posted
Barbara Johnson of CDC, as many of you know, is an arch-Denialist, who uses her powerful public health position to organise counter-moves to discredit important research breakthroughs which contradict the Steerite line.
She recently published a paper claiming Advanced Labs' blood culture method (which has been finding the bacteria in so many chronic Lyme patients) is unreliable, and that Dr Sapi's results were due to lab contamination.
Below Dr Macdonald shows basically how dishonest Johnson and her colleagues have been:
"Improved Borrelia burgdorferi Blood culture Method Preview: Re: Improved Borrelia burgdorferi Blood culture Method CDC Critique of Sapi et al Blood Culture for Borrelia in Human Blood:Many Mistakes by the CDC critique methods and False Conclusions: _________________________________________________________________________ CDC Analysis of the DNA sequencing Data for the Advanced Labs Blood culture isolates: by Dr. Barbara Johnson et al. ________________________________________________________________________ An Official CDC critique and an Official CDC accusation of alleged Flawed Advanced Laboratory techniques resulting in Only 3 genovars instead of 60 + Genovars of Borrelia as reported by Sapi __________________________________________________________________________ The CDC Analysis is flawed for the reasons posted below and the CDC manuscript must be withdrawm _________________________________________________________________________
The Reader of the CDC manuscript will infer that The CDC had in their possession aliquots of each of the isolates from Advanced Labs If this is NOT the case.
The CDC may be required to issue a Retraction of theirmanuscript to clarify this point for the reader and to address the BLASTn data which follows for a single isolate . Advanced Laboratories and the CDC agreed had 21 nucleotide mismatches with B31 were present in the exemplary Isolate. [Isolate JX867376}
CDC analysis of isolate JX86 7376 detected 21 base mismatches with respect to B31 and the Sapi Paper also reported 21 base mismatches with respect to B31 [97% identity with B31]
I did a BLASTn search on isolate JX867376 against all borrelia.
A 100% match was obtained with JX867376 itself as deposited in GenbBank.This is expected and this 100% match indicates that the 603 bases were correctly entered into the NCBI BLASTn Search Engine. -------------------
B31 borrelia complete DNA sequence produced a result with 21 mismatches against Sapi deposit JX867376 for a congruence percentage of 97% It is interesting that the BLASTn search also revealed 97% matches for the additional Borrelia on Deposit in GenGank: N40, CA382 ZS7 and multiple numbered haplotypes of Borrelia spp. A 96% match was noted for multiple genotypes of B. garinii and B. Bavariensis.
So if the truth be told, based on a BLASTn search of all Borrelia in GenBank, it is very very misleading to state that isolate JX867376 was UNIQUE for B31 as is posted at position 49 in the CDC Table.....AND ..... and to omit any mention of the following borrelia genotypes which also yielded 97% matches with JX867376 according to BLASTn search. ST12 N40 ST8 CA382 ST4 ST51 ST56 St1 ZS7
Each and every one of the above genotypes should have been posted at postion 49 in the CDC table.
To post only B31 is very misleading to the reader who does not use the BLASTn tool for sequence analysis and borrelia genotyping.
______________________________________________ Correction to the CDC Table of Results for (97%) [21 base mismatches against reference strain borrelia burgdorferiB31] against Advanced Labs Isolate JX867376.
" This Advanced labs isolate may indicate ANY of the following Borrelia species: B31, N40,ZS7,ST! ST4, ST8ST12,,ST51,ST56, CA382, _______________________________________ _______________________________________
Mismatches of Bases by BLASTn analysis should now be initiated for Each and Every Advanced Lab nucleotide sequences and the original manuscript should be withdrawn and re-written to accommodate BLASTn search data for each of the Advanced Lab PyrG nucleotide sequences.
I look forward to CDCreconciliation of BLASTn data with the observed Advanced Lab dep[osited nucleotide sequences with the hope that the issue of Contamination of Patient Recovered Borrelia from blood cultures may be viewed in the full context of BLASTn search Data to embrace all possible borrelia species with closely matching nucleotide sequences.
The maximum number of polymorphic sites in CDC analysis of the Sapi Data was 21. CDC speciated only 3 strains of borrelia in Their analysis : B31 burgdorferi [N=22], B023 afelii [N=2}, and Fuji P1 garinii [ n=27]
These assignments conflict with the Sapi paper as follows: In the Sapi manuscript Table 3 : Sapi et al reported 5 isolates of Garinii - [ no identical garinii genotypes noted by Sapi } 1 isolate of afzelii Pko [consistent with European type afzelii] 3 kurtenbachii [ all genotypically distinct] 1 americanum and 6 burgdorferi [B31=1] , [ZS7=1} , [ N40=1], { ST1 =1], { ST11 =1}, { St8=1}.
For the remaining: "JX86***** series isolates I will consult the GenBank accessions as I have for isolate JX867376.... and perform my own Clustal analysis. of nucleotide Base alignments
CDC group registered the following genovars [ your results in parentheses] among the JX86**** series: 7424 51 polymorphic sites [Called Afzelii B023 by CDC group] 7398 49 polymorphic sites [called Afzelii B023 by CDC group] 7394 43 polymorphic sites { Not classified by CDC group} 7417 42 polymorphic sites [Called Garinii Fuji P1 by CDC group} 7380 42 polymorphic sites {called Garinii Fuji P1 by CDC group} 7378 42 polymorphic sites { Called Garinii Fuji P1 by CDC group} 7379 42 polymorphic sites Called Garinii Fuji P1 by CDC group}
Twenty one isolates with 41 polymorphic sites EACH [ isolates not collated here] 7393 39 polymorphic sites [Called garinii Fuji P1 by CDC group} 7376 21 polymorphic sites [[See above - called B31 burgdorferi by CDC group}} 7419 2 polymorphic sites [ Called burgdorferi B31 by CDC group}
CDC also indicate that CDCS equence analysis yielded 27 Identical isolates of Garinii 2 i dentical isolates of Afzelii. 22 isolates of B31 { with only 2 cases #48 and 49 called B31 burgdorferi with "mismatched" bases : #48 n=1 miusmatch and #49 with 21 mismatches] So instead of 60+ unique Borrelia genovars, the CDC reduced the Sapi/Advanced Labs results to just 3 genovars ----------------------------------------------------- I insist the the genotyping of the Advanced Labs GenBank deposits speaks for heterogeneity of genovars, and reinforces the concept that So called European type borrelia may very well be now recognized as vectored by USA Ixodid ticks. Mexico, Central America and Brazil are geographies in which GARINII has been proven to be vectored by ticks.
To make matters more complex, the Amblyomma family of ticks (Amblyomma cajenesse) are competent vectors for Garinii infections in the Western Hemisphere. We need not look to Sea bird migrations to explain USA cases of Ixodid scapulairs and Amblyomma spp. vectored human infections.
The uniqueness of the Sapi report of Advanced Labs Human Blood culture Borrelia strains is therefore CORRECT.
No Laboratory Contamination of patient material with any living borrelia ever occurred European Strains of borrelia were recovered from the blood of USA patients in the Advanced Labs study of Borrelia blood cultures
Respectfully submitted, Alan B. MacDonald MD FCAP FASCP August 16,2013"
Elena Cook
-------------------- Justice will be ours. Posts: 786 | From UK | Registered: Oct 2007
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Keebler
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posted
- Elena,
Thanks so much for this, and for the Dr. MacD comment in your other post today from the NYT article.
So much appreciated that you continue to post such key pieces. So sad, of course, but we really need to know the current events as they unfold just to keep up (though sure wish it were not so necessary).
thanks, again -
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poppy
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posted
And didn't we know those liars at the CDC would do this? Evidently there is nothing too low and dishonest for them to do.
Once again you can either believe they are criminally incompetent or evil.
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Keebler
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- It's just so very lonely and such a terribly rough road, in every phase & aspect of a life with lyme. -
Posts: 48021 | From Tree House | Registered: Jul 2007
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poppy
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posted
Aint that the truth.
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TF
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posted
They made the same types of discrediting statements about Dr. MacDonald's research years ago when he was finding living spirochetes in patients who had been treated for months with antibiotics. The purpose was to get the world not to believe what the man was finding.
No different here. Using same tactics so that they won't look like they have been wrong all of these years.
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posted
Hilarious post for proposed remake of Wizard of Oz posted on CDC Facebook page. Go there to "Like"!
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lpkayak
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posted
grrrrrrrr. too mad to say anything.
-------------------- Lyme? Its complicated. Educate yourself. Posts: 13712 | From new england | Registered: Feb 2004
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Catgirl
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posted
Typical. They have brain issues. I'd lay odds the right side of their brains are barely functioning, which would explain why they cannot think outside the box.
So maybe the right brained people will live longer because we're open minded and smart enough to treat, and the left brains will die off from disease (evolution). Surely, something is not functioning properly in their brains.
-------------------- --Keep an open mind about everything. Also, remember to visit ACTIVISM (we can change things together). Posts: 5418 | From earth | Registered: Mar 2011
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This is reading like a graphic novel with underground lyme warriors fighting for justice. What
is the next step? MacD had written a well reasoned argument as to why CDC is wrong. So, now what? Also, "Grrrrrr!"
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Razzle
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posted
They're blinded by greed, ego, and politics.
-------------------- -Razzle Lyme IgM IGeneX Pos. 18+++, 23-25+, 30++, 31+, 34++, 39 IND, 83-93 IND; IgG IGeneX Neg. 30+, 39 IND; Mayo/CDC Pos. IgM 23+, 39+; IgG Mayo/CDC Neg. band 41+; Bart. (clinical dx; Fry Labs neg. for all coinfections), sx >30 yrs. Posts: 4167 | From WA | Registered: Feb 2011
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posted
I hope Dr. MacD does another youtube in response. I don't know why he can't sue them for liable.
-------------------- I'm not there yet but I'm closer than I was yesterday.---- Lyme Band 31,41,58. Being treated for Lyme and Bartonella. Posts: 149 | From Maine | Registered: Oct 2010
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posted
I have always felt that we cannot win this war through science alone. We are not dealing with honest people. We do need a political expose of these liars.
CDC will use American taxpayers' money to ensure that their flawed article gets as wide an audience as possible - I would not even be surprised if they arrange for it to go out via mainstream mass media as well as medical media.
Meanwhile they will manoeuvre and use their enormous influence to try and deny Dr Macdonald, Dr Sapi or anyone else who would clarify the issues, access to the medical press.
If any of you had a positive from Advanced Labs and are now facing a skeptical GP or Infectious Disease specialist, why not print out Dr Macdonald's post and invite them to do the Blastn search themselves, and see who is telling the truth.
Elena
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Catgirl
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posted
Dr Sapi found that a large number of her US patient blood samples contained Borrelia which were closely matched to a Japanese strain of Borrelia garinii called HP1.
This is NOT one of the lab test strains so there is no possibility of contamination.
If you are familiar with using BLASTn, please go there and input the accession number of borrelia HP1 which is AB555778.
Please confirm that you get the output below which confirms Dr Sapi's findings and indicate that CDC's allegation that many of her cultured strains were derived from lab strain garinii Fuji P1 as totally misleading.
Please copy your result here so that everyone can see. Thanks Elena ps The size of the display box in Lymenet may distort some of the blast columns. If you recopy the text into Word this may help.
NCBI LogoBLAST ® Basic Local Alignment Search Tool My NCBI My NCBI help [Sign In] [Register] Jump to Page Content
Download GenBankGraphics Next Previous Descriptions Borrelia garinii pyrG gene for CTP synthase, partial cds, isolate: HP1 Sequence ID: dbj|AB555778.1|Length: 603Number of Matches: 1 See 20 more title(s) Related Information Range 1: 1 to 603GenBankGraphics Next Match Previous Match Alignment statistics for match #1 Score Expect Identities Gaps Strand 1160 bits(603) 0.0 603/603(100%) 0/603(0%) Plus/Plus
Download GenBankGraphics Next Previous Descriptions Borrelia sp. enrichment culture clone c612pg CTP synthase (pyrG) gene, partial cds Sequence ID: gb|JX867417.1|Length: 603Number of Matches: 1 Related Information Range 1: 1 to 603GenBankGraphics Next Match Previous Match Alignment statistics for match #1 Score Expect Identities Gaps Strand 1154 bits(600) 0.0 602/603(99%) 0/603(0%) Plus/Plus
Download GenBankGraphics Next Previous Descriptions Borrelia sp. enrichment culture clone c503pg CTP synthase (pyrG) gene, partial cds Sequence ID: gb|JX867411.1|Length: 603Number of Matches: 1 Related Information Range 1: 1 to 603GenBankGraphics Next Match Previous Match Alignment statistics for match #1 Score Expect Identities Gaps Strand 1154 bits(600) 0.0 602/603(99%) 0/603(0%) Plus/Plus
Download GenBankGraphics Next Previous Descriptions Borrelia sp. enrichment culture clone c113pg CTP synthase (pyrG) gene, partial cds Sequence ID: gb|JX867380.1|Length: 603Number of Matches: 1 Related Information Range 1: 1 to 603GenBankGraphics Next Match Previous Match Alignment statistics for match #1 Score Expect Identities Gaps Strand 1154 bits(600) 0.0 602/603(99%) 0/603(0%) Plus/Plus
Download GenBankGraphics Next Previous Descriptions Borrelia sp. enrichment culture clone c112pg CTP synthase (pyrG) gene, partial cds Sequence ID: gb|JX867379.1|Length: 603Number of Matches: 1 Related Information Range 1: 1 to 603GenBankGraphics Next Match Previous Match Alignment statistics for match #1 Score Expect Identities Gaps Strand 1154 bits(600) 0.0 602/603(99%) 0/603(0%) Plus/Plus
Download GenBankGraphics Next Previous Descriptions Borrelia sp. enrichment culture clone c63pg CTP synthase (pyrG) gene, partial cds Sequence ID: gb|JX867378.1|Length: 603Number of Matches: 1 Related Information Range 1: 1 to 603GenBankGraphics Next Match Previous Match Alignment statistics for match #1 Score Expect Identities Gaps Strand 1154 bits(600) 0.0 602/603(99%) 0/603(0%) Plus/Plus
Download GenBankGraphics Next Previous Descriptions Borrelia sp. enrichment culture clone c204pg CTP synthase (pyrG) gene, partial cds Sequence ID: gb|JX867394.1|Length: 603Number of Matches: 1 Related Information Range 1: 1 to 603GenBankGraphics Next Match Previous Match Alignment statistics for match #1 Score Expect Identities Gaps Strand 1148 bits(597) 0.0 601/603(99%) 0/603(0%) Plus/Plus
Download GenBankGraphics Next Previous Descriptions Borrelia garinii pyrG gene for CTP synthase, partial cds, isolate: NP76 Sequence ID: dbj|AB555834.1|Length: 603Number of Matches: 1 See 2 more title(s) Related Information Range 1: 1 to 603GenBankGraphics Next Match Previous Match Alignment statistics for match #1 Score Expect Identities Gaps Strand 1148 bits(597) 0.0 601/603(99%) 0/603(0%) Plus/Plus
Download GenBankGraphics Next Previous Descriptions Borrelia sp. enrichment culture clone c198pg CTP synthase (pyrG) gene, partial cds Sequence ID: gb|JX867393.1|Length: 603Number of Matches: 1 Related Information Range 1: 4 to 603GenBankGraphics Next Match Previous Match Alignment statistics for match #1 Score Expect Identities Gaps Strand 1142 bits(594) 0.0 598/600(99%) 0/600(0%) Plus/Plus
Welcome to LymeNet! Here it is customary to say "hello" first, to introduce yourself, rather than begin by saying you're "no CDC fan". There is no need to be so defensive. I, for one, believe that you may not be a CDC fan. After all, there is plenty of rivalry between CDC and NIH.
I was wondering when you would turn up.
You ignore the Blast output I have posted, and say you are "troubled" by Dr Sapi's results. You fear she found no Lyme at all, just contamination.
Well, I am going to ease you're troubled mind, Mr 1hctom. And this time, I will do it in a manner that everyone here will understand, even if they have never studied science in their entire lives.
So please, come, sit at our table; it's so cold outside - here it's comfortable. Relax, make yourself at home, make yourself at ease. Let us take your troubles from you....
Je vous connais milord...
Now. Mr Ihctom please explain to me, how did Dr Sapi manage to contaminate her cultures, when the live control strains she used were stored in a different lab, which was situated IN A DIFFERENT STATE?
There, you feel less troubled already, don't you, Mr "lkctom"? Don't you feel the stress just melting away?
I'm so glad we have been able to relieve you of your "troubles".
Friends (that's not you, Mr Ihctom), please do not report him to the moderator this time round.
I know some of you find it unbearable to be in the same corner of cyberspace as him. Believe me, I feel exactly the same as you. But let's give the miserable rodent a chance. He is going to explain to us how the live control strains of Borrelia managed to transport themselves from one state to another, just to contaminate Dr Sapi's cultures.
So tell us, Mr 1hctom. Please. Explain it to us. We are burning to know. Did the germs hitch-hike? Take a plane? I haven't been to the States in so many years. Do you still have Greyhound buses? If so, perhaps the strains hopped on a Greyhound bus? You tell us, Mr Ihctom. Enlighten us.
It's so much better to have an open debate, don't you think? Let us all put our cards on the table. So much more honourable than a government official hacking into people's Medscape accounts, desperately trying to stop certain borrelia-related facts from reaching a medical audience, don't you think?. Of course you would never stoop to such pathetic behaviour, would you, Mr 1hctom. No. Of course not.
So tell us. How did the lab strains transport themselves from one lab to the other? Tele-transport, like Star Trek?
Elena Cook
quote:Originally posted by lhctom: I'm no CDC fan but its troubling that 29 patients from across the US were found to have the garinii species not found in the US and at least 21 had the exact same 603 letter pyrG gene that also matched the Japanese JujiP2 garinii strain that was acquired by ALS and used to test the culture.
The odds of finding so high a percentage of garinii infections in the US is quite low. The odds of spirochetes from multiple US sites having the exact same 603 letters in their pyrG gene is even lower. To have 21 matches to the 603 letters of the ATCC test FujiP2 isolate is very low. The odds all three would happen is the product of the three very low odds. This is not good.
-------------------- Justice will be ours. Posts: 786 | From UK | Registered: Oct 2007
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susank
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posted
All this is Greek to me - could someone explain?
I was positive on the ALS test.
Results from my four Igenex tests are in my sig. line. Lots of bands - from different tests dates - considered negative.
I think the ALS confirmed I have Lyme.
-------------------- Pos.Bb culture 2012 Labcorp - no bands ever Igenex - Neg. 4 times With overall bands: IGM 18,28,41,66 IND: 23-25,34,39 IGG 41,58 IND: 39 Bart H IGG 40 Posts: 1613 | From Texas | Registered: Aug 2009
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susank
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posted
Am tired - will try to reply.
My lifestyle was riding horses, walking dogs, birdwatching/hiking etc in the woods. Have pulled ticks off all my animals. And myself.
No rash. I feel I was infected in Texas. About a year ago it was in the news that Texas A&M Univ. was testing ticks throughout the state. 25% tested pos. for Bb.
I knew I was sick. Weird bad sick/symptoms. Started with my eyes and mouth getting dry and eyes very sensitive to light. Tested neg. to everything.
First test with Igenex came back with some pos. and Ind bands. So tested and re-tested after various challenges. Some bands repeated. Some only appeared on one test result.
I did the HLA tests and I fit the group for Lyme susceptible. Bad detoxer etc.
CD57 low.
Discovered I also have Hypogammaglobulinemia. ie deficient amounts of total serum Imm.G and subclasses.
Perhaps caused by Lyme disease?
Perhaps is why so few IGG bands?
So I begged for the ALS culture test. To my surprise - because I had really given up - the tenth week I got the call that I was positive.
I suppose I will always have my doubts - that's just me. I have lost faith in about everything having to do with medicine - testing, diagnosis, treatment etc.
Oh - my Bart. Hens. came back from Igenex as positive. Or better said - not negative with IGG of 40 - which under their changed ranges implies positive.
Would be rather hard to believe I had Bart with no Lyme.
Anyway, my pea brain cannot grasp the controversy over the ALS test - and contamination - ??? I cannot connect the dots/understand the techno stuff.
An issue is that a strand of Lyme from another country was detected or something? That is where I get lost. So lost that I cannot even determine if the strain was found in patients' blood or test medium.
As an aside - and unrelated - I found it interesting to read what antibodies were found in different IVIG brands from different manufacturers/countries/donors. IIRC four of the five brands showed Bb antibodies to varying degrees.
Try searching for that info. You won't find it. I printed a copy years ago. Maybe it is meaningless info - maybe not.
To add; re: sequencing. That part of the culture test was not available when I tested. I think that was called an "extended" part of the test? Whatever - I really wanted my specimen - if positive - to be "typed". Regret that it wasn't. If the test was not so expensive I would do it again. That IS the part of the ALS test that you are questioning, right?
-------------------- Pos.Bb culture 2012 Labcorp - no bands ever Igenex - Neg. 4 times With overall bands: IGM 18,28,41,66 IND: 23-25,34,39 IGG 41,58 IND: 39 Bart H IGG 40 Posts: 1613 | From Texas | Registered: Aug 2009
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susank
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posted
Really tired...... CD57 below 60.
When Cornell came out with their new multiplex Lyme test I had my horse tested - and soooooo wish I could have slipped a tube of my blood in the shipping container.
How can Cornell come up with such an accurate test and no one else can? I wish they would test humans - far less drama.
And BTW my horse was neg. IIRC an antibody test on him prior had band 41.
Reasonably, how many people in the US would test pos. for Bg or Ba? AFAIK TBI's did not originate in the US. Bb got here somehow - as well the others, right?
Who else reading here has had the ALS gene sequencing? Results? Bb? Bg? Ba?
I know I need to research all this more in depth.
My ALS said pos. for Bb - that is all I know.
Geez - could folks have BB and or Bg/Ba?
So really the "exact" matching is the problem? The results look too much like the test medium?
Really - this needs to be dumbed down for some of us.
Have treated - not aggressively - overall I guess am worse than when I "crashed" in 2006. First "crash" of 1996 was thought to be CFS/EBV/Fibro.
So more studies being done? Results expected when? This does concern me.
Whatever the outcome - the truth would be nice.
-------------------- Pos.Bb culture 2012 Labcorp - no bands ever Igenex - Neg. 4 times With overall bands: IGM 18,28,41,66 IND: 23-25,34,39 IGG 41,58 IND: 39 Bart H IGG 40 Posts: 1613 | From Texas | Registered: Aug 2009
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posted
Posted by Dr alan Macdonald on Lyme forums:
Re: Improved Borrelia burgdorferi Blood culture Method Postby inmacdonald » August 22nd, 2013, 2:21 pm BLAST searches are good ......[ by that we are speaking of BLASTn or the nucleotide blast, there are also other BLAST menu choices such as Protein sequence BLAST..... but for MUTATION DETECTIVES, please use the BLASTn- as it provides maximum detail]
for Further site by site analysis exquisite Detail of Nucleotides with precision and minimal human Eyeball analysis type errors in scanning sequences of 603 base length... Always use CLUSTAL analysis. because the Color stripes of like bases (see below link) allows for easier graphical Locus by Locus analysis [ with no hocus pocus}
.....do the math..for BLASTn RESULTS... 1. BLAST result of 100% match for a sequence of 603 bases = identity of 603 out of 603 bases Blast result of 99% match for a sequence of 603 bases = Identity of 597 out of 603 bases Blast result of 97% match for a sequence of 603 bases = identity of 585 out of 603 bases
2. Now for example in a 99% blast identity comparing 2 GenBank depoists, What were the exact LOCus positions in the 603 sequence for each and every on of the the mismatches?? AND what were the letters for each and every locus mismatch at Each site.??
Answers: You can examine the sequence print outs for BLAST for each of the "Found" mismatches. You will soon go blind trying to manually analyze 100 different retrievals each 603 bases long in BLASTn Search, Or You can do Clustal Analysis and get color coded alignments - which highlight the areas of mismatch among many may DNA sequences, and allow for easy determination of the Specific identity of substitution/mutation at Each Locus.
Clustal Analysis for Garinii type DNA sequences including both GenBank Reference Garinii individuual deposits from around the world and For ALL of the Sapi et al GARINII - like isolates in the Advanced Labs blood Culture paper.
Clustal analysis - for Garinii-like isolates From Advanced labs shows: A. perfect alignments at 100% identity for 21 of the Advanced labs GenBank deposits and 5 Advanced Lab deposits with Single Base Mismatch [ each a a different locus and Each with a unique base substitution.} and 1 Advanced Labs deposit with TWO Base mismatches This does not provide evidence for a "cookie cutter" population of Garinii-like isolates, but rather shows mutated bases in 6 of27 Advanced lab deposits For an overall rate of 22% of Advanced labs deposits Positive for mutations against reference garinii strain AB55778 ( haplotype 603 base deposit Garinii Hp10)
Among the remaining Garinii 603 base haplotype deposits Jf331248.1, JF331231.1, JF 331269.1 and JF331265.1 Identities of 100% were seen in this group of Four reference garinii strains. This identical group of four Garinii had 166/603 mismatches with the Advanced labs deposits. There is no reason to suspect that 105 dna sequence identity among the "group of four" was a result of "Contamination". The Lab of Origin, Date of Deposit,and Source of the Deposit(isolated from what life form)for the "Group of Four" are as follows: JF331248.1 Gomez-Diaz, Barcelona,spain/Feb 15,2011/ Ixodes uriae tick/ strain name T1913 JF331231.1 Gomez-Diaz,Barcelona,Spain/Feb15,2011/ Ixodes uriae tick/ strain name T1697 JF331269.1 Gomez-Diaz, Barcelona, Spain/ Feb 15,2011/ Ixodes uriae tick / strain name Conn A3/3 JF331265.1 Gomez-Diaz, Barcelona, Spain / Feb13, 2011/ IXODES RICINUS tick/strain name IPT114 So Four separate Garinii isolates from Spain with 100% identity in the "group of Four" - with separate tick species showing 100% identity in DNA from Garinii strains (4 different) recovered. -------------------------------------------------------------------------------------------------------------
Ref: Gomez-diaz, E ,et al, "Genetic structure of marine borrelia garinii and population admixture with terrestrial cycle of Lyme borreliosis", 2011, Environ.Microb. 13(9):2453-67. ________________________________________________________________________________________ Now a source for the GenBank reference Strain HP1 of Garinii GenBank AB555778.1 which shows extensive 100% identity with the Advanced Labs human blood borrelia isolates [ 21 cases out of 27]
Source of this specimen: Fujita, H, et al, HokKaido Japan/ April 12, 2010/ Ixodes persulcatus tick / strain name HP1
There is no possibility of contamination of any of the Advanced labs Isolates with this Garinii HP1 since it is Not for SALE at the American Type Culture Collection.[ATCC} That is correct!! Not For Sale!!! Not available in any store !!!
Plain and simple: Contamination did not occur in Barcelona ,Spain in the lab of Gomez-Diaz in year 2011. [ 100% identities of 603 bases from the group of four" notwithstanding] Contamination did not occur in Philadelphia, Pennsylvania Advanced labs in the year 2012-2013. [ 100% identities of 603 bases in the group of 21 notwithsatnding. { 6 Advanced labs human blood culture isolates showed mutations which make them Unique among ALL GARINII Deposits in the National Center for biotechnology Information(NCBI) }
Let us get used to the concept that GARINII type borrelia are present in the blood of some USA patients who acquired Lyme disease , chronic type,and who were willing to spend upwards of $1000.00 to secure this precious information.
Respectfully submitted, Alan B. MacDonald, MD, FCAP, FASCP August 22,2010
PS: Yes many,many words in the CDC paper: "Assessment of New Culture Method to Detect Borrelia species in Serum of Lyme Disease Patients" Barbara J.B. Johnson, Mark A. Pilgard, and Theresa M. Russsell J. Clin Micro ,14 Aug 2013 epub ahead of print, doi 10.1128/JCM.01674-13 Are False statements, not buttressed by Bench laboratory work by any of the authors, who as CDC employees [ as listed on the title Page} represent the full force and power of the Centers for Disease Control and Prevention.
Collectively, the authors of the CDC official critique of a legitimate private Scientific Laboratory, Licensed and certified by the State of Pennsylvania to provide diagnostic medical services to patients, engaged in concerted action to Discredit Advanced Laboratories. The CDC employees FABRICATED mis-truths and engaged in Unsubstantiated Speculation that Advanced labs had living Borrelia in the building which houses the Advanced Laboratories facility. Furthermore, the CDC employees speculated, without ever conducting a Site visit to the Advanced laboratories Facilities, that carelessness in laboratory technique CAUSED results to be issued to patients and to the physicians caring for them.
Finally, the employees of the CDC who authored the above captioned paper gave written instructions to patients concerning their medical care based on laboratory clinical diagnostic reports to disregard the Advanced Laboratories results as spurious, flawed and misleading. All of this from CDC employees holding positions of highest authority, without ever Fact checking the accusations made in their paper.
So did the CDC authors write untruths? Yes Should disciplinary action be taken against CDC employees , who are public servants? Yes Should the CDC paper captioned above be RETRACTED because of its many flaws and false assertions? Yes Should the Director of the CDC issue a Written Statement of apology to Advanced Labs? Yes Should the CDC issue a National Press release to apologize for publishing a false and unscientific document? Yes Under the Freedom of Information Act is the public permitted to view the basis for the statement in the CDC manuscript page 2 line 64 which states..." the Centers for Disease Control and Prevention has received numerous inquiries from National and State Health departments and clinicians about the performance of this culture method since Advanced Laboratories began offering it in 2012>,," Freedom of Information Act States "Yes" Did Advanced Laboratories Fully Disclose ALL DETAILS of their method for Borrelia culture from human blood in the Materials and Methods ?? Yes and in great detail. Reference { pp 363 to 373 International Journal of Medical Science :2013: 10:362-376- covering TEN single spaced DATA loaded manuscript pages of all aspects of media preparation, quality controls, and detailed EXACT instructions for the handling of cultures from blood commencing with the patient pre-analytics through the Incubation conditions and quality controls, to the use of Antibody assisted identification of each positive culture, to the divers borrelia morphologies of the patient isolates, to the PCR Reaction conditions to DNA Sequence analysis for each and every positive culture, to formal acceptance of Each patient isolate described in their manuscript to the National Center for Biotechnology Information [NCBI] and the GenBank ACCEPTANCE of each of the Advanced laboratories deposit as scientifically justified by GenBank oversight. Did Advanced laboratories fulfill its scientific obligations, and regulatory oversight demands in great detail, freely, openly, and conscientiously, with no details overlooked??? Yes
Where is the Greater Science in this unprovoked vitriolic attack by employees of the Centers for Disease Control on a scientifically conscientious and carefully managed patient diagnostic service, fully Licensed by the State of Pennsylvania?? Verdict for the Advanced laboratories. { Centers for Disease Control claims are Rejected.}
Respectfully submitted, Alan B.MacDonald , MD, FCAP, FASCP
-------------------- Justice will be ours. Posts: 786 | From UK | Registered: Oct 2007
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posted
OK, "1hctom", that's enough now. You've had your fun. Tell them who you really are, Ed. Tell them the truth. If you had the slightest leg to stand on you would not come here, pretending to be a patient, and playing your silly games, the same games you have been playing for maybe 20 years now, or at least as long as the Web has existed.
Tell them who you really are, you snivelling coward.
Tell them what you did in the 1990s all those years at NIH.
tell them how hard you worked to funnel all the Lyme grant money to Denialists ONLY.
Tell them all the rest, too.
How many pseudonyms have you invented to play these games, to come here and laugh at and taunt your victims, Ed? "hv808ct", "chuch padams" "nnecker" and a million others...
How many victims are you PERSONALLY responsible for? Tens of thousands? Hundreds of thousands?
Millions?
Tell them who you really are, you monster. Elena
-------------------- Justice will be ours. Posts: 786 | From UK | Registered: Oct 2007
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posted
Oh yes Ed, try and fool the Americans into thinking the C6 Elisa is something other than the pile of trash it has always been.
"lhctom" says:"The C6 peptide is a good test and is being considered as a CDC 2T replacement. Its used in Canada. I had the C6 peptide ELISA 3 times at 3 labs and it was positive. "
Dr Burrascano says:
"Low Sensitivity- Elisa: Sensitivities range from 29% to 68% Stricker, BMJ 2007; 335 (7628):1008
posted
The C6 Elisa only detected 5 out of 57 PCR and Igenex western blot positive patients.
(paraphrased; source is recent ILADS presentation by Dr Nick Harris, director of Igenex)
----------- The C6 elisa has been in use in Europe for years. It was first launched by Allen Steere. It has been used in Britain for years and in fact Immunetics C6 Elisa is exactly the brand that is in use here now at Porton Down.
Here in Britain we probably have the LOWEST detection rate of Lyme in all of Europe.
Our neighbour, Holland, just across the water, has a reported rate of 100 new cases per year per 100 000 inhabitants. That figure is based on EM rashes ONLY, so is a massive underestimate of course. For as most of you know, many many people never notice a rash, and 90% of the EM rashes do not appear like the "typical" Bullseye, so will not be recognised by doctors in the first place.
So I absolutely concede that the Dutch figure is a gross understatement of the true incidence, and I don't wish in any way to play down the suffering of Dutch Lyme victims, who are also denied adequate treatment thanks to the adoption of IDSA-style criteria in Europe.
But I just want to point out that while the Dutch have an official incidence rate of 100 per 100 000, ours is 1.7 per 100 000.
I repeat, 1.7 per 100 000.
There are NO significant differences between the Lyme-related ecologies of our two countries.
We both have the same ticks, the same mice, the same birds, the same sheep, the same deer, etc etc etc.
We have the Immunetics C6 Elisa, and our OFFICIAL incidence is less than 2 per 100 000 inhabitants!
"NIAID-supported investigators are now working closely with CDC to determine if the C6 ELISA can eventually replace the two-step standard ELISA and Western blot tests (Clin Immunol 132(3): 393, 2009)."
And our guest is the Monster from the NIH who, I see, has been using this particular false name for nearly a year to pretend to be one of us, and to surreptitiously push the C6 elisa. He has also impersonated REAL Lyme patients for the same purpose, I see.
It is not the Moderators we need to call on to deal with the Monster from NIH. It is the international human rights organisations we need to call on!!!
He and his colleagues need to be tried for crimes against humanity.
Elena
-------------------- Justice will be ours. Posts: 786 | From UK | Registered: Oct 2007
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poppy
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posted
I would feel more confident this was a real patient, instead of a troll, if there had been other posts which gave us a clearer picture, instead of something that just appears out of nowhere to discredit this newer lab test. Which is behavior that trolls use.
So, not saying this is a troll, but have question marks here.
The thing is that there was an earlier culture test that was published on, and immediately trashed by the powers that be. It is a pattern to do this with any test, including PCR, that might actually be better than the two tier process endorsed/enforced by the CDC, which is not very good at all.
So, when the people who push bad tests on us then criticize other tests, we have to be suspicious of their motives.
I am not able to comprehend the science behind these allegations, so cannot say anything useful on lab contamination.
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poppy
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I see. Well, the way it looks to me is that the CDC has no credibility on lyme disease. They have done everything possible to ensure more people do not get diagnosed, and then, not get treated adequately. So, in my book, they are liars from the get go. So, with that kind of record, am I going to believe they have this one right? No.
It is going to take more than this to be convincing, a lot more.
If these other places are checking this procedure and if they are competent and qualified, then their results will be useful. If they are somehow beholden to govt for funding (and most big universities are), then maybe the results might reflect it.
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The above captioned paper Must be Retracted for the J.ClinMicrobiology. The rationale for a demand for Retraction are: A crucial ERROR in the CDC paper criticizing Advanced Labs and Dr Eva Sapi was the CDC assumption that the BSK media testing which used LIVE control strains of Borrelia burgdorferi, B. Garinii, and B. Afzelii was done in Philadelphia, Penn- --- the location of Advanced Laboratories. Actually the TRUTH is: Dr. Eva Sapi did ALL of the BSK Media Testing of ATCC control living borrelia strains in her West Haven Connecticut Laboratory at the University of New Haven.
Therefore: In Philadelphia, Penn at the Advanced Laboratories There were NO LIVE BORRELIA CONTROL CULTURES EVER!! Geographic separation of Advanced Laboratories from the University of New Haven Laboratories makes the CDC contamination argument an IMPOSSIBLE EVENT.
The Advanced Laboratory received tubes of human blood for Testing. The Only living borrelia in the Advanced Laboratories building were PRIMARY [New} { Unique} isolations of Borrelia from Human blood.
It is IMPOSSIBLE TO CONTAMINATE human blood specimens with CONTROL STRAINS (3) of BORRELIA SPIROCHETES if the location of the Control borrelia {allegedly the source of positive cultures held in Philadelphia by Advanced Labs] i was Only ON SITE in the University of New Haven Research Lab of Dr Eva Sapi. hundreds of miles from Philadelphia, Pennsylvania.
A second error perpetrated by the CDC manuscript is as follows: The CDC authors testify that they "developed" their own pyrG sequences and that same sequences were deposited in the National GenBank for all to examine. There is NO RECORD that the CDC ever deposited pyrG sequences in the national GenBank at the time of the publication of their paper. Without the availability of the MISSING CDC pyrG sequences, There was NO POSSIBLE WAY for Impartial Expert Reviewers at the Journal of Clinical Microbiology to perform a REVIEW and then the vote to either Approve for Publication OR vote to REJECT for publication The CDC submitted paper
Respectfully submitted, Alan B. MacDonald, MD, FCAP FASCP August 24, 2013
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susank
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lhctom: could you copy and post your sequencing results? i never did that part of the test and have been curious about what the results would look like. thanks.
-------------------- Pos.Bb culture 2012 Labcorp - no bands ever Igenex - Neg. 4 times With overall bands: IGM 18,28,41,66 IND: 23-25,34,39 IGG 41,58 IND: 39 Bart H IGG 40 Posts: 1613 | From Texas | Registered: Aug 2009
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I am surprised you continue to treat "LHCTom" aka Ed as if he is genuine Lyme patient, and not the Monster from NIH playing his usual game of infiltrating Lyme patients' forums, pretending to be a Lyme patient.
After all, someone has just kindly posted for us a rebuttal from Dr Alan Macdonald, sent to the journal in which the lying CDC allegations were published, which proves conclusively that "LHCTom"'s comments on contamination are nonsense.
Dr Alan Macdonald, as you would know unless you are very new to Lyme, is the world's greatest Lyme scientist.
I accept that some people may be fooled by Ed aka LHCTom's little act. It can at times look a bit realistic. After all, if any one of us were to do something for twenty years non-stop, we would become good at it too.
But if all of you watch very closely, and pay attention to exactly what he says, you will eventually realise what he is.
Elena
quote:Originally posted by susank: lhctom: could you copy and post your sequencing results? i never did that part of the test and have been curious about what the results would look like. thanks.
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posted
SusanK, I forgot to mention, I had not met you before, but a quick glance into the archive reveals that you are a very original thinker. I see, for example, that you believe that antibiotics might be causing false positive results on Lyme western blots.
That is very original. In fact, I have never heard of that before! Not even from the Denialists, whose agenda, of course, it would serve perfectly.
Would you mind explaining to me, scientifically, how it would be possible for antibiotics to cause positive results on a Lyme western blot? I cannot for the life of me understand it.
Thanks. Elena
-------------------- Justice will be ours. Posts: 786 | From UK | Registered: Oct 2007
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Stop misrepresenting me. I clearly stated that my info was from as ILADS presentation by Dr Nick Harris, not from any other site.
Anyway, let's look at the quote YOU yourself have posted. It includes this information:
"In a set of 30 patients with late Lyme disease, all having CDC-positive IgG and IgM Western Blots, the C6 ELISA was positive in ONLY 10% OF THE PATIENTS. It is NOT A GOOD TEST FOR LATE-STAGE Lyme disease."
(my capitalisation)
Look at your membership number, Mr "LHCTom" aka Monster from the NIH. It is Number 41,709. Now, as you have just joined Lyme Net the other day, we know that it is a very recent number. In other words, this group has over 40 000 members.
Do you not comprehend that the VAST MAJORITY of those 40 000 plus people are here because of the issue of "late-stage" (or rather, CHRONIC) Lyme?
And this is just ONE, mostly US-based, group. Do you have any idea how many people are out there in the world, who have had to join groups like this one, because their CHRONIC Lyme is not recognised?
Do you think there was a Worldwide Lyme Protest, for the first time ever, because of something other than CHRONIC Lyme being ignored?
And then you recommend to us a test which you imply Igenex are RECOMMENDING, which is only TEN PERCENT SENSITIVE for chronic Lyme?
Are you out of your tiny mind?
Igenex offered the test not long after it first came out, in 2003. I believe the study they refer to, which was 73% positive in finding VERY EARLY Lyme cases which were also CDC blot-positive, is from 2003.
Actually, as YOU KNOW WELL as you are a scientist yourself, 73% sensitivity is a pretty lousy figure.
My reference from Dr Harris is a lot more recent than yours.
The Americans are unfamiliar with the C6 Elisa, as I gather it's not widely in use in USA. And you are trying to con them into thinking that it's a good and sensitive test.
If you have chronic Lyme, it might just pick it up. But it is FAR MORE LIKELY not to, and then you will have an official, FDA-endorsed BIG FAT NEGATIVE on your medical notes that will just prejudice doctors even more against you.
ALL Antibody tests are useless in Lyme, because of the myriad ways in which Lyme dysregulates and suppresses parts of the immune system.
We need antigen-based tests, and GOLD standard tests like blood culture for chronic Lyme, such as Dr Sapi and her colleagues worked hard to produce, and the Monster and CDC are working hard right now, to discredit.
Elena
quote:Originally posted by lhctom: Below is the actual quote by Nick Harris from IGenex.
Lisa aka Elena, would have you believe the test is 10% sensitive. But she is conveniently leaving off most of what Nick Harris actually said. The test has been shown to be 75-90% (other studies have shown 96%) except late stage infections where a small study at IGenex showed only 10%. Since this is the only other test offered in the US that is recognized by ID doctors, if you want to get a diagnosis that is believed, the C6 is one way to try. Its very dishonest to partially quote someone or a study just to give the impression you want. We all know this is exactly what the IDSA does. So isn't this the same? Lisa, Elena or whoever she is is giving out information intentionally altered from a direct quote. This is exactly the anti-science behavior that has led to all the problems. We need honest activists if we want the truth to emerge. I said the C6 has problems but we are very limited to accepted and validated tests here in the US. Igenex offers the test. I have late stage Lyme and I was positive at IGenex and tony Brook on the C6. It helped me. Why would IGenex offer the test if Nick Harris did not see some value?
The ELISA test works quite well for patients with EM rash and a known tick bite, within 3-4 months of the tick bite. After 3-4 months, the test loses sensitivity. The C6 peptide ELISA detects the C6 found within the antibody formed against borrelia, so this is an antibody test. In a study with patients with CDC-positive IgG and IgM Western blot tests, the C6 ELISA was positive in 73% of these patients. In a set of 30 patients with late Lyme disease, all having CDC-positive IgG and IgM Western Blots, the C6 ELISA was positive in only 10% of the patients. It is not a good test for late-stage Lyme disease. Other studies have been done with various results, all with 100% of patients CDC-positive by Western Blot. The best result for the C6 ELISA was just under 90% - results varied widely from study to study.
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poppy
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Did Susan really say abx could cause a false positive WB? The FDA said the opposite....that abx could abrogate the antibody response.
But maybe what Susan is trying to do is discredit a positive test after an abx challenge. Hmmm, does sound like a troll, or a seriously confused patient.
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Try It. You will find detail that is present in BLASTn but easier on the Eye.
22% of Sapi's Garinii-like isolates had either one or two base substitutions with reference strain AB55778.1 haplotype (n==603) Garinii. With Barcelona haplotypes (n=603)in GenBank Jf331248.1 Jf331231.1, and Jf331265.1 Japanese haplotype the identity among this reference group of 4 was 100 each with each other. Net take home message: all bona fide Garinii haplotypes, but difference by 166 base mismatches with the Sapi GenBank Deposits. Have you ever successfully made a GenBank deposit which passed muster and was published by Genbank? I would venture a guess that you have not.
So make the move over to Clustal analysis for DNA sequence alignments. It works! By the way in B31 the complete pyrG sequence is 1602 bases,-- Soooo with 603 bases to examine we are only seeing a part of th total pyrG ORF Alan MacDonald MD , FCAP FASCP Aug 25 2013 PS:It is now Aug 25 2013 at 14:38 hours. Do you know where your CDC deposits Kf170280 KF170281 , KF170282 are?? They are not presently available to the Public. Perhaps missing in action/ Perhaps prisoners in a CDC Remote site with Cheney. Perhaps they will never see the clear light of day.
With No CDC GeneBank Deposits available to the public, How is it that the Outside expert reviewers were able to complete their review of the CDC paper [ without the missing 3 DNA CDC reference pyrG sequences? ] Did the paper bypass Outside Impartial review? Who paid between $2000 to $3000 for the CDC paper to have accelerated paper-less publication { epub ahead of print}?? Were taxpayer funds used to advance a CDC false scenario? Alan b. MacDonald MD
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poppy
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Sounds pretty convincing to me. Thanks for the explanation.
If the labs involved in this were separated geographically by nearly 200 miles, then it seems to me that gene sequencing is not even needed to show that the CDC totally blew this, and defamed the lab. If I had a lot of money, I would finance a libel case against Dr. Johnson and her buddies. When are we going to see some CDC heads roll for this kind of malfeasance?
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poppy
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And does anyone think there is impartial review of lyme articles at this IDSA journal?
No.
They will print any pack of lies anyone cares to send them so long as it prevents diagnosing and treating lyme.
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susank
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posted
Hold your horses. Somebody must be misreading something I wrote. Re: antibiotics and testing.
I did challenges to provoke a response.
-------------------- Pos.Bb culture 2012 Labcorp - no bands ever Igenex - Neg. 4 times With overall bands: IGM 18,28,41,66 IND: 23-25,34,39 IGG 41,58 IND: 39 Bart H IGG 40 Posts: 1613 | From Texas | Registered: Aug 2009
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poppy
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Or a misquoted patient. Sorry about that, Susan.
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susank
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posted
If someone will show me a post where I wrote against Abx and testing I will correct it.
I should have never entered into this discussion.
Will "tom" share his results - ie actual copies?
Would be interesting if he would.
-------------------- Pos.Bb culture 2012 Labcorp - no bands ever Igenex - Neg. 4 times With overall bands: IGM 18,28,41,66 IND: 23-25,34,39 IGG 41,58 IND: 39 Bart H IGG 40 Posts: 1613 | From Texas | Registered: Aug 2009
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poppy
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If you think the culture has problems based on contamination that did not actually exist because the two labs were several hundred miles apart, then you are not thinking very well, if not actually a troll. On that issue, it is unclear. So before you accuse people here of being a cult, maybe you should review the evidence.
And I am questioning your credentials to say these sequences are impossible, when the missing CDC samples are not to be found, and are irrelevant if the contamination could not have occurred.
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poppy
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I think you are right, and since you are quacking, you are a duck (troll). Didn't want to rush to judgement, but pretty clear now.
And addressing my next comment to someone who is not a troll and does understand these genetic issues, unlike myself.
Why would the exact same sequences found in multiple spirochetes of the same species be thought to be evidence of contamination anyway? Would you not expect a recently introduced pathogen from a place of more genetic variability to be less variable? In other words, if this is a European species brought here by a bird in recent years, then it would have more genetic variability at its origin (Europe) than at a new location where it was recently established (the U.S.).
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susank
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posted
Poppy - its all over my head but was having the same thoughts.
I have not studied Bgar - but the bit I did read about - seems Bgar found in colder climates. Saw a ref to Alaska?
Dunno - does Igenex test for Bgar?
Wonder why ALS would? Of course people travel to other countries and could be exposed. And folks move here from the endemic countries.
It gave me a bit of a scare in regards to popssible problems with the ALS culture - else I would not be in on this discussion.
I feel confident my Bb pos. test from ALS was not compromised.
Its just all weird about the Bgar and Baf.
To add - re: Elena?s questions to me:
I "believe Abx cause false positive WB's"???? then I "believe Abx cause positive WB's" ???
I thought I might have still a few marbles left in my head - Abx are taken pre-test to "help" get the pathogens out/into the blood - to be detected on a WB? Right?
No one wants a positive test. But if you are Bb positive you sure want one. Instead of wandering in the wilderness wondering what the "h" is wrong with you.
-------------------- Pos.Bb culture 2012 Labcorp - no bands ever Igenex - Neg. 4 times With overall bands: IGM 18,28,41,66 IND: 23-25,34,39 IGG 41,58 IND: 39 Bart H IGG 40 Posts: 1613 | From Texas | Registered: Aug 2009
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Carol in PA
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Who is lhctom and why are all his posts deleted?
His profile says ten posts, but none are there.
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susank
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posted
I guess we won't be seeing his actual Bgar test results. Hmmmmmmmmmm
-------------------- Pos.Bb culture 2012 Labcorp - no bands ever Igenex - Neg. 4 times With overall bands: IGM 18,28,41,66 IND: 23-25,34,39 IGG 41,58 IND: 39 Bart H IGG 40 Posts: 1613 | From Texas | Registered: Aug 2009
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poppy
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posted
People who read this thread are going to be confused, because some posts won't make any sense with the troll's deleted. But, goodbye, don't come back and mess with sick people.
No, don't think we will be seeing his test results, probably because they don't exist.
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susank
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posted
"Tom" - I have been giving you the benefit of the doubt - a wee bit - that you are a "good guy" but that is looking very doubtful.
But you did write something that piqued my interest. I guess its old news - but it did give me some thoughts in regards to Bb strains B31 and 297.
It is a fact that Labcorp uses only B31 in their tests?
I have lost count of how many times I have been tested by Labcorp for Lyme - starting in 1996.
Every band - every single time was negative.
Just last month on my Labcorp orders I ended up somehow being tested again. Not one band showed positive. Not even 41. (Arup lab at least picked that one up years ago).
ALS - pretty much supported by Igenex - shows I have Lyme. Could I deduce that I don't have strain B31 - only 297? And would that be of any significance? Different treatment? Where geographically is 297 most likely to be found? Anyone?
-------------------- Pos.Bb culture 2012 Labcorp - no bands ever Igenex - Neg. 4 times With overall bands: IGM 18,28,41,66 IND: 23-25,34,39 IGG 41,58 IND: 39 Bart H IGG 40 Posts: 1613 | From Texas | Registered: Aug 2009
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beaches
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posted
I'm a bit late to post here on this thread.
But I did get a chance to read what lhctom/Ed had to say.
I'm no scientist, but even I, ignorant layperson that I am, was able to follow the logic.
I did notice that lhctom/Ed got a bit agitated when confronted with the science and began to spew all sorts of accusations/generalizations against the membership here...
Posts: 1885 | From here | Registered: Jul 2012
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posted
Friends, let's welcome the legendary Dr Alan Macdonald to LymeNet.
Thank you so much for coming here, Dr Macdonald. I did see your earlier post, but I thought it was just a patient posting a text you had written.
Thank you for debunking the evil Ed (aka "LHCTom" aka "Thomas Eames" etc), who is a notorious Denialist scientist whose real name shall be revealed very shortly.
And thank you so much for all the incredible work you have done for us, all these years, which one day, when the cover-up is over, and its perpetrators all exposed, will be rewarded with a Nobel Prize.
Elena Cook
quote:Originally posted by Shadrach: Dear Ed, Have You ever used CLUSTAL X?
Try It. You will find detail that is present in BLASTn but easier on the Eye.
22% of Sapi's Garinii-like isolates had either one or two base substitutions with reference strain AB55778.1 haplotype (n==603) Garinii. With Barcelona haplotypes (n=603)in GenBank Jf331248.1 Jf331231.1, and Jf331265.1 Japanese haplotype the identity among this reference group of 4 was 100 each with each other. Net take home message: all bona fide Garinii haplotypes, but difference by 166 base mismatches with the Sapi GenBank Deposits. Have you ever successfully made a GenBank deposit which passed muster and was published by Genbank? I would venture a guess that you have not.
So make the move over to Clustal analysis for DNA sequence alignments. It works! By the way in B31 the complete pyrG sequence is 1602 bases,-- Soooo with 603 bases to examine we are only seeing a part of th total pyrG ORF Alan MacDonald MD , FCAP FASCP Aug 25 2013 PS:It is now Aug 25 2013 at 14:38 hours. Do you know where your CDC deposits Kf170280 KF170281 , KF170282 are?? They are not presently available to the Public. Perhaps missing in action/ Perhaps prisoners in a CDC Remote site with Cheney. Perhaps they will never see the clear light of day.
With No CDC GeneBank Deposits available to the public, How is it that the Outside expert reviewers were able to complete their review of the CDC paper [ without the missing 3 DNA CDC reference pyrG sequences? ] Did the paper bypass Outside Impartial review? Who paid between $2000 to $3000 for the CDC paper to have accelerated paper-less publication { epub ahead of print}?? Were taxpayer funds used to advance a CDC false scenario? Alan b. MacDonald MD
-------------------- Justice will be ours. Posts: 786 | From UK | Registered: Oct 2007
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posted
Susank, I was not making any accusations against you.
I said you were an original thinker, because you seemed to think antibiotics could cause FALSE positive Lyme tests.
Perhaps I should have written "False" twice, instead of once, to be clearer.
My apologies.
Both sides of the Lyme War accept that at times the antibody response can be abrogated by antibiotics.
Some on our side believe that after treatment, at times, antibodies not seen before on western blot may appear.
No one, to my knowledge, has ever suggested that antibiotics can cause FALSE positive blots.
That's why I asked you how it could happen? After all, that could only be the case, if a molecule of antibiotic, which is nearly always a synthetic chemical compound, had almost the identical chemical composition to an epitope, ie part of a protein on the surface of a living Lyme bacteria, which can elicit an immune response.
I had glanced randomly into the archive and found a thread (see below) from 2011 in which you wrote this:
"Is what kind of makes me wonder if Abx could cause false pos LD tests."
Icon 1 posted 27 June, 2011 05:41 PM Profile for susank Send New Private Message Edit/Delete Post Reply With Quote Razzle - yes have read that. Is what kind of makes me wonder if Abx could cause false pos LD tests. I cannot connect the dots how that could happen. and with non tetracycline drugs. I have so many bands but not positives on the "specific" bands - only IND's. During a phone conversation in general discussing my results - was told that I need to look elsewhere since I did not seroconvert on the "specific" "hot" bands after Abx challenges. I did actually "convert" a bit - but to what? Has to be something antibiotic sensitive?"
It's no big deal, Susan. but I am curious as to why you still think that "Tom" ("LHCTom" aka "Thomas Eames") who is really named Ed, has anything of value to tell us. when you have just seen the greatest Lyme scientist in the world treat him as if he is a fraud. Which of course he is.
Do you think a scientist of the stature of Dr Macdonald would risk his reputation by making accusations against someone who claimed to be a "suffering patient", if there was the slightest doubt in his mind as to what that man really was ?
Elena
-------------------- Justice will be ours. Posts: 786 | From UK | Registered: Oct 2007
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posted
So it seems that "LHCTom"/"Thomas Eames" aka Ed has disappeared, and so have all of his messages.
One of two things has happened.
1. After being exposed and dealt a stunning blow by Dr Alan Macdonald, the Monster from NIH has turned tail and fled, like the coward he is.
or
2. Our good moderators, seeking to protect us from frauds and con merchants, have realised that he is back here for the nth time, pretending,yet again, to be a patient.
And though Ed still has a position at NIH, and still retains respectability as a member of various prestigious scientific societies like the American Association for the Advancement of Science (A.A.A.S.). our good moderators have understood what a hateful fraud he is, and slung him out right on his A.A.A.S..
Regardless of which has happened, I would like to make an URGENT request, not only of the moderators, but of every person here, whether you have participated in this thread, or merely read it:
Please SAVE any files you may have showing what he said on this forum.
Please SAVE them both in electronic form, and in HARD COPY.
Moderators, please RETAIN any technical, server-based or other data in any form that you may have, that might allow the origins of his messages to be traced.
Please everyone SAVE this material, and STORE it SAFELY. Because one day it could form part of a huge dossier of important evidence of the FRAUD perpetrated by US government scientists, and their colleagues in other countries such as mine, fraud that has resulted in the suffering of MILLIONS of people.
I know I joke a lot and use a lot of sarcasm. But I am deadly SERIOUS about this point. Things will never improve until all these morally-challenged Denialists are EXPOSED.
Elena Cook
-------------------- Justice will be ours. Posts: 786 | From UK | Registered: Oct 2007
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If you watch the videos, you will learn that B. garinii is in Mexico and south america - these are not cold countries.
It is all over Europe -hot and cold. Dr Macdonald posted info about 4 identical garinii pyrG sequences from four distinct strains of garinii in Spain. (Clearly Genbank didnt consider them "contamination" just becuase they had the identical portion of pyrG gene.)
Spain is very hot - English people flock their every summer for that reason.
Now, remember that Mexico is connected to the US by LAND, so we dont even need to look at seabirds.
It's very unlikely that Mexican borrelia garinii are stopped at the border and asked to produce their documents before they can proceed any further. Elena
quote:Originally posted by susank: Poppy - its all over my head but was having the same thoughts.
I have not studied Bgar - but the bit I did read about - seems Bgar found in colder climates. Saw a ref to Alaska?
Dunno - does Igenex test for Bgar?
Wonder why ALS would? Of course people travel to other countries and could be exposed. And folks move here from the endemic countries.
It gave me a bit of a scare in regards to popssible problems with the ALS culture - else I would not be in on this discussion.
I feel confident my Bb pos. test from ALS was not compromised.
Its just all weird about the Bgar and Baf.
To add - re: Elena?s questions to me:
I "believe Abx cause false positive WB's"???? then I "believe Abx cause positive WB's" ???
I thought I might have still a few marbles left in my head - Abx are taken pre-test to "help" get the pathogens out/into the blood - to be detected on a WB? Right?
No one wants a positive test. But if you are Bb positive you sure want one. Instead of wandering in the wilderness wondering what the "h" is wrong with you.
-------------------- Justice will be ours. Posts: 786 | From UK | Registered: Oct 2007
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