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Infections and Chronic Disorders

Chronic diseases (health problems that last for months or years, like arthritis and cancer) are draining and frustrating. Often, doctors can only treat the symptoms – and often, even that isn’t particularly effective. For many people a Paleo diet can bring relief from the symptoms of chronic diseases, especially gut diseases like Crohn’s Disease, celiac, or diabetes. For others, though, symptoms persist even on the best of diets – and many people feel frustrated and discouraged when the purest nightshade-free, FODMAPs-free, gluten-free, dairy-free, egg-free autoimmune Paleo protocol isn’t helping.

In a community focused on diet, the temptation to solve every problem with some kind of dietary change is very strong. But it’s important to remember that poor health might have causes outside your kitchen. In the case of chronic health problems, researchers are increasingly discovering that conditions like cancers, autoimmune disorders, and neurological diseases are strongly linked to infections by viruses, bacteria, or fungi. These infections can trigger the onset of a chronic disease,* or worsen one that already exists. Although many infections don’t ever become chronic, and many chronic infections don’t ever develop into anything worse, the physiological burden of fighting off a chronic infection can strain your body’s resources and undermine your health and vitality even on the most inoffensive and nourishing diet.

*(for the sake of clarity, in this article, “chronic disease” will refer to a chronic non-infectious, disease like cancer; “chronic infection” and “chronic infectious disease” will refer to a chronic infectious disease like herpes or hepatitis B)

Infections: The Basics

Medically speaking, an infection is any damaging invasion of the body by a harmful microorganism. Unlike genetic diseases or deficiency diseases, infectious diseases require foreign attackers (pathogens): these pathogens can be bacteria, fungi, parasites, or viruses. Bacteria are single-celled organisms that take a variety of forms and can thrive in many different conditions; most bacteria (such as your gut flora) are actually beneficial or harmless to humans, but an invasion by harmful bacteria or an imbalance of beneficial bacteria can cause disease. Viruses are even smaller: they aren’t even complete cells. Each virus contains nothing but a protein coating wrapped around its DNA and RNA. Unlike bacteria, viruses aren’t considered to be alive because they can’t reproduce on their own or survive outside the host’s body; this is why antibiotics are useless against them.

Fungi are usually multicellular (although yeasts are a type of unicellular fungus), and are actually very primitive plants. Like bacteria, fungi can be either helpful (Penicillin is made from a type of fungus) or damaging. Parasites include protozoa (unicellular organisms ) and helminths (parasitic worms). More recently, scientists have also conducted research on another type of infectious agent, prions. Prions are built entirely of protein, and most famous for causing mad cow disease.

Infectious agents are almost everywhere – even people who take reasonable care to wash their hands and clothes are exposed to germs from almost every substance they touch, the air they breathe, and the water they drink. Attempting to prevent all exposure to potential pathogens would be useless, and even potentially harmful. Fortunately for us, a healthy human immune system can stop the vast majority of these pathogens at the door. But sometimes a harmful invader does get through the body’s defenses, causing an infectious disease.

Infections by any of these agents can be either acute or chronic. Acute infections come and go rapidly; chronic infections develop more slowly and last longer. For example, the flu is an acute infection: although a person with the flu might feel sick for longer, the virus itself usually comes and goes within a week. Staph infections, on the other hand, can frequently be chronic, lasting up to several years. Infections can also be latent; that is, the pathogen can stay in the body without producing any symptoms. Chicken pox is a classic case of a latent infection: the chickenpox virus can stay dormant in the body for years, to recur as shingles later in life.

Infections and Chronic Disease

While infections are nasty enough on their own, they also pose a more long-term danger: they can cause or complicate other chronic diseases, even diseases that aren’t contagious or typically associated with infectious agents. For years, scientists dismissed the role of infections in chronic disease, simplistically classifying infectious diseases as universally acute. Cancer isn’t contagious, so how could it possibly be caused by a transmissible viral or bacterial infection? But two Australian scientists, Robin Warren and Barry Marshall, challenged this model in 1982, when they proved that chronic infection by a type of bacteria called H. Pylori could actually cause peptic ulcer disease, a noninfectious and chronic stomach disease.

Warren and Marshall won the 2005 Nobel Prize in Physiology or Medicine for their discovery. Since this breakthrough, scientists have found an increasing number of connections between various infections and other chronic diseases that were previously thought to be unrelated to infectious agents. This doesn’t mean that you can “catch Parkinson’s” the same way you catch a cold; the chronic diseases themselves are not contagious. But infection with other diseases that are contagious can affect the development of a noncontagious disease in a variety of complicated ways. Sometimes, infections are directly responsible for the development of a noncontagious chronic disease; in other cases, they contribute more indirectly.

Infections can directly lead to other chronic diseases in 3 key ways. First, an infection can slowly damage the tissues or organs of the human host, or provoke the body’s own immune system into doing so (an autoimmune response). Some pathogens are molecularly similar to your own cells, and so an immune response directed against them can mistakenly attack your own body as well (this is called molecular mimicry). The immune response in this case can continue even after the original pathogen is no longer in the body. Chronic Hepatitis B, for example, can provoke an autoimmune response against the liver, often leading to Chronic Liver Disease over a period of several years. Thus, an infection can set off a chronic autoimmune problem that persists long after the original infectious agent has been destroyed.

Second, the infection can cause such serious damage immediately that it produces lifelong problems. Poliomyelitis, a disease caused by the poliovirus, sometimes causes permanent paralysis (Franklin D. Roosevelt is the most famous victim of this). Finally, acute infections can lead to chronic follow-up conditions (known as sequelae) that stem from the original infection. For example, foodborne pathogens like E. Coli can induce chronic sequelae including reactive arthritis and chronic joint pain.

It’s important to note that most infections don’t develop into chronic autoimmune conditions, or give rise to serious sequelae like arthritis. Claiming that “E. Coli gives you arthritis” is hyperbolic and inaccurate; “the damage caused by E. Coli may cause conditions that make you more susceptible to arthritis” would be more precise (if not as catchy of a headline). Nevertheless, a high infectious burden (the amount of energy the body has to spend fighting chronic infections or their aftereffects) can seriously increase a person’s likelihood of developing a chronic disease. Even if the infection doesn’t explicitly cause an autoimmune response or one of the other problems above, it can still contribute to overall poor health, and suppress immune function.

The specific biological processes involved in this kind of damage are as varied as the infections themselves, but it’s possible to identify at least two common factors: inflammation and oxidative stress. These two problems both represent systemic physiological damage, and they’re both very closely linked to both infectious diseases and non-contagious chronic diseases.

Oxidative stress is an imbalance between oxidative free radicals and antioxidants. During normal oxygen metabolism, your body forms a type of free radical called a Reactive Oxygen Species (ROS). ROS are very chemically unstable; in their attempts to become more stable, they can change the molecular composition of other cells, causing tissue damage. Normally, your body can handle these ROS through molecules called antioxidants, which control the potential damage of ROS and prevent them from accumulating. Infections, however, reduce antioxidant production, thus causing a kind of cell damage known as oxidative stress. Oxidative stress is also the primary driver of the aging process, and also implicated in chronic diseases of old age like Parkinson’s and Alzheimer’s. Thus, the oxidative damage caused by an infection could exacerbate the symptoms of these chronic diseases. Oxidative stress also impairs an effective immune response and causes inflammation, which scientists have linked to chronic conditions like cancer, diabetes, and neurological disorders.

Inflammation is the natural consequence of any kind of infection: it’s the immune system’s first response to any kind of tissue damage (from an infection or any other cause). This is very useful for an acute illness or injury like the flu: your body senses the invading virus, responds with an inflammatory immune reaction, clears the virus from your body, and repairs the damaged tissues. But in the case of a chronic infection, the initial inflammatory response never gets entirely turned off – when the pathogen stays in the body, the acute inflammatory immune response becomes chronic and self-perpetuating (i.e. hormones and chemicals produced during the inflammatory response trigger further inflammation). Inflammation then triggers further oxidative stress, provoking a vicious cycle of positive feedback.

The inflammation and oxidative stress caused by a chronic immune response have been strongly linked to many kinds of chronic diseases, including many types of cancer, neurological/psychiatric diseases (like Alzheimer’s Disease, autism, and depression) and autoimmune disorders (like Type 1 Diabetes or Hashimoto’s thyroiditis). An immune system burdened by chronic inflammation also can’t fight off other pathogens as effectively, so one chronic infection makes you more likely to get another. Some infections (such as Hepatitis A and some parasites) even do double damage by suppressing your immune system to survive. On top of this, the inflammation and oxidative stress of the infection add to the damage that any existing chronic disorder might be doing.

The biological evidence for the role of infections in causing chronic disease is supported by a high prevalence of chronic infections among people with other chronic diseases. But even though infections are clearly related to noncommunicable chronic diseases, it’s difficult to identify a clear cause-and-effect relationship because most chronic diseases are so complicated and related to such a wide variety of causes. Several infections are associated with more than one chronic disease, and any given chronic health problem might be caused or exacerbated by more than one infection. Some infections also contribute to chronic disease through a postinfectious immune response, or remain latent for years (meaning that a test will show up negative even though the bacteria are still in your body). Tests for these infections are difficult, expensive, and often mutually contradictory, making diagnosis even more difficult. But if you have a chronic disease (and probably even if you don’t), it’s a safe bet that you’re also suffering from an increased infectious burden.

Chronic Infections: A Modern Problem

From an evolutionary perspective, an infectious cause of chronic diseases makes sense, because these diseases confer no survival benefit: if they were genetic, they should have been slowly weeded out of the gene pool. Surviving genetic diseases do have a survival advantage to go along with their disadvantages (the gene that causes sickle-cell anemia, for example, also causes resistance to malaria). Thus, the description of chronic diseases as being rooted in infections is evolutionarily plausible.

An evolutionary perspective on chronic infections and diseases, however, raises one important question: why are they such a characteristically modern problem? Although there is some evidence for the existence of chronic diseases in the ancient world, until very recently, acute illnesses accounted for the vast majority of the death toll. In 1900, the top three killers in the United States were tuberculosis, pneumonia, and diarrhea (all acute). In 1997, they were heart disease, cancer, and stroke. By 2,000, almost half of all Americans had at least one chronic condition with approximately one-fifth of the population suffering from more than one.

To some extent, the modern prevalence of chronic (rather than acute) noninfectious diseases can be explained by the differences between ancient and modern lifespans, but Paul Jaminet has recently put forward another fascinating theory regarding chronic infections in particular. Drawing on the work of biologist Paul Ewald, Jaminet proposes that bacteria (which evolve much more rapidly than humans, often developing traits such as antibiotic resistance within a few years) are evolving to increase their evolutionary fitness by becoming less noticeable. In the modern world, we can use antibiotics and other medicines to kill any pathogens we notice, so the bad guys have to go underground to survive. An acute case of pneumonia is impossible to miss: if the chest pain and the fever don’t clue you in, hacking up a rainbow of mucus is a sure sign that something is very, very wrong. But a chronic case of candida overgrowth can develop slowly over several years: sometimes it’s better, sometimes it’s worse. Through oxidative stress, chronic infections imitate the aging process, so many people assume that they’re simply getting old. Thus, the pathogens can survive by lurking undetected as a chronic disease, rather than flaring up as an acute condition.

Chronic Infections and a Paleo Diet

Since chronic infections are so damaging, and since the damage they cause isn’t always immediately apparent, the ideal solution would be to avoid them entirely. Unfortunately, most adults are almost certain to already have at least one chronic infection; even people who feel healthy might be hosting a dormant viral or bacterial infection. Considering how many pathogens are constantly surrounding us, escaping infections altogether is probably not possible.

For people who aren’t currently experiencing symptoms of a chronic disease or infection, a sensible middle ground is damage control: do what you can to support your immune system by preventing oxidative stress and reducing inflammation as much as possible. This will set up our body to handle the pathogens in your environment as well as it can, sparing you at least some of the problems these infections can cause.

One of the most important ways you can support your body’s defenses through diet is by healing your gut. Leaky gut is an autoimmune, inflammatory condition that generates systemic inflammation (much like chronic infections). On the other hand, healthy gut flora strengthen your immune system. Healing your gut and restoring a healthy balance of gut flora involves eating a healthy diet free from inflammatory grains and legumes (and any other foods you personally might be intolerant to), and avoiding excessive exercise and chronic stress. It’s also important to get enough micronutrients to keep your immune system and your body’s natural defenses running smoothly. Vitamin C and Vitamin D are especially important for immune function.

Reducing oxidative stress also gives the immune system a boost. To combat oxidative stress, it can be useful to eat foods high in antioxidants (like berries), but dietary antioxidants aren’t a magic cure-all; taking antioxidant supplements isn’t generally advisable. A more effective strategy is to reduce the factors causing the stress in the first place. Obesity and metabolic syndrome contribute to oxidative stress, so loosing excess weight and stabilizing any metabolic issues can help. Intermittent fasting is also useful, since IF promotes autophagy, the process that your body uses to process ROS and prevent them from becoming problematic.

In general, anything that reduces the physical stress load on your body will help reduce oxidative stress and inflammation, and thus help keep your immune system functioning properly. Since Paleo as a whole is designed specifically to reduce the overall stressors that cause inflammation and oxidative damage, following a basic Paleo eating plan is usually sufficient, without the need for supplemental antioxidants or special restrictions.

As well as taking care of your body and immune system on a daily basis, make sure you take advantage of the benefits of modern science by getting vaccinations when they’re available. The vaccine against Human Papillomavirus (HPV), for example, protects women against cervical cancer, which results from chronic HPV infection. Vaccines for Hepatitis A and Hepatitis B can prevent you from getting these viruses, which might develop into chronic liver disease. Obviously, not every type of infection has an associated vaccine, but where the vaccines are available, it’s a good idea to get them.

These recommendations are sufficient for healthy people, but people who are already suffering ill health from a chronic infection might need to take further steps to regain their health. These steps will depend on what kind of infection you’re suffering from, and where in the body the infection is located. In general, a ketogenic diet is useful for treating bacterial and viral infections, because bacteria and viruses don’t have mitochondria, so a ketogenic diet starves them of their favorite fuel source, glucose. Fungi and protozoa, on the other hand, have mitochondria of their own, so a ketogenic diet won’t help because they can just use ketones for energy. Before you try any kind of dietary intervention, make sure you’ve identified what problem you actually have.

Gut infections are particularly difficult to treat, since it’s necessary to not only kill the unfriendly pathogens but also preserve the helpful gut microbiota. In its natural and healthy state, the innate immune system needs a very complex process to recognize which gut bacteria are helpful and which are harmful (perhaps this is why gut dysfunction can trigger so many autoimmune conditions). Ideally, a treatment for a chronic infection should also preserve this distinction. Simply taking an antibiotic to wipe out all microbes living in the gut can backfire, since destroying the beneficial bacteria leaves the gut wide open to colonization by superbugs like C. Diff. In some chronic infections, it might be necessary to take an antibiotic, but this should always be accompanied by a remedial course of probiotics and/or probiotic foods like sauerkraut and kefir (if you tolerate dairy well), to restore the helpful gut flora.

Dietary intervention can be very helpful in treating chronic diseases (and the infections that cause them), but for serious health conditions, always make sure to try dietary therapy in conjunction with a treatment plan prescribed by an actual doctor. A reasonable course of action would be to sit down with your doctor, and discuss the possibility that an infection might be causing or exacerbating your health conditions, and then develop a comprehensive treatment plan that incorporates diet and supplements. This can be frustrating if you’re stuck with a doctor who isn’t Paleo-friendly, but resist the urge to give up and attempt to treat yourself. You cannot cure cancer with bone broth and ketosis.


Chronic infections are a uniquely modern problem, and they can contribute to all kinds of chronic diseases, from cancers to psychiatric disorders to autoimmune conditions. Some infections are specifically associated with particular diseases (such as the relationship between hepatitis and chronic liver disease); others can trigger autoimmune reactions or chronic sequelae; still others do more general damage by causing inflammation and oxidative damage that impairs the immune system and stresses the body in general. Even if these infections don’t lead to another chronic condition, they can still result in what doctors call “failure to thrive,” a general lack of energy and vitality.

The chronic infectious burden that most of us are carrying certainly takes a toll on our well-being – for some people, treating an infection might be the missing link to restoring their health with a Paleo diet and lifestyle. With the increasing amount of research devoted to potential infectious origins of chronic diseases, hopefully mainstream medicine will start developing more effective integrative cures that treat the underlying infections, not just the symptoms, of chronic diseases. Until then, taking appropriate steps on your own, or bringing up the evidence with your doctor can help prevent or treat a chronic infection as part of the Paleo lifestyle.