There's no question that chronic Lyme disease is a controversial illness and one that doesn't play by the usual rules. If it did, all stages of the disease would be easily dispatched by a short course of antibiotics, sufferers would rapidly return to health, and their lives would go on as if nothing significant had happened. Sadly, that's not the way it goes for many Lyme disease patients who continue to labour under the weight of debilitating symptoms for several months, years, or even decades after what should have been effective treatment.
There is considerable debate in the medical and scientific communities over why so many Lyme disease patients experience symptoms associated with the illness for such extended periods of time and that debate, from what I've seen, is not a particularly polite one. Fractious would be a better description.
I'd like to take a moment to reflect on the major theories regarding the causes of chronic Lyme disease symptoms. Keep in mind that these are not the only theories. Rather they're the ones that have clawed their way to the top of the heap since Lyme disease patients first started reported lagging symptoms back in the 1970s, long before Borrelia burgdorferi was identified as the illness's causative agent.
Here are the big three, in no particular order:
Theory #1: Autoimmune syndrome - The autoimmune syndrome theory revolves around the premise that a short course of antibiotics (typically 2 to 4 weeks) is sufficient to kill off the Lyme bacteria. Any symptoms that remain are most likely the result of the patient's immune system continuing to react as it did when the now defeated infection was still active. Several better understood infectious diseases cause exactly these sorts of syndromes, so this theory wasn't exactly pulled out of thin air. Since the 1980s, this Lyme-induced autoimmune syndrome has been the dominant theory for ongoing symptoms and if you read the existing treatment guidelines for Lyme disease, you will discover that this theory remains front and centre to this day. In recent years, however, it has been losing significant ground to the novel pathogen theory which, for many researchers, is the more plausible explanation for persisting symptoms.
Theory #2: Novel pathogen(s) - The idea here is that when someone is bitten by a tick that's infected with Lyme bacteria, that tick may also be infected with another pathogen (or pathogens) and while antibiotic treatment eradicates the Lyme bacteria, it does not eradicate the unknown pathogens. We already know that the ticks that carry Lyme disease can carry several other disease-causing organisms such as Bartonella, Babesia, Anaplasma, and Ehrlichia. Tick researchers readily confess that they know very little about what organisms live on and in ticks, making the contraction of a pathogen that is either entirely unknown to medical science or that is not yet known to cause illness in humans a realistic possibility. Research is ongoing at several sites throughout Canada to try to identify any and all organisms associated with ticks and, eventually, to determine what impact, if any, these organisms have on human health. Many will, no doubt, have no impact whatsoever, but a handful may hold the answers Lyme sufferers have been waiting for. This is an area of research that is expected to yield significant results over the next decade.
Theory #3: Bacterial persistence - This theory stems from the idea that after Lyme bacteria has been in the body for more than a few weeks, it begins to employ several unique survival techniques that both antibiotics and the immune system have a great deal of difficulty defeating. It's these survival techniques that have been put forth as the reason for why short courses of antibiotics appear to fail in a large number of people with advanced infections. The bacteria persistence theory has been picking up steam in recent years, but it has yet to make it into mainstream thinking. There is significant push back against this theory by old guard researchers and there has traditionally been very little research funding channelled in this direction. But several research groups have been looking into these survival techniques and their results have so far been compelling. More pressure will need to be placed on this theory by many more researchers worldwide before it challenges the other two theories in a meaningful way.
It will take time and lots of research to determine which of these theories are correct. It's possible that all three are and that Lyme patients with ongoing symptoms are suffering from a complicated stew of persistent bacteria, novel pathogens, and autoimmune foul-ups. That would certainly go a long way towards explaining why the symptoms of Lyme disease are so diverse, seem to vary from one patient to the next, and often require a kaleidoscope of treatments. It's also possible that none of these theories is correct and that the real reason for Lyme's persistent symptoms is one of the lesser known theories or possibly something that hasn't been considered yet. Only time will tell.