Ribotyping

Ribotyping involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes
coding for the 16S and 23S rRNA. Conceptually, ribotyping is similar to probing restriction fragments of chromosomal
DNA with cloned probes (randomly cloned probes or probes derived from a specific coding sequence such as that of
a virulence factor).
Ribotyping is a method that can identify and classify bacteria based upon differences in rRNA. It generates a highly
reproducible and precise fingerprint that can be used to classify bacteria from the genus through and beyond the
species level. DNA is extracted from a colony of bacteria and then restricted into discrete-sized fragments. The DNA
is then transferred to a membrane and probed with a region of the rRNA operon to reveal the pattern of rRNA genes.
The pattern is recorded, digitized and stored in a database. It is variations that exist among bacteria in both the
position and intensity of rRNA bands that can be used for their classification and identification. Databases for Listeria
(80 pattern types), Salmonella (97 pattern types), Escherichia (65 pattern types) and Staphylococcus (252 pattern
types) have been established. In addition over 35 different genera have been tested and RiboPrint® patterns
obtained. These databases continue to grow as more bacteria are ribotyped.
Fig:examples of ribotype pattern.
Why Ribotype?
Contamination source bacteria in finished products can originate from any one of the ingredients, processing
personnel or the environment. Ribotyping allows the establishment of unequivocal relationships between bacterial
isolates recovered from any of these sources and the finished product. Molecular epidemiology A number of diseases
in animals that are caused by bacteria can be traced to the consumption of contaminated feed. Ribotyping can help to
identify the contaminated feed source for elimination. Spread of infection within a group of animals can also be
followed by ribotyping and routes of animal-to-animal transmission identified. Identification RiboPrint® patterns can
be used to identify a bacterium if that pattern is in the database. Currently well over 600 patterns are in the database
representing both Gram positive and Gram negative bacteria and this database grows continuously The largest
number of RiboPrint® patterns have been collected for Listeria, Salmonella, Staphylococcus and Escherichia coli.
Custom identification databases can be developed for virtually any need.
How is the RiboPrinter® System's typing method superior?
Key to the utility of a typing method is its reproducibility and standardization. The most common technique for typing
is using a panel of antisera which selectively react with a certain degree of nonoverlapping specificity. Establishing a
serotyping scheme for a new microorganism is tedious and dependent upon the quality of the panel of antisera.
Furthermore the dissemination of this technique to other laboratories is usually limited and the longevity of the assay
dependent upon antisera stocks. Virtually no typing method has been developed to the stage that allows standards to
be established especially when classifying below a species level. Although a number of techniques have been
explored and practiced in different laboratories, there is no method whose output is easily standardized. Ribotyping
has over the past 10-15 years been established as a robust classification and typing method. It was originally
developed as a manual method, but took a quantum leap in reproducibility and standardization with the development
of the RiboPrinter® Microbial Characterization System by Qualicon (a subsidiary of DuPont). This instrument
automates all of the steps in the process from cell lysis to data capture and database comparisons. Further, reagent
cassettes including the enzymes, enzyme conjugated-hybridization probe, electrophoretic gel and membrane have
been developed with aim of delivering consistent performance. Data capture is accomplished via a CCD camera and
the patterns stored in a digitized format. It is therefore relatively easy to compare results among laboratories and to
exchange data electronically.
Institute for Environmental Health

Ribotyping Protocol
Genomic DNA Isolation and Restriction Endonuclease Digestion
Confluent growth was scraped with a sterile flat-head toothpick and suspended in 200 microliters (μL) 50mM Tris,
50mM EDTA (pH 8.0). Six hundred μL more of 50mM Tris, 50 mM EDTA was then added and the suspension was
thoroughly mixed by pipetting up and down. Then 45 μL 20% sodium dodecyl sulfate (SDS) and then 10 μL
proteinase K (20 μg/mL; Pharmacia, Piscataway, N.J.) were added. This solution was then incubated at 40°C for 1
hour. After an equal volume of phenol was added to each tube, samples were vortexed, and centrifuged for 5
minutes. The top layer was extracted, and an equal volume of chloroform was added. The preparation was vortexed
again, centrifuged, and extracted. Two and a half volumes of absolute ethanol were added and the DNA was
precipitated out and spooled onto a glass capillary pipette. The DNA was washed with a few drops of absolute
ethanol, dried, and re-suspended in 50μL dH2O. Separate restriction endonuclease digestion reactions were set up
using EcoR1 and PvuII, 10 units/μL (Boehringer Mannheim, GmbH, Germany) as instructed by the manufacturer
using 2 μL DNA. They were incubated at 37°C overnight. The samples were then centrifuged and 0.5 μl of enzyme
was added. The samples were re-incubated at 37°C for a minimum of 3 hours. They were centrifuged again and 3 μL
stop dye was added. Every batch of restriction enzyme reaction contained two reactions with a positive control
strain that was included on two lanes on each gel.
Gel Electrophoresis and Southern Blot Hybridization
Samples were run on a 0.8% agarose gel in 1X Tris-borate-EDTA at 22 volts and 17 milliamps, for 17 hours. λ HindIII
was used as a size standard along with a known E. coli isolate designated as 3915. Each agarose gel was assigned
a number, and when more than one gel was run, the position of the first standard reference strain was changed in
each gel (1st lane on the first gel, to the Nth lane on the Nth gel). Electrophoresis gels were stained in ethidium
bromide. If two gels were stained in a single container, one corner of the gel with the higher number was clipped. The
label for each gel was also transferred to the staining container. Each gel was then photographed and a hard copy of
the print was labeled with the gel sheet (containing the isolate numbers loaded on each lane, and the enzyme used to
cut the DNA, plus date, gel number, voltage, current, gel strength, buffer strength, and electrophoresis time
information). After photography each gel was returned to the same staining container. The DNA fragments were then
transferred to a Nitran filter (Schleicher & Schuell, Keene, N.H.), baked at 80°C for 1 hour, and probed with 32P-
labeled copies of E. coli rRNA, which were made by extension of random hexanucleotide primers using Avian
Technical Support Document Upper Oyster Creek (Segment 1245) Appendix C C-2 Myeloblastosis Virus reverse
transcriptase (Stratagene, La Jolla, California) under conditions specified by the supplier. Each membrane filter was
labeled with the gel number, restriction enzyme designation, date, and technician’s initials. Hybridization was done in
5X SSC (1X SSC is 0.15 M NaCl plus 0.015 M sodium citrate), 0.1% SDS, 1mM EDTA, and 50% formamide at room
temperature overnight. Salmon sperm DNA and blocking reagent (Boehringer Mannheim GmbH, Germany) were
used to block nonspecific binding. Three washes were done with a solution of 2X SSC and 0.1% SDS, once at 25°C
for 20 minutes and twice at 65°C for 20 minutes to wash off low-homology, non-specific binding. Blots were then
exposed with an intensifying screen to x-ray film (Kodak, Rochester, New York) for 24 hours at -70°C. Two to three
exposures were done to ensure all possible bands would show up. All reagents and buffers were made according to
formulas in the MEI standard operating procedures. Reagents and buffers were tested for sterility.
Restriction Fragment Length Polymorphism Analysis
Each ribotype was then analyzed by assigning an alphanumeric pattern based on the distance between the bands.
Bands more than 3 mm apart were counted as singles while bands that were within 3 mm of each other were counted
as doubles or triples. For example, two bands that were closer than 3 mm were designated “2” and a group of three
bands with 3 mm or less between each band were designated “3.” A “1” designated a single band more than 3 mm
distant from another band. Each unique banding pattern was called a ribotype and assigned an alphanumeric pattern.
Two isolates that had the same numeric value but different banding patterns were assigned letters to differentiate the
two ribotypes. For example, two isolates with an identical numerical pattern of 2122111, but with the bands shifted so
the two isolates did not have identical banding patterns, were labeled 2122111A and 2122111B. The ribotypes were
then entered into a Microsoft Access® database and compared to the other ribotypes of known source in the library
database. Ribotype patterns that numerically appeared to be similar were compared side-by-side visually to judge
matching. Isolates with the same PvuII and EcoR1 ribotypes are deemed to be members of the same
ribogroup. Using this approach only isolates with two identical ribotypes were grouped together.

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Ribotyping involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes

Fig:examples of ribotype pattern.

How is the RiboPrinter® System's typing method superior?

Institute for Environmental Health

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