Table 3.

RD4 mapping and genotypes of 12 representative M. caprae isolates from southern Bavaria and accession numbers of amplified gyrB and RD4 deletion-adjacent sequences

Isolate no.	PCR result		Accession no.		Genotyping		Type
	RD4 internal left portion	RD4 internal central portion	Amplified gyrB sequencea	RD4 deletion-adjacent sequence	MIRU-VNTR codeb	Spoligotypec
11/D028	−	+		d	2364212535222534133363322	SB2174	Karwendel
10/RW079	−	+	JX420304	KC007398d,e	2364212535222534133363322	SB2174	Karwendel
V-09-425	−	+		d	2364212535222534133363322	SB2174	Karwendel
11/D133	−	+		d	2364212535222534133363322	SB2174	Karwendel
V-09-274	−	−		JX420311	2264242433224534132553323	SB0418	Lechtal
11/D102	−	−	JX308291	JX420308	2264242433224534132553323	SB0418	Lechtal
11/Roe010	−	−	JX420306	JX420309	2264242433224534132553323	SB0418	Lechtal
12/Rd52799	−	−	JX420307	JX420310	2264242433224534132553323	SB0418	Lechtal
09/RW044	+	+	JX420305		2354242534224534122243322	SB0418	Allgäu
10/RW314	+	+	JX420303		2354242534224534122243322	SB0418	Allgäu
11/Rd152461	+	+			2354242534224534122243322	SB0418	Allgäu
D6431	+	+			2354242534224534122243322	SB0418	Allgäu

^aIn addition to the GenoType MTBC assay, sequences provide information about the SNPs in the gyrB gene.

^bCopy numbers in loci MIRU2-4-10-16-20-23-24-26-27-31-39-40 and VNTR424-577-1982-2401-3690-4156-1955-2163b-2165-2347-2461-3171-4052. Copy numbers differing from the Lechtal genotype are in bold type.

^cAccording to www.mbovis.org.

^dA 700-bp fragment was obtained, but the nucleotide sequence could not be determined because of high guanine-cytosine content.

^eResults from contig sequences in the next-generation sequencing of the 2.5-kb PCR approach produced a 2,224-bp fragment spanning the 5-kb deletion.