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May 2006

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Subject:
From:
"Stapleton, Raymond D" <[log in to unmask]>
Reply To:
The Pharmaceutical Microbiology Forum Email List <[log in to unmask]>
Date:
Mon, 1 May 2006 10:06:04 -0400
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Ed,

We replaced our Vitek with a sequencer in order to perform microbial
identifications via 16S ribosomal gene sequence analysis in early 2005.  In
summary, it has been a huge improvement.  Our lab had prior experience with
Vitek, Biolog, and API strips.  Please see below for a few specific
thoughts.

*  Initial capital expense can be significant, however we have found routine
samples cost about the same as Vitek, as we were repeating at least 50% of
our samples in attempt to get an ID.  We now repeat about 1% or less.

*  We have greater confidence that our sample ID's are accurate.  

*  The ability to generate custom databases allows you to track specific
organisms.

If you perform a large number of ID's, I feel it is a worthwhile investment.
If you only perform a few, it may be easier to send to an outside vendor
(such as Accugenix, etc.).

Regards,
Ray

*****************************************************
Ray Stapleton, Ph.D.
Merck & Co., Inc.
Stonewall Quality Operations
Microbiology Section Manager
Elkton, Virginia   22827
*****************************************************


-----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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=================================
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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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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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