Multilocus variable-number tandem repeat analysis for molecular typing and phylogenetic analysis of Shigella flexneri

Wang, You-Wun; Watanabe, Haruo; Phung, Dac Cam; Tung, Sheng Kai; Lee, Yeong-Sheng; Terajima, Jun; Liang, Shiu-Yun; Chiou, Chien-Shun

doi:10.1186/1471-2180-9-278

Table 1 Allelic diversity of VNTR loci in various serotype groups.

From: Multilocus variable-number tandem repeat analysis for molecular typing and phylogenetic analysis of Shigella flexneri

VNTR locus (alias)^a	Range of copy number^b	Typability^c (%)	Allele diversity for serotype group:
			1a/1b/NT (n = 12)	2a/2b/X/NT (106)	3a/3b (n = 12)	4a/4b/Y (110)	6 (n = 2)	Total (n = 242)
SF1	N, 1-4	49.6	0.50	0.02	0.64	0.02	0.00	0.55
SF2 (ms09)	1-3, 283	100.0	0.15	0.04	0.28	0.31	0.00	0.52
SF3 (O157-11)	2-18	100.0	0.75	0.78	0.72	0.60	0.00	0.77
SF4	1-12	100.0	0.65	0.69	0.65	0.00	0.00	0.70
SF5	N, 1-3, 155, 161	99.2	0.00	0.16	0.57	0.00	0.00	0.62
SF6	N, 2-19	54.1	0.61	0.87	0.00	0.02	0.00	0.76
SF7	2-12	100.0	0.00	0.66	0.00	0.00	0.50	0.63
SF8 (ms22)	2-8	100.0	0.00	0.57	0.00	0.00	0.00	0.65
SF9	1-9	100.0	0.57	0.63	0.00	0.07	0.00	0.60
SF10	1-6	100.0	0.00	0.32	0.00	0.02	0.00	0.61
SF11 (ms25)	1-3	100.0	0.00	0.48	0.61	0.00	0.00	0.62
SF12 (ms07)	2-8, 389	100.0	0.00	0.00	0.50	0.05	0.00	0.54
SF13	1-3	100.0	0.00	0.39	0.00	0.00	0.00	0.44
SF14	N, 1-3	94.2	0.15	0.04	0.40	0.00	0.00	0.56
SF15	1-2	100.0	0.00	0.04	0.00	0.00	0.00	0.49
SF16	1-2	100.0	0.00	0.00	0.50	0.00	0.00	0.50
SF17	1-2	100.0	0.00	0.42	0.00	0.02	0.00	0.43
SF19	1-2	100.0	0.00	0.00	0.50	0.04	0.00	0.50
SF20	2-3	100.0	0.00	0.00	0.00	0.00	0.00	0.02
SF21	N, 1-2	97.1	0.00	0.07	0.57	0.00	0.00	0.22
SF22 (ms21)	1-4	100.0	0.00	0.11	0.00	0.07	0.00	0.54
SF23	N, 2-3	54.5	0.00	0.00	0.15	0.04	0.50	0.55
SF24	3-4, 241, 258	100.0	0.00	0.02	0.50	0.02	0.00	0.53
SF25	2-11	100.0	0.00	0.00	0.79	0.02	0.00	0.10
SF26	N, 1-3	47.9	0.44	0.20	0.28	0.00	0.00	0.57
SF27	2-4, 241	100.0	0.40	0.48	0.50	0.00	0.00	0.62
SF28	1-2	100.0	0.00	0.00	0.00	0.00	0.00	0.50
SF29	3-4	100.0	0.00	0.00	0.49	0.00	0.00	0.50
SF30	2-3	100.0	0.00	0.02	0.00	0.00	0.00	0.49
SF31	2-11	100.0	0.00	0.00	0.63	0.00	0.00	0.05
SF32	1-2	100.0	0.00	0.02	0.00	0.00	0.00	0.49
SF33 (ms06)	2-4	100.0	0.00	0.11	0.00	0.00	0.00	0.15
SF34	1-3	100.0	0.00	0.48	0.00	0.00	0.00	0.49
SF35	2-3	100.0	0.00	0.00	0.00	0.00	0.00	0.50
SF36	N, 1-2	97.1	0.00	0.02	0.57	0.00	0.50	0.53
SF37	1-2	100.0	0.00	0.02	0.00	0.00	0.00	0.49

^aAlias loci described by Gorgé et al. [21] and by Keys et al. [25]
^bAlleles with numbers greater than 100 contain an imperfect copy due to deletion or insertion and are reported instead as the lengths (in bp) of amplicons.
^cTypability % = (number of isolates with PCR amplicon/number of isolates analyzed) × 100.

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