C
haracterization methods for bacteria
T. Mandala, P.Palitb , S. Goshamic, D.
Mukhopadhyayd, B. Bhuniad*,
a
Department of Chemical Engineering, National Institute of Technology,
Durgapur, Mahatma Gandhi Avenue, Durgapur-713209, India.
b
Dr. B.C.Roy College of Pharmacy and allied Health Sciences , Durgapur
-713206, India
c Department of Biotechnology, BIT, Meshra, Ranchi, Jharkhand 835215
d
Department of Biotechnology, BCET, Durgapur, Durgapur 713212.
Running Title:
Characterization Methods for Bacteria
* Corresponding author
E-mail: bbhunia@gmail.com
Abstract
Accurate and definitive microorganism identification, including bacterial
identification and pathogen detection, is essential for correct disease
diagnosis, treatment of infection and trace-back of disease outbreaks
associated with microbial infections. Bacterial identification is used in a
wide variety of applications including microbial forensics, criminal
investigations, bio-terrorism threats and environmental studies. So in this
review we have discussed several methods for identification of bacteria.
Keywords:
Bacteria, Phenotype , Genotype, Plasmid, Rybotype, DNA, PCR
Introduction
Traditional methods of bacterial identification rely on phenotypic
identification of the causative organism using gram staining, culture and
biochemical methods. However, these methods of bacterial identification
suffer from two major drawbacks. First, they can be used only for organisms
that can be cultivated in vitro. Second, some strains exhibit unique
biochemical characteristics that do not fit into patterns that have been
used as a characteristic of any known genus and species. In the past decade
or so, molecular techniques have proven beneficial in overcoming some
limitations of traditional phenotypic procedures for the detection and
characterization of bacterial phenotypes (Cullimore, 2000; Barrow and
Feltham, 2004).
Through the early part of the twenty-first century, there appeared to be a
general feeling that the same observations and tests could be used to
characterize and identify any kind of bacterium. But as different, "exotic"
types of bacteria were discovered, it was found that they would tend not to
grow in the standard test media nor even in the usual conditions of
incubation. Obligate parasites and strict anaerobes were among the emerging
groups of bacteria needing special methods for growth and characterization
(Cullimore, 2000; Barrow and Feltham, 2004). By the 1930s, a standard
descriptive chart was developed for uniformity in recording the
characteristics of the "aerobic saprophytes" (which are equivalent to what
we call the "commonly-found" or "easy-to-grow" chemoheterotrophs in our
general courses today).
Morphological Methods
In identifying bacteria, the morphological features are of importance in
that they constitute the first step in characterization. The form,
diameter, elevation and margin of colonies, pigment formation can be
observed directly. Cellular morphology, Gram status, sporulation and
motility of an isolate can be determined by microscope after different
staining methods. Phase contrast microscopy is also used to determine spore
presence and cellular morphology without staining.
Phenotypic Methods
Phenotypic methods include biotyping, antibiogram, phage typing,
serotyping, PAGE/immunoblotting and multilocus enzyme electrophoresis
(MLEE). In biotyping an organism can be identified and classified at the
genus and/or species level using various biochemical reagents and
parameters. Antibiogram includes the analysis of the growth of strain in
the presence of antibiotic. However it is not very discriminatory and for
example antibiogram patterns can change with transformation of plasmids
(Busch and Nitschko, 1999). In phage typing, a particular bacterium is
infected by a specific phage. Thus, the isolates can be differentiated
based on the infection capability. Serotyping involves identification of
microorganisms according to their reaction to a given antiserum. Proteins
from whole-cell lysate can be separated by SDS-PAGE. Protein patterns are
used in classification of strains (Busch and Nitschko, 1999).
Genotypic Methods
Genotypic methods are based on DNA analysis of chromosomal or
extrachromosomal (plasmid) genetic material. The main advantages can be
summarized as follows: - They are able to distinguish between two closely
related strains: High discriminatory power. - All strains are typeable
since it is always possible to extract DNA from bacteria - Analytical
strategies can be applied to DNA of any source since it is always possible
to extract DNA from bacteria. - The composition of DNA is not affected by
cultural conditions or preparation methods. - Resulting data can be
analyzed statistically (Farber, 1996). Genotypic methods include plasmid
typing, pulse-field gel electrophoresis, ribotyping, polymerase chain
reaction based methods, nucleotide sequencing, DNA-DNA hybridization
(Farber, 1996, Goodfellow, 2000). Some of these methods were summarized
below.
Plasmid Typing
Plasmids are self-replicating, extra chromosomal, usually supercoiled
genetic elements (Bush and Nitschko, 1999, Farber, 1996). Plasmids
generally encodes for products and/or functions which modify the phenotype
of the cell. In plasmid typing, plasmids are isolated from bacterial
strains, then their number and size are determined by gel electrophoresis.
However different plasmids can be of the same size. Using restriction
enzymes, this problem can be solved. Different plasmids will give different
fragment patterns (Farber, 1996). The main drawback of the method is the
transfer of plasmid between strains and species
Chromosomal DNA Restriction Endonuclease Analysis
In this method, DNA is cut with a frequent-cutting restriction enzyme and
the fragments are electrophoresed on agarose gel. A difference in fragment
patterns between isolates is referred to restriction fragment length
polymorphism (RFLP). Different patterns are due to DNA composition
variations. This method is rapid, inexpensive, relatively easy to perform
and universally applicable. But interpretation of fragment pattern is not
easy since numerous fragments are obtained and they are closely spaced on
agarose. In order to obtain interpretable results, several restriction
enzymes must be used.
Ribotyping
Ribotyping is based on the use of nucleic acid probes to recognize
ribosomal genes. In a prokaryotic ribosome there are three types of RNA
(23S, 16S and 5S rRNA). The genes coding for rRNA sequences are highly
conserved and multiple copies of the rRNA operon exist in most bacteria.
Thus, chromosomal fragments containing a ribosomal gene are revealed after
hybridization with probes. Resulting hybridization bands (approximately 1
to 15) are compared between isolates. Ribotyping refers to the grouping of
bacteria based on this method.
PCR-Based Methods
PCR is based on the amplification of DNA by a heat stable DNA polymerase
enzyme. Depending on the special primer used, the region of interest is
amplified. Reaction includes repeated cycles of high temperature for
denaturation of the DNA, oligonucleotide (primer) annealing and an
extension step mediated by thermostable DNA polymerase. Amplification cycle
is repeated 25-35 times to produce a >106 fold amplification of the
target DNA. The amount of the target DNA is exponentially increased.
PCR-Ribotyping
In a prokaryotic ribosome genes coding for rRNA are separated by spacer
regions which are variable in length or sequence at both the genus and
species level (Farber, 21 1996). Thus, multiple bands are obtained after
amplification of spacer regions in different rRNA coding operons for a
particular strain. Besides, spacer region between 16S-23S rRNA or 23S-5S
can be amplified and amplification products can be compared on agarose gel.
In this method, availability of universal primers is the major advantage.
Sequence variation between ribosomal operons, described especially in the
ISR between the 16S and 23S rDNA genes in individual strains (Gürtler and
Stanisich, 1996), has been used for bacterial identification (Jensen et al., 1993, Tilsala-Timisjarvi and Alatossava, 1997). Ribosomal
internal spacer regions have been found to be more variable than 16S and
23S rDNA between bacterial species (Barry et al., 1997). For
example, closely related species B. subtilis andB. atrophaeus have been differentiated by comparing ISRs (Nagpal et al., 1998). Flint et al. (2001) have shown that ISR
sequences have varied in length among the different lactic acid bacterial
species and have varied also within some strains of the same species.
LH-PCR (Length Heterogeneity Analysis of Polymerase Chain Reaction
Amplified DNA)
This method is based on the natural length variation within 16S rDNA genes.
The variable region is amplified by PCR with fluorescently labeled
universal primers that recognize the region in all eubacteria (Tiirola et al., 2003).
PCR-RFLP
In this method PCR amplicons are digested with suitable restriction
enzymes. Digested amplicon is run onto an agarose gel and DNA fingerprint
results are obtained. 16S, 23S and 16S-23S rRNA spacer regions have been
used for locus specific RFLP (Olive and Bean, 1999, Caccamo, 2001).
Genomic DNA Based RFLP
PFGE (Pulse Field Gel Electrophoresis) is a very discriminating and
reproducible typing method. In this method, intact cells are embedded in
agarose plugs to 22 prevent the shearing of DNA during DNA extraction.
Then, these plugs are treated with detergent and enzymes to isolate the
DNA. In the following step, the isolated DNA is cut with an infrequently
cutting restriction endonuclease which recognizes specific 8-base cutter or
6-base cutter sequences. These enzymes are chosen depending on the G+C
content of the bacterial genome. After digestion, very large DNA fragments
(10-800 kb) are obtained. Bacterial plugs are inserted into agarose gel and
they are subjected to electrophoresis. In PFGE system the electrical field
is alternated at predetermined intervals. At these intervals, called switch
time or pulse time, the direction of electrical field is changed.
Consequently, the separation of high molecular weight DNA fragments is
performed. Agarose concentration, buffer concentration, pulse times,
voltage and electrophoresis run time are important parameters which affect
the separation of fragments (Olive and Bean, 1999, Busch and Nitschko,
1999, Farber, 1996 ).
DNA Sequencing
In this method, the nucleotide composition of a DNA molecule is determined.
Generally the 16S rRNA gene or the 16S rRNA is sequenced because they
contain variable and conserved regions within bacterial species. Besides,
sequencing of whole genome is not practical. Evolutionary trees are
constructed based on 16S rRNA.
DNA-DNA Hybridization
Denatured complementary strands of DNA can reassociate to form native
duplexes under suitable experimental conditions. Nucleic acid fragments are
paired according to the similar linear arrangements of the bases along the
DNA. Nucleotide sequence similarity between bacterial strains can be
detected by measuring the amount of molecular hybrid and its thermal
stability (Goodfellow, 2000). Microbial species are extensively delineated
using DNA-DNA relatedness data (Stackebrandt and Goebel, 1994).
Conclusion
In this review we report a comparative study between conventional and
unconventional identification methods for bacterial identification in the
Clinical Microbiology Laboratory. Bacterial clinical isolates
identification obtained by DNA sequencing shows excellent correlation with
identification obtained by conventional microbiological methods. Moreover,
DNA sequencing allows the identification of bacteria from colonies grown on
agar culture plates in just a few minutes, with a very simple methodology
and hardly any consumable costs, although the financial costs of this
experiment can be high.
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