demonstrate the presence of the toxin, and they do so with the Elek’s Test. Developed in 1949, the Elek’s Test uses immunodiffusion to demonstrate the toxin. The patient’s isolate is placed on the agar in a straight line, alongside a known toxic and non toxic strains (which serve as positive and negative controls). Then a strip of paper containing antitoxin is laid across them in a perpendicular fashion. The antitoxin reacts with the toxin, forcing it to visibly precipitate out into the agar.


If the patient’s isolate contains the diptheria toxin, then peripitin lines will be formed. Iron will inhibit toxin production, so the Elek’s Test must be performed on a media with low iron content and an alkaline pH.

The toxin itself is pretty interesting. A bacteriophage with the Tox gene will infect a C.diptheriae bacterium, which will incorperate the Tox gene into its own genome and thus become a toxin producer. The toxin is secreted and actually nontoxic until it encounters trypsin, which will result and two fragments: A and B. Fragment B binds to receptors on eukaryotic cells and mediates the entry of Fragment A into the cell. Once in the cytoplasm, Fragment A disrupts protein synthesis. This disruption of protein synthesis is what contributes to the toxigenicity of the toxin.

Diptheria itself is characterized by a grey-white pseudomembrane formation on the throat, which honestly looks pretty nasty. And while I am usually all for disgusting photos of medical conditions, today I feel more like posting a photo of sled dogs, who hold the award for the most ridiculous tongues ever.

(All the better to lick your face with, my dear.)

So thank you, C. diphtheria, for giving Alaskans kickass piece of history that displays the extremes we will endure to help fellow Alaskans, a wonderful mid-winter celebration, and hilarious photos of sled dogs.

If you are interested in learning more, especially about the history of Diptheria epidemiology, Todar’s Online Textbook of Bacteriology is a wonderful resource.

E.coli Is Pretty Damn Cute.

29 Feb

Not many people would consider Escherichia coli to be cute. Or any other bacteria, really.
But this little Gram-negative darling deserves some respect and appreciation. There are many strains, ranging from peacefully non-pathogenic to potentially fatal food poisoning, with an impressive range of genetic and phenotypic diversity. And don’t forget the menacing H0157:H7, a sneaky little punk who stole the notorious shiga toxin from Shigella.

E.coli 0157:H7 would totally have a mohawk.

Science owes a lot to E.coli.  It was one of the first organisms to have its genome sequenced. Since the initial sequencing in 1997, there have been 60 completely sequenced strains. So diverse is this organism that these 60 sequenced strains only share 20% of their DNA. The other 80% of each strain is wildly different!
In the 1940’s, Joshua Lederberg and Edward Tatum used E.coli to describe the phenomenon bacterial conjugation, where bacteria exchange and transfer genetic material via direct contact, much like a flash drive can transfer info between computers. In 1988, a long-term experiment involving 12 identical cultures of E.coli was set up.
In 2010, the cultures reached 50,000 generations, and display a wide variety of diversity, including one culture which can now utilize citrate. Citrate utilization is a common test used to differentiate Salmonella (positive) from E.coli (negative) in medical microbiology labs. While there has yet to be a known case of wild E.coli utilizing citrate, we now know that they can evolve to adapt that characteristic on their own.
You may have heard of Mutaflor, a probiotic used to treat gastrointestional disorders. That’s actually a specialized strain of E.coli! (I like to pretend that it wears those old-fashioned nurse uniforms).

E.coli has taught us so much about microbiology, genetics, and evolution. And if that isn’t adorable enough, E.coli is peritrichous, meaning that it has beautiful flagella everywhere!


Seriously, flagella everywhere! They probably give the best hugs! The flagella are like itty bitty rotary-powered protein tentacles. It’s basically the bacterial version of Cthulhu. Good thing they never bothered to evolve wings. (Yet.)

(First image from shardcore.com. They have wonderful art.)