TABLE 2.

Species-specific and nucleotide-sequencing PCR primers used in study

Specificity and primer name	Sequence (5′ to 3′)a	Position	PCR annealing temperature (°C)	Product size
Universal 16S rDNA primer
UNI2	GACTCCTACGGGAGGCAGCAG	336–356b	60	1,020 bpc
UNI5a	CTGATCCGCGATTACTAGCGATTC	1337–1360b
B. cepacia complex recA
BCR1	TGACCGCCGAGAAGAGCAA	2–20d	58	1,043 bpd
BCR2a	CTCTTCTTCGTCCATCGCCTC	1044–1024d
recA sequencing primers
BCR3	GTCGCAGGCGCTGCGCAA	513–530d	58	532 bp,d 3′ half of B. cepacia complex recA gene in combination with primer BCR2
BCR4a	GCGCAGCGCCTGCGACAT	528–511d	58	527 bp,d 5′ half of B. cepacia complex recA gene in combination with primer BCR1
B. cepacia genomovar I
BCRG11	CAGGTCGTCTCCACGGGT	112–129e	62	492 bpe
BCRG12a	CACGCCGATCTTCATACGA	603–585e
B. multivorans (Bm)
BCRBM1	CGGCGTCAACGTGCCGGAT	321–339d	62	714 bpd
BCRBM2a	TCCATCGCCTCGGCTTCGT	1034–1016d
B. cepacia genomovar III-A
BCRG3A1	GCTCGACGTTCAATATGCC	294–309f	62	378 bpf
BCRG3A2a	TCGAGACGCACCGACGAG	671–654f
B. cepacia genomovar III, RG-B
BCRG3B1	GCTGCAAGTCATCGCTGAA	228–246g	60	781 bpg
BCRG3B2a	TACGCCATCGGGCATGCT	1008–991g
B. cepacia genomovar IV, RG-4
BCRG41	ACCGGCGAGCAGGCGCTT	361–378h	64	647 bph
BCRG42a	ACGCCATCGGGCATGGCA	100–990h
B. vietnamiensis, RG-BV
BCRBV1	GGGCGACGGCGACGTGAA	84–101i	62	378 bpi
BCRBV2a	TCGGCCTTCGGCACCAGT	461–444i

^aBase positions in primer sequence which were mismatched in other genomovars are underlined. 

^bPosition in relation to Escherichia coli 16S rRNA gene (GenBank accession number J01859). 

^cSize in relation to B. cepacia 16S rRNA gene (GenBank accession number X87275). 

^dSize and position in relation to B. multivorans ATCC 17616 recA sequence U70431. 

^eSize and position in relation to B. cepacia genomovar I strain ATCC 17759 recA (Table 1). 

^fSize and position in relation to B. cepacia genomovar III-A strain K56-2 recA (Table 1). 

^gSize and position in relation to B. cepacia genomovar III-B strain C1394 recA (Table 1). 

^hSize and position in relation to B. stabilis strain LMG14291 recA (Table 1). 

ⁱSize and position in relation to B. vietnamiensis strain C2822 recA (Table 1).