Several molecular techniques has been introduced recently for the differentiation of
microbial isolates: plasmid profiles, restriction fragment length polymorphism of
chromosomal DNA or plasmids, ribotyping, arbitrarily primed PCR, pulsed-field gel
electrophoresis(PFGE), and phylogenetic analysis. Molecular strain typing became an
essential tool for epidemiological investigation. And conventional serotyping or phage
typing methods are so time-consuming and labor-intensive that molecular fingerprinting
methods are used as a substitute. Clinical microbiology laboratory cannot help doing
strain typing for infection prevention and control, and should make a good choice among
them in respect of efficiency and cost effectiveness.
PFGE, compared with other methods, can provide a high level of discrimination and is
used as a method of choice for strain typing of a wide variety of organisms. For
example, bacteriophage typing is not used but PFGE is recommended for the
classification of methicillin-resistant Staphylococcus aureus isolates. Results are
reproducible and easy to interpret. Guideline has been proposed for evaluating whether
PFGE patters represent the same or different strains. But other genotyping methods
such as plasmid profiles or arbitrarily primed PCR occasionally may be useful for
further evaluation of isolates. The major disadvantage is that the method is more
complicated and expensive than other genotyping methods.
The introduction of diagnostic procedures based on nucleic acid sequences, in
particular PCR, has recently increased the need for precise classification of
microorganisms in accordance with their molecular characteristics. Statistical methods in
molecular phylogenetics have been developed and amenable to use in the clinical
microbiology laboratory for the classification of some microorganisms. Currently used
methods such as neighbor joining, minimum evolution, likelihood, and parsimony methods
produce reasonably good phylogenetic trees when a sufficiently large number of
nucleotides or amino acids are used. For example, clinically significant serotypes of
enteroviruses, which are presently composed of 67 individual serotypes and distinguished
on the basis of the neutralization tests with restricted amount of antisera, can be
identified by the phylogenetic approach based on RT-PCR and nucleotide sequencing of
the 3' half of genomic region encoding VP 1.
In the near future, the number of microorganisms available for molecular strain typing
will be increased and the molecular techniques for strain typing will be a routine test in
clinical microbiology laboratory. It is essential to keep a close communication between
the clinical microbiology laboratory and the hospital epidemiologists for the efficient and
appropriate use of molecular strain typing results.
|