DIFFERENTIATION BETWEEN PHENOTYPIC AND GENOTYPIC IDENTIFICATION MECHANISMS
Recently, a Blog was published that identified the fifteen most common bacterial isolates identified by Accugenix, Inc, Newark, DE during 2010. This Blog created an interest in other related areas to include the best methods to assure a definitive identification of an isolated bacterium.
In a poster presented at the most recent American Society for Microbiology, Accugenix compared multiple technology solutions to determine the fitness for use studies beyond routine panels provided by manufacturers to understand both the performance and operation impact vs. the various environmental monitoring systems. The goal was to assure each customer the highest percentage of accurate identification to the species level. The systems compared permitted identification by either phenotypic or genotypic methods.
The data suggests that the greatest percentage of satisfactory matches occurred in the following order (from highest to lowest):
Accugenix (DNA Sequencing using the Accugenix Bacterial library 04APR11)*
Applied Biosystems MicroSEQ® v. 2.2*
Bruker MALDI-TOF® v. 3.1.2*
bioMerieux Vitek® v. 2.2**
NOTE: *=Genotypic Method; **=Phenotypic Method
One additional system, MIDI, also known as Fatty Acid Methyl Ester (FAME), which had been utilized by Accugenix for a number of years, was not included since its use had been discontinued (by Accugenix).
None of these systems is designed to compare microorganisms of the same species. The DuPont Qualicon RiboPrinter® system is available to compare strain-specific characterization where additional subspecies identification is required.
The above systems also exhibit some unique features and requirements. For example, the Vitek, Biolog and MALDI-TOF systems require living microorganisms to obtain identification. The Applied Biosystems and the Accugenix modification of the same do not require living cells, but it is desirable to use them if possible. In selected instances, testing laboratories will not test nor will postal authorities permit the shipment of live, hazardous or pathogenic microorganisms and these bacteria can only be shipped to the testing laboratories once they have been killed.
Other limitations of the MALDI-TOF system include the age of the culture, temperature of storage, not in a sporulation state and requirement for fresh growth. Please discuss exact requirements with your testing facility.