As mentioned, comparing the complete sequence of entire genomes will reveal any and all genetic differences between the organisms compared. Mul-tilocus sequence typing (MLST) is a technique that can be used to compare microorganisms based on the DNA sequence of a set of genes rather than a single gene. This technique is usually used to compare microorganisms based on the sequences of conserved "housekeeping" genes (i.e., genes that are always expressed in the organism because they are essential for life functions).23 This technique incorporates a PCR step to amplify the target regions to produce enough DNA for accurate sequencing.23 Entire gene sequences can be examined, but generally only portions of the genes (some of which can be quite large) are sequenced and compared. MLST has been used in typing many bacterial pathogens of epidemiologic significance including Neisseria meningitidis, Listeria monocytogenes, Eschericia coli O157:H7, and antibiotic-resistant strains of Staphylococcus aureus.23-26
Some advantages of MLST include a high degree of reproducibility between laboratories, the easy portability of sequence data between laboratories, and the ability to tailor the technique to examine nearly any set of genes for comparison. A major disadvantage of this technique becomes obvious when MLST is used to type genetically monomorphic microorganisms. For organisms such as Bacillus anthracis whose strains show very little genetic variability, it is very difficult to differentiate between isolates. In such strains, housekeeping genes and most other genes often show little or no variability, and, thus, other targets will need to be selected.14,27 Another disadvantage to MLST arises from the possible introduction of bias when selecting genes to sequence, and even the region of a gene selected may not turn out to be the best choice, because the selected region may be less variable than other regions of the gene.
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