TABLE 1.

Summary amended MTC PCR typing panel results^a

MTC species	PCR-targeted locus [no. in profile]b
	16S rRNAc [1]	cfp32 (Rv0577) [2]	MiD3 (IS1561′) [3]	RD4 (Rv1510) [4]	RD7 (Rv1970) [5]	RD1 (Rv3877 to Rv3878) [6]	RD9d (Rv2073c) [7]	RD12 (Rv3120) [8]	General profilee
“M. canettii” (n = 5)	+	+	+	+	+	+	+	−f	1234567•
“Ancestral” M. tuberculosis [PGG1b] (n = 6)	+	+	+	+	+g	+	+	+	12345678
“Modern” M. tuberculosis (PGG1b) (n = 14)	+	+	+	+	+	+h	+	+	12345678
“Modern” M. tuberculosis (PGG2) (n = 19)i	+	+	+j	+	+	+k	+	+	12345678
“Modern” M. tuberculosis (PGG3) (n = 5)	+	+	+	+	+	+	+	+	12345678
M. africanum subtype Ib (n = 12)	+	+l	+	+	+	+	−m	+	123456•8
M. africanum subtype Ia (n = 18)	+	+	+	+	−	+	−	+	1234•6•8
Dassie bacillus (n = 4)	+	+	+	+	−	−n	−	+	1234•••8
Oryx bacillus (n = 2)	+	+	+	+	−	+	−	+	1234•6•8
M. microti (n = 10)	+	+	−o	+	−	+	−	+	12•4•6•8
M. pinnipedii (n = 7)	+	+	−o	+	−	+	−	+	12•4•6•8
M. caprae (n = 1)	+	+	+	+	−	+	−	−	1234•6••
M. bovis (n = 14)	+	+	+	−	−	+	−	−	123••6••
M. bovis BCG (n = 8)	+	+	+	−	−	−o	−	−	123•••••

^aIncludes strains previously described (38) as well as strains evaluated herein for the first time.

^bBased upon the presence of (+) or a failure to amplify (−) a PCR fragment of the expected size; confirmatory PCR amplification of secondary targets from all strains (n = 125) was also performed as previously described for the loci MiD3, RD4, RD1, and RD9 (38), and the results were coincident with those of the primary targets (data not shown).

^cIn addition to this gene, all MTC strains (n = 125) also amplified for the genetic elements hsp65, rpoB, IS1081, mpb70, gyrA, gyrB, katG, oxyR′, pncA, and Rv0911.

^dThe locus introduced to expand the MTC PCR typing panel (38).

^eBased upon the presence or absence of a PCR fragment for each numerically assigned locus; not included are the isolates with independent overlapping strain-specific LSPs.

^fAs a result of RD^can.

^gAs an exception, M. tuberculosis strain CA-74 failed to amplify; resulting profile, 1234•678.

^hAn alternate RD1 target amplicon (Rv3879c; 1,000 bp) was truncated by 57 bp (943 bp) in M. tuberculosis strains 97-803, 97-1177, and 97-1438.

ⁱIncludes Uganda genotype M. tuberculosis strains (n = 4).

^jAs exceptions, M. tuberculosis strains 94-1055, 2002-1330, 2002-1384, and Percy47 failed to amplify; resulting profile, 12•45678.

^kM. tuberculosis strain CA-56 failed to amplify for an alternate RD1 target amplicon (Rv3879c) because of the RD1^tbA LSP (62).

^lAs an exception, M. africanum subtype Ib strain Percy13 failed to amplify; resulting profile, 1•3456•8.

^mFailure to amplify from M. africanum subtype Ib strain 15082 was supported by a flanking PCR that produced a bridge amplicon of the predicted size.

ⁿAs a result of RD1^das; the alternate RD1 target amplicon (Rv3879c) was PCR positive.

^oFailure to amplify was supported by a flanking PCR that produced a bridge amplicon of the predicted size.