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infectious disease

Lyme disease: Disease staging and typical treatment recommendations (Part 1)

Vectorborne diseases are infectious diseases transmitted to people via blood sucking arthropods, like mosquitos, flies and ticks. Lyme disease, caused by spirochete bacteria of the genus Borrelia, is the most common such disease in North America. In the US, more than 20,000 cases have been reported annually in the years since 2002. 94% of cases occur in New England, the Mid-Atlantic, and the upper Midwest. (CDC, 2010) Every year, 1-3% of people living in endemic regions of the US become infected. Cumulatively, you can see infection rates of as high as 15%. (Tugwell 1997)

Most people with Lyme are diagnosed in early disease. A hallmark erythema migrans (EM) rash, commonly called the Bull’s eye rash, is found at the site of the tick bite in the majority of Lyme patients. Accompanying symptoms include fever and headache. However, up to 16% of patients never develop a rash. In the absence of this rash, many people think they had a virus and do not seek treatment. (Steere 2003)

Lyme disease has three distinct phases:

  1. Early localized infection. This is the initial presentation of viral type symptoms, like headache, soreness, fever, tiredness, and often the Bull’s eye rash. At this point, the infection is in the skin where the tick bite occurred. (Auwaerter 2004)
  2. Early disseminated infection. This is when the bacteria enter the bloodstream and spread. The EM rash may occur in places other than the site of the bite. In Europe, patients may develop borrelial lymphocytomas, which are darkly colored bumps. This symptom is specific to the European species of Borrelia. Neurologic problems affect 10-15% of patients in this stage. It can cause meningitis, facial palsy, memory loss, shooting pains, psychiatric changes and sleep disturbances. Some patients may also experience cardiac problems such as atrioventricular block (AV block.) (Stanek 2012)
  3. Late disseminated infection. Untreated or undertreated patients can progress to this stage after several months. About 5% of untreated patients develop chronc neurologic problems, including polyneuropathy and Lyme encephalopathy. (Seltzer 2000) Encephalomyelitis can cause cognitive impairment, weakness in the legs, difficulty walking and balance disturbances, among other things. Psychosis, panic attacks and anxiety can all occur. Lyme arthritis can occur, usually in the knees, but sometimes elsewhere. (Puius 2008)

Early localized or early disseminated infection (without neurologic or cardiac symptoms) is treated with short courses of antibiotics: doxycycline 100mg twice daily; or amoxicillin 500mg three times a day; or cefuroxime axetil 500mg twice daily, for 14 days. In the presence of neurologic symptoms of early disseminated disease, the recommended treatment is ceftriaxone 2gm daily IV for 14 days; or cefotaxine 2gm IV every 8 hours, or penicillin G 18-24 million units per day, in divided doses every 4 hours, for 14 days; or oral doxycycline 200-400 mg daily in 2 divided doses for 10-28 days. These recommendations are for adults. Patients with cardiac issues secondary to Lyme should be treated with either oral or IV antibiotics for 14 days while hospitalized. Ceftriaxone is usually used for this purpose. (Wormser 2006)

In late disseminated infection, Lyme arthritis can be treated successfully with doxycycline, amoxicillin or cefuroxime axetil as detailed above. Adults with arthritis and evidence of neurologic disease should receive IV ceftriaxone for 2-4 weeks. If joint swelling recurs, retreatment for 4 weeks of oral antibiotics or 2 weeks of IV antibiotics is recommended. Late neurologic disease can be treated with IV ceftriaxone for 2-4 weeks. Existing inflammation may take some time to wane and response to treatment may be slow. (Wormser 2006)

About 10-20% of patients treated for Lyme disease with 2-4 weeks of antibiotics continue to have fatigue and joint/muscle pain for some time after treatment is completed. These ongoing symptoms can last upwards of six months and indeed can last for years. This is termed Post-Treatment Lyme Disease Syndrome (PTLDS) and the exact reason for this is unknown. Many people also refer to this as “chronic Lyme disease.” (Aucott 2012) We are going to go through the competing theories on “chronic Lyme” and the evidence presented for both sides in the upcoming posts.



John N Aucott, Ari Seifter and Alison W Rebman.  Probable late lyme disease: a variant manifestation or untreated Borellia burgdorferi infection.  BMC Infectious Diseases 2012, 12:173.

Wormser, Gary P. The Clinical Assessment, Treatment, and Prevention of Lyme Disease, Human Granulocytic Anaplasmosis, and Babesiosis: Clinical Practice Guidelines by the Infectious Diseases Society of America. Clin Infect Dis. (2006) 43 (9): 1089-1134.

Seltzer EG, Gerber MA, Cartter ML, Freudigman K, Shapiro ED (February 2000). “Long-term outcomes of persons with Lyme disease”. JAMA 283 (5): 609–16.

Puius YA, Kalish RA (June 2008). “Lyme arthritis: pathogenesis, clinical presentation, and management”. Infect. Dis. Clin. North Am. 22 (2): 289–300, vi–vii.

Auwaerter PG, Aucott J, Dumler JS (January 2004). “Lyme borreliosis (Lyme disease): molecular and cellular pathobiology and prospects for prevention, diagnosis and treatment”. Expert Rev Mol Med 6 (2): 1–22.

Stanek G, Wormser GP, Gray J, Strle F (February 2012). “Lyme borreliosis”. Lancet 379 (9814): 461–73.

Tugwell P, Dennis DT, Weinstein A, Wells G, Shea B, Nichol G, Hayward R, Lightfoot R, Baker P, Steere AC: Laboratory evaluation in the diagnosis of Lyme disease. Ann Intern Med 1997, 127(12):1109-1123.

Steere AC, Dhar A, Hernandez J, Fischer PA, Sikand VK, Schoen RT, Nowakowski J, McHugh G, Persing DH: Systemic symptoms without erythema migrans as the presenting picture of early Lyme disease. Am J Med 2003, 114(1):58-62.

Centers for Disease Control. Lyme disease data, 2010.

Immunity, vaccination and disease transmission

Okay, everyone. Cold and flu season is upon us, so it’s time to talk to you about immunity and disease transmission.

Herd immunity occurs when a large portion of the population is immune or less susceptible to a disease. It is mostly mediated by humoral immunity, when B cells have made antibodies and memory cells in response to an earlier infection.  Infectious diseases are transmitted from person to person, but when herd immunity is achieved, the chains of transmission are broken. This means that susceptible persons are much less likely to interact with infectious persons, thus reducing the risk of infection by those susceptible.

Practically speaking, herd immunity is achieved mostly by vaccination. The number I see most often to achieve herd immunity is 95%, meaning 95% of the population needs to be vaccinated in order to prevent widespread transmission of the disease. In reality, the requisite percentage is very specific to the disease and its natural history. For most diseases for which we vaccinate, 80-95% vaccination rate is needed to achieve herd immunity.

I’m going to tell you guys a secret now. A few months ago, someone was rolling out some unsubstantiated facts and figures on vaccination in my facebook group. I asked them to cite their source. Their response was to mock me and insist that it wasn’t worth it since I would never read them anyway. Being as I have feelings and go out of my way to be accepting even to lines of thought I do not personally endorse, I got pretty fucking mad. I don’t know what other people do when they get mad, but when I get mad, I learn everything I can about the subject in question. In this case, that included reading a vast amount of garbage and dangerous misinformation. I am talking 1-2 hours a day of reading articles and watching videos on completely inaccurate myths about vaccination.

So let me be really clear here: I read lots of posts and memes and even “scientific articles from medical doctors” supporting the anti-vaccination movement and I fervently, wholeheartedly, and without reservation of any kind, reject its merit. This information does not convey an accurate understanding of epidemiology, immunology or microbiology of infectious disease. I agree that, rarely, vaccine injury can occur. My niece had an ADEM reaction at the age of four which may or may not have been due to a vaccine (but probably not, because correlation does not equal causation.) I also agree that the risk of death or serious injury from illnesses for which we vaccinate is greater than the risk from vaccination.  I do not agree that any scientific link exists between vaccination and autism.

There is a very small portion of the population who have truly valid reasons for not vaccinating, and an even smaller portion who have truly valid reasons for completely not vaccinating. These include people with primary immunodeficiencies (for whom vaccination cannot be effective), those too young to be vaccinated, transplant recipients, and those with severe secondary immunodeficiencies (such as from medications.) Universally, these are also the people at highest risk from infection. These people cannot be vaccinated and are more likely to be killed by communicable diseases.

Mast cell patients are recommended to receive all vaccines per CDC (or relevant governmental body) guidelines. Premedicating with antihistamines is practiced by many mast cell patients prior to receiving vaccines. (Please note that steroids can interfere with vaccine action, and as such should be avoided if possible.) Simply having mast cell disease is not a contraindication to vaccination.


One of the best descriptions of how herd immunity works goes like this:

There is a population of 1,000,002 people. 1,000,000 are vaccinated for disease X and 2 are not.

An outbreak of disease X causes infections in 101 people. 100 are vaccinated and 1 is not vaccinated.

This means the rate of infection among the vaccinated population is 0.01% and the rate among the unvaccinated is 50%, 5000x higher.

A vaccinated person can still become infected, it is just less likely. They often experience less severe disease, but not always. It is also important to get boosters at appropriate intervals to maintain strong immunity.


Let’s address some specific cases.

Seasonal flu viruses are spread by droplets dispersed by coughing, sneezing or talking. Most often, the flu is spread when these droplets contact with the mouth or nose of another person. Less often, an uninfected person may become infected by touching a surface upon which droplets still rest and then touching their mouth, nose or eyes.

If you are infected, you can start infecting others more than a full day before you have any symptoms and for up to a week after. Young children and those with weakened immune systems can be contagious for even weeks longer.

For some, the flu is just a painful and unpleasant inconvenience, with no permanent damage to their health. However, for others, it can be disabling or fatal. In the 2012-2013 flu season, 171 children died from the flu. 50% of the children had no previous risk factors for complications. 90% of the children who died were not vaccinated.

In the 2010-2012 seasons, the risk of PICU admission for flu related illness was reduced by 74% through vaccination. The CDC estimates that 7.2 million flu related illnesses will be prevented by vaccination in the 2014-2015 flu season.


Measles is seeing a resurgence in the US, largely due to increased rates of vaccine refusal. Measles is still very common in other parts of the world. Prior to vaccination in the US, measles caused about 450 deaths a year. From 2000-2013, there were 37-220 cases annually in the US, with most being contracted by unvaccinated individuals outside of the country. This year, we have had a record 610 cases in 24 states, most as a result of 20 individual outbreaks.

Measles is unbelievably contagious. It has an R0 (pronounced “R naught”) of 12-18, which means that 12-18 other people can be infected by one person. 90% of the people close to a measles patient will contract it. An 83-94% vaccination rate is required for herd immunity against measles. It is transmitted by droplets as described above and can live on a surface for up to two hours. An infected person can infect others up to four days before they have a rash and up to four days after.

Measles is a very serious disease. It can cause a wide array of complications, including death. It can cause severe ear infections resulting in permanent deafness. Approximately 5% of children with measles get pneumonia, the most common complication resulting in death. It can also cause a fatal condition affecting the central nervous system 7-10 years after infection.


Pertussis, also known as whooping cough, has an R0 of 12-17. Almost everyone in the same house will be infected if not vaccinated. It is also spread by droplets and 92-94% herd immunity is required to be effective. A person can be contagious for up to three weeks before they have symptoms. Once the cough appears, they are most contagious, for up to 2-3 weeks after. After five days on antibiotics, a person is usually no longer contagious. A really important thing about pertussis is that the laboratory test used to detect it is not great. A negative test does NOT mean you don’t have pertussis, especially if you have been exposed.

Pertussis is especially dangerous for infants and young children, and can transmitted by holding infants too young to be vaccinated. 23% of infants under 1 year who get pertussis will develop pneumonia. 1.6% will die. People of any age can develop complications, including permanent loss of bladder control, rib fractures from severe coughing, and encephalopathy. Uncomplicated pertussis can cause severe coughing for up to 10 weeks.

In 2012, 48,277 cases of pertussis were reported in the US, but it has historically been underreported. 20 people died. This was the most cases in a year in the US since 1955.

I am going to California this February and I am literally terrified that I am going to get pertussis while I’m there and end up in the hospital. How unfortunate and unnecessary.

So how do you prevent getting sick and spreading illnesses?

  • Wash your hands often. Soap and water is best.
  • Regularly disinfect surfaces that might be contaminated.
  • Avoid close contact with sick people.
  • If you get sick, the CDC advises staying home for at least 24 hours after the fever is gone.
  • Cover your nose and mouth when you cough or sneeze.  Coughing or sneezing into your elbow is better than into your hand.
  • If you are sick, or have been exposed to someone who is, especially stay away from people at increased risk of danger from infection. This includes people with chronic diseases like mast cell disease. Infections are activating to mast cells. Furthermore, many of us have other health conditions and/or take medications that suppress our immune system. Patients with primary or secondary immunodeficiencies are at greatest risk. For these people, infection with even mundane diseases can be fatal.

All information on this topic is available at the CDC or WHO websites, with citations for corroborating peer reviewed literature on the applicable pages.