Application Note

The role of microbial genotyping in the clinical lab

A case study of Clostridium difficile

Clostridium difficile is emerging as one of the most common and expensive hospital-acquired infections estimated
to cost over $600 million annually.1 The increasing rise in infections has been attributed to increased reporting,
increased use of alcohol-based hand sanitizers that do not effectively eradicate spores, and the emergence of a new
strain.2 The new, more virulent strain commonly referred to by its PFGE type of NAP1 is increasingly being seen
in countries throughout the world.3 The discovery and isolation of this strain is important for increased patient
health and decreased nosocomial costs.

Similarity
How DiversiLab™ can help percentage
The DiversiLab System is a microbial indicates a high
genotyping system that allows the level of similarity to
characterization and strain discrimination of both NAP1 strain.
bacterial and fungal isolates.4 Optimized
fingerprinting kits are available for multiple
bacteria, including Clostridium. In The virtual gel-
images are
addition to strain-level discrimination of indistinguishable.
C. difficile isolates, the DiversiLab System
provides a library of C. difficile fingerprints
that contains the virulent NAP1
strain. All other library
samples show a low
When multiple C. difficile isolates are level of similarity.
obtained in a geographical region or in a
single healthcare facility, an outbreak is
suspected. Each of these isolates can be A Top Match report showing the comparison of an outbreak sample to the
genotyped using the DiversiLab System to DiversiLab C. difficile Library. The outbreak sample shows high similarity
determine similarities in the fingerprints. to the virulent strain (CL03).
The DiversiLab System can then answer
the following questions.

• Do I have an outbreak of C. difficile samples?

If all isolates show an indistinguishable fingerprint pattern, the patients may be part of the same outbreak. Prevention
procedures such as isolation precautions, decontamination of equipment and increased infection control measures
can be enacted immediately to prevent further spread of the infection.

• What is the source of my outbreak?

Isolates obtained from personnel, potentially contaminated equipment or the environment can be compared to patient
samples. Analysis of the fingerprint patterns can direct the IC team to concentrate on specific areas of
contamination.

• Are my isolates similar to the new, virulent strain?

The fingerprints of your isolates can be compared to our library of characterized isolates. Similarities or differences
to library strains can indicate the presence of virulence factors.

• Why is the DiversiLab System a preferred method for typing C. difficile?

The DiversiLab System provides strain-level discrimination of C. difficile in an easy-to-use, automated format. With
results in a single day, the outbreak can be eradicated quickly. Unlike other standard methods that encounter
problems with the endonucleases found in anaerobes, the DiversiLab System works reliably with all tested strains of
C. difficile.5 Additionally, a database is available for comparison of your samples to previously characterized
isolates, including the NAP1 strain.
 Advanced microbial genotyping

The DiversiLab System at a Glance

• Highly accurate, reproducible
rep-PCR technology with
standardized protocols and
reagents

• Automated analysis with multiple

data viewing features to aid with
analysis

• Same day strain-typing for real-

time investigations Included with the DiversiLab System:
Agilent 2100 Bioanalyzer
• Data storage to allow tracking Desktop Computer
and comparison of pathogens DiversiLab System Software for Data Analysis
from users proprietary database Agilent Software for Instrument Operation
or DiversiLab reference Chip Priming Station
database Vortex Mixer
Training Course
• Ability to genotype both bacteria
and fungi at the strain-level If you already have a Bioanalyzer,
you only need to add the
DiversiLab System Software.
• An expanding list of libraries for
identification and comparison to
standard samples For more information about how the DiversiLab System
can be incorporated into your lab, please call us today.
© 2007 bioMérieux, Inc. BBI-004-08

Not for Use in Diagnostic Procedures.

1. McDonald LC, Owings M, Jernigan DB. 2006. Clostridium difficile infection in patients discharged from
US short-stay hospitals, 1996-2003. Emerging Infectious Dis. 12(3):409- 415.
2. Barkclay L, Vega C. 2005. Two studies report new, resistant strain of Clostridium difficile. Medscape
Medical News. http://www.medscape.com/viewarticle/518602.
3. McDonald LC, et al. 2006. An epidemic, toxin gene-variant strain of Clostridium difficile. N Engl J Med. bioMérieux, Inc.
353(23):2433-41. 100 Rodolphe Street
4. Healy M, Huong J, Bittner T, Lising M, Frye S, Raza S, Schrock R, Manry J, Renwick A, Nieto R, Woods Durham, NC 27712
C, Versalovic J, and Lupski J R. 2005. Microbial DNA Typing by Automated rep-PCR. J Clin Microbiol. (800) 682-2666
www.biomerieux-
43(1):199-207. usa.com/diversilab
5. Spigaglia P, Mastrantonio P. 2003. Evaluation of repetitive element sequence-based PCR as a
molecular typing method for Clostridium difficile. J Clin Microbiol. 41(6):2454-7.