Allele distribution and genetic diversity of VNTR loci in Salmonella enterica serotype Enteritidis isolates from different sources

Table 2 VNTR loci on the genome of S. Enteritidis

Locus (alias)	Dye labeled	Primer sequences (5'-3')	PCR set	Conc. (uM)	Location (size)^b; gene	Repeats size (bp)	No. repeats^c	Reference
SE1	D3	F – AGACGTGGCAAGGAACAGTAG			LK5 Contig 1680_10.15
		R – CCAGCCATCCATACCAAGAC	A	0.10	283–549 (267 bp)	7	5	[15]
SE3	D2	F – CAACAAAACAACAGCAGCAT			LK5 Contig 1921_10.15
		R – GGGAAACGGTAATCAGAAAGT	A	0.10	537–856 (320 bp)	12	4	[15]
SE8	D2	F – TTGCCGCATAGCAGCAGAAGT			PT4
		R – GCCTGAACACGCTTTTTAATAGGCT	A	0.15	2812703–2813171 (469 bp)	87	1	[15]
SE10^a(STTR1)	D4	F – GCTGAAGAAGCGGCAAAAC			PT4
		R – GTACCGCTATCTTTCGATGGC	A	0.05	774231–774760 (530 bp); SEN0697	45	8	[15, 27]
SE2	D4	F – CTTCGGATTATACCTGGATTG			LK5 Contig 1930_10.15
		R – TGGACGGAGGCGATAG	B	0.05	906–1106 (201 bp)	7	5	[15]
SE5 (STTR5, Sal16)	D2	F – CGGGAAACCACCATCAC			PT4
		R – CAGGCCGAACAGCAGGAT	B	0.10	3073216–3073427 (212 bp); SEN2867	6	12	[15, 27, 28]
SE6^a(STTR3, 3629542)	D3	F – CGGTGGCGGAGATTCTAATCA			PT4
		R – ACGCCGTTGCTGAAGGTAAT	B	0.10	3510975–3511412 (438 bp); SEN3305	33	11	[15, 27, 29]
SE7	D4	F – CCGACCCAATAAGGAG			LK5 Contig 1168_10.15
		R – CTTACCGTTGGTAGTTTGTTA	B	0.03	323–867 (545 bp)	61	8	[13, 15]
SE9	D2	F – CGTAGCCAATCAGATTCATCCCGCG			PT4
		R – TTTGAAACGGGGTGTGGCGCTG	B	0.10	533132–533460 (329 bp); SEN0475	9	3	[15]

^a: Primer sets were redesigned in this study to remove non-specific PCR amplicons when multiplex PCR is applied.
Repeats sequences for locus SE6: TCGTCATCGCCGCTATCGTCGGGCGGGGTTACA
Repeats sequences for locus SE10: TTCGGCATCCGCTTTCTTCTTCGCGTCCGCCGCCGCTTTCGCCGC
^b: The locations were based on the genome sequences of Salmonella enterica serovar Enteritidis LK5 http://www.salmonella.org/genomics/sen.dbs and PT4 http://xbase.bham.ac.uk/colibase strains
^c: Alignment parameters chosen to weight for match, mismatch and indels were 2.3.5 or 2.5.5 which is more permissive than other options http://tandem.bu.edu/trf/trf.html. Repeat numbers for locus SE7 were counted manually due to imperfect repeat sequences. Repeat numbers for all loci are rounded to the nearest integer. For example, repeat number at locus SE7 in LK5 strain was rounded from 7.5 to 8.

ISSN: 1471-2180