A multi locus variable number of tandem repeat analysis (MLVA) scheme for Streptococcus agalactiae genotyping

BMC Microbiology

Table 1 Characteristics of the 6 VNTR loci selected for MLVA scheme to genotype the 186 strains of S. agalactiae

VNTR¹	Repeat size bp²	Putative function³	Expected number of repeats⁴			PCR product bp⁵	Number of alleles	min-max size of amplicons (bp)	HGDI ⁶
			2603 V/R	A909	NEM316
SAG2_32pb_244pb_3U	32	Non-cds⁷	3	3	3	244	3	212 - 276	0.474 [0.427 - 0.522]
SAG3_24pb_126pb_2U	24	Protein DnaJ	3	2	3	126	2	126 - 150	0.481 [0.452 - 0.511]
SAG4_60pb_114pb_1U (SATR1)*	60	Hypothetical protein	3	1	1	114	6	114 - 414	0.713 [0.691 - 0.735]
SAG7_18pb_285pb_8U (SATR2)*	18	Hypothetical protein	6	8	-	285	9	231-573	0.745 [0.701 - 0.789]
SAG21_48pb_783pb_14U (SATR5)*	48	FbsA	-	14	18	783	26	117 - ≈2000	0.893 [0.867 - 0.919]
SAG22_159pb_928pb_5U	159	Hypothetical protein	2	5	2	928	7	292 - 1246	0.713 [0.666 - 0.761]

¹, Tandem repeat locus name defined as follows: common name_size of the repeat sequence_size of the amplicon for the A909 reference strain_corresponding number of repeats
², Size of the repeat sequence
³, Putative function of the open reading frame concerned
⁴, 2603 V/R, A909 and NEM316 number of repeats (-: lack of VNTR)
⁵, Expected size of PCR product for the A909 reference strain
⁶, HGDI: Hunter and Gaston's diversity index, 95% confidence intervals are noted in brackets
7, 69 bp upstream from the ribosomal protein S10 sequence
*, Locus name described by Radtke

ISSN: 1471-2180