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)

HGDI6

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

Haguenoer et al. BMC Microbiology 2011 11:171   doi:10.1186/1471-2180-11-171

Open Data