Germ warfare / Cannibalism and antibiotic resistance

There are cruel, savage, depraved people in the world.  We see evidence of this from concentration camps, prisons, dictators, and terrorists.  But none of these people have anything on bacteria.  Whatever cruel thing humans can think up, bacteria do 10 X worse and they don't even have brains. 

They cause tremendous pain in diseases like tetanus where the victim's muscles all tighten to the point that their spine breaks.  They cause diptheria, which causes the victim to slowly suffocate by growing a membrane across their throat that blocks their breathing.

You may be thinking that bacteria only do this to humans.  Surely they wouldn't do this to their own kind.  Hah.  They have no morals or bounds.

When bacteria stop growing due to scarcity of food, they produce secondary metabolites which include molecules such as pigments and antibiotics (yes most antibiotics come from bacteria).

When times get tough and food is scarce, bacteria produce antibiotics and kill and eat each other.  Most bacteria have lots of resistance genes.  The resistance genes are necessary so that the bacteria don't get killed off by their neighbors.  It's like being in the Donner / Reed party, but with some defenses in place to make sure you are not the one being eaten.

It is possible to extract bacteria from fossilized mud and lake sediments because the bacteria got trapped in the sediments and have been surviving ever since on what little nutrition was available from the rocks and sand.  The deeper the sediments, the lower the nutritional content of the rocks.  Bacteria from deep and ancient sediments tend to be resistant to more antibiotics than bacteria from newer and more shallow sediments, which suggests that the bacteria surviving in fossilized mud actually can't eat the mud....they mainly just eat each other.  The more time that passes, the more intense the competition becomes.........

Friday Fun!!!!! Infectious disease goodies!

Happily, there are warped individuals in this world besides myself.....You know.....people who laugh about the earliest recorded act of bioterrorism  which involved catapulting plague victims over city walls (though I am sure it wasn't fun at the time).....or people who kind of enjoy figuring out what dish gave them food poisoning and what infectious agent was the cause of their trouble!  For people such as this, here are some recreational infectious disease sites for you.

Who knew that you could send love through STD Greeting Cards!

My favorite is the Chlamydia one.  Please notice that other health related greeting cards are also available.  

My long time favorite!  Now available on line Infectious Disease Trading Cards!

I only have sets one and two and I sometimes think about going to the CDC museum in Atlanta to pick up set 3.  I am happy they are on-line so I don't have to make the cross country flight.

I love E. coli, but considering where it comes from, I don't know that I want to cuddle with it.  However, if you are slightly more warped than I, you may enjoy this plush Stuffed animal E. coli!

I hope you have all kinds of fun with this.

Confessions of a Germophobe-How clean is too clean?

I have to admit, as a small child, I was a big nerd.  My favorite television program was 20/20 with John Stossel and Barbara Walters.    I think Barbara Walters was even my role model for a while.  She was so poised and dignified.  So, of course, when I heard a 20/20 report on HIV in the early 1980's, (and was still too young to have had any sex ed.), I panicked.  I was worried that I would get HIV from petting the dog and not washing my hands before I ate.  I agonized about the time that my big sister dared me to eat dirt and wondered if I should get tested for HIV.  

I started washing my hands every time I touched anything....my desk at school, my hair, my shoes and especially other people.  Eventually my hands started bleeding from washing them too much so I guess that it was fortunate that in that time frame I saw a 20/20 report on obsessive compulsive disorder and learned that people go to the hospital with that too.

I had to seriously evaluate my habits and decide what health patterns seemed to take priority.   I think that there may be a lot of people out there who face the same struggle.  They want to avoid getting sick, so they might go on overkill to wipe out the germs around them.  So how clean is too clean?  I still probably don't know the answer to that question, but I know of some things that are definitely dirty and should be avoided.

1) Promiscuous sex.  Okay, this seems like a no brainer, but there are girls out there terrified of the seats in public restrooms, who sleep with all kinds of strange men.   There are all kinds of sexually transmitted diseases that you can pick up through intercourse... HIV, chlamydia, gonorrhea, and so on.  So you practice "safe sex"and the list gets smaller, but still includes syphilis, scabies, herpes, human papilloma virus, and bacterial vaginosis  because close body contact is all that is required for transmission of those diseases and condoms don't prevent that.  Probably being monogamous with a monogamous partner or abstinent is the #1 thing you can do to keep yourself free of infectious diseases. More info at CDC STD link.

2)Sewage.  Most of us take sewage treatment for granted, but in parts of the world that lack proper sewage and water treatment plants, diseases such as cholera and typhoid are still rampant.  Sewage treatment saves a lot of lives.

3)Restaurants.  Food poisoning is super common in some parts of the world 

(like Merced, CA).  I end up with food poisoning about 1/3 of the time that I eat out in Merced and so I have come to the conclusion that restaurants make people sick.  I didn't always feel that way, but I do now and I eat out a lot less.

The most common form of food poisoning is Norwalk virus.  This comes from people not washing their hands after using the bathroom, and then handling your food.  Only about 1/3 of the population is susceptible to Norwalk virus so lots of people are carriers and they get everyone else sick.  The symptoms of Norwalk, if you are susceptible, are vomiting and diarrhea for 24 hours.  You know, the 24 hr flu....it's really food poisoning...probably from a restaurant.  

4) Cuts and abrasions.  These weren't such a big deal 20 years ago, but now they are because Staph aureus strains are becoming more virulent and more resistant.  It makes you a lot sicker a lot faster and is harder to get rid of.  Athletes especially are prone to getting Staph infections.  This doesn't mean that you have to freak out every time you get a cut or scrape though.  Just take care of the wound.  I prefer hydrogen peroxide because bacteria aren't going to become resistant to it because peroxide oxidizes and destroys the molecules they are made of. Probably any disinfectant will work though.

5) Rodents and cockroaches.  When tested, these organisms really do carry more pathogens than other creatures.  There is a good reason we hate them.  

6)Bathrooms.  This one is reminiscent of #2.  Human waste is dirty and people touch knobs and handles and all kinds of other places in the bathroom before they wash their hands.  If there is one room to keep super clean, it's the bathroom.  I think bleach is the best disinfectant in a bathroom because bacteria will never become resistant to it.  Bleach oxidizes the molecules bacteria are made of so as long as life is carbon based, bleach will disinfect.

7) The noses of little children.  Little kids carry around Streptococcus in their nasal passages.  Children in both clean and dirty living arrangements have Strep in their noses....it's just part of being a kid.  Little kids now get Strep vaccinations and that helps some, but there are so many different types of Strep that no vaccination can wipe all of them out.  There is not a lot else to be done with this one, but if you want to keep your kids from getting sick, probably keeping them away from other sick little children with runny noses and coughs is a good idea.

8)Pets. I guess it depends on where they go and what they eat, but pets can spread diseases.  Rabies is an example, but of greater concern is probably intestinal parasites.  There are other diseases that are spread by pets, but they aren't very common. Check out the CDC link for more info.

9) Shoes, keys, money, security badges, wallets, purses, and things that get handled a lot, dragged everywhere, set down everywhere and rarely to never get washed.  This is honestly starting to get pretty picky, because I can't think of ever really getting sick from any of these things, but I confess that I occasionally run my keys through the dishwasher and I cringe when parents let their little children suck on keys.

So the upshot of all of this is that with the exception of so many people having multiple sex partners, most of us are probably clean enough. All you people out there who aren't neat freaks might be doing better than you thought.

The best question on Earth / What we should know about hospitals

There are all kinds of questions people ask me .  I get asked A LOT about the genetics of homosexuality, which I know almost nothing about.  I get asked about the origins of life which I know absolutely nothing about.  I get asked how do two blue eyed people have brown eyed kids and I do know something about that, but wish that I didn't as the best explanation is probably the milkman.  I always feel awkward when asked these questions, and I find myself wishing that people would ask me a different question.  In fact, I know exactly what question I wish people would ask because it is one of the more important questions I could answer, but NO ONE...I repeat NO ONE has ever asked me this question.  I sometimes wonder if people know that they should be asking this question....Maybe the general populace doesn't even realize the need for this question.  The question is: Are hospitals safe? 

I try to work this into conversation.  For example...

Random stranger I just met:   "Could you tell me um .... what do you think about a gene for people being gay?...... Not that I am... just that I can't imagine anyone being gay and so I was wondering why people sometimes are....hem."

Me: "You know, I was just pondering that question the other day and I was thinking it was really important because there are gay people in hospitals and they need to know whether hospitals are safe places ...."

OR

Another random stranger I just met: "You know, people say that life evolved from pond scum, well what do you believe?  I mean how do you resolve God and scum?"

Me: You know, I wasn't alive back then and so I just really don't know how life began, but I can tell you about the kind of stuff growing in the scum in hospitals and whether it's safe to go to the hospital or not..."

(You get the idea)

So now are you dying to know the answer to the question...Are you?   Are you?

Well then ask it.

Are hospitals safe? 

(Hooray!!! Someone finally asked it!)

Now that you know the question, maybe you can guess the answer...

Which is of course a resounding NO!

People who are deathly ill go to hospitals.  It's why hospitals exist.....  To save people from dying (and to perform surgeries and other dangerous or complicated health procedures).  You get really sick people in there.  You might catch what they have.  A couple of years ago I was really sick with RSV no one wanted to be around me.  Well people lots sicker than I was are in hospitals, and being in a hospital doesn't magically take away the contagious nature of disease.

 Worse, hospitals are places where antibiotics get used a lot so there is a lot of resistance to antibiotics inside of hospitals.  

Worse yet, health care workers who are not careful can carry really bad germs from one patient to the next if they don't change their gloves, change pens and clipboards (or wash their hands before touching them), talk on their cell phones with unwashed hands, etc.

Lots of people get infections that ultimately kill them while they are in hospitals.  Sure a death may  be attributed primarily to a stroke, but what really killed the patient was the pneumonia they picked up while they were on a ventilator recovering from the stroke.

Now I don't think that hospitals are bad places.  There are lots of doctors and nurses in them and the combined expertise of those individuals saves a lot of lives.  Also, there is really great equipment in hospitals that saves a lot of lives and if you need the expertise or the equipment present in hospitals, then it is fine to go there.

However, hospitals are not safe places.  There are some people I know who prefer to recover in hospitals (Ackk!!!) when they could probably recover just as well at home (perhaps with a nurse assisting at home from time to time).    Recovery at home, when possible is a better option usually.  There are far fewer sick people in our homes.  Even if homes do not appear as clean as a hospital, the multitudes of germs present in our homes probably have less lethal potential than the resistant bugs that manage to survive in the seemingly sterile environment at a hospital.  The bugs that survive around hospitals are among the toughest and hardest to kill of the bacteria.  They are like the most elite groups of the military who are able to survive in almost any conditions and kill even when the strongest defenses are in place.  They are not good bacteria to hang out with.

So next time you go to visit your doctor or see a nurse or go to the hospital, instead of asking them bizarre questions that don't pertain immediately to your health (like whether they think you might be genetically gay because your second cousin is gay.....sorry, I really do get this one a lot),  you should instead ask them about whether they have washed their hands and whether they used the same pen and clipboard with the last patient.

What's grosser than gross?

Okay, This is a game I used to play when I was a kid.  Now I'm going to play it with you. (You're lucky).  This is how you play.  You ask the questions.  I give the answers.

You: What's grosser than gross?

Me: Squirting out bloody diarrhea.

You: What's grosser than that?

Me: Squirting someone else's poop back inside you.

You: What's grosser than that?

Me: Dripping someone else's poop down your throat through a tube.

You:  That is the most disgusting thing I have ever heard.  I would rather die than do that!

The truth is that most people, when faced with that choice prefer not to die. But when could someone else's poop save your life?  The answer is when you have a Clostridium difficile infection.  

When people get C. diff it is always after they are treated with antibiotics.  C. diff is a natural, but uncommon part of our gut microbial flora.  Normally it passes through without disturbing us.  However, when we take antibiotics, our normal gut flora gets killed off, which leaves our guts as unclaimed territory.  If C. diff are the first microbes to stake claim on our bowels, we are in deep (well...umm...) trouble.  They take over completely and cause severe abdominal cramping, bleeding, and diarrhea.  C. diff infections can become so severe that the affected individuals actually die.  

Now you may be thinking that C. diff only affects people in developing countries in the Southern Hemisphere, but that isn't true.  There are regularly occurring cases of C. diff in North America.  

So if this is something that affects people in developed countries, and always occurs as the result of taking antibiotics, how do we treat it?  Well, sometimes different antibiotics can kill off the C. diff and sometimes they can't.  When antibiotics don't work, another course of action is available.

If C. diff took over an uncolonized colon (and other guts too) because the other bacteria were dead, then clearly, the answer is to put the normal bacteria back.

You may ask, Can't I just eat yogurt?  Nope, it isn't close enough to our intestinal flora.

What about other probiotics?  Not close enough.

The only thing that is close enough is the real deal from a healthy person. 

So what do you do?  You find a close friend or family member (this adds whole new dimensions to intimacy) that you would trust with your life and you take a large sample of healthy bacteria from their guts (aka poop), stick it in a blender (yuck!), and then get their healthy bacteria inside of you.  Dripping those bacteria down from the top end of the digestive tract seems to work better than going in from the bottom end because the whole intestinal tract gets exposed that way.  

Patients respond well to this treatment and are healthy and happy again in no time!

(I hope I never get C. diff. ; )

Use it and lose it?

I recently heard that a friend of mine with two extremely premature twin babies took her children to the doctor because they had fevers and ear infections. Their ears ruptured and drained and it was clear from the odor of what drained that this resulted from a bacterial infection. The doctor refused to give them any antibiotics. The twins didn't improve, and frantic for her children's health, she finally found a doctor willing to prescribe some antibiotics and the children are okay now.

WHAT WAS THAT DOCTOR THINKING? Despite his seeming lack of medical skill, he was probably trying to be responsible.

Overuse and misuse of antibiotics are almost always cited as the reasons for resistance. Doctors are being taught this and encouraged to withhold antibiotics from patients.

The accusation that misuse of antibiotics is the cause of resistance is unduly strong considering there are very few data to support it. This accusation has never been experimentally tested and the observations leading to it have never been statistically tested. It is based in general observations, and far reaching assumptions. For every observation that supports the accusation, there are several to refute it.

In support of the accusation, antimicrobial resistance is less frequently observed in Scandanavian countries and the Netherlands than it is in Italy, France, Greece, Turkey, and Tunisia. Scandanavian countries and the Netherlands use antimicrobials less often than the more southern European countries. That would seem to support the accusation.

On the other hand, when hospitals stop using an antimicrobial, resistance to it usually doesn't decrease. Sometimes resistance actually increases in frequency after the antibiotic is no longer in use.

Also, resistance is found in bacteria located at the most pristine parts of the earth where humans have never used antibiotics.

Also, for brand-new antibiotics that have barely been used, resistance emerges rapidly, and is often present in bacteria before the antibiotics are even released.

These observations all seem to refute the idea that by reducing antibiotic use, we can stop resistance.

A well tested pillar of evolutionary theory is that in a really large population, genes that confer even a small increase in fitness will tend to spread through the population.
Bacteria have unfathomably large populations. The bacteria inside one person outnumber all the humans alive on the earth. When all of the bacteria on earth are considered, it is usually pretty accurate to think of them as an infinitely large population. This means that even if an antibiotic is very rarely used, resistance to it might spread because there could be some fitness advantage associated with the resistance gene. In other words, if we use antibiotics at all, resistance will follow. We can't stop it unless we give up antibiotics completely, which simply isn't an option.

Does this mean that we should use antibiotics with reckless abandon? No, certainly not. Many antibiotics are mildly toxic to humans and from that perspective alone, they should be used judiciously.

Also, even though any use of an antibiotic might cause resistance to spread, using an antimicrobial a lot will cause resistance to spread more rapidly.

However, we certainly need to explore options for controlling resistance that extend beyond indoctrinating doctors to use fewer antibiotics. That just isn't an effective way of preventing resistance, and it sometimes compromises the health of patients.

Horizontal Inheritance

Compared to humans, bacteria are very advanced in some ways. For example, consider the attention and the investment that went into cloning "Dolly" the first cloned sheep. And then there were the aftershocks, worries about human cloning and ethical considerations and debates about how and when humans would be cloned and if they could be cloned. Now in no way do I support human cloning, but as I consider the millions that have been spent to reach those technologies, I feel a little smug about the cloning of bacteria that takes place in a nickles worth of broth made from yeast and liver extract.

Cloning bacteria is the easiest thing on earth. They just copy their DNA and then split themselves in half with one copy of the genome in each half. The end products are two exact duplicates of each other that can then go on to divide some more. For humans, cloning is a lot harder, because we come from two parents and four grandparents. As humans, variation is the norm, but in bacteria, it is the exception.


Bacteria do however, have variation. Rather than getting their variation from unique combinations of parental DNA, they get it from their neighbors. This process is called horizontal gene transfer. It's kind of like a white elephant exchange. Sometimes you win, sometimes you lose. They don't know what they are going to get. Except in this case their lives depend on it. If they get worse genes, they'll die. If they get better genes, they live and do better than their neighbors.

Antibiotic resistance genes are often spread through bacteria via horizontal gene transfer and getting a resistance gene is like winning the lottery (for the bacteria) if the antibiotic it blocks is being used. Without the gene , the bacteria die and with it, they live. The problem with this kind of lottery is that the bad bacteria aren't the only ones that win. For example, if someone uses penicillin for a long time, it stops working on their illness because the bacteria that were causing the illness have become resistant to penicillin. When they become resistant, they can spread resistance to bacteria that don't make us sick, like the beneficial bacteria that live in our guts. We need those bacteria, but if they become reservoirs of resistance genes they can spread the resistance into new strains of bacteria that us sick.

This is why doctors tell us to finish our whole course of antibiotics even if we get better. It is important to kill of the disease causing bacteria before they become resistant, but it it also important to kill of the innocent bystander bacteria that might become resistant to the antibiotic as well.

Antibacterial Handsoap

The question I am most commonly asked is whether I think that antibacterial handsoap is a good idea or not.... The answer is that it depends. Bacteria grow on our skin. There is no way around this. They will always be there. They are called "skin flora". This name reminds me of my garden in the back yard, and it really is similar. There are good plants such as lilies and gladiolas and there are bad plants such as ragweed and dandelions. There are also plants that are a mixed bag ... like grass.....it's fine in the lawn but bad in the flower beds.

Bacteria are the same. There are good ones and bad ones and some that are a mixed bag. Some of the good ones, like lactobacillus are mainly found in the gut, but may also help to ward off yeast infections externally. An example of a bad one is Propionibacterium which causes acne , (and incidentally also is the bacterium used to make Swiss cheese). Staphylococcus is a mixed bag. It is found all over the skin and is just fine when it's there, but if it gets inside a cut or scrape it can cause infections and be deadly sometimes.

A lot of people try to kill the Staph on their skin. In essence, this is the same as killing a lawn. The grass may die, but something else will move in. Like a dead lawn that gets taken over by weeds, the "something else" that replaces Staph on the skin is usually worse. One of the bad species of bacteria being found on skin right now is Acinetobacter baumanii. This is a worse pathogen than Staph when it gets inside of us. It is resistant to nearly all antimicrobials. No one is sure why it is being found so regularly in skin flora these days. There are people who might blame global warming. As global warming has not yet affected the temperature of human beings, I am more inclined to think that antimicrobial soaps are the cause.

I do not think that antimicrobial soaps are always bad however. If someone gets exposed to worse bacteria than Staph, then antibacterial soap is probably a good idea. Health care workers, for example, are probably justified in using antibacterial soaps. After visiting a hospital, or having physical contact with someone who is obviously sick, it is probably a good idea to use antibacterial handsoaps. For the rest of us however, we have to consider that if we kill off our natural skin flora, the greatest likelihood is that something worse will take its place.

Antimicrobial Resistance...the untold story

I guess that I spend a good fraction of my life thinking about antibiotic resistance. Probably more than sleeping, but less than my friends and families. It's fun to think about resistance because all of the processes that cause it occur inside of a little cell that is only a few microns in diameter. I think about bacteria in cross sections and when I do that, they seem like video game screens with enzymes running around like Pacman and chewing up the antibiotics, or changes in cell walls that are like a force field that keeps antibiotics from getting in.

It's fun to think about them this way, but always, in the back of my mind are the articles I read that describe elderly people dying from multidrug resistant urinary tract infections (Since when did those become lethal?), multidrug resistant pneumonia that they acquired in the hospital, and multidrug resistant skin infections from minor abrasions. Those weigh on me heavily. I remeber reading a bunch of articles about sepsis and septic shock and wondering what those terms meant. I literally started crying when I read a definition that included the phrase "liquification of internal organs". Who knew that was so common?

Last year, more people in America died of multidrug resistant Staph aureus than AIDS. That's only the tip of the iceberg of resistance. That is only one organism and there are so many resistant organisms.

My mood changes from sad to angry when I think about how few resources are given to solving this problem. In the US, there are no major lobbying groups for this problem, no private organizations dedicated to it, and very few federal funds available for studying and solving this problem. Research from developing countries in Latin America has already surpassed US research of drug resistance on some fronts!

I am not sure what to do about this problem. I give much of my time and thought to researching resistance. Sometimes I think I have nothing more to give to the problem, but then I think, maybe there is a little more I can do. So, I am going to start keeping a blog about this problem. Hopefully it will be more enjoyable than a text book and more relevant.