Infectious Disease in the TEOTWAWKI World- Part 2, by Militant Medic

Bacteria, Virus, Fungi, Parasites, and Prion defines an infection as “The invasion and multiplication of microorganisms such as bacteria, viruses, and parasites that are not normally present within the body. An infection may cause no symptoms and be subclinical, or it may cause symptoms and be clinically apparent. An infection may remain localized, or it may spread through the blood or lymphatic vessels to become systemic (bodywide). Microorganisms that live naturally in the body are not considered infections. For example, bacteria that normally live within the mouth and intestine are not infections.”

There is a lot there, in that little definition and beyond, that the definition is not even accurate! Germs that normally live in your body can cause infections and do frequently. Any woman who has ever had a yeast infection knows this. Yeast are a natural part of a woman’s genital tract. Usually kept in check by the natural competition with other bacteria that live “down there” and by the natural acidity of the genital tract. However, if she takes an antibiotic that kills those competing bacteria, yeast can overgrow leading to a yeast infection. So we see the definition above is not even right.

First, I would like to present a few definitions we use a lot in medicine that some of you may not be familiar with. (Some of these are not textbook thorough but simplified for our conversation):

Germ: any microorganism in existence. This includes bacteria, virus, parasite, fungi, and prions.

Pathogen: a germ that infects you and makes you sick (i.e. Strep pyogenes, which causes strep throat)

Commensal: a germ that generally lives in or on you but does not make you sick; it doesn’t help you either. (For example, staph epidermidis is a germ that lives on your skin but only in very rare cases makes you sick.)

Symbiote: a germ that gains a benefit from living in or on you but that provides a benefit to you in return. A current buzzword for some of these are probiotics. (E. coli live in our intestines where they absorb nutrients but in return secrete Vitamin K– an important clotting factor– that our body absorbs and uses.)


Now let’s gain an understanding of each of the different types of germs. I tried to keep from getting too technical.

Bacteria are single-celled organisms that are prokaryotic (in that they lack a membrane-bound nucleus and other intercellular structures common to more advanced organisms). They are very small, usually no larger than a few micrometers (or 0.0001 inch) and come in a variety of shapes. They are found all over the earth from deep sea vents to the arctic. Obviously, we are most interested in the ones that inhabit or infect humans. We are filled and covered with bacteria, and it is estimated there are 10 times more bacteria on and in us than we have cells in our body! Most are commensals, which basically mind their own business and help keep more pathogenic bacteria in check through normal mechanisms of competition.

Bacteria can be classified in a number of different ways. Most are beyond the scope of this article. One classification that is helpful to understand is Gram staining. Gram stain is a purple dye that selectively stains cell walls. Gram positive bacteria (which have thick cell walls) stain purple, and Gram negative (which have thin cell walls) stain pink. The two most important Gram positive bacteria are the Strep and Staph family. An understanding of whether a bacteria is Gram positive or negative is important because many antibiotics are much better at killing one or the other. For example, antibiotics that target cell walls (like the penicillins) are much better against Gram positive bacteria with their thick juicy cell walls than Gram negative with their wimpy unappetizing thin cell walls.

Another classification that is helpful are anaerobic vs. aerobic. Aerobic bacteria can tolerate the presence of oxygen and include Streps, Staphs, Mycoplasma (the cause of tuberculosis), and Enterobacteriaceae (Salmonella, Klebsiella, E. coli, Yersinea (plague), and Shigella). Anaerobic bacteria tolerate oxygen poorly and will not grow well in areas with a lot of oxygen. Some examples of anaerobic bacteria include Clostridium (C. diff, botulism, gas gangrene, and tetanus), Fusobacteria, Corynebacterium (diptheria). Some antibiotics (like Metronidazole) only work against anaerobic bacteria.

Many of the classic diseases of mankind are caused by bacteria. These include scarlet fever, cholera, tuberculosis, syphilis, anthrax, bubonic plague, tetanus, gangrene, and leprosy.

Almost all bacteria can be killed by one antibiotic or another.

Viruses are small infectious particles (notice I did not say cells) that require a host cell to replicate and reproduce. Viruses come in a wide variety of forms, including plant viruses, animal viruses, and even viruses that infect bacteria and parasites. Viruses are so small they cannot be seen, even with the most powerful light microscopes.

Because they have to “hijack” your cells to divide, all human viruses are considered pathogenic. There are not any viruses that I am aware of that are commensals or symbiotes.

Many famous diseases of mankind are caused by viruses, including smallpox, polio, influenza, herpes, chickenpox, HIV/AIDS, hepatitis A, B, and C, right down to the lowly common cold (Rhinovirus). Viruses have been in the news a lot lately, as they are the cause of Ebola and Avian flu.

To my knowledge, we have discovered treatment for only a few strains of viruses, and I say “treatment” instead of “cure” because the medications we have discovered only slow and weaken the virus as opposed to kill them, but this is better than nothing. The few viruses we can treat are HIV, chickenpox, herpes, hepatitis B and C, and influenza. For all other viruses THERE IS NO TREATMENT. Understanding this one simple point is really important if you do not want to waste your antibiotics on a viral illness you cannot treat.

Fungi are a large family of eukaryotic organisms, which means they have membrane bound nuclei and other advanced cellular structures. They range in size from single-celled yeasts to very large underground branching structures that create mushrooms when ready to reproduce.

While fungi can be very damaging to plants, only a few bother humans. The pathogenic species are the Dermatophytes (Greek for “Skin Lovers”, which are the causative agents of ringworm, toenail fungus, athletes foot, and jock itch) and Yeasts (which can infect a woman’s genital tract or our skin). There is also a triad of geographically localized fungi that can also make you sick. These are Histoplasmosis (endemic to the Ohio River Valley), Coccidiomycosis (endemic to the central valley of California), and Blastomycosis (endemic to the Great Lakes region). These three usually cause lung disease, due to inhalation of the spores. A bunch of other fungi are less dangerous and generally only cause disease in people with weakened immune systems, like AIDS patients.

There are many good treatments against fungi, and all can be killed by one antifungal or another. Regular antibiotics (used to kill bacteria) do NOTHING against fungus and can actually make them grow more by removing their bacterial competition. (Just ask any woman who has had a yeast infection after a course of antibiotics.)

Parasites are a large family of critters where the parasite benefits from the host, while the host is harmed. While bacteria and viruses are technically parasites for our discussion, we will not consider them as such. We will also not be considering important but largely foreign parasites (like malaria) in our discussion.

We will be focusing on endoparasites (parasites that live in us, like worms) or exoparasites (parasites that live on us, like lice) of the human body. Parasites are multicellular and in this regard more closely related to humans than viruses, bacteria, or fungi.

Parasites are an additional concern because many act as vectors in spreading other viral, bacterial, or parasitic illnesses. The classic example is bubonic plague (Yersinia pestis), which was spread by fleas. If you could avoid being parasatized by the flea, you could avoid the plague.

We have good treatments against parasites, but the more closely the parasite resembles a human the more likely the treatment will hurt you as well. Significant side effects are common with many parasite treatments. Like viruses and fungi, parasites are usually unaffected by antibiotics.

Prions are infectious proteins that can cause other proteins to change shape, leading to harmful effects to the host. As they do not contain any genetic material and cannot reproduce in the classical sense, technically they are not living organisms. Prions were not discovered until 1982 and are rare. They are the causative agents of Mad Cow Disease and Kuru. Prion disease is transmitted by eating infected brain and spinal cord tissue. Once acquired there are no treatments and prion disease is universally fatal. So, don’t eat brains.

How Do Antibiotics Work?

Before we talk about how antibiotics work, I want to discuss something called Antibiotic Spectrum of Activity. Antibiotics are generally classified as Broad-spectrum, Intermediate- spectrum, or Narrow-spectrum. This refers to how many different types of bacteria the antibiotic can and will kill. I will discuss the spectrum of each of the antibiotics in greater detail below, but in general Broad-spectrum kill a wider variety of bacteria than narrow-spectrum, which kills fewer and more specific bacteria. While some may think “The antibiotic I want to take is the one that always kills the most different kinds of bacteria. Give me the broadest-spectrum you have!”, this is a mistake. Remember, most of the bacteria in your body either don’t hurt you or they actually help you, and sometimes just their presence keeps other harmful bacteria in check. Using a broad spectrum, like Clindamycin, to treat strep throat is like taking out a foxhole with a tactical nuke. You kill everything on the battlefield– good guys and bad. While it will cure the strep throat, it will wipe out all your friendly gut bacteria too, leaving you with a case of diarrhea, if you are lucky, and a case of Clostridium difficile colitis, if you are not. In general, the only time doctors use broad spectrum antibiotics is when there is not a narrow spectrum that will do the job (Clinda to kill MRSA) or you have a wound that potentially has a lot of different bacteria in it and you want to kill all of them (Augmentin for a dog bite). If you know the bacteria that is causing the problem, use a narrow-spectrum antibiotic that will kill the pathogen and only the pathogen.

WARNING!! Like other meds, many antibiotics can cause unpleasant side effects. If you are lucky, you just get a little loosening of the stools or a mild yeast infection. However, others can cause changes in red or white blood cells or liver or kidney problems. Many can also interact with other medications you might be taking. Before taking any drug you should read about it and gain an understanding of potential side effects you might experience. This is especially true if you are pregnant or breastfeeding. I have discussed some of the bigger potential complications below, but it is by no means an exhaustive list. Before starting an antibiotic you will need to evaluate whether the risks are outweighed by the benefits. In some cases, it’s easy. “The risk is a rash, but if I don’t take it I will die!” Obviously the benefits outweigh risks in this case. More difficult will be “I have a runny nose. It might be a sinus infection, but it could just be a virus and the only antibiotic I have will likely give me severe diarrhea.” This is a harder choice to make.