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Polyphasic Taxonomy and the use rpoB Gene as an
Alternative Biomarker for Identification of Clinically
Important and Ambiguous Bacteria:
Synthesis and Review
CESAR M. MENDOZA, JR., RMT, M. Bio. Ed.
Introduction
• One vital area within the
practice of clinical
microbiology is the system of
identification of microbial
isolates.
• Identification of the etiologic or
causative agent responsible
for the disease and correlate
pathological condition is a
crucial part of clinical
microbiology.
• In conventional system,
accurate morphologic and
phenotypic description is
used but with the rapid
sophistication of
microbiological assays
intended for clinical isolates,
automation and genotypic
identification became an
alternative system in some
cases (Clarridge, 2004).
Introduction
Phylogenetic
relationships
not only a
taxonomic concern
a salient force in
bio-molecular
applicability and
maximum
advancement of
scientific constructs
especially in clinical
laboratory and
management.
Gram Positive Organisms
Introduction
• Polyphasic Taxonomy
a consensus type of taxonomy that aims to maximize all
available data and come up with a decisive conclusion on
taxonomical aspect. (Gillis, et. al., 2005).
BBL Crystal ID (Beckton Dickinson) Thermo cycler
Introduction
• On the current setting, phylogenetic
analyses based on the 16S rRNA gene
is considered vital, important, and
universal tool for the validation and
reconstruction of evolutionary history
and phylogenetic relationships of
various bacterial organisms (Woese et
al. in Kupfer, et; al, 2006).
Introduction
• This paper evaluates the present protocols in the
identification of clinically isolated bacteria
including the ambiguous identities using
phenotypic and genotypic protocols
• Traces the development of various systems used
in clinical microbiology in the identification of
bacterial isolates both in routine and reference
laboratories.
• Identifies alternative biomarker as a potential
housekeeping gene or sole gene determinant for
identification of clinically-isolated bacteria
Objectives
Conventional Method of Bacterial ID –
Present state: On the verge of collapse?
• Conventional methods:
appropriate culture
media and phenotypic
characterization -
staining techniques
such as gram stain,
morphological
descriptions, cultural
requirements, and
biochemical reactions.
Successful in identification of
some bacterial species
Limitations on discriminating
clinically relevant taxa
because individual test may
not be reproducible and that
species metabolic phenotype
is not an absolute property
and may exhibit variability.
Conventional Method of Bacterial ID –
Present state: On the verge of collapse?
Conventional Methods:
Presumptive Test
-Triple strength Lauryl Tryptose
Broth
Confirmatory Test
-If positive inoculate in Brilliant Green
Lactose Broth
Thermotolerant Coliform
-If positive inoculate in EC Broth at 44oC
24 hours
These techniques allow the identification of most bacterial
isolates with good accuracy but are laborious, tedious and
expensive (Bizzini, A., et. al. 2010).
Questions on Specificity
and Accuracy
Conventional Methods:
Staining, Biochemical Reactions, Physiological Requirements
Gram Stain Spore Stain Hemolytic Patterns
Biochemical
Reaction
Conventional
Methods:
Use of Culture Media
Preparation of Culture Media
Speed and Time for ID
The speed of microbial identification can
produce critical impact on clinical
management and diagnosis
Staining Technique Isolation of bacteria
Speed and Time of ID
1. appropriate antimicrobial agents
can be identified and initiated
unnecessary treatment with
ineffective antibiotics can be
avoided;
2. the prognosis of the patients
can be improved
3. Antibiotic resistance can be
avoided; and
4. expenditure on antimicrobials
and overall hospital costs can be
markedly reduced.
Conventional Methods-
Setbacks: (Woo, et. al, )
1. not applicable for non-cultivable
and non-culturable organisms.
2. there are organisms that do not
conform to patterns of known
bacterial species in terms of
biochemical reactions.
3. there are also bacteria that are
slow growers and are difficult to
isolate.
• Studies indicated that compared
to phenotypic tests, gene
sequence-based identification
schemes are superior in the
identification of strains
considered ambiguous.
• “Ambiguous” - Atypical
biochemical, profiles, slow-
growing bacteria, rarely
encountered bacterial species,
and non-cultivable strains. (Woo,
et. al., 2003)
Conventional Methods:
Staining, Biochemical Reactions, Physiological Requirements
Current Trends on Microbial Identification – Clinical
Setting
• Microbial identification in
clinical setting both in
routine and reference
laboratory has evolved
in the past few decades.
• Current trends include
highly automated
identification systems that
have been introduced in
many medium- to high-
throughput clinical
microbiology laboratories
worldwide.
• Conventional Methods
• Rapid Automated ID systems
• Molecular Techniques
• Phenotypic characterization and
automated strips were not enough to
identify accurately some clinical isolates
• Gene sequence can discriminate far more
finely among strains of bacteria than
phenotypic methods
(poorly described, rarely isolated, or
phenotypically aberrant strains)
• This is an area in which 16S rRNA gene
sequence identification might have an
immediate impact on patient care
(Clarridge, 2004).
Current Trends on Microbial Identification – Clinical
Setting
Molecular Marker – Is Newer
Better?
Vital Criteria:
presence in a wide
distribution among
bacteria
uniqueness in the
genomic structure
size of phylogenetic
information that can be
derived
diverse sequence
among related species.
• Molecular diagnostic
methods based on the
detection of bacterial
nucleic acids from
clinical samples hold
the promise of rapid
detection and
identification of the
etiologic agent of the
disease (Pingle, M., et.
al. 2007).
The search for a new biomarker:
The “rpoB gene”
DNA-dependent RNA polymerase is a
multi-subunit enzyme that consist of two α
subunits encoded by the rpoA gene, one β
subunit (rpoB) and one β’ subunit (rpoC)
(Kupfer, et. al. 2006).
• Comparison of rpoB sequences has been
used as a basis for phylogenetic analyses
among some archaea and bacteria
• The protein is approximately 150kD in size
and is a subunit of RNA polymerase with
the beta subunit involved in the synthesis
and elongation of the RNA chain
(Donnabella, 1994)
The search for a new biomarker:
• The rpoB gene
contains many
characteristics that
have made the SSU
rRNA gene important
in the field of
taxonomic studies
and molecular
research since its
introduction as a
universal
phylogenetic marker.
universal distribution,
highly conserved
presence of conserved
and hypervariable regions
of the gene.
in contrast to SSU rRNA,
rpoB has not been
detected in multiple
copies in any complete
sequenced of the
prokaryotic gene (Walsh,
D., et. al., 2004).
The search for a new biomarker:
Usage of rpoB gene in Bacterial
ID of Clinical Isolates
• In a study on the comparative phylogenies
of the housekeeping gene that contains
rpoB compared with 16S RNA for the
phylogenetic study of Pasteurellaceae
(Christensen, 2004),
concluded that:
……..analysis of housekeeping gene
like rpoB is a promising approach for
the revision and study on the taxonomy
of various organisms such as
Pasteurellaceae.
• In Comparative genetic relationships of Aeromonas strains
using 16S rRNA, gyrB, and rpoB gene sequences were done
with gyrB evaluated against rpoB gene and the 16S rRNa
sequencing as the reference:
The study revealed: both gyrB and rpoB can be use to clarify
the taxonomical and evolutionary relationships among
strains of human, animal (carriers or patients) and
environmental species of Aeromonas in contrast with 16S
rRNA gene sequencing which is useful only in identifying
the organism in genus level only…
……. rpoB sequences are more preserved in the genus
Aeromonas…
……. using rpoB gene sequencing, controversial and
issue-laden taxa of Aeromonas are better understood….
Usage of rpoB gene in Bacterial
ID of Clinical Isolates
• A study on the potential utilization of rpoB - fast and direct
assay on the presence of Mycobacteria spp. (various
respiratory specimens) and compared it with concentration
technique using flurochrome staining.
• Study revealed: A high percentage yield for sensitivity
(92.3%) of rpoB-PCR was noted as compared to CF
(concentration fluorochrome) staining (88.4%)
• 94.5% of resistant isolates exhibited mutations in the
hot-spot variable region of the gene while no mutation
within the 305-bp region for any of the rifampin-sensitive
strains tested and isolated - sequencing of the DNA of
the rpoB gene may result in the early detection of strains
that may later on exhibit resistance to rifampin (Hirano,
K., et. al., 1999).
Usage of rpoB gene in Bacterial
ID of Clinical Isolates
Other Related Studies - rpoB
• Partial utilization of rpoB gene sequence
also proved to be critical for identification
of emerging Acinetobacter species
• Partial rpoB was also utilized in
comparative analysis of Pasteurella
pneumotropica isolates from laboratory
rats and mice.
Conclusion:
• phenotypic and genotypic characterization
for the polyphasic taxonomy clearly
indicated that proper identification of the
bacterial isolates in clinical setting is a
critical matter needed to be resolved.
• The available systems in placed in routine
and reference laboratories are still the
rapid and automated system
• it still cannot address fully the issues on
proper taxonomy and relationships of
ambiguous profiles
• Time and speed of the conventional method is a major
drawback
• Immense need for an alternative biomarker gene to
augment the usage of 16S rRNA and definitely the
utilization of rpoB can be an alternative biomarker for the
accurate identification of bacteria in clinical setting
including the ambiguous ones.
• As a conclusion, the rpoB gene is an alternative
biomarker as it encodes the β-subunit of RNA
polymerase and common to all bacteria as it exist as a
single copy in the genome with highly conserved and
variable sequence.
Conclusion:
• It is not only of primary importance in the
identification of rifampin-resistant
Mycobacterium spp. but also of various
genera such as Pasteurellaceace,
Aeromonas, Acinetobacter, and
halobacteriales previously identified to
produce inaccuracy using the 16S rRNA
gene.
Conclusion:
Thank you very
much!!!