Chapter 1
Infections, Antibiotics, Vaccines, and their Relationship
to Autism and ADD: Alternative Treatments
By Dr. William Shaw

 Is There an Autism Epidemic?

The late Bernard Rimland Ph.D., at the Autism Research Institute (1), asked the question “Is there an autism epidemic?”  His data in Table 1 shows that, between 1965 and 1969, only 1% of parents who contacted him were inquiring on behalf of a child with autism less than 3 years old. However, between 1994 and 1995, 17 % of the parents who called him were inquiring on behalf of a child under the age of 3. Presumably, the higher percentage of inquiries on behalf of children under three could be attributed to two factors: (1) a greater knowledge about autism on the part of physicians and parents, leading to an earlier diagnosis and/or (2) a higher incidence of autism in the younger age group. Furthermore, a large number of professionals, including pediatricians and physicians with large practices in the field of autism, have noticed an increase in the incidence of autism.  William Crook M.D., a pediatrician who started his practice in the 1950’s, although being aware of the symptoms of autism, says that he did not see a case of autism until 1973, 24 years later. From that point on, it seemed to him that the incidence of autism accelerated.  Acknowledging this increase is critical for determining whether autism is mostly caused by genetic or environmental factors. If autism is mainly due to genetic factors, the incidence of autism would be constant. Furthermore, the percentage of individuals with autism in a particular age group would be the same. Thus, if the incidence of autism in three year olds is one in a thousand, the incidence of autism in fifty year olds should also be one in a thousand.

Table 1

Is there an autism epidemic?


% under 3 years

















Fortunately, similar data has been reported in Iceland (2). Iceland is an ideal country for this evaluation since a single institution confirmed all cases of autism in the entire country and since the investigators personally reviewed all the diagnosed cases, data variability was minimized. These investigators found that the incidence of autism had doubled over the last 20 years. Furthermore, the male to female ratio had increased significantly over the same time period. This study is extremely important since it shows that factors other than genetics may be causing autism. What could some of these nongenetic factors be?

Data in Table 2 shows the extraordinary incident of cases of Autism in the United States.

Table 2

Kontstantareas and Homatidis (3) at the University of Guelph in Ontario, Canada found a high correlation between the prevalence of ear infections and the incidence of autism. They found that the earlier a child with autism had an ear infection, the more likely that child had a more severe form of autism. They also found that the increased incidence of ear infections was also associated with the more severe rather than mild form of autism. Many similar studies have been conducted in the field of attention deficit hyperactivity (ADHD).  These studies also indicate that increased ear infection early on in life results in much greater incidents of hyperactivity (4-8). Roberts and his colleagues (4) reported that recurrent otitis media during infancy was correlated with increased distractibility of the students later in life. Other studies (5-8) correlated recurrent otitis media in infancy with later low IQ scores, poor performance on reading, spelling, and math tests, increased retention in grade levels, increased attention deficits, and increased behavior problems in school.
Both the autism and ADHD research groups have assumed that this abnormal development is caused by hearing impairment brought on by the ear infection.  My own interpretation of this data is that the abnormal development is instead caused by abnormal byproducts of yeast and drug-resistant bacteria being absorbed into the body from the intestines following the excessive use of antibiotics.  Later chapters will deal with the mechanism of this problem in great detail.

 The Antibiotic Revolution

Antibiotics were first produced on a commercial scale around the end of World War II. In 1949, the amount of antibiotic production was very low, about 80 tons per year (9).  In addition to this low production, the kind of antibiotic used was mostly of the injectable type. But by the 1950’s, the use of oral antibiotics became more predominant.  As a child in grammar school in the 1950’s, I got most of my antibiotics injected into the buttocks. By 1954, 250 tons of antibiotics per year were being produced. By 1990, 20,000 tons (40 million pounds) of antibiotics per year were being produced (9). I believe that this explosive growth in the use of antibiotics is a major factor for the increased incidence of autism, developmental disorders such as ADD, as well as a number of adult disorders such as fibromyalgia. In the United States, one of the main reasons for antibiotic use in children is to treat the condition called otitis media or ear infection.

 Ear Infections

According to a publication (10) by The Panel for Otitis Media, a group of prominent pediatricians and scientists from throughout the United States concluded that:

  • Ear infections account for one-third of all visits to the pediatrician and 75% of all follow-up visits.
  • Between 1975 and 1990, office visits for otitis media increased by 150% to 24.5 million visits per year.
  • Children under age two had the highest rate per year of office visits to the doctor for evaluation of otitis media and also the greatest increase in visits per year between 1975 and 1990: 224%!
  • A two year study of children between the ages of 2 and 6 years in day-care showed that 53% had at least one episode of otitis media during their first year and 61% during their second year. Thirty percent of the children had recurrent bouts of otitis media.
  • A cost analysis in 1991 estimated that the cost per episode, including direct and indirect costs, prescription drugs, and parents’ time lost from work at $406 for a total yearly cost in 1991 of about ten billion dollars.

Otitis media has proven to be a cash cow to both primary care physicians and the drug industry. Now consider another 30 billion dollars a year spent on specialized speech and developmental therapy (11) and billions of dollars more spent to treat ADD, PDD, autism, and other disorders. If, in fact, the overuse of antibiotics is related to the increase in these disorders, then the financial impact of otitis media is very large indeed.

 Nonhuman Use of Antibiotics and the Rise of Antibiotic-Resistant Bacteria

In addition to the marked increase in antibiotic use in humans, the use of antibiotics in food animals has also sky-rocketed, not because the animals are sicker than usual, but because they gain weight much faster when antibiotics are given with their feed. According to regulations, the animals are supposed to be withdrawn from antibiotic use prior to slaughter so that most of the antibiotics they are exposed to will have been eliminated by the time of their death.  However, the abnormal microbial ecology in the intestines of these animals caused by the use of antibiotics persists.  It seems likely that chemical byproducts (such as gliotoxins) produced in the intestines of these animals by yeast, fungi, and antibiotic-resistant bacteria may be absorbed into their bloodstream and are likely to be present in their meat as well. It is difficult to know how much of a problem this is for humans who eat this meat. Pamela Scott, who has written a later chapter in this book, was so concerned about this problem that she only fed her son meat from range animals not exposed to antibiotics in feedlots.

According to Stuart Levy M.D. a professor at Tuft’s University School of Medicine in his book The Antibiotic Paradox: How Miracle Drugs Are Destroying the Miracle (9), the use of antibiotics for fattening animals and other agricultural uses also selects for more drug-resistant bacteria. These bacteria then enter the ecosystem through the meat and feces of these animals and, in turn, may infect humans. Dr. Levy found that six months after the use of antibiotics in feed for chickens, stool samples from humans in the surrounding community contained the same drug-resistant bacteria that had developed in the chickens. The use of human antibiotics in animal feed has been banned in Great Britain but is still allowed and is widely used in the United States. Antibiotics have even been added to the water in which salmon and catfish are raised, and as a result, antibiotic-resistant bacteria have been found in the flesh of these fish.  In addition, antibiotics such as Streptomycin and oxytetracycline have been sprayed from airplanes to control diseases in fruit trees and potatoes, allowing the development of drug-resistant bacteria in soils over a wide geographic area. Some pathogenic bacteria may now be resistant to as many as 10 different antibiotics.

 Bacteria That Causes Ear Infections

The three most common bacteria causing ear infection are Streptococcus pneumoniae, Haemophilus influenza, and Moraxella catarrhalis. These organisms account for 70-90% of all ear infections (12). These organisms commonly inhabit the nose and throat of children and can easily move into the ear via the Eustachian tube. Streptococcus pneumoniae accounts for 30-40% of all cases.  As many as 28% of strains of this organism have been found to be penicillin resistant. Haemophilus influenza is responsible for about 21% of otitis media cases; 15-30% of strains of this bacteria are resistant to several types of penicillin. Moraxella catarrhalis accounts for 12 % of all cases. As many as 96% of strains of this organism may be resistant to penicillin such as amoxicillin (12). Moraxella catarrhalis is present at some time in the nose or mouth of 75% of infants before the age of two years.

The Panel for Otitis Media (10) stated: “It is characteristic of health care providers in the United States to intervene for otitis media with effusion, but the panel was impressed by data suggesting that otitis media usually follows a benign course without treatment.  Thus, although such a study might be difficult to implement because it runs counter to prevailing attitudes, research to document the natural course of otitis media with effusion is essential.”

Translated into simple English, this means that doctors and parents are used to using antibiotics for ear infections. The proof that they work over the long run is shaky. However, it is going to be extremely hard to change the way things are done because habits are difficult to change.

A large Dutch study was done using 1,439 children, divided into two groups with one of the groups receiving no treatment and the other receiving antibiotics and antihistamines. In the untreated children, 60% of the children recovered without medical intervention within three months. This kind of treatment would almost never be done in the United States.  To understand the cultural differences between the two countries for treating ear infections, only about 30% of physicians in Holland prescribe antibiotics compared to the United States, where close to 99% of physicians prescribe antibiotics on a regular basis. Parents and employers must also share in the blame for this antibiotic overuse because with so many two-income families, mothers are under pressure to be at work rather than stay home with a sick child. The parents put pressure on the physicians to use antibiotics even when inappropriate. The physician knows he may lose the patient unless he complies.

In another study of 518 children with ear infection, Cantekin (13) found that six weeks after stopping the antibiotic amoxicillin, the recurrence was 2-6 times higher in the antibiotic-treated children than those in the placebo group. Van Buchem (14) treated one group of otitis media patients with antibiotics, one with tubes in the ears, and a third with neither. The outcome in the three groups was essentially the same.

After examining the medical histories of many children with autism, I became very interested in otitis media due to the fact that a very high percentage of these children had a history of frequent ear infections or other infections treated by antibiotics. In hundreds of medical charts I examined at a hospital, children with seizures, autism, and even psychosis had a history of antibiotic use prior to the development of these conditions. The urine organic acid testing of these children frequently revealed high concentrations of compounds derived from yeast and/or bacteria that are commonly resistant to broad-spectrum antibiotics. The pattern was so prevalent and so striking that there is little doubt in my mind that there is a relationship between the high concentrations of yeast and bacteria byproducts and the resulting disorders.

Exposure to cigarette smoke is also a significant risk factor for otitis media. In a study of seven year old British children, the authors found cotinine, a metabolite of nicotine was present in the saliva of children exposed to secondhand smoke and that the level of cotinine increased with the number of smokers in the household. The authors (15) found that one-third of the cases of otitis media could be attributed to exposure to secondhand smoke.

In addition, allergies can frequently be the major underlying cause of ear infection because an allergic reaction can cause swelling of the tissues in the ears which interferes with proper drainage enabling bacteria to grow more readily. McMahan (16) and Nsouli (17) both found that treatment of underlying allergies greatly diminished the recurrence of otitis media. Because ear infections are such a difficult medical problem for both parents and children, I have compiled a list of different approaches for treating these ear infections, which is given at the end of the chapter.


Numerous parents have reported the regression of their normally developing child within hours or days of vaccination with the MMR, DPT, or hepatitis B vaccines. The most serious research linking the vaccination to autism and PDD can be seen in the work of Andrew Wakefield, a British gastroenterologist. Dr. Wakefield perceived a significant increase in the incidence of Crohn’s disease, an inflammatory bowel disease that he believes is related to the MMR (measles, mumps, rubella, vaccine). After parents of children with autism begged him to examine the gastrointestinal tracts of their children, Wakefield found that lymphoid hyperplasia was prevalent in children with autism who had been vaccinated with the MMR vaccine. Some of the children had severe fecal impaction with stool masses as large as a grapefruit. Many of the parents mistakenly thought that their children had diarrhea because much of the time, a limited amount of liquid stool would ooze around the fecal impaction.  In some cases, the lymphoid hyperplasia was so severe that the intestinal lumen was nearly closed off. Wakefield describes the lymphoid hyperplasia as being similar in appearance to pus-filled tonsils. Data gathered in California indicates an increased incidence of autism that correlates with the introduction of the combined MMR vaccine (Figure 1). A significant increase in the incidence of autism appears to occur about three years after the MMR introduction. The vaccine issue is covered in greater detail in a separate chapter on vaccinations. 

Figure 1
Distribution of Birth Dates of Regional Center Eligible Persons with Autism Figure-1


 Ear Infections and Other Recurrent Infections: How to Break the Cycle or At Least Reduce the  Damage

The following are different techniques that will help break the cycle and minimize the damage. Remember that there are exceptions to every rule and antibiotics may sometimes be needed.

  • Tough it out or employ watchful waiting. Use ear drops containing benzocaine and a decongestant to stop the pain. A large study conducted in Holland showed no difference in outcome when children receiving antibiotics were compared to a placebo group. Antibiotics are not used nearly as much in Europe as in the United States. Only 31% of general practitioners in Holland use antibiotics to treat ear infections. By not treating the infection immediately, your child’s immune system is allowed to react and build up a defense against future infections. If infections are treated immediately, the immune system will not have a chance to strengthen itself.
  • Eliminate milk, wheat, and other allergy causing foods from the diet. Milk is one of the most common food allergies, often causing sinus infections, leading to blockages of the Eustachian tubes, and resulting in ear infections. If milk and dairy elimination does not clear up the infections, get a comprehensive IgG food allergy test to determine if other foods are a problem.
  • Stop any cigarette or other smoking inside the house.
  • Never use antibiotics for colds or flu since antibiotics kill only bacteria, not cold or flu viruses.
  • If you have to use antibiotics for your child, have your doctor prescribe the antifungal drug nystatin along with the antibiotic. There are no adverse reactions between nystatin and antibiotics because nystatin is only minimally absorbed into the bloodstream from the intestine.  If your doctor won’t prescribe nystatin, give one of the natural antifungal products such as garlic, caprylic acid, or grapefruit seed extract along with the antibiotic. Giving the beneficial bacteria Lactobacillus acidophilus while taking antibiotics may not help since the antibiotics may kill the acidophilus bacteria as well. Penicillin, chloramphenicol, erythromycin, tetracycline, oxacillin, vancomycin, and ceftriaxone all will kill the acidophilus bacteria. After antibiotics are completed, give supplements of Lactobacillus acidophilus for at least 30 days. Actually, giving acidophilus supplements regularly, on a daily basis, will help maintain a healthy intestine.
  • Get a throat culture done if your child has frequent infections. The most common organisms causing ear infection commonly inhabit the nose and throat. There is a vaccine available for Streptococcus pneumoniae, which is the most common cause of ear infections. If your child has a positive throat culture for Streptococcus pneumoniae, ask your pediatrician about getting vaccinated against this organism. The vaccine is termed the 23-type pneumococcal polysaccharide vaccine.
  • Consider having one parent stay home with your child until he is at least two years old and avoid preschool and day care centers. Day care is a breeding ground for germs.
  • Breast-feed your child for as long as possible since breast-milk contains antibodies against the bacteria that cause ear infections and other infections as well. Children who are breast-fed are much less likely to get frequent infections during the first six months of life (18,19).
  • Echinacea, the coneflower, was used extensively by the Plains Indians of the United States to treat infections and this knowledge was transferred to the settlers. Echinacea is a stimulant of the immune system and is available in pediatric doses in many health food stores such as Wild Oats.  It can also be ordered over the phone (800-494-WILD) if a store is not nearby. This therapy is even more effective if drops of garlic and mull (also called mullein) oil are placed in the ears while giving the Echinacea. (My son used this method and resolved his earache overnight.) Three days of this therapy will clear up most ear infections.  If this doesn’t work, there is still always the option of using antibiotics. Echinacea will help to decrease the incidence and severity of colds and flu because of its stimulating effect on the immune system. This product has been used extensively in Germany for many kinds of illnesses.  Although much of the literature documenting its use is written in German, some of the articles in English are listed in the references (20-23). Echinacea works best if it is given for 10 days and then discontinued for two weeks before starting again.
  • Ask your doctor to give your child a “shot” of rocephin in the buttocks instead of oral penicillin.  As a child in the 1950’s, I regularly received shots of penicillin as did millions of other people. The main benefit of the injection over oral antibiotics is that it will not kill the beneficial bacteria in the intestinal tract. Killing the beneficial bacteria often leads to an overgrowth of the intestinal tract with yeast and harmful bacteria like Clostridia. Therefore, the antibiotic “shot” will reach the human cells in the intestine, but will not reach the bacteria inside the intestinal cavity.
  • If your child has four or more infections in one year, consider an evaluation of their immune system. Many children with autism have an inborn weakness of the immune system called an immunodeficiency.  It is best to consult with a clinical immunologist, a physician (M.D. or D.O.) who specializes in these diseases. Usually these physicians are also part-time researchers and are associated with a medical school. If your child has a significant immunodeficiency, ask your physician about the possibility of using antibody infusions (called IVIG or intravenous immunoglobulin) to help your child’s immune system fight off new infections.  Sudhir Gupta M.D. at the University of California at Irvine has obtained complete remissions of some cases of autism (24) using IVIG therapy. See the chapter on the immune system for more detailed information.
  • Consult a health practitioner trained in homeopathy. The technique called homeopathy was shown to be more effective (25) than conventional antibiotic treatment in a German study of 103 children between 1 and 11 years. Homeopathy drops are also available at most health food stores. After one year, 70.7% of the children treated with homeopathy had no relapses compared to 56.5% of children treated with antibiotics. The average number of relapses was also much higher in the children treated with antibiotics than in those treated with homeopathy. 
  • Consider tubes in the ear (tympanotomy tubes) if all else fails.


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