TABLE 1.

Comparison of available molecular epidemiology tools for M. tuberculosis

Method	Attributes	Strengths	Weaknesses
Spoligotyping	May be used directly on clinical samples or early cultures	Low DNA concentration required	Less discriminatory than other genotyping methods
	Rapid initial PCR amplification step	Short turnaround time	False clustering
	Involves probe hybridization	Objective and reproducible results	Unable to resolve transmission events within outbreaks
	Numerical results	Fingerprint defined with a numerical code, which facilitates comparisons	Interrogates only a small fraction of the entire genome
IS6110-based RFLP analysis	Cultured isolates are required to obtain sufficient DNA for RFLP analysis	High discriminatory power	High DNA concentration required
	Restriction digestion followed by gel electrophoresis and blot transfer		Banding pattern may be difficult to interpret and standardize
	Hybridization of IS6110-specific probe		Technically demanding and has a long turnaround time
	Generates a band pattern fingerprint		Not suitable for strains with no or low-copy-number IS6110
			False clustering
			Unable to resolve transmission events within outbreaks
			Interrogates only a small fraction of the entire genome
15- and 24-locus MIRU-VNTR analyses	Require cultured isolates	Low DNA concentration required	Interpretation of unexpected fragment sizes is challenging
	Rapid initial PCR amplification step	Short turnaround time	False clustering
	Fragment lengths can be resolved using gel or capillary electrophoresis systems	Objective and reproducible results	Unable to resolve transmission events within outbreaks
		Medium-high discriminatory power (less than that of IS6110-RFLP assay)	Interrogate only a small fraction of the entire genome
		Fingerprint defined with a numerical code, which facilitates comparisons
WGS	Currently requires culturea	Superior tool for resolving transmission dynamics	Technically demanding for sample preparation and data analysis
	Fragmentation of genomic DNA followed by addition of sequencing adapters	Interrogates 100% (or close to 100%) of the genome	Not globally available due to higher costs
	Desktop-sized sequencers perform sequencing by synthesis	Yields information about virulence factors, antibiotic resistance, and epidemiology	No standardized methods for data analysis and data sharing
	Data analysis requires bioinformatics expertise		Current methods have long turnaround times

^aNewer sequencing technologies may be able to generate whole-genome sequences without culture.