Friday, April 29, 2011

1 The Friday Four

In this week's Friday Four, we'll look at how some bacteria avoid antibiotics by shutting down and hiding until it's safe to come out again,  students who go bacteriophage hunting,  disrupting bacteria's communication or quorum sensing in future antibacterial treatments,  tests which use bacteria's scent to detect not only their presence but species, strain, and their antibiotic resistance profile.

CO message to readers: The Friday Four postings will be on hiatus for at least the month of May during Lyme Awareness Month.

1) 'Going off the grid' helps some bacteria hide from antibiotics


ScienceDaily (2011-04-25) -- Call them the Jason Bournes of the bacteria world. Going "off the grid," like rogue secret agents, some bacteria avoid antibiotic treatments by essentially shutting down and hiding until it's safe to come out again.


I want to keep this one short and sweet: What if those few Borrelia burgdorferi left behind in collagen that some researchers say are not viable or non-dividing are just basically in stasis instead? What if they have shut down their metabolic processes and only look mostly dead? (This is starting to remind me of the scene in that movie, The Princess Bride, where Westley is... Oh, never mind, if you haven't seen it, I don't want to spoiler it for you. It's a fun movie. I will tell you the Bourne series is one of the best action series in my opinion - along those lines, I like Memento too...)

Source Reference:
Xiaoxue Wang, Younghoon Kim, Seok Hoon Hong, Qun Ma, Breann L Brown, Mingming Pu, Aaron M Tarone, Michael J Benedik, Wolfgang Peti, Rebecca Page, Thomas K Wood. Antitoxin MqsA helps mediate the bacterial general stress response. Nature Chemical Biology, 2011; DOI: 10.1038/nchembio.560

2) Phage hunting students find new bacteriophages in soils of St. Louis suburbs


ScienceDaily (2011-04-25) -- Twelve students who had participated in an unusual biology course as freshmen have found two bacteriophages, viruses that prey exclusively on bacteria, in the soil of two suburbs of St. Louis, Missouri. As the finders, they had the naming rights; the new phages are called Angelica and Uncle Howie.


This is as awesome as being an amateur astronomer. If you're an amateur astronomer, if you find an object in the sky no one has discovered before, it can be named after you or you can decide what you want to name it. Here, students are discovering their own bacteriophages in the dirt and naming them anything they want.

I posted this mainly because I think it's cool, and I wish I had gotten the opportunity to do this in school, too. Well, who knows... maybe I'll go back to school someday, just to be able to take a course like this and name my own bacteriophage Camp Other. If I did, though, I'd try to find one that consumed Borrelia burgdorferi.

Source Reference:
Pope WH, Jacobs-Sera D, Russell DA, Peebles CL, Al-Atrache Z, et al. Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution. PLoS ONE, 2011; 6 (1): e16329 DOI: 10.1371/journal.pone.0016329

3) Bacteria interrupted: Disabling coordinated behavior and virulence gene expression


ScienceDaily (2011-04-22) -- New research reveals a strategy for disrupting the ability of bacteria to communicate and coordinate the expression of virulence factors. The study may lead to the development of new antibacterial therapeutics.


Bonnie Bassler is up to it again. I love her presentation on TED, and if you haven't seen it, you really should set aside 18 minutes of your time to watch her video on how to get bacteria to talk and how to get them to shut up.

And recently she was on a team that did more research on how to stop bacterial infections by shutting up them up.  Four points in turn outlined their strategy for how one could stop bacterial infection by stopping quorum sensing:

  1. Quorum-sensing (QS) antagonists represent potential antibacterial therapeutics
  2. They can bind LuxR-family transcription factors in competition with autoinducers
  3. The antagonists stabilize a closed conformation incapable of binding operator DNA
  4. This inhibition strategy may be generalizable to other multidomain receptors

Which means that there are antagonists which can bind to certain factors that normally autoinducers would bind to - the antagonists are competition for them,  much like Saccharomyces bouldarii can be competition for other yeasts and C. difficle. When the antagonists bind to the factors, they will not bind to operator DNA.

So to sum up: If you can stop autoinducers, you can stop the bacteria from communicating. You can shut it up. If you shut it up, you can tell it to stop having sex and the immune system police will evict it, much like a loud annoying neighbor.

You think I'm kidding, and making this story up? I'm not - I'm merely telling the story to illustrate a point: In order for gene transcription to be activated in the bacteria, the cell must encounter autoinducers secreted by other cells in its environment.

Here's a basic diagram of how Gram-negative bacteria engages in quorum sensing (noting that Borrelia burgdorferi is not exactly Gram-negative or Gram-positive here, it is somewhat closer to Gram-negative so I include that model here):

What you need to imagine here is that this oval represents a bacterium, and that initially a small number of bacteria are doing this all at the same time in their host, whether that be human or not.

Here the LuxI protein makes the autoinducers (green pentagons) which then diffuse freely outside. Each bacterium doing the same, the concentration of external autoinducer is a measure of the size of the population (quorum).

When the autoinducer concentration is high (meaning the bacteria has reproduced to a certain population)  the autoinducer binds to a cognate receptor LuxR (cognate means having the same form and ad hoc characteristics to bind specifically to the molecule it receives).

This is quorum sensing.

The complex auto inducer-Lux R then binds at target gene promoters and activate their effect (transcription) which has behavioral consequences.

In other words, once the bacteria reaches a certain threshold, the level of autoinducers is very high, and the number of bacteria goes up. The high autoinducer level means more bacteria, and more bacteria means more autoinducers. It's a self-perpetuating feedback loop. If you can prevent the loop from even getting started, bacterial numbers will remain low.

So, you're probably wondering, does Borrelia burgdorferi engage in quorum sensing, and if so, can we get it to shut up also?

This has actually been somewhat under debate. Some research has stated that Borrelia burgdorferi has an autoinducing cognate receptor called LuxS, but it doesn't have the necessary autoinducer to bind to it, which in this case would be AI-2.

More recent research has shown that there might be a more complicated method for Borrelia burgdorferi involved for synthesizing its own autoinducers... Might.

To draw from this Polish research paper from 2009 (

"...the studies of von Lackum et al.[62] demonstrated that B. burgdorferi encodes functional Pfs and LuxS enzymes for the breakdown of toxic products of methylation reactions. According to these observations, B. burgdorferi was shown to synthesize the final product, 4,5-dihydroxy-2,3-pentanedione (DPD) during laboratory cultivation. DPD undergoes spontaneous rearrangements to produce a class of pheromones collectively named autoinducer 2 (AI-2). The addition of in vitro-synthesized DPD to the culture of B. burgdorferi manifested in differential expression of a distinct subset of proteins, including the outer surface lipoprotein VlsE. Although many bacteria for regeneration of methionine can utilize the other LuxS product, homocysteine, B. burgdorferi did not show such an ability. It is hypothesized that B. burgdorferi produces LuxS for the express purpose of synthesizing DPD, and utilizes a form of that molecule as an AI-2 pheromone to control gene expression [4]."

Those cited papers are:

[62] Von Lackum K, Babb K, Riley SP, Wattier RL, Bykowski T, Stevenson B: Functionality of Borrelia burgdorferi LuxS: the Lyme disease spirochete produces and responds to the pheromone autoinducer-2 and lacks a complete activated-methyl cycle. Int J Med Microbiol 2006, 296, 92-102 -and-
[4] Babb K, von Lackum K, Wattier RL, Riley SP, Stevenson B: Synthesis of autoinducer 2 by the lyme disease spirochete, Borrelia burgdorferi. J Bacteriol 2005, 187, 3079-3087

I need to read more about it, at this point the above is currently hypothetical and an in vitro test, so the answer to your question is (unless you know something I don't): the jury is still out on this one.
Source Reference:
Guozhou Chen, Lee R. Swem, Danielle L. Swem, Devin L. Stauff, Colleen T. O'Loughlin, Philip D. Jeffrey, Bonnie L. Bassler, Frederick M. Hughson. A Strategy for Antagonizing Quorum Sensing. Molecular Cell, Volume 42, Issue 2, 199-209, 22 April 2011 DOI: 10.1016/j.molcel.2011.04.003

4) Get a whiff of this: Low-cost sensor can diagnose bacterial infections


Colorimetric sensor array
overlaid on petri dish
ScienceDaily (2011-04-28) -- Bacterial infections really stink. And that could be the key to a fast diagnosis. Researchers have demonstrated a quick, simple method to identify infectious bacteria by smell using a low-cost array of printed pigments as a chemical sensor. In only a few hours, the array not only confirms the presence of bacteria, but identifies a specific species and strain. It even can recognize antibiotic resistance -- a key factor in treatment decisions.

Comments: So the abstract for this paper is as follows:
"Rapid identification of both species and even specific strains of human pathogenic bacteria grown on standard agar has been achieved from the volatiles they produce using a disposable colorimetric sensor array in a Petri dish imaged with an inexpensive scanner. All 10 strains of bacteria tested, including Enterococcus faecalis and Staphylococcus aureus and their antibiotic-resistant forms, were identified with 98.8% accuracy within 10 h, a clinically important time frame. Furthermore, the colorimetric sensor arrays also proved useful as a simple research tool for the study of bacterial metabolism and as an easy method for the optimization of bacterial production of fine chemicals or other fermentation processes."
The full text requires paid access, however, just looking at what is known here between the article and abstract, I have to wonder how accurate a test this could be to detect Borrelia burgdorferi. I could see this rapid strain identification being useful for identifying bacteria for bacteriophage treatments and also for detecting the presence of bacteria on specific surfaces in hospitals or from open wounds. This wouldn't work well for something that is deeply embedded in collagen, but it might work from a synovial fluid sample better than current detection tests for Bb there.

Source Reference:
James R. Carey, Kenneth S. Suslick, Keren I. Hulkower, James A. Imlay, Karin R. C. Imlay, Crystal K. Ingison, Jennifer B. Ponder, Avijit Sen, Aaron E. Wittrig. Rapid Identification of Bacteria with a Disposable Colorimetric Sensing Array.Journal of the American Chemical Society, 2011; : 110427110353066 DOI: 10.1021/ja201634d
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4 Top 10 Tips For Doing Your Own Lyme Disease Research

Here are my top 10 tips to share for doing your own Lyme disease research. Pretty simple and straightforward - and if you have any to add, please share in comments below.

1) Use the scientific, Latin terms for everything. You can use common terms, too, but Latin will give you more results and more specific results.


Instead of "Lyme disease" use "Borreliosis".
Instead of "Neuro Lyme" use "neuroborreliosis".
Instead of "Lyme bacteria" or "infection" use "Borrelia burgdorferi".

2) Find out which terms microbiologists and scientific researchers use in their own papers and classes and then apply them to your search.


Instead of "coinfection" use "polymicrobialism" or "polymicrobial".
Instead of "can't think straight" use "cognitive symptoms".
Instead of "spinal tap" use "lumbar puncture".
Instead of "shooting and burning pains" use "paresthesia".
Etc. - you get the idea.

Look at online and offline medical dictionaries for words that describe your symptoms and plug those into a search engine.

3)  Move your search away from general Google search to Google Scholar. You can get specific results for only scientific papers and patents that way.

4) Whenever you don't understand a term, use Wikipedia for an explanation.

I add a note of caution here: Wikipedia is not always right, though it usually is correct on basic science definitions.

If you aren't sure, double-check by doing a more general search and rely on college and university web sites for definitions. You may want to restrict your domain search to .edu web sites.

5)  Read educational institution web sites in general.

You may be surprised to find out what research is being done now on Lyme disease and coinfections which hasn't been published yet. Bookmark these items and check PubMed for the university name and researcher(s) name(s) periodically, as a paper will eventually be published.

6) Passively collect research information on your own web site or inbox by using RSS feeds.

If you look at the right column of this page and scroll down, you will see a number of Lyme disease and other disease-related and alternative medicine articles that are directly getting posted to this site all the time.

You can do the same with your own web site - or if you don't have a web site - by using an RSS reader or by subscribing to an RSS feed that gets sent to your email address.

This way, research comes to you and you don't have to always go do a search for it.

7) Look at major professional organizations' web sites - even if you may not agree with everything said - at least you will know what's going on.

Read the IDSA's web site periodically and be aware of how they view the issues around Lyme disease and infectious diseases in general. See what the NIH, CDC, and organizations have to say, and even more, dig deeper and look at what people from those organizations say in their research on PubMed and other online publication hubs. Some of what you find may surprise you.

8) Look at major online science web sites geared towards  a more general audience  (not specifically written for professionals) periodically.

Science Daily is a good example of this, and if you look at the bottom of each article, you will often see a link to the original paper or source on which they based their article. Check out the original source for more information - often it leads to finding out about other research the same researchers did on Lyme disease and coinfections.

Also, use the search function in Science Daily to look up terms such as "Lyme disease", "Borrelia", "Babesia" and even "Malaria". You may find interesting articles and older research from their archives this way.

9) Buy microbiology, acarology, and entomology text books for cheap and used at college bookstores which are trying to get rid of all old textbooks, "fire sales",, and independent used bookstores near you.

While these textbooks can be dated, you might find information in them that could be useful and give you ideas of where to search next. Note that a lot of the basic information on Lyme Borrelia hasn't changed - but there has been a more refined and detailed understanding of what Borrelia is about over time, though, and those details need to be picked up by reading more recently published papers and books. (I say this, stating that a lot of Lyme disease research I see being cited online for and by patients is a bit outdated - we need to update these sites to reflect the state of the science.)

(You can also see if any friends or relatives have some lying around they're willing to lend or give to you.)

10) Search various libraries online, and participate in your local interlibrary loan program.

Can't afford that $500. book on microbiology? See if you can borrow it through your library's interlibrary loan program.

You will usually have a shorter time limit on borrowing books that are in high demand - some books have to be returned in a week. So if you need more time to work on it, ask someone to copy select passages for you from it to make notes on them later after you return the book.

Also, in many areas you can sign up for a program that will allow others to pick up books for you at the library on your behalf if you are housebound and too ill to go out - see if your area has one and sign up if you need it. This is good program to use in general for any material you may want to borrow for your own personal use.

And a bonus, Number 11:

Have a family member, friend, or friend of a friend who is already studying clinical microbiology, molecular biology, and/or genetics (immunology is helpful, too) help you decipher what you don't understand - and to tell you whether or not they think the findings are significant and which questions are not answered by a particular study that would be useful to have answered.

This may be a tricker bit, because not everyone is going to either have the time to respond to your request for help on this or hold the belief that your research is not worth the effort because they may believe that Lyme disease cannot persist and you are wasting your time.

Unfortunately, this is the truth of it - but in the true spirit of scientific inquiry and basically being stubborn, some people may be willing to help you at least a little bit.

My advice here is the less well-known the person is to you, the better it is to keep personal details out of the query. Also, keep your email or discussion brief, polite, and to the point while avoiding discussing the controversy. This is not to invalidate or dismiss your experience - but being said out of practicality and diplomacy: Busy people are more likely to respond to something in an unbiased fashion if you keep it simple and short.

Happy researching!

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Wednesday, April 27, 2011

0 IOM Summary Report: Neuroborreliosis Notes #2

This is Part 2 of part 1, IOM Summary Report: Neuroborreliosis Notes...
(Read that first...)

After Dr. Stephen Barthold's presentation, the following discussion came up:

"Another participant questioned how neurologic symptoms occur if the bacterium is just in collagen,even if it is associated with neural tissue. Barthold noted that mice do not get central nervous system disease, possibly because they don’t have much connective tissue in their brain. However, central nervous system disease is seen in larger mammalian species that have more collagen in their meninges and perivascular spaces. Under those circumstances, Barthold has observed spirochetes in the collagenous areas and along the perivascular spaces into the brain. Because there is a dearth of good analysis of human neuroborreliosis cases, it is not known if the spirochetes are located in other areas.  He noted that a tissue bank or biorepository would be very valuable to allow for these types of analysis."

Has Dr. Barthold talked to Dr. Alan MacDonald at all? I have to wonder... aren't there other tissue banks out there which already have neuroborreliosis samples?

So all these people - a portion of which knew they were bitten by ticks - have cognitive and neurological symptoms, but there is little good analysis of human neuroborreliosis cases.

Why is that?

Does it have anything to do with how difficult it is to determine whether or not a patient has neuroborreliosis, especially once you're read the European data on testing the CSF for IgG antibodies and realize that the initial positive rate is at it's best within two weeks of clinical presentation (assuming this means symptom onset)?

When they say there isn't enough data on human neuroborreliosis... let's start with this chart:

No news is good news?

I note that there also is no independent measurement for Late disease-Neuroborreliosis  in this table, either. Just arthritis and the measure for culture is labeled "anecdotal". So data is lacking there, too. (I have to wonder why the author used "ancedotal".)

But then there is always two-tier testing, which is indirect detection testing (does not test for the organism itself, but tests for antibodies to it):

As you can see from this chart, depending on which kind of testing you use (ELISA, two-tier Western Blot, or this other proposed test), supposedly serological testing for early Lyme disease is poor, and early disseminated neurological infection is better. Not perfect, but better.

Is that late neurological and arthritis disease detection rate correct? I want to see the cited research (this requires finding the original full text publication) before commenting more on it. But I will say that even with the correct distribution of findings here,  neuroborreliosis that occurs within the first week after being bitten is not going to show up in the early group, and 13-37% of early disseminated neuroborreliosis cases are missed, depending on the test set.

Note on page 7-4 that:

"The C6 testing protocol has performed comparably in accurately detecting the presence of antibodies to B. burgdorferi in sera of patients with acute EM, but was slightly less effective in the case of neurological Lyme disease."

And also, this is an important point, related to the first chart at the top and information in my previous neuroborreliosis notes post:

"One scientific gap is the testing of cerebrospinal fluid for antibodies. Europeans measure intrathecal production of antibodies by measuring antibodies in CSF and comparing these results against the concentration of antibodies in the serum to produce a ratio. U.S. Scientists have not had a sufficiently large population in which to evaluate the efficacy of this approach because fewer cases of neuroborreliosis are documented in the United States as compared to Europe and CSF sampling is not routinely done in patients with Lyme disease. The absence of this type of testing is a gap in diagnostics for neuroborreliosis caused by B. burgdorferi in the United States."

Is this the case - that the gap in diagnostics for neuroborreliosis is to be blamed on the bacteria? I think that's unfair to the bacteria. As far as I can see, what's happened is that the fact of neuroborreliosis is not something that has been discussed or emphasized when pathogenic Borrelia are neurotropic to varying degrees. Neurological symptoms should be included when educating doctors, nurses, and patients about the disease, and not sidelined to "that only happens in European strains". It doesn't, and besides, Americans do sometimes visit Europe. And hey, if B. garinii and B. afzelii are beginning to show up in southern ticks, well, maybe in a while you'd be seeing more cases of early neuroborreliosis anyway.

I don't know about you, but many Lyme disease patients I've spoken with only got an ELISA test for Lyme disease from their primary care physician, and when that came back negative, there was no further testing.

CSF testing when I had early neurological symptoms is not something I was offered, either.

Which is ludicrous when early serological testing is especially prone to not detecting an infection. What should happen is if the person has a lot of neurological symptoms shortly after a tick bite, they should have a LP. And also the Western Blot. Repeated Western Blot testing which shows an increasing and changing serological profile would be useful in demonstrating antibody response.

It is also stated elsewhere in the summary report:

"An increment in immunoreactive bands is observed in the IgG immunoblots of sera of patients with neuroborreliosis and Lyme disease arthritis."

Saying that Borrelia burgdorferi doesn't cause neuroborreliosis isn't true. Saying it's rare isn't a helpful statement, and aside from utility, it's not even clear how rare it is because we simply lack that data. We don't know. What we have is a guess.

Referring to some studies (there are more studies on neuroborreliosis in the paper):

Page 7-15

"Turning to the literature pertaining to patients with chronic persistent symptoms, Fallon noted a number of areas need additional research. A European study compared patients with neurologic Lyme disease to those with erythema migrans 3 years later and found that 50 percent of those with neuroborreliosis experienced persistent symptoms versus 16 percent of the EM patients (Vrethem et al., 2002). These results suggest that follow up studies on chronic symptoms, rather than focusing solely on early EM, should focus on the subpopulation of patients who present with neurologic or other disseminated symptoms."

Page A-94:

"In a study of 60 U.S. patients with neuroborreliosis (16 with early and 44 with late neuroborreliosis), the sensitivity of PCR in CSF was 38% in early and 25% in late neuroborreliosis, and an inverse correlation was found between duration of antimicrobial treatment and PCR results (Nocton et al., 1996)."

So clearly, PCR isn't so great at detecting neuroborreliosis in early or late stage infection.

Page 7-16
"With respect to pathophysiology, Borrelia act directly and can invade neural cells in vitro (Livengood and Gilmore, 2006); there are also indirect actions, such as the induction of local cytotoxins or inflammatory mediators (reviewed in Fallon et al., 2010). European studies show that pro-inflammatory cytokines are increased, and chemokines, excitotoxin, and quinolinic acid are increased in patients with neuroborreliosis (Weller et al., 1991; Halperin and Heyes, 1992; Widhe et al., 2004; Rupprecht et al., 2005)."

(An aside: For all of those readers getting excited about the excitotoxin, it's not produced by the Lyme Borrelia spirochete - it's produced by your own body. If you're thinking about detoxing that, I'll be discussing it in a different post.)

A discussion item on this was noted at some point during the workshop:

"...Dumler noted that large-scale human clinical studies that have sufficient statistical power are needed. As discussed by previous panelists, such studies would allow the acquisition of large numbers of subjects and potentially bring together all of the involved communities — patients,advocate groups, physicians, academicians—to address research uncertainties on a large scale. These clinical trials for tick-borne diseases could easily be assimilated into modern high-throughput methods that may make whole genome surveys feasible.There would need to be some discussion on how many patients would be needed for a single-nucleotide polymorphism (SNP) analysis for neuroborreliosis. A large-scale clinical study would be intense and difficult, but it would rely on the communities coming together. These clinical trial groups could provide critical corroborated subjects and a biorepository of samples for pathogenesis studies. Within the group, one could create and validate the next generation of diagnostics. It would also provide a critical structure for the assessment of the new diagnostics, clinical interventions, and therapeutics.

Here's one action item: Organize a large-scale human clinical study involving single-nucleotide polymorphism (SNP) analysis.

But is this the most relevant test for people who are ill and have persistent symptoms? I wish Dumler would outline the process for patients as to what he sees in the future for patient treatment using this data.

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0 IOM Summary Report: Neuroborreliosis Notes

Well, I said in recent comments that I was going to write my own summary of the Institute of Medicine (IOM) tickborne diseases workshop, but then I thought better of it:

This report is a whopping 485 pages.

I don't have the focus required to get through the entire thing in one sitting, and it would take me a long time to write up a comprehensive summary that hit on what others may want to hear.

Besides, from the patient perspective, the big bullet points about how well the workshop went in terms of advocacy and awareness and the follow-up summary report have already been covered by Lyme Policy Wonk, NatCapLyme, and others.

So I'm going to take another  approach here, and write about specific topics I pick out of the report and cite them.

The focus of this post will be Neuroborreliosis, which means when Lyme disease infects the CNS and brain.

I find it interesting to juxtapose the comments I see made by someone in discussion in one part of the report and then in the research portion of their report, information which at least partially contradicts what was stated.

Let me show you what I'm talking about here...

For example, page 9-12 has as part of the end of workshop discussion stating the following:

"A question was raised about who should comprise a clinical management team to treat patients with long-term symptoms. O’Connell noted that Lyme disease affects a number of different systems, depending to some degree on the borrelial genospecies causing the infection.Borrelia burgdorferi, which is the most common strain in the United States and also occurs in Europe, tends to cause Lyme disease arthritis. Borrelia garinii, which is strongly associated with neuroborreliosis, and Borrelia afzelii, mainly causing skin manifestations, are more common causes of Lyme borreliosis in Europe."

And when you read page A-180, Susan O'Connell has this to say:

"Although the differences between presentations of European and American Lyme neuroborreliosis have been stressed over the years, they may have been overemphasised in the case of early neuroborreliosis (Halperin, 2008). This is also supported by clinical experience in the UK, where between 10 and 20% of patients with serologically confirmed Lyme borreliosis acquired infections abroad, in mainland Europe or USA (HPA, 2011). Clinicians in the UK have noted marked similarities in acute neurological presentations of patients with USA-acquired infection and those acquired in the UK and other parts of Europe (Dillon, O'Connell and Wright (2010)."

In reading this, what is the reader to assume? Based on this information, it would appear that American patients suffering from a Borrelia burgdorferi infection could also be more likely to have acute neurological presentations - because if traveling Europeans are coming back from the US having received a tick bite in an endemic area, what are the odds they are showing an acute neurological presentation from an imported strain of B. garinii or B. afzelii? According to information presented elsewhere in this report, evidence of those strains in the US has been very isolated and found only in ticks in the southeastern portion of the US.

I also found this to be interesting information on patients in Europe, on page A-178:
"Neuroborreliosis has been notifiable in Denmark since 1994; with an annual average of 83 cases (1.5/100,000), ranging from 41 in 2002 to 104 in 2006 (Christiansen and Mølbak, 2005) and 61 cases (1.1/100,000) in 2009 (EpiNorthData, 2011). Cases of disseminated and late borreliosis have been notifiable in Norway since 1995. Annual incidence of neuroborreliosis varied from 75 to 200 cases in the ten years 1995-2004 (average 3/100,000), with a marked increase of nearly 100 cases between 2003 and 2004 (Nygard et al., 2005). There were 273 notifications in 2009, a rate of 5.6 /100,000 (EpiNorthData, 2011). As neurological complications are the most significant manifestations of disseminated and late Lyme borreliosis in Europe data on neuroborreliosis obtained from the Slovenian, Danish and Norwegian notification schemes can give useful information on epidemiological trends in widely geographically separated areas of Europe."

So, in Denmark, Neuroborreliosis is actually treated as a diagnosis which is medically notifiable separate from non-Neuroborreliosis Lyme disease - and in Norway, disseminated and late borreliosis are also notifiable there.

If there is evidence patients are returning to Europe having been infected with Borrelia burgdorferi in US, and they develop neuroborreliosis and it's reportable in these countries, one would think they have a better epidemiological picture than the US does about neuroborreliosis as well as greater awareness.

I don't know, though - I'm not living in Denmark, Norway, or Slovenia. So perhaps someone who is and reading this could leave me a comment on this issue.

At any rate, at least by characterizing diagnosis in this way and tracking this data, one would think that those patients who are not found to be positive by serological testing early in their infection or when early diagnosis of infection is missed that these cases of Lyme disease will be counted later on for a bigger epidemiological picture.

If there is great concern about the significance of neuroborreliosis in Europe, why aren't all countries adopting the reporting schemes these countries are using?

So here's an interesting counterpoint...on page A-180, the following is stated:

"Less than 5% of European neuroborreliosis patients present with late neuroborreliosis with duration of symptoms from six months to several years (Mygland et al., 2010). This condition is likely to have a chronic course if left untreated and can affect the central and peripheral nervous system."

And prior to this, on page A-179, the following is stated:

"Neuroborreliosis accounts for between 10% and 20% of laboratory-confirmed cases each year and appears to be a useful sentinel for year-on year comparison. It has been estimated that there may be 2,000-3,000 cases of Lyme borreliosis annually in the UK (Health Protection Agency, 2011)."

So, to make a distinction here - if I'm reading this correctly - O'Connell is saying that 5% of all European neuroborreliosis patients present with late neuroborreliosis, but the overall percentage of cases of neuroborreliosis reported is 10-20% of all reported Lyme disease cases.

Also on that same page, it is stated:

"The EUCALB case definitions acknowledge similarities between the major manifestations of Lyme borreliosis and North America, including erythema migrans, early neuroborreliosis and Lyme arthritis."

This is the piece that, between what I cited earlier and now concerns me: When Lyme disease is discussed in the US, many medical advice sites and articles written about Lyme disease seem to focus on it being a mild, flu-like illness where Lyme arthritis can develop if it's not treated early on.

And I think that may be how it is for a segment of the patient population who has an uncomplicated case, one involving a clear EM rash, and no coinfections, where one receives antibiotics soon after infection.

My concern is that the frequency of neuroborreliosis isn't something we're tracking that well in the US - and maybe it is being undiagnosed or misdiagnosed with other conditions.

Does anyone know how we track and record neuroborreliosis cases in the US? Or follow up on patients with tick bites who may not have shown symptoms immediately after the bite and only got a prophylactic dose of Doxycycline?

Regardless of anyone's thoughts and feelings about long-term antibiotic treatment, by missing a neuroborreliosis diagnosis early on, everyone is harmed by it - the patient, the patient's family and caregivers, the patient's workplace, and society in general. Without greater awareness, there is a risk of the diagnosis turning into something far more devastating, and the Lyme disease going untreated.

If anything the push to diagnose Lyme disease early on is just one piece of the prevention of long-term chronic symptoms related to Lyme disease - the push is to really be sure one catches neuroborreliosis early because that is often where the worst problems start.

On page A-180, it is stated:

"Central nervous system manifestations of late neuroborreliosis include encephalitis or encephalomyelitis with tetraspastic syndrome, spastic-ataxic gait disorder and disturbed micturition, which may lead to misdiagnosis with other conditions such as multiple sclerosis if the possibility of neuroborreliosis is overlooked.Clinical awareness of this possibility is crucial, as antibiotic treatment will arrest progression. The degree of clinical recovery following microbiological cure depends on the severity of tissue damage. Recovery may be slow, especially in older patients, and can be incomplete, particularly in those who had been severely affected prior to treatment."

And on page A-182...

"In neuroborreliosis only about 10-30% of DNA detection tests on CSF are positive, and highest rates are obtained on samples taken within the first two weeks of a clinical presentation. It is considerably more sensitive than culture for synovial tissue and fluid, for which culture has rarely been successful (Wilske et al., 2007)."

So just to lay this all out there for the reader, here you have a disease that can infect the brain early in infection and the infection cannot be detected in the CSF by using a DNA detection test anywhere from 70-90% of the time.

If you get bitten by a tick, and show symptoms of neuroborreliosis and get a lumbar puncture test to look for Borrelia DNA within the first two weeks of symptoms, then you have a better chance of getting a solid diagnosis. But once that window closes, then it will be harder to get a positive CSF reading.

This tip on page A-183 may help in diagnosing patients with neuroborreliosis after that two week window:

"Lymphocytic pleiocytosis is almost always present in both early and late neuroborreliosis and many patients have raised protein and oligoclonal IgG bands."
But in using this diagnostic measurement, one has to make sure that the medical professional is willing to consider neuroborreliosis as a differential diagnosis and run an IgG test and not just a general test to determine if a patient has bacterial or viral meningitis when they actually have neuroborreliosis.A negative test for bacterial meningitis will be labeled as viral when it might have been neuroborreliosis all along.

You'd better have a good diagnostician in your corner who knows what you have and will treat it, because neither a CSF test nor a blood test has a good chance of returning a positive result for neuroborreliosis in early and early disseminated Lyme disease infection.

Continued at: Part 2: IOM Summary Report: Neuroborreliosis Notes

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Monday, April 25, 2011

0 Exercise: A Better Lyme Disease Case Defintion

CDC painting by numbers: The numbers
need to represent reality - actual cases are much
higher than those reported to the CDC.  
Since many patients do not like the case surveillance definition for Lyme disease, I have an exercise for my readers.

I'm going to provide you with a case definition for Lyme Disease, and see what you have to say about it.

Do you think it is better than the current CDC case definition? Or worse? Why or why not?

What do you think needs to change, and how would you change it?

What do you think is missing? What should be added?

Please share your view in comments -
I want to see what people say about this provided definition first and then see if we can collectively rewrite a better one.

Lyme Disease

Clinical description

A systemic, tick-borne disease with protean manifestations, including dermatologic, rheumatologic, neurologic, and cardiac abnormalities. The best clinical marker for the disease is the initial skin lesion, erthyma migrans, that occurs among 60-80% of patients.

Clinical case definition

  • Erythema migrans, or
  • At least one late manifestation, as defined below, and laboratory confirmation of infection

Laboratory criteria for diagnosis

  • Isolation of Borrelia burgdorferi from clinical specimen, or
  • Demonstration of diagnostic levels of IgM and IgG antibodies to the spirochete in serum or CSF, or
  • Significant change in IgM or IgG antibody response to B. burgdorferi in paired acute and convalescent phase serum samples

Case classification: a case that meets one of the clinical case definitions above


This surveillance case definition was developed for national reporting of Lyme disease; it is not appropriate for clinical diagnosis.

Definition of terms used in the clinical description and case definition:

A. Erythema migrans (EM)

For purposes of surveillance, EM is defined as a skin lesion that typically begins as a red macule or papule and expands over a period of days to weeks to form a large round lesion, often with partial central clearing. A solitary lesion must reach at least 5 cm in size. Secondary lesions may also occur. Annular erythematous lesions occurring within several hours of a tick bite represent hypersensitivity reactions and do not qualify as EM. For most patients, the expanding EM lesion is accompanied by other acute symptoms, particularly fatigue, fever, headache, mild stiff neck, arthralgia, or myalgia. These symptoms are typically intermittent. The diagnosis of EM must be made by a physician. Laboratory confirmation is recommended for persons with no known exposure.

B. Late manifestations

Late manifestations include any of the following when an alternate explanation is not found:

Musculoskeletal system

Recurrent, brief attacks (weeks or months) of objective joint swelling in one or a few joints, sometimes followed by chronic arthritis in one or a few joints. Manifestations not considered as criteria for diagnosis include chronic progressive arthritis not preceded by brief attacks and chronic symmetrical polyarthritis. Additionally, arthralgia, myalgia, or fibromyalgia syndromes alone are not criteria for musculoskeletal involvement.

Nervous system

Any of the following, alone or in combination:

Lymphocytic meningitis; cranial neuritis, particularly facial palsy (may be bilateral); radiculoneuropathy; or rarely, encephalomyelitis. Encephalomyelitis must be confirmed by showing antibody production against B. burgdorferi in the cerebrospinal fluid (CSF), demonstrated by a higher titer of antibody in CSF than in serum. Headache, fatigue, paresthesia, or mild stiff neck alone are not criteria for neurologic involvement.

Cardiovascular system

Acute onset, high-grade (2nd or 3rd degree) atrioventricular conduction defects that resolve in days to weeks and are sometimes associated with myocarditis. Palpitations, bradycardia, bundle branch block, or myocarditis alone are not criteria for cardiovascular involvement.

C. Exposure

Exposure is defined as having been in wooded, brushy, or grassy areas (potential tick habitats) in a county in which Lyme disease is endemic no more than 30 days before onset of EM. A history of tick bite is NOT required.

D. Disease endemic to county

A county in which Lyme disease is endemic is one in which at least two definite cases have been previously acquired or in which a known tick vector has been shown to be infected with B. burgdorferi

E. Laboratory confirmation

As noted above, laboratory confirmation of infection with B. burgdorferi is established when a laboratory isolates the spirochete from tissue or body fluid, detects diagnostic levels of IgM or IgG antibodies to the spirochete in serum or CSF, or detects a significant change in antibody levels in paired acute and convalescent phase serum samples. States may determine the criteria for laboratory confirmation and diagnostic levels of antibody. Syphilis and other known causes of biologic false-positive serologic test results should be excluded when laboratory confirmation has been based on serologic testing alone.

Well, what do you think? What works? What needs rewriting and why?
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Friday, April 22, 2011

0 The Friday Four

In this week's Friday Four, we'll look at antimalarial trees that are threatened with extinction but may yet be saved to make natural medicine, how our own bacteria use immune cells to help save us from bad infections, a six-fold risk of death from C. diff in patients with IBD, and genetically engineering mosquitoes so that they have less ability to spread disease.

1) Antimalarial trees in East Africa threatened with extinction

Source link:

Olea europaea Africana -
African wild olive - antimalarial tree
ScienceDaily (2011-04-21) -- Research released in anticipation of World Malaria Day finds that plants in East Africa with promising antimalarial qualities -- ones that have treated malaria symptoms in the region's communities for hundreds of years -- are at risk of extinction. Scientists fear that these natural remedial qualities, and thus their potential to become a widespread treatment for malaria, could be lost forever.


According to this article, researchers at the World Agroforestry Centre (ICRAF) and the Kenya Medical Research Institute (KEMRI), Common Antimalarial Trees and Shrubs of East Africa, are documenting and studying 22 of the region's malaria-fighting trees and shrubs which have been found to be antimalarial by both traditional medicinal practitioners and scientists.

Time is running out for these trees, though, because of deforestation and overexploitation for medical use without replacing the trees and cultivating new ones, but scientists are preserving them in a genebank as well as a nursery.

Here is one thing I want all alternative medicine lovers to be aware of, and it saddens me, too. The article states:
"Today, the world's newest, most-effective therapeutic treatment for malaria also comes from a plant, the Artemisia annua shrub. However, access to malaria therapies based on artemisinin compounds remains low -- around 15 percent in most parts of Africa and well below the World Health Organizations' 80 percent target. Additionally, the malaria parasite's ability to resist artemisinin is already beginning to emerge in Southeast Asia."
Here is our note of humility, humanity...

Mother Nature is in charge. She always was, and we will be one step behind her. Get a bacterial infection, then take an antibiotic, then the bacteria grows resistant to the antibiotic. Get an infection, then take an herb, then the bacteria grows resistant to the herb, too.

It's evolution in action, and there's nothing we can do to stop it. All we can hope to do is keep up, and try to maintain balance. But Mother Nature is crafty. Beautiful, mysterious, and creative, and has many tricks up her sleeve.

So just because it's an herb doesn't mean a parasite or bacteria won't develop resistance to it.

This aside: I really hope these scientists can protect and save as many of these trees as they can from destruction. It sounds like they are working hard on this problem. If they do, they may have in their hands future treatments for not only malaria but babesia, too.

Additional Sources:

2) Learning to tolerate our microbial self: Bacteria co-opt human immune cells for mutual benefit

Source link:

B. fragilis
ScienceDaily (2011-04-22) -- The human gut is filled with 100 trillion symbiotic bacteria which we blissfully live with, although they have many features similar to infectious bacteria we react against. What decides whether we ignore -- or fight? In the case of a common "friendly" gut bacterium, Bacteroides fragilis, researchers have discovered the surprising answer: The decision is not made by us, but by the bacteria, which co-opt cells of the immune system for our benefit ... and theirs.


So these scientists discovered that these friendly bacteria in mice, B. fragilis, can control regulatory T-cells in their immune system. These T-cells, by the way, are what protects our immune systems from attacking our own cells - they are basically anti-autoimmune cells.

B. fragilis can "trick" the immune system into activating these regulatory T-cells so they themselves will not get attacked.

How does this happen? The bacteria produces a molecule that receptors (called Toll-like receptors) on the regulatory T-cells pick up. When these regulatory T-cells get this "message", they suppress T helper 17 cells. By shutting those cells down, the bacteria is able to colonize the intestines.

This is not usually how Toll-like receptors are thought of - they are thought of as being part of a chain of communication in the immune system that works to get rid of bacteria - not keep it alive.

Question to my readers: What is the relationship between Toll-like receptors and Borrelia burgdorferi in people?

I'll give you time to research it if you don't know the answer, and will tell you next week.

Original Reference:
June L. Round, S. Melanie Lee, Jennifer Li, Gloria Tran, Bana Jabri, Talal A. Chatila, and Sarkis K. Mazmanian.The Toll-Like Receptor 2 Pathway Establishes Colonization by a Commensal of the Human MicrobiotaScience, 21 April 2011 DOI:10.1126/science.1206095

3) C. difficile increases risk of death 6-fold in patients with inflammatory bowel disease

Source link:

Patients admitted to hospital with inflammatory bowel disease face a sixfold greater risk of death if they become infected with Clostridium difficile, a new study has found.


The It-Could-Be-Worse News: A review published in 2010 estimated the overall mortality rate for patients with C. difficile to be 6 per cent.

Okay, 6%. I rather it'd be 0%, but 6% is a relatively small number compared to the rate of fatalities for other conditions.

The Bad News: Those most severely ill and the elderly are in a high risk for fatality from a nasty C. diff infection.

That's not good.

The Worst News: The mortality rate for IBD patients with C. difficile at 30 days was 25 per cent, compared with 3 per cent for patients with IBD alone.

25%. That's really not good.

I really don't know what to say to this other than it's scary. I hope research finds a way to prevent and cure IBD, and that we can prevent and more effectively treat C. difficile infections.

My advice:

1) Take your probiotics if you are using antibiotics. Eat yogurt  and/or take probiotics 3 hours after and before taking antibiotics daily.

2) Take Saccharomyces boulardii. There is some evidence it stops C. diff infections.

3) Avoid taking antibiotics unless it's absolutely necessary.

4) Get evaluated for Inflammatory Bowel Disease if you suspect you have it.

This not something to mess around with.

Original Reference:
 J.A. Karas et al. A review of mortality due to Clostridium difficile infection. Journal of Infection (2010) 61, 1-8.

4) 'Disease-Proof Mosquito' Could Spread Like Wildfire

Source link:

Scientists have identified several mosquito genes that, when tinkered with, decrease the mosquitoes' ability to transmit a virus or a parasite; they have also given the insects new genes that do the same.

My only comment for this is: Will we ever see a tick that is bred to not spread Lyme disease bacteria and coinfections? 

Is there anything beneficial in having any of these hosts carry these infections for anyone but the pathogenic agents? Any whatsoever at all?


Then stop these pathogens in their tracks, please.
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0 Phage Therapy and Borrelia burgdorferi

EDITED February 27, 2012 to include information on specific phages of B. burgdoferi.

Earlier this week, we discussed the use of phage therapy - the medical use of viruses found in nature that kill bacteria.

Phage therapy has been a part of regular medical treatment in Eastern Europe for over 85 years, but most of the research published has been in the Russian and Georgian languages since the primary former Soviet institution for the research and collection of a huge phage library has been in Tblisi, Georgia.

Eliava Institute of Tblisi, Georgia -
major bacteriophage research center
Those familiar with the Georgian language have stated that detailed documentation for double-blind controls was lacking in research mentioned, so the work as a whole wasn't taken seriously once translated. However, if research came from patient case studies, then documentation wouldn't require blind controls and simply record individual patients' responses. Either way, it is unknown to me how much of the research has been translated or has been made available for translation, given many people do not speak Georgian and because part of the research was written in the era of censorship in Soviet Georgia, some research may not have been published at all - even in a Russian translation.

Tbilisi's Eliava Institute, however, is not the only place in Eastern Europe that has conducted phage research - the Polish Academy of Science has a special institute that is also involved in phage research and therapy. You can learn about their current research here:
The Ludwik Hirszfeld Institute of Immunology and Experimental Therapy (Polish Academy of Science) and read specific research papers in English right here: Evergreen College Guide to Polish Phage Research.

Both of these institutions have had success in treating local patients as well as visitors from abroad. And with growing antibiotic resistance worldwide, one has to wonder why is it phage therapy isn't being used in the west to treat more patients? Why isn't it being used to treat Borrelia burgdorferi, the bacteria which causes Lyme disease?

These are two different questions, one of history and politics, and one of science. To explore them both requires a bit more backstory and examination of the FDA's regulations regarding the adoption of new medical therapies.

In the 1990's, entrepreneurs from the US and Canada traveled to the Eliava Institute to investigate their use of phage therapy and see if they could use the same medical treatment to help patients in the United States. Due to the FDA's regulatory system on all new therapies - especially combination or "cocktail" drug therapies - the use of phage therapy on patients in the United States would be a long way off, and any company investing in phage therapy would be using it for other purposes first.

As a result, in the United States, phage therapy is being used as a spray to protect all kinds of food (the FDA approved of treating cheese first, then other foods) from developing Listeria monocytogenes, bacteria that can lead to severe infection and sometimes even be fatal in vulnerable populations. There have also been treatments developed for veterinary healthcare, such as ear drops for dogs to treat ear infections (otitis media), and the most recent application of phages is using them on surgical equipment and clinic surfaces.

The road to adopting phage therapy for use on treating people in the western hemisphere has been a somewhat rocky one, given that the first entrepeneurs who went to Tblisi and came back to form a phage therapy research startup company had a bit of a falling out: The main financial backer for the company, Canadian Caisey Harlingten, was rumored to have had arguments over who would receive patent rights on work created with the company's new CEO, Richard Honour, and Honour decided to shut down work being done at the Eliava Institute and develop genetically modified phages in the US.

After this, personnel which had been recruited from Tblisi to go work in the United States for Harlingten's company were not happy with this arrangement, jumped ship, and went on to form their own startup, Intralytix. Intralytix - unlike other pioneering phage startups - decided to focus on phage treatments for animals and general products instead of human therapy.

After three years of operating at a loss, Caisey Harlingten resigned from his company, Phage Therapeutics - as did Richard Honour and the chief financial officer.

Last I read, Phage Therapeutics was supposed to have a particular phage that kills 93% of a broad spectrum of over 1,000 of S. aureus and S. epidermidis strains that were isolated from patients in the US, Canada, and South America. This phage was supposed to have been in preclinical trials and was supposed to enter clinical trials against eye infections.

But somewhere along the line, Phage Therapeutics changed hands, their stock devalued, and I discovered that as of February 22, 2008, Phage Therapeutics International Inc. was acquired by Surge Solutions Group, Inc. in a reverse merger. SSGI, Inc., through its subsidiary, Surge Solutions Group, Inc., provides construction and environmental services in Florida. Nothing to do with phage technology. What happened to the above mentioned broad spectrum phage mix?

Where one company falls, others spring up to take their place. There are a growing number of startups in the phage business, but mostly doing business like Novophage, which specializes in using phages to remove biofilms from industrial equipment.

The first clinical trials using phage therapy were conducted in Europe and America. One clinical trial involved a cocktail of eight bacteriophages (five against Pseudomonas aeruginosa, two against Staphlococcus aureus, and one against Escherichia coli) on leg ulcers in 2008 at The Wound Care Center in Lubbock, Texas.  Following that trial, the Southwest Regional Wound Care Center used bacteriophages along with other methods to treat antibiotic-resistant infections under a limited study. Further information on this study has not been published to date.

Bacteriophages are being studied in fighting against E. coli infections in Bangladesh, and phase 2a clinical trials in the UK have been conducted for using phage therapy on chronic inner ear infections caused by Pseudomonas aeruginosa at the Royal National Throat, Nose, and Ear Hosptial in London. Very positive results on clinical and bacteriological efficiency and safety concerns have been reported on this latter trial.

In 2010, a nebulizer treatment using bacteriophages of Burkholderia cepacia complex (full text) to treat cystic fibrosis was developed, and earlier study was completed on the development of an inhaler to treat Staphylococcus aureus or Pseudomonas aeruginosa. So far, the inhalers have yet to be tested on people.

There is an international conference on bacteriophages that is held in Olympia, Washington, and hosted by Evergreen College. Dr. Elizabeth Kutter, professor of microbiology at the college took a keen interest in bacteriophage therapy years earlier, and had traveled to Tbilisi herself to investigate the treatment and their results. Since then, she has been actively pursuing research into bacteriophages and promoting it for use in medicine. The college has its own special phage projects page you can look at to see research conducted on phage therapy around the world.

Even though there is interest in bacteriophages, few clinical evaluations have been published on them because the data available are at a very early stage, making it difficult to attract further funding - and as mentioned earlier, the use of phage often involves a "cocktail" of more than one virus to treat a patient and this challenges the FDA's regulatory standpoint on cocktail treatments.

Also, using phage therapy in Eastern Europe focused mainly on treatment for wounds and intestinal infections - conditions which could be treated using phages topically in ointments, sprays, and dressings or capsules and enemas. Intravenous therapy (IV) - while used on occasion - did not make up the majority of treatments given, so little has been known about their effectiveness.

There is some evidence that phage therapy can work in IV therapy, but it was suggested that in this form it is more likely to come with a drawback: just as Lyme disease patients experience a Herxheimer reaction from antibiotic therapy, patients receiving phage therapy can also have a Herxheimer reaction from phage therapy. One veterinary study, though, has shown that no notable negative reactions or effects were noted (Soothill, 2004).

As as a commenter on my previous post mentioned, there are shortcomings as well as benefits to the use of phage. But overall, the risks of using phage therapy seem lower than those of antibiotics so far because the antibiotic resistance issue and risk of C. difficile are gone (someone is even working on phage therapy for C. difficile).

Despite the growing evidence that phage therapy can be safe and effective, there are some challenges that even people who are most unfamiliar with phage therapy have pointed out at least one of them:
  • We don't know much about how phages interact with gut flora. Suspicions are most are benign if not helpful because we already have bacteriophages living in our stomachs and intestines all the time.
  • Some research has shown one kind of phage - T-even bacteriophage - show inhibition of lysis in low-oxygen environments. 
  • Both carbohydrates and bile salts can interfere with bacteriophages ability to replicate in the stomach. 
  • If a bacteriophage that was lytic becomes lysogenic, it will integrate with its host, enabling it to transfer bacterial virulence genes into other bacteria. This is why therapeutic phages must be entirely lytic and cannot carry toxic or housekeeping genes associated with lysogeny.
Even though these drawbacks exist, research is underway to find solutions that address them because the risk of not having phage therapy can be worse for some patients with very deadly infections which are becoming increasingly antibiotic resistant.

Can phage therapy work on killing Borrelia burgdorferi?

So far I have not seen any phage therapy research for Borrelia burgdorferi - however, the Phage Therapy Center for patients in Tblisi, Georgia claims they have phage therapy to treat Lyme disease coinfections.

In terms of phage therapy for Lyme disease itself, though - the best answer I can give at this writing is a theoretical maybe someday.

This is based on the idea that there is a phage for every bacteria out there if we were only to look for it and find it. It's also based on the idea that we have the technology available to potentially modify Lyme disease's known phages in order to change its behavior - or perhaps create a delivery system which could lyse Borrelia in a manner that phage does.

But so far - unlike Staphloccocus and other bacteria - few phages which attack and kill Borrelia have been documented. Publications on virulent phages of Borrelia are sparse, and there is only a little more documentation on phages in spirochetes as a whole.

B3-like morphology
phage on spirochete
In 1982, Hayes, Burgdorfer, and Barbour recorded their observations of a phage attacking Borrelia burgdorferi in vivo and took photographs to record the event. The images captured are of a B3-like bacteriophage, described by the researchers as having a "40- to 50-nm elongated head and a tail 50 to 70 nm in length. It appears devoid of collars or kite-tail structure".

There are two aspects of these images below which are  compelling: One is that they give us a rare glimpse of a phage which can actually kill Borrelia burgdorferi. (Wouldn't it be fabulous if we could somehow find a way to harness this as a treatment method, and find phages for all strains of Borrelia?) The second is that we have a photo of gemmae - a form of Borrelia which is not mentioned much in today's genomic oriented Borrelia research.

  •  (a) Section profile of a gemma with its attendant membrane bound granules or spherical bodies. Arrows indicate cross-section profiles of bacteriophage heads. (b) Internal attachment of bacteriophage to outer membrane material after plasmolysis of the spirochete. Arrows indicate remnants of plasma membrane.
A passage within the text, "Bacteriophage in the Ixodes dammini Spirochete, Etiological Agent of Lyme Disease", sheds some light on what is known about this phage and its relationship to Borrelia burgdorferi:
"Thus far, only those spirochetes showing left-handed coiling have been found to be phage infected. Figure ld shows phages that are associated with a spirochete with left-handed coiling. Bacteriophage heads in longitudinal and cross-sectional profiles were also observed within granules located within the aneurysmic blebs (Fig. 2a).

Completely assembled phages were more clearly seen in rarely occurring plasmolysed cells (Fig. le and 2b). In negatively stained preparations of spirochetes, they have only been detected internally (Fig. 2c). Bacteriophages previously reported to infect other spirochetes (15-17) are described as polyhedral and tailed (7) or cubic (5) in symmetry."
It appears that only those spirochetes which coil in a counterclockwise direction had phages. Why didn't any spirochetes with a clockwise coil have phages? Is there some inherent difference in their surface which makes it harder for phage to adhere to them?

In 1993, Neubert et al wrote about finding phage which were induced while introducing the antibiotic, ciprofloxacin, to Borrelia spirochetes. These A-1 and B-1 type phages were not virulent phages such as Hayes et al's B3-like phage.

The ultimate Borrelia book, "Borrelia: Molecular Biology, Host Interaction and Pathogenesis", has some passing mention of phages of Borrelia as well as a map of known and possible prophages in its plasmids. It also mentions a more recent discovery than Hayes, Burgdorfer, and Barbour's B3-like phage.

phiBB-1, prophage of
Borrelia burgdorferi
In 2001, Eggers et al published their discovery of a phage of Borrelia burgdorferi (Bb) named phiBB-1 (also written as φBB-1). It is not the best candidate for use in bacteriophage therapy because it is a prophage - also known as a temperate phage or lysogenic phage.

Lysogenic phages remain inactive as viruses when they are prophages, and only replicate together with the host genome unless mobilized. In contrast, virulent phages, having replicated and assembled into complete virions, cause rapid lysis and death of the bacterial cell, with release of 10–100 virions per phage; these virions then find more prey and die out when they cannot find any more bacteria.

Every time Borrelia burgdorferi divides, the viruses internalized in its plasmids divide with it. The viruses are an integral part of the plasmids and contribute to the functionality and antigenic variation of the spirochete - they have become part of the bacteria. In technical terms: The phiBB-1 prophage is capable of transducing a cp32 (circular plasmid) between cells of the same isolate and between different Bb isolates (gene transfer between different Borrelia spirochetes). This means this prophage could play a role in the genetic diversity of different Bb isolates.

Lytic-Lysogenic Phage Cycles
image by Suly12, Wikipedia
See the image to the left. If a bacteriophage is virulent, it will deposit its genes into bacteria so that it replicates and kills the bacteria from inside by lysing its membrane. The viruses then continue in search of more of the same bacteria to feast on. This is called the lytic cycle.

But if a bacteriophage is temperate or lysogenic, though - a prophage - then it will deposit its genes into bacteria so that they mix with the bacteria's own genes and divide with them each time the bacteria divides. This is called the lysogenic cycle.

Borrelia burgdorferi's plasmids contain virus genes which are locked into the lysogenic cycle.

Hypotheses Of Altering Phages To Lyse Borrelia

In order to put phiBB-1 to work at killing Bb, someone would have to genetically engineer it or introduce some agent which turns it into a virulent phage that kills Bb rather than adding its own DNA to its plasmids. Or, maybe phiBB-1 could be modified in a different way: don't bother changing its prophage nature, just program it to turn off DNA replication and gene expression in the bacteria's plasmids.

Another thing that could be done is to have someone extract the lysing proteins that work with phiBB-1 and find a method of delivery to Bb so those proteins could go to work on killing Bb outside in - maybe attach it to a non-pathogenic adenovirus that is programmed for such an adventure. There are such delivery systems being experimented with in general right now - but nothing yet for Borrelia.

These are wild hypotheses about how an existing phage we know about could be used to kill Bb, but it is not proven this would work. People are thinking of the biotech applications of phiBB-1 - but so far, I have seen only one patent application referring to its use.

The best option, obviously, would be to find naturally occurring phages which lyse Borrelia burgdorferi (as well as other strains) and find a method for using them to treat patients - though there are likely to be technical challenges in applying this as well.

Wired magazine:
A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy. Wright A, Hawkins CH, Anggård EE, Harper DR. Clin Otolaryngol. 2009 Aug;34(4):349-57.
Viruses Vs. Superbugs: A Solution to the Antibiotics Crisis? By Thomas Häusler
Soothill, J.S. Hawkins, C. Anggard, E.A. & Harper, D.R. (2004) Therapeutic use of bacteriophages. Lancet Inf. Dis. 4, 544-545.
Microbiologist, the magazine of the Society for Applied Microbiology (June 2009, Vol.10 No.2)
Bacteriophage Therapy: Exploiting Smaller Fleas. Stan Deresinski. Clin Infect Dis. (2009) 48 (8): 1096-1101. doi: 10.1086/597405 link:
Bacteriophage in the Ixodes dammini Spirochete, Etiological Agent of Lyme Disease. Stanley F. Hayers, Willy Burgdorfer, Alan G. Barbour. Journal of Bacteriology, June 1983, p. 1436-1439. link:
Demonstration of Cotranscription and 1-Methyl-3-Nitroso-Nitroguanidine Induction of a 30-Gene Operon of Borrelia burgdorferi: Evidence that the 32-Kilobase Circular Plasmids Are Prophages. Hongming Zhang and Richard T. Marconi. Journal of Bacteriology. December 2005, Vol. 187, No. 23 p. 7985-7995.
Bacteriophages induced by ciprofloxacin in a Borrelia burgdorferi skin isolate. Neubert U, Schaller M, Januschke E, Stolz W, Schmieger H. Zentralbl Bakteriol. 1993 Aug;279(3):307-15. link: Bacteriophage-like particles associated with a spirochete. Berthiaume L, Elazhary Y, Alain R, Ackermann HW. Can J Microbiol. 1979 Jan;25(1):114-6.

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Wednesday, April 20, 2011

34 News: Institute of Medicine Releases Lyme Disease Workshop Summaries

Source link:

To read the Workshop Summaries, click on the link at the top and look in the righthand column - you'll see gray buttons that say "Download Report" or "Read Report Online For Free". If you want to download a pdf of the report, you'll need to supply your email address and other info. If you just want to view it online, click "Read Report Online For Free" and there will be no request for personal information.

Once you select "Read Report Online For Free", by the way, you have an opportunity to download a 21 page summary of the report (direct download) by clicking on a link for it on the lefthand column. Otherwise, the full report is 468 pages long.

[CO update: The 21 page summary gives the barest of outlines of what was discussed, along with a list of those who attended - you are much better off reading the 468 page report.]

One thing to note here is that this appears to be a report on what was discussed at the Institute of Medicine (IOM) workshop on tickborne diseases in October 2010 and not a final position piece stating the IOM's consensus on how Lyme disease and tickborne infections should be approached through research, prevention, or treatment.
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Tuesday, April 19, 2011

0 Chart: Effectiveness of different alternative medicine ingredients

I found this link on alternative medicine online that you might find interesting:

LINK: A visualization based on the effectiveness of different alternative medicine supplements, spices, oils, and herbs

Each item represented there is based on PubMed and Cochrane reports on large human blind placebo-controlled studies only.

If you click on the bubbles, you'll be taken to abstracts which support the use of those particular alternative medicines for specific conditions.

Note these directions found at the bottom of the page before you go there:
"The higher a bubble, the greater the evidence for its effectiveness. But the supplements are only effective for the conditions listed inside the bubble. (Mouseover the bubble to see what I mean.) 
You might also see multiple bubbles for certain supplements. These is because some supplements affect a range of conditions, but the evidence quality varies from condition to condition. For example, there’s strong evidence that Green Tea is good for cholesterol levels. But evidence for its anti-cancer effects is conflicting. In these cases, we give a supplement another bubble."
The chart is Flash based, but there is a link to a non-Flash version there if you prefer that (iPhone users take heed.)
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Monday, April 18, 2011

0 Research And A Personal Story: Computer scientist researches own Lyme disease

Well, this has been posted elsewhere, but I just had to share it here, too:

Computer scientist researched her own condition, Lyme disease

Source link:

Read the above article, and see if you see yourself (or someone you care about) in this woman's shoes. (I know that I can relate to her own search for reliable medical information, that's for sure.)

After much research from many different medical sources, Ms. Mankoff decided to try long-term antibiotics. After 18 months of antibiotic use she could stop treatment and go on to write professional papers, work full time, and do research on how members of the Lyme patient community seek out information on Lyme disease diagnosis, treatment, and support.

There is mention in the Post-Gazette article above that the paper based on her research of the Lyme patient community will be presented at an upcoming conference on computer-human interaction, CHI 2011.

That paper is:

J. Mankoff, K. Kuksenok, J. A. Rode, S. Kiesler & K. Waldman, Competing online viewpoints and models of chronic illness. In Proceedings of CHI 2011. To Appear (Full Paper)

And here is a link to the FULL TEXT (no subscription required):

If anyone happens to be in the Vancouver area this May 6 and would like to attend the session, it will be from 4:00-5:20 pm. (A link to the conference appears at the bottom of this post.)

A description is as follows:

Session Chair: Julie Kientz (University of Washington)
Competing Online Viewpoints and Models of Chronic Illness - Paper

Session Chair: Julie Kientz (University of Washington)
Competing Online Viewpoints and Models of Chronic Illness - Paper
Jennifer Mankoff Carnegie Mellon University,
Kateryna Kuksenok University of Washington,
Sara Kiesler Carnegie Mellon,
Jennifer A. Rode Drexel University,
Kelly Waldman Duke

Abstract »

People with chronic health problems use online resources to understand and manage their condition, but many such resources can present competing and confusing viewpoints. We surveyed and interviewed with people experiencing prolonged symptoms after a Lyme disease diagnosis. We explore how competing viewpoints in online content affect participants’ understanding of their disease. Our results illustrate how chronically ill people search for information and support, and work to help others over time. Participant identity and beliefs about their illness evolved, and this led many to take on new roles, creating content and advising others who were sick. What we learned about online content creation suggests a need for designs that support this journey and engage with complex issues surrounding online health resources.

If you wish to attend CHI 2011 for only a day session on site, you must be warned that registration is steep:

If you can't make it to Vancouver and pay for admission, consider sitting at home, reading the pdf of the paper above, and emailing Ms. Mankoff with comments and questions.

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The Camp Other Song Of The Month

Why is this posted? Just for fun!

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Lyme Disease