Table 3.

Overview of methods that were used to detect mycobacterial MSIs.

Methoda	Targetb	Output or readoutc	Sample typed
Insertion sequence based RFLP	Species specific insertion sequences	Differences in restriction enzyme band hybridization patterns	Culture
Variable number tandem repeat	Species specific tandem repeat loci	Differences in copy numbers based on PCR	Specimen or culture
Whole genome sequencing	Entire genome	Heterogeneous SNPs	Specimen or culture
Spoligotyping	Direct repeat spacers (CRISPR)	Differences in spacer sequences based on hybridization	Specimen or culture
Region-specific PCR	Chromosomal targets depending on the specific method and species	Differences in PCR band patterns	Specimen or culture
Phage typinge	Lysis of colonies by mycobacteriophages	Susceptibility to a select mycobacteriophages	Culture
Pulse field gel electrophoresise	Enzymatic digestion of chromosomal DNA	Differences in restriction enzyme band patterns	Culture
pTBN12 digestione	Species specific plasmid fingerprinting	Differences in restriction enzyme band patterns	Culture
hsp65 PCR-RFLPe	hsp65 gene	Differences in restriction enzyme band patterns	Culture
Random amplified polymorphic DNAe	Species specific chromosomal DNA	Differences in PCR band patterns	Culture
Other RFLPe	Species specific DNA sequences	Differences in restriction enzyme band hybridization patterns	Specimen or culture

^aReferences for methods are present in the main text and Supplementary Table 2.

^bThe component or property of the bacterial cell analyzed by the respective methods.

^cThe result obtained for interpretation using the respective methods.

^dThe type of material that can be used for the assay. Note that all methods except for phage typing use extracted DNA for analysis.

^eMethods listed come under the “other” category in Table 2.