Sapi - Antibiotic susceptibility different forms of Bb

Topics with information and discussion about published studies related to Lyme disease and other tick-borne diseases.
Claudia
Posts: 1448
Joined: Wed 14 Nov 2007 1:19
Location: Connecticut, USA

Re: Sapi - Antibiotic susceptibility different forms of Bb

Post by Claudia » Tue 10 May 2011 0:55

RitaA, your posts with your questions, thoughts and opinions were appropriate for the topic and, most importantly, added to the discussion here, so I am sorry that you removed them.

admin
Site Admin
Posts: 342
Joined: Wed 25 Jul 2007 21:06

Re: Sapi - Antibiotic susceptibility different forms of Bb

Post by admin » Tue 10 May 2011 1:18

RitaA wrote:Sorry -- I just noticed this was under the "Science" section -- not the "General" one where personal opinions are welcome.

Rita
RitaA wrote:Again, my apologies for muddying the waters with a personal perspective -- which I have removed.

Rita
IIRC your posts were relevant to this topic and not inappropriate, and nowhere it says that there can't be any personal opinions and perspectives in the "Science" section.

If anything is "muddying the waters", it's your removal of the text from your posts. Such is not appreciated, because it mutilates discussions and takes other people's posts out of context.

If you still have the original texts of the posts, I want to ask you to put them back.

Martian
Posts: 1944
Joined: Thu 26 Jul 2007 18:29
Location: Friesland, the Netherlands

Re: Sapi - Antibiotic susceptibility different forms of Bb

Post by Martian » Tue 10 May 2011 2:21

FYI:

"Relative Risk" also wrote a commentary on the paper in a post titled "Lyme disease: bad research, bad data, bad conclusions": http://relative-risk.blogspot.com/2011/ ... a-bad.html

Some quotes:
It’s a nice looking paper with lots of colorful graphs and darkfield photos. Unfortunately, it’s just sloppy work masquerading as competent, peer-reviewed research by people who have preconceived ideas about Lyme disease. Stricker and Sapi have used questionable techniques, very bad data presentation, and ill defined terminology to generate the data they believe in and their backers paid for.
First, it’s old news that bacteria undergo morphologically changes in response to various environmental stresses.
Second, it’s not clear what Sapi and Stricker mean when they refer to borrelial round bodies or cysts, or the equally vague term, “biofilm-like bodies.”
Blebs, cysts, round bodies, particles, membrane fragments, vesicles and gemmae. It’s hard to tell intact cells from debris, and live cells from dead. The methods used by Sapi and Stricker to tell round from spiral and dead from living—undergrads staring through microscopes at counting chambers, and the BacLight Live/Dead assay—are both suspect. It’s hard, real hard, to count cells under a microscope. As for the Live/ Dead assay, there are problems with that simple yes/no interpretation as noted back in 2007
Finally, Sapi and Stricker went to some trouble to graph out all their various combinations of Borrelia strains and morphologies and antibiotics. The result is a headache-inducing presentation of 20 graphs and lots of mysterious photos. It’s another case of bad graphing…not to mention bad data.
What do they conclude from all these graphs? “The presence of atypical forms of B. burgdorferi may be the reason the spirochetes can survive in infected tissues for years or even decades.” Big surprise. Sounds like the perfect justification for pumping patients full of antibiotics for long periods of time. (Time being measured by how long their insurance and bank accounts hold out.)

Of course, the persistence of strange forms of bacteria or bacterial remnants may be more innocuous than Sapi and Stricker suggest.

RitaA
Posts: 2768
Joined: Thu 1 Jul 2010 8:33

Re: Sapi - Antibiotic susceptibility different forms of Bb

Post by RitaA » Tue 10 May 2011 2:51

I did a "quote" from the Admin message above, so I can only assume that's Claudia or there's something wrong with the quote function:
Claudia wrote:IIRC your posts were relevant to this topic and not inappropriate, and nowhere it says that there can't be any personal opinions and perspectives in the "Science" section.

If anything is "muddying the waters", it's your removal of the text from your posts. Such is not appreciated, because it mutilates discussions and takes other people's posts out of context.

If you still have the original texts of the posts, I want to ask you to put them back.
Unfortunately, I don't keep copies of my posts. My general message (in both posts) is that I appreciate having the opportunity to read the results of research even if it has not been peer-reviewed or replicated or published in a mainstream medical journal. I also included personal information that I decided was inappropriate for a "Science" section. I don't believe anyone was addressing my personal comments, but rather reiterating their points of view.

Sorry if I have caused any confusion at all.

Rita

rlstanley
Posts: 1637
Joined: Mon 3 Dec 2007 2:53

Re: Sapi - Antibiotic susceptibility different forms of Bb

Post by rlstanley » Tue 10 May 2011 3:45

RitaA:
Unfortunately, I don't keep copies of my posts. My general message (in both posts) is that I appreciate having the opportunity to read the results of research even if it has not been peer-reviewed or replicated or published in a mainstream medical journal. I also included personal information that I decided was inappropriate for a "Science" section. I don't believe anyone was addressing my personal comments, but rather reiterating their points of view.
My response to your post: http://www.lymeneteurope.org/forum/view ... 299#p23859

Indeed, the main point, the leading point, you made in the post that you deleted was that you felt Sapi used Dove to rapidly publish results. And that is exactly what I responded to. I explained why that reasoning had major problems and that rapid communication of results is done at symposia and meetings. Following that, publication in a good peer reviewed journal is expected.

In addition, you felt that it was important to get results out rapidly because that could be used for treatment. I responded to that as well.

Next time, your entire post will be quoted.
.

Martian
Posts: 1944
Joined: Thu 26 Jul 2007 18:29
Location: Friesland, the Netherlands

Re: Sapi - Antibiotic susceptibility different forms of Bb

Post by Martian » Tue 10 May 2011 4:12

Regarding the questionable publishing of the paper, also note that another paper from Sapi et al. "In Vitro Effectiveness of Samento and Banderol Herbal Extracts on the Different Morphological Forms of Borrelia Burgdorferi" was published in the Townsend Letter (July 2010).

Regarding the content of the paper, of course it should go without saying that in vitro results cannot simply be translated to in vivo. Regarding the substances alone there are several things to take into account, like bioavailability, pharmacokinetics, pharmacodynamics, and substance penetration in various body tissues and fluids. A poor performing drug in vitro may actually perform well in vivo, and visa versa.

rlstanley
Posts: 1637
Joined: Mon 3 Dec 2007 2:53

Re: Sapi - Antibiotic susceptibility different forms of Bb

Post by rlstanley » Tue 10 May 2011 17:47

CO:
Maybe the best thing anyone could do here is email her and ask her why she decided to publish with DP, and if a more detailed paper will be published in the near future?
Good idea. Go for it.
Thinking off the cuff here... and this is wild speculation on my part, but what if Sapi is working on a patent for novel culture methods? It won't show up on Google patents (I've already been there; haven't seen anything thus far and it only shows processed patents not ones mid-process) now but it would require an NDA. This might be some way to split the difference so that people know what she's working on without doing full disclosure? I don't know.
I've never heard of someone 'publishing' in low level journals because of some patent. New concept here?
As for the rest of it, in terms of content:

I'm asking a number of the same questions you've already brought up here (methods? statistical analysis? "bio-film like" definiton?)

When there is essentially no peer review, you get this kind of stuff. This paper should have been kicked back to the authors with severe warnings to clean it up and define terms for starters. How can you have a paper based on stuff that isn't even defined? I've seen better 6th grade science projects. When a kid makes a mistake like that, you kindly tell them what to do. There is no excuse for someone in the scientific field.

Either way, this is in vitro. More in vivo tests are needed that examine the relevance of the round body issue - if there is any. Barthold doesn't think they're as important - he's already found live whole spirochetes post-treatment that could be transmitted by ticks to a new host.
Any way at all, when something isn't even peer reviewed well enough to define terms, then IMO everything else is suspect. I wouldn't even put Barthold's name in the same sentence as this Dove publication. Barthold has done respectable, well-published work.

Camp Other
Posts: 996
Joined: Wed 2 Mar 2011 4:32
Contact:

Re: Sapi - Antibiotic susceptibility different forms of Bb

Post by Camp Other » Tue 10 May 2011 18:51

rlstanley,

I tried to take the paper at face value even with it having been published at DP and look at the results shared and see if any of it mapped to existing research anyway. It doesn't validate her research and if anything, independent confirmation of her findings are necessary and that's harder to confirm on any level because the paper is so weak on process and analysis.

In the end, I'm puzzled about her choice to use DP given her previous track record with other journals her work had been published in. I mean, what changed? I could only speculate that the patent-in-process had something to do with it, but then why publish at all? Why not wait until the patent has been approved and then publish in greater detail including methods and analysis?

Maybe I will email her. The worst that can happen is I don't receive an answer.

rlstanley
Posts: 1637
Joined: Mon 3 Dec 2007 2:53

Re: Sapi - Antibiotic susceptibility different forms of Bb

Post by rlstanley » Tue 10 May 2011 19:58

CO:
I tried to take the paper at face value even with it having been published at DP and look at the results shared and see if any of it mapped to existing research anyway.
Yes, I know that is what you did.

My point is that when something is so poorly reviewed to allow glaring flaws to pass, then it does not deserve a thorough analysis because the content is suspect to begin with. Relative Risk did a good enough overview of the paper http://relative-risk.blogspot.com/2011/ ... a-bad.html His analysis of the methods used is an eye-opener; here's one:
As for the Live/ Dead assay, there are problems with that simple yes/no interpretation as noted back in 2007:

The commercially available LIVE/DEAD BacLight kit (Invitrogen) has enjoyed increasing popularity among researchers in various fields since it was released about 10 years ago. The kit consists of two stains, propidium iodide (PI) and SYTO9, which both stain nucleic acids. Green fluorescing SYTO9 is able to enter all cells and is used for assessing total cell counts, whereas red fluorescing PI enters only cells with damaged cytoplasmic membranes. The emission properties of the stain mixture bound to DNA change due to the displacement of one stain by the other and quenching by fluorescence resonance energy transfer.

LIVE/DEAD staining was shown to work not only with (eu)bacteria but also with archaea or eukaryotic cells, such as yeast (Saccharomyces cerevisiae). Although this kit enables differentiation only between bacteria with intact and damaged cytoplasmic membranes, it is often used to differentiate between active and dead cells. While it seems accurate to assume that membrane-compromised bacterial cells can be considered dead, the reverse (that intact cells are active cells) is not necessarily true.

Microscopic assessment of LIVE/DEAD-stained bacterial cells is usually simplified to either “green”-labeled (live) or “red”-labeled (dead) cells. However, experience with this dye combination and flow cytometry during the last few years by our group and others has shown that the staining of bacterial cells with SYTO9 and PI does not always produce distinct “live” and “dead” populations; intermediate states are also observed. In the kit manufacturer’s manual, the region of intermediate states is referred to as “unknown.” This can lead to difficulties in the interpretation of results and can be critical when, for example, decisions have to be made about the effectiveness of disinfection methods or the amount of viable bacteria in water distribution systems. (2007, Michael Berney, et al.)


If they wanted accurate counts of live and dead bacteria they should have made those determinations the old fashioned way: plate counts. (Kurtti, T.J., Munderloh, U.G., Johnson, R.C., Ahlstrand, G.G., 1987. Colony formation and morphology in Borrelia burgdorferi. J. Clin. Microbiol., 25, 2054–2058.)
The scientific review process of competent journals is harsh and exacting. I speak from experience. There is no pussy footing around in academia, as there should be. You are not treated with kid gloves by any means by review boards of journals of quality.

Generally warnings are issued & rewrites demanded when expected substance is excluded. So, if the peer review is such that it overlooks major flaws, well does that paper deserve anyone's time and effort to analyze it as if it were a serious piece of work?
.
edit to add color
Last edited by rlstanley on Sun 15 May 2011 19:39, edited 1 time in total.

Camp Other
Posts: 996
Joined: Wed 2 Mar 2011 4:32
Contact:

Re: Sapi - Antibiotic susceptibility different forms of Bb

Post by Camp Other » Wed 11 May 2011 9:03

rlstanley wrote:
CO:
I tried to take the paper at face value even with it having been published at DP and look at the results shared and see if any of it mapped to existing research anyway.
Yes, I know that is what you did.

My point is that when something is so poorly reviewed to allow glaring flaws to pass, then it does not deserve a thorough analysis because the content is suspect to begin with. Relative Risk did a good enough overview of the paper http://relative-risk.blogspot.com/2011/ ... a-bad.html His analysis of the methods used is an eye-opener; here's one:
As for the Live/ Dead assay, there are problems with that simple yes/no interpretation as noted back in 2007 ... (RR's review snipped for brevity)

Thanks, that is useful information to have on that particular assay - I appreciate it.

I do read RR on occasion, but it's difficult for me to read it at times because he is pretty scathing in his commentary about Lyme disease patients and paints them all with the same brush of crazy.

It's gotten old. I don't see why he can't just state his opinion without having to insult people all the time.
The scientific review process of competent journals is harsh and exacting. I speak from experience. There is no pussy footing around in academia, as there should be. You are not treated with kid gloves by any means by review boards of journals of quality.
I'm aware of that fact, I can speak of similar experience - possibly in a different field of study. I know how hard they have to be and should be. I've had to review others' papers in the past.
Generally warnings are issued & rewrites demanded when expected substance is excluded. So, if the peer review is such that it overlooks major flaws, well does that paper deserve anyone's time and effort to analyze it as if it were a serious piece of work?
.
Are you asking me indirectly why I would analyze it the way I did? I didn't give it the analysis RR did, and he decided to shred it. That's his idea - he's good at shredding.

I'm aware that results don't mean a thing if the bedrock they are built on (statistical analysis, methods, materials, etc.) aren't supported and lack validation and verification. And I chose not to focus on that because I had a different set of reasons to approach the research the way I did:

1) To build a bridge for other Lyme patients between what they are reading via Lyme sites all the time and something they possibly are not, in terms of related research.
2) To get them to consider questioning parts of the research they are generally handed without any commentary at all.
3) To use this as a starting example that will be drawn upon later to discuss how to evaluate a research-related publication. ( I could have done that here, but I decided to do it later once my audience knew they could be reading about Dr. Sapi's work on the site and I have yet to find a good specific direct comparison paper.)
4) This came later: As a sort of bookmark to myself to remind me about this patent because I'm curious about it and want to see if it bears mentioning later.

It's a stepwise approach. I don't expect all Lyme patients will want to read about any research I post in the first place.

At baseline, some people simply won't be interested in reading anything unless it answers the question, "How can this benefit me and stop me from feeling so sick?" Because that is what most of us are seeking: relief from persisting symptoms, whatever the cause is.

Frankly, on a different note... I'm still wondering about Sapi in general, and her whole track record. How familiar are you with her earlier research, pre-Lyme disease research?

Post Reply