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May 2006

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Subject:
From:
Mary Dollenmaier <[log in to unmask]>
Reply To:
The Pharmaceutical Microbiology Forum Email List <[log in to unmask]>
Date:
Mon, 1 May 2006 12:23:14 -0400
Content-Type:
text/plain
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We have weighed the cost and expertise required for gene sequencing and
are not able to justify the investment for routine IDs.

Excerpts of non-binding recommendations in some trade journal
advertising suggest the FDA prefers gene sequencing:

 

'Genotypic methods have been shown to be more accurate and precise than
traditional biochemical and phenotypic techniques.'

 

In the actual FDA guidance document, the excerpted paragraph reads in
full:

 

'These methods are especially valuable for investigations into failures
(e.g., sterility test; media fill contamination). However, appropriate
biochemical and phenotypic methods can be used for the routine
identification of isolates.'

 

We subcontract gene sequencing for critical test results to confirm our
FAME IDs.

 

Mary


 


-----Original Message-----
From: The Pharmaceutical Microbiology Forum Email List
[mailto:[log in to unmask]] On Behalf Of Balkovic, Ed
Sent: Friday, April 28, 2006 2:12 PM
To: [log in to unmask]
Subject: [PMFLIST] Anyone doing all of their microbial IDs using genetic
techniques?

Fellow Microbiologists:

Since I'm an "Ancient Microbiologist" ( who came out of the clinical lab
doing research on the pathogenesis and immunology of influenza virus in
a mouse model and then moved onto QC testing of influenza vaccines at
Connaught Labs before getting into Biotech) and not a "Gene-Jockey"; I
was
wondering:

Has anyone converted from using biochemical characterization systems
(VITEK, Biolog, API, RapID, Crystal, etc.) or fatty acid analysis
systems (MIDI) as their primary microbial identification methods to
totally using genetic techniques (16s rRNA sequencing or ribotyping) for
all of their isolates in the QC Micro Lab?


If so, how is it working out?


Any problems that the rest of us should be looking out for?


Is anyone considering making the total shift in the future?


Has anyone at least incorporated genetic methods in their lab for use in
special cases?  If so, how is this working out?


It appears to me that 16s rRNA sequencing is better for IDs and
ribotyping is better for comparing the relatedness of 2 different
isolates?  Would others agree?


We are still using the biochemical characterization systems, VITEK, API,
RapID, for our IDs.  Is it time to think about making the change?  I
know the vendors of these genetic systems say it is.



Thanks, in advance.
Ed Balkovic

Ed Balkovic, Ph.D.
QC Microbiology Technical Support
Genzyme Corporation
45 New York Ave.
P.O. Box 9322
Framingham, MA  01701
(T) 508-271-3660
[log in to unmask]

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------------------
The PMFList (http://microbiol.org/PMFList_info.htm) is operated from
The Microbiology Network (http://microbiol.org) and supported by
our sponsors (http://microbiol.org/sponsor.htm) as a service to
the scientific community.

Please take a second to visit our sponsors' web sites and say thank you for their support of this service.

Accugenix - http://www.accugenix.com

American Type Culture Collection - http://www.atcc.org

ATS Laboratories - http://www.ats-labs.com

Biolog - http://www.biolog.com

Biomerieux - http://industry.biomerieux-usa.com

Dupont Qualicon - http://www.qualicon.com

EMD Chemicals - http://www.emdchemicals.com

EMSL Analytical, Inc. - http://www.emsl.com

Genomic Profiling Systems, Inc. - http://www.genprosys.com

MIDI, Inc. - http://www.midi-inc.com

Millipore - http://www.millipore.com

Pall - http://www.pall.com

NovaTek International - http://www.ntint.com

Raven Biological Labs - http://www.ravenlabs.com

Veltek Associates, Inc - http://www.sterile.com

=================================
The nature of this service is to provide a medium for communication.  The specific statements and endorsements of individuals participating in the discussions are not necessarily those of The Microbiology Network, Inc., the PMF, or the sponsors of the list.

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