Ed,

Like you I have the feeling there would be something missing in a microbiology
lab without traditional identification procedures. 
We have rationalized and reduced the number of species identifications performed
in the lab. We use Vitek with Crystal ID as a backup for this purpose. Results
are mostly passable, but there are many repeats and a lot of judgement calls.
Anything critical or of special interest that we cannot obtain a good or
acceptable ID with these methods is sent out to a contract testing lab for 16s
rRNA sequence IDs. This works well.
I have come to understand that while 16s rRNA IDs are good as they are obtained
from an extensive database, you need ribotyping for fingerprinting and
relationship between strains (although you may not get an ID) and intend to use
a contract lab for that service.
I am convinced that it would be a retrograde step to invest in new and upgraded
versions of conventional phenotypic systems.  Mainly this is due to the new
taxonomy that is being developed based on DNA sequencing which the phenotypic
systems are having great difficulty keeping up with. Contract testing labs offer
an efficient and timely service, and the cost involved is not unrealistic if you
take into account capital cost of a new system, cost per test, plus repeats when
necessary, analyst time saved, maintenance and service costs etc. 
The only reson I have hesitated over the switch to genetic IDs is that we shall
have lab staff (who mostly have biology degrees and rely on learning their
microbiology on the job) who have no knowledge of microbial taxonomy,
biochemistry and identification procedures. But then, other automated rapid
methods that are increasing being implemented use technologies not based on
traditional culture methods, so microbiology as a whole will change drastically
over the next few years.

That is my perspective. I shall be interested in other responses.

Jackie Hewitt
Microbiology Manager
Luitpold Pharmaceuticals
Tel.  (631) 924-4000 x 321
FAX (631)205-2075
E-mail  [log in to unmask]


-----Original Message-----
From: Balkovic, Ed [mailto:[log in to unmask]] 
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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