Table.

Advantages and Disadvantages of Three Common Bacterial Subtyping Methods

Subtyping Method	Advantages	Disadvantages
Whole Genome Sequencing (WGS)	Analysis may be tailored for low or high discriminatory power May potentially be automated Provides phylogenetically relevant subtyping data Reproducibility likely to be high if method of data interpretation is standardized, but this requires demonstration in clinical use Typability high Data acquisition methods are applicable to any species without significant adaptation (customizing)	Expensive, but cost is falling Requires technical expertise to perform Labor intensive Requires high informatics capacity and special software Requires bioinformatics expertise, typically doctoral level, to analyze and interpret data; analytical approach must be adapted for each organism and research question Generally long turn-around time, although can be performed in days with concerted effort Currently an experimental method for outbreak investigations
Pulse Field Gel Electrophoresis (PFGE)	Current gold standard for highly discriminatory subtyping, i.e. outbreak investigations Reproducibility high if rigorously standardized Typability high Readily adapted to a variety of species, methods already well described for many species Inexpensive	Fairly labor intensive Requires expertise to interpret the data Do not produce phylogenetically relevant information
Multilocus Sequence Typing (MLST)	Used for phylogenetic subtyping Repeatability, reproducibility high Typability high	Low to moderate discriminatory power, i.e. little use in outbreak investigations Moderately expensive Labor intensive Requires expertise to interpret data Requires significant labor and expertise to adapt and validate for each species