Superbugs Super Suck

So by “tomorrow” I would have another post, I meant “the tomorrow after I trying to learn how to poach eggs and twerk in my kitchen”. Also no, I’m not joking; I’ve never poached an egg before.

ANYWAY. Superbugs.

You know I have one of these.

Like the lice that evolved as humans and human habits changed, so have superbugs have evolved. “Superbug” is a blanket term referring to any bacteria that has evolved antibiotic resistance. Strains that were once easily susceptible to mild antibiotics, now require stronger and stronger drugs to be eradicated. So not only are the chances or prolonged illness and death increased, but more people have to deal with harsher drugs to cure an infection. Not good.

How does this happen? By frequent exposure, or infrequent, low-level exposure to antibiotics. I can explain how this works with one of my convoluted analogies (cause I haven’t done one of those in a while).

Many of you have probably heard of the businesses that will blast classical music outside in order to discourage hoodlums. The idea being that angry punks have no appreciation for Bach and Brahms and, finding the music annoying, will leave. If only one business were pumping the Baroque jams, then the kids would leave and find somewhere else to hang. Should a lot of businesses try this (whether or not angry punks are actually a problem), the kids would quickly become accustomed to the music. Similarly, if only a few businesses tried it, but not at volumes loud enough to be a proper annoyance, the kids would easily develop a tolerance and never leave. As a result, the businesses that actually have a problem with angry punks and hoodlums will have to play less and less mainstream music (like opera or free-form jazz) louder in order to clear their sidewalks. But at a certain point, they’ll alienate their own customers on top of the kids that want to smoke and curse outside. Either way, the business now has a lot of Classical Resistant Angry Punks (CRAP) to deal with.

In this scenario, the kids are the bacteria and the music is the antibiotic. When people use antibiotics unnecessarily (like when folks demand some for a viral infection), not only does it kill off your natural microbiota, but the frequent exposure ensures that only bacteria tough enough to withstand the drugs will survive. Remember, even your natural bacteria can be dangerous in the right place or population size.

Another problem occurs when patients do not finish their course of antibiotics. Many people assume that just because they feel better, they can stop taking medicine. However, this can end up only killing off the weaker bacteria, leaving resistant strains to proliferate and evolve stronger resistance. Bacteria can also pass their resistance on to or receive resistance from others. That’s how we get multiple-resistant pains in the neck like Staph.

If you have a bacterial infection that will not clear up on its own (like many ear infections), ABSOLUTELY take the antibiotics your doctor prescribes. Just make sure you finish the dose and do NOT demand antibiotics if they’re not necessary. Many people (especially parents) want to feel like they’re doing something about an infection, but antibiotics are not always the answer.

Hugs not drugs, guys.

Although hugs will not cure TB.

I strongly recommend drugs if you have TB.

The RIGHT ONES though.

Minocin will not help.

Just talk to a doctor, OK?

Ophid out.

Source

–. 2014. “Stop The Spread of Superbugs.” NIH News In Health. March 6, 2015. < http://newsinhealth.nih.gov/issue/feb2014/feature1&gt;

Raw Power- Clarification

Some things have been been bugging me since I posted Raw Power the other day, and I want to make a clarification. First of all, food poisoning is serious business. Bacteria like E Coli and Salmonella can make you very sick, some strains can even kill you. Things like improper butchering or storage techniques allow for bacterial contamination and proliferation, as a result, humans invented cooking to kill any potential bacteria living in their food. Eating raw meat means you trust yours or the restaurant’s butcher and the chef that prepared it. Although there are grades of bacterial exposure (called inoculum) that range from unnoticeable to the body to lethal, it does NOT take much time for bacteria to proliferate to a lethal inoculum size (which varies between species). It can take as little as 20 minutes for a population on your food to double. So ALWAYS keep food cold and separate from other things when not preparing it and wash everything well and frequently.

Sushi, conversely, is a greater concern for parasitic contamination. Preparing sushi means choosing fish that have been carefully inspected for any parasites. They’ve also been flash frozen at incredibly cold temperatures to kill any lingering buggies (your freezer is not cold enough to do this). If you’re making sushi (or steak tartarre, for that matter) tell your butcher so they can help you choose the best and safest cuts.

Lastly, I addressed bacterial contamination at large, but it remains to be said that E Coli, Salmonella and other enteric bacteria reside in the gut, so contamination with such bacteria is indicative of exposure to fecal matter (usually due to nicking the intestines during butchering). These do not just live in your environment if you are a safe cook. Be a safe cook.

Again, there are safe ways to eat raw meat, but you and the meat have to be safe. The FDA is strict about testing for the serious stuff like E Coli and Salmonella, so I focused on other types of bacterial exposure. However, I realized my post might have minimized the dangers and thus I wanted to clarify some things.

That is all.

Raw Power

Have I expressed my love of eating? I love eating. Food is beautiful and delicious and beautifully delicious. I will tunnel my way through a box of Cheezits or meander my way through some world class Thai cuisine. If it’s edible, I will try it at least once. Some of my favorite foods involve raw meat: sushi, venison carpaccio, steak tartarre. As a result, I am often pronounced “brave” (sometimes also “semi-feral”, if they’ve seen me eat) by some of my friends and family.

Raw and undercooked foods, particularly meat, do have a risk of causing food poisoning. If they’re contaminated with hostile bacteria, it can make you all kinds of BLEAH. Veggies have a decreased chance of carrying such bacteria, and they don’t make for as tasty of an environment for them, either.

So why would anyone eat raw or undercooked meat? As I’ve covered previously (see previous) our bodies have natural microbiota and other strong defenses against pathogens. Anything that makes you sick has to overwhelm the initial defense. A few bacterial cells won’t even make a dent; those bastards need a LOT of buddies before they pose a significant health threat. Smaller children, the elderly and the immune compromised can get sick a lot more easily because their immune systems are not as strong; it takes less bacteria to make them sick.

Think about all those times you’ve had everyone’s favorite raw treat: cookie dough. We’ve all had some, yeah? Cookie dough is DELICIOUS and anyone who says otherwise is lying. And you know, a little cookie dough that goes straight from the mixing bowl to my mouth, with little waiting around is not going to be a hospitable environment for bacteria to grow. At no point does the dough get warm enough for any bacteria present to multiply into significant numbers. Ideally, it has also never been exposed to harmful bacteria, cause we know that even beneficial bodily microbiota can be dangerous if they’re in the wrong place at the wrong time. Besides, unless you sterilize your kitchen constantly, there WILL be bacteria in your kitchen. And if you do, well…you got issues, man.

Delicious, delicious salmonella risk…

As with the raw cookie dough, raw meats are kept chilled until serving, at temperatures too cold for bacteria to proliferate. By the time they make it to my plate, exposure to foreign bacteria is minimal and it’s perfectly safe to eat.

Although ideally there is some exposure to Worcestshire, maybe some rock salt or a nice vodka marinade.

Hm, pardon me while I get some lunch. Next time I’ll address why duck is safe undercooked but chicken is not.

Cheers!

Sources

-. 2010. GRE Subject Test: Biology 5th Ed. Kaplan, New York.

On Drinking Texas Tea

Following the Deepwater Horizon rig explosion and subsequent spill into the Gulf of Mexico there was a lot of talk about clean up efforts, including talk of oil-degrading bacteria. Seems mighty helpful of the bacteria, degrading all this crap we spilled, but the fact is that the bacteria are entirely selfish. I’ve thought that saying the bacteria are “degrading” the oil sounds more like they’re kindly disassembling molecules for us. The fact is that oils are hydrocarbons and there are many kinds of bacteria that need it as a carbon and energy source. These bacteria possess specialized enzymes for digesting the oil into carbon dioxide and water. However, oil is made up of a variety of chemicals so no one species of bacteria can digest all of it. Different species chow down on different hydrocarbons using different enzymes. But! Species without the gene for producing such enzymes can receive the gene for these enzymes either via human-mediated bioengineering, or the natural process of horizontal gene transfer. Bacteria can actually give good genes to other bacteria. It requires a sex pilus to connect two cells and through which the donor can send a copy of their genes for oil-degrading enzymes.

Unfortunately, oil digestion is not a quick process. The speed depends on environmental conditions such as temperature, pH and availability of other nutrients, as well as the actual size and composition of the oil spill in question. Regardless, the presence of bacteria make a big difference in controlling and shortening long term effects of hydrocarbon contamination in the environment. By the way, I’ve been talking a lot about oil spills, but microbes are widely used for a variety of chemical spills involving hydrocarbons.

 

Source

American Academy of Microbiology. 2011. “Microbes and Oil Spills-FAQ”. Fisheries and Oceans Canada. June 16, 2013. < http://www.dfo-mpo.gc.ca/science/publications/microbes/index-eng.html&gt;

Photo credit LBNL (Lawrence Berkeley National Laboratory)

CORRECTION: Fermenterss for Father’s Day

While researching my post for tonight, I’ve found sources contradicting what I found last night regarding oil-degrading bacteria. Namely that those are typically aerobic, rather than anaerobic, bacteria.

That is all.

Fermenters for Father’s Day

What started as a request from my father for a Father’s Day blog topic ended in my education being denounced as incomplete because I don’t read Superman. Also I think my dad wants to be silicon-based. Maybe. That part was slightly unclear. Anyway, I think that means his present will be a bit more difficult to accomplish this year. I guess that’s what I get for waiting until the last minute. But! The Dado did express a desire to learn about microbes that do not rely on oxygen to survive, and what The Dado wants, The Dado gets (whether we like it or not…like the soul patch).

The reason for the different oxygen requirements of different microbes lies in cellular respiration. Respiration is essential for gleaning ATP (adenosine triphosphate, a high energy molecule that acts as “energy currency” in cells) from organic (or inorganic, depending on the microbe) compounds. Microbes have a variety of respiratory pathways, but I won’t bore you with all those right now (I can always bore you with them later). All the different pathways require a terminal electron receptor. That is, a molecule or atom that accepts electrons from the molecule being oxidized during respiration. Microbes that utilize oxygen as the terminal electron acceptor are called aerobes and those that use other compounds are called anaerobes. These groups can then be further broken down based on oxygen tolerance.

Aerobes that absolutely NEED oxygen are called obligate aerobes and contrast from facultative aerobes that may grow anaerobically, depending on conditions. E. coli is one such bacteria. Microaerophiles, as the name suggests, love only a little air. Much more than 5-10% oxygen concentration (atmospheric oxygen concentration is 20%) and they can’t grow. Likely they have oxygen sensitive proteins, so despite the fact they need oxygen for respiration, too much of the stuff will kill them. More oxygen tolerant bacteria produce more enzymes (such as catalase and superoxide dismutase) that work together to break down toxic oxygen compounds into safer compounds.

Obligate anaerobes are the opposite of obligate aerobes; they are completely oxygen-intolerant. These stroct anaerobes ferment or respirate anaerobically using compounds such as sulfates and nitrates as their terminal electron acceptors. However, their sensitivity to oxygen is not necessarily due to a lack of the detoxifying enzymes mentioned previously and could be cause by other factors. Aerotolerant anaerobes, on the other hand, don’t give a crap about oxygen and will grow with or without its presence. Typically they use fermentation as their respiratory pathway with pyruvate as the terminal electron receptor.

Aerobes have gotten a bit of press lately for their applications in degrading hydrocarbons associated with chemical spills. But more on that later; got to go figure out how to surprise The Dado with a silicon-based biology. I have a feeling a blindfold won’t cut it.

Enjoy the view, Dad. You’re going to be a metalloid soon.

Source

Brown, Alfred E. 2009. Benson’s Microbiological Applications: Laboratory Manual in General Microbiology. McGraw Hill, New York.

Photo credit, me.

Political (Single-Celled) Animals

Time to talk politics. Not Dems vs. Reps or left vs. right, up vs. down, etc. I’m talking the politics of science, specifically medicine. Although the scene is changing, there have been (and still are) strong inclinations to believe Western scientific/medical practices are the end-all-be-all and everything else is foreign bunk. However, studies and reviews are few and far between actually confirming or denying the actual bunk-itude of non-Western/”traditional” medical practices. But again, this is changing; the World Health Organization now has a list of ailments treatable with acupuncture and other various Eastern therapies are becoming more popular in conjunction with Western ones. This brings me to what I really want to talk about: bacteriophage therapy.

Bacteriophage are viruses that target bacteria, hijacking bacterial genetic machinery in order to replicate themselves. Phage may be lytic or lysogenic. Lytic phage will get to work right quick replicating before making the bacteria literally explode with baby viruses. Cute. Lysogenic phage on the other hand are patient. They hide viral DNA or RNA (viruses may have either) in the bacterial genome until the time is right. Then the bacteria explodes. Furthermore, phage are species specific, so one kind of virus will only attack one kind of bacteria. Beginning to see the possibilities? Human bacterial pathogens don’t stand a chance. And unlike antibiotics, phage will evolve alongside their prey, making them virtually immune to the resistances plaguing modern medicine. So why aren’t we all taking bacteriophage instead of antibiotics? Researched off and on since the latter 1800s, phage were even produced commercially to fight bacterial infections. But challenges were made to the efficacy of phage therapy and antibiotics quickly became much more popular so phage were largely forgotten. In the West, anyway, in Eastern Europe and the Soviet Union, bacteriophage therapy use and research persisted, displaying success in combating multi-drug resistant bacteria with phage. It’s like a miracle cure, but politics prevented phage from staging a comeback in the West. Despite the mounting evidence in support of phage therapy, the reports were all in Georgian, or Polish to a lesser extent (the leading institute in this field since the 1920’s is in Georgia, the one in Poland popped up in the 1950’s). Not terribly popular languages outside Eastern Europe even today. When some papers were eventually produced in English, the writer apparently never spoke to the scientists or even had a basic knowledge of medicine because it claimed (among other things) that the phage were useful against allergies, besides mixing up which phage were to be used on which infections. The Western scientists were not impressed. Even if the English papers were accurate, the most research came from “damn, dirty Commies” so it never really had a chance. UNTIL NOW.

Damn, dirty Commie phage, curing all our shit.

OK, not really “NOW” now, but “now” twenty-some years ago. In the ‘80s phage research experienced a revival in Great Britain at the hands of William Smith. Since then papers have been piling up in support of phage therapy and its superiority over antibiotics. However, more rigorous studies need to be conducted to further understand its efficacy, so it will be a while before you can use a virus on your E. coli infection. Still, when the headlines of multi-drug resistant bacteria loom, remember that for every superbug there’s a superflyswatter.

It just needs to go through clinical trials.

 

Source

Sulakvelidze, Alexander, Zephira Alavidze and J. Glenn Morris, Jr. 2001. “Bacteriophage Therapy”. Antimicrobial Agents Chemotherapy. 45(3): 649-659.

Photo credit Dennehy Lab, Queens College: http://dennehylab.bio.qc.cuny.edu/

Gifts of the Spices and Seasonings Part 2

After yesterday’s post, I’m sure you’re all wondering HOW your curry is antimicrobial. If not, then I’m not doing my job right! Or you’re not eating enough curry. Anyway, the true heroes of microbial inhibition are sulfur dioxide and phenols. For those of you unaware, a sulfur dioxide molecule contains one atom of sulfur bonded to two oxygen atoms (hence the “dioxide” bit). In your bloodstream after a nice garlic-and-onion-filled meal, it relaxes the blood vessel walls and thereby reduces blood pressure while giving you the kind of breath that would scare buzzards. Great stuff, right? Bacteria would not agree. While some bacteria LOVE sulfur, those involved in food spoilage do not. Sulfur dioxide gets all up in bacterial protein business, completely messing up their shit by binding to components of oxidation. Enzymes are particularly affected and their reduced function is lethal for the bacteria.

Phenols on the other hand don’t roll that way. Carbon rings with an alcohol group and other various bells and whistles, “phenol” is a very broad chemical term. However, when you’re thinking of antimicrobial components of spices, you’re thinking of eugenol, thymol and carvacrol. Found in cinnamon, cloves, sage and oregano, these phenols are badass. Quite simply, they destroy cell membranes. Doesn’t matter where, doesn’t matter what, fungi, bacteria, in a box with a fox, whatever. They’ll take it down.

So next time your coworkers commence sniffling and sneezing, grab what cold remedy you will, but to really battle the bugs, just spice things up a little.

 

Oh, and since I don’t have any fun, pertinent pictures today, here’s a sea otter washing his face.

 

 

Source

-. 2009. Winemaking. Practical Winery and Vineyard Journal. March 26, 2013.

-. 2010. GRE Subject Test: Biology 5th Ed. Kaplan, New York.

Billing, J and PW Sherman. 1998. Antimicrobial functions of spices: why some like it hot. Quarterly Review of Biology 73(1):3-49.

Oyedomi, SO, AI Okoh, LV Mabinya, G Pirochenva and AJ Afolayan. 2009. The proposed mechanism of the bactericidal action of eugenol, terpineol and terpinene against Listeria monocytogenes, Streptococcus pyogenes, Proteus vulgaris and Escherichia coli. African Journal of Biotechnology 8 (7): 1280-1286.

Sherwood, Lauralee, Hillar Klandorf and Paul Yancey. 2005. Animal Physiology: From Genes to Organisms. Thomson Brookes/Cole, Belmont, CA.

Photo courtesy of me, otter courtesy of the Seattle Aquarium

Gifts of the Spices and Seasonings

Sadly, this is not a post about bacon, or bacon-flavored ice cream, for that matter. However bacon is a good segue into the science I AM going to toss your way and that is antimicrobials. Why do you think such a salty, blood-pressure destroying thing was invented (without knowing how delicious it would be)? Salt-cured meats are HIGHLY resistant to spoilage via microbes and fungi. The salty environment sucks moisture from microbial and fungal cells, making them so hypertonic (thirsty and shriveled) they die.

Yet salt is not the only antimicrobial seasoning out there. In hot, tropical climates, a lot of salty food is a very bad idea unless you enjoy severe dehydration. Instead, hot, tropical cooks employ various spices containing compounds that naturally reduce spoilage by inhibiting the growth of bacteria, yeasts and mold. Now for some anthropology/microbiology crossover action: a study examining the use of 43 different spices in meat-based dishes from 36 different studies found that the higher the average annual temperature, the more spices were used in individual recipes. In addition, recipes of total studied used more spices and the more of the most potently antimicrobial spices (Billing and Sherman, 1998). But wait! There’s more…Not only can spices keep your food germ-free, but they keep you healthy too. Cinnamon alone helps with cholesterol and bloodsugar management, while garlic and onion (a vegetable, but often used as a seasoning) are excellent for lowering blood pressure and warding off vampires.

More microbe mauling spices include allspice, clove, oregano and various peppers. As well as sage, rosemary and thyme. Haven’t found anything scientific supporting parsley though.

Tomorrow I plan on exploring the compounds that help these spices work these wonders. But right now it’s sunny in Seattle and I need to enjoy this while it lasts.

 

Sources

Billing, J and PW Sherman. 1998. Antimicrobial functions of spices: why some like it hot. Quarterly Review of Biology 73(1):3-49.

Snyder, P. 1997. Antimicrobial Effects of Spices and herbs. Retrieved March 25, 2013, from Hospitality Institute of Technology and Management, St.Paul, Minnesota Website: http://www.hi-tm.com/Documents/Spices.html.

 

Bonus points if you got the song I attempted to reference.