Submitted by Jim K on Wed, 2005-10-12 23:58


Cpn Simple- The shortest explanation we could think of!

  • Cpn has been clearly proven to have persistence in the body despite “standard” antibiotic treatment (two weeks of a single antibiotic).
  • Cpn has been implicated in a wide variety of diseases (see bottom of this page).
  • Blood tests and cultures are not reliable indicators of whether Cpn is part of your disease.
  • If you have any of the diseases in which Cpn has been implicated, it may be worth trying an “empirical” (based on symptoms alone) combination antibiotic protocol (Link).
  • Most doctors are not familiar with this, and you will have to present a rational and evidence based case to them for prescription of the appropriate antibiotics through information such as on this site.

Is this right for you? 


Four indicators can be used to help you determine if an empirical test of the full combination antibiotic protocol is useful for you. You should be on it for for a minimum of 6 months to a year. The first three suggest that you have Cpn and you should continue this treatment.

1. You experience distinct reactions to the antibiotics indicative of Cpn die-off (see Reactions to Treatment link).

2. You have improvement of disease symptoms.

3. You have noticeable halting of symptom progression.

4. Nothing at all and decide this isn’t for you.

Killing Cpn In Different Phases

Diagram from David Wheldon ( used by permission. 

Phases of the Cpn bacteria and what agents effect those phases:

EB’s- Elementary Body What are they? EB’s are spore-like forms which are infectious and metabolize minimally (aren’t using nutrients, replicating, exchanging with the environment, etc.). They are tough, tiny and reside in the intercellular tissues (outside of actual body cells). What do they do? EB’s attach to your body’s cells and invade them. Since there can be more EB’s than can get into cells, EB’s build up in local tissues causing inflammation and immune response.

What kills them? They are killed by amoxicillin, which is transformed to penicilamine in your own body, and destroys the bonds which hold the EB cell wall together. An amino acid NAC (N-acetyl cysteine) also is used for this purpose. What happens? When you kill them, they release toxin into the tissues in which they have built up, and you get inflammation and pain there, which can last for days or weeks afterwards before you feel relief of symptoms. Most people taking NAC report a period of flu-like feeling of malaise, achyness, nunning nose, perhaps coughling.

RB's- Reticulate Body What are they? Once an EB enters a host cell it transforms into a form which can replicate new EB's which is called a Reticulate Body or RB. The RB has no energy source of it's own for this, so it must steal energy (ATP) from the host cell, leaving the host cell weakened and less functional. The RB also inhibits the natural cell death of the host cell so that it can survive while it replicates. After the production of many new EB's the host cell bursts and dies, spreading the infectious new EB's into the surrounding tissue.RB's are inhibited in replicating by various antibiotics such as doxycycline, azithromycin, roxythromycin and others, and subject to this will convert into the Cryptic (and nonreplicating) form where they can be killed by metronidazole. RB's are prevented from forming by rifamcin.

Cryptic form What are they? When RB’s face an environment which threatens their survival inside a cell (lack of food, antibiotic attack, etc) they can transform into a “Cryptic” form which stays inside the cell, but is in hibernation, so to speak. What do they do? In this form it is not vulnerable to regular antibiotics and can reside there until conditions change, then become an RB again and start to replicate and reinfect with EB’s. What kills them? Flagyl (metronidazole) or Tinactin (tinidazole) are used to kill the cryptic forms of Cpn. Nitrofurantoin, an old urinary tract infection drug, also has antichalmydial effect in this phase. These drugs can be hard to tolerate for various reasons, and so are commonly “pulsed” by taking a course for 5 days every 3-4 weeks, rather than taken continuously. Some protocols may eventually have one of these drugs taken continuously for some period as the patient can tolerate. Patients may experience fatigue, nausea, bowel upset, deep joint achyness and muscle pain as the cryptic orgnanisms are killed and the immune system engages in clean up.

Much of the discomfort from treating Cpn is a combination of the organism's endotxin itself, and the inflammation caused by your own immune system (cytokine) reactions to that.


Amoxicillan and NAC kills the infectious spore-like EB forms which build up in the tissues.

Rifamcin kills EB’s transforming to RB’s in a vulnerable enzyme transformation phase.

Doxycycline and either Rozithromycin or Azithromycin, are used in combination to interfere with the RB’s ability to replicate. Two are used which work on different proteins to minimize creating resistance.

Five days a month of metronidazole or tinidazole (added to the first two continuous antibiotics) targets the cryptic formi, to kill the bacteria outright.

Supplements are recommended to help counter the impact of Cpn on the body, and of the inflammatory effect of the die off during treatment.

Treatment can take months to years to completely eradicate Cpn from the body.

What diseases has it been implicated in?

Additionally: chronic obstructive pulmonary disease, uveitis, optic neuritis, radiculitis, nerve deafness, transverse myelitis, sarcoid, myocarditis, pericarditis, culture-negative endocarditis, atheromatous arterial disease, aneurysm, giant-cell (temporal) arteritis, polyarteritis nodosa, Wegener's granuloma, primary sclerosing cholangitis, reactive arthritis, Reiter's syndrome, Behcet's disease, cutaneous vasculitides including pyoderma gangrenosa. Wheldon adds: "Conditions which may suggest the possibility of flare-ups of chronic Chlamydia pneumoniae infection deserving serological investigation include the following — a multiplicity being more strongly suggestive: recurrent sinusitis, recurrent chest infections, chronic fatigue (especially if following a respiratory infection), focal neurological deficits, myalgia, muscle fasciculation's, recurrent episodes of bronchospasm, unexplained pleuritic pain, angina, recurrent arthralgia, unexplained recurrent abdominal pain, unexplained menorrhagia, recurrent fistula-in-ano, recurrent cutaneous vasculitides, achalasia, intestinal dysmotility."