Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay

Le Flèche, Philippe; Jacques, Isabelle; Grayon, Maggy; Al Dahouk, Sascha; Bouchon, Patrick; Denoeud, France; Nöckler, Karsten; Neubauer, Heinrich; Guilloteau, Laurence A; Vergnaud, Gilles

doi:10.1186/1471-2180-6-9

BMC Microbiology

Table 2 List of tandem repeat loci investigated

From: Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay

22 tandem repeats with a predicted different length in the 3 genomes:
vntr^a	alias name^a	Chr	% ^b	upper primer	lower primer	b.suis^c	b.mel^c	b.abor^c	nb of different alleles^d	min-max bp^e	HGDI ^f
BRU1938_8bp_371bp_9u	Bruce01 or TR7	1	100	GGTCTGGGAAAACATGAAAAGC	AGCCGATCCTGCAAAACATAAT	395	371	419	12	331–435	0.95
BRU1923_339bp_787bp_3u	Bruce02	1	94	AACGCAGCATCACCAATGT	CCCAGATGTTCGGCTATAGTATG	448	787	2143	6	448–1974	0.8
BRU1627_9bp_199bp_3u	Bruce03	1	82	GGCTATTATTTCACCGGCAAGA	TCTTGATTTCCTTGCGATACCA	208	199	217	4	154–217	0.48
BRU1543_8bp_152bp_2u	Bruce04 or TR6**	1	100	CTGACGAAGGGAAGGCAATAAG	CGATCTGGAGATTATCGGGAAG	184	152	160	8	152–208	0.87
BRU1365_8bp_185bp_3u	Bruce05	1	84	AAGTATCAGGAAGGGCAGGTTC	GGGAGTAGGGGAATAAGGGAAT	193	185	201	4	185–217	0.59
BRU1322_134bp_408bp_3u	Bruce06*	1	94	ATGGGATGTGGTAGGGTAATCG	GCGTGACAATCGACTTTTTGTC	274	408	542	4	140–542	0.73
BRU1250_8bp_158bp_5u	Bruce07**	1	100	GCTGACGGGGAAGAACATCTAT	ACCCTTTTTCAGTCAAGGCAAA	166	158	150	5	150–190	0.78
BRU1134_18bp_348bp_4u	Bruce08*	1	75	ATTATTCGCAGGCTCGTGATTC	ACAGAAGGTTTTCCAGCTCGTC	330	348	366	4	312–366	0.53
BRU588_8bp_156bp_7u	Bruce09 or TR8**	1	94	GCGGATTCGTTCTTCAGTTATC	GGGAGTATGTTTTGGTTGTACATAG	140	156	124	8	124–244	0.72
BRU221_19bp_127bp_2u	Bruce10	1	90	ATCAATTCGCGGATATTTCACT	AGTGCGTTTCATATGTTTGCTG	146	127	165	2	127–146	0.26
BRU211_63bp_257bp_2u	Bruce11*	1	80	CTGTTGATCTGACCTTGCAACC	CCAGACAACAACCTACGTCCTG	509	257	383	6	257–698	0.84
BRU73_15bp_392bp_13u	Bruce12*	2	58	CGGTAAATCAATTGTCCCATGA	GCCCAAGTTCAACAGGAGTTTC	345	392	375	7	302–452	0.82
BRU19_8bp_196bp_2u	Bruce13	2	100	CGAACGATAGACCAGAACATGC	TTGAAAGAATCAGATAAGATAAAGCA	204	196	220	10	196–300	0.85
BRU18_8bp_102bp_7u	Bruce14	2	100	TTGCTTTATCTTATCTGATTCTTTCAA	GGTGTCGTTGGAGATAGAGGTC	142	102	94	11	70–214	0.93
BRU1112_264bp_346bp_1u	Bruce15	2	81	GCGGTGTTGTGTCTGTGGATA	GCCGTCAGTATCCACGTCATAG	875	346	4112	7	346–2458	0.83
BRU548_8bp_152bp_3u	Bruce16**	2	100	ACGGGAGTTTTTGTTGCTCAAT	GGCCATGTTTCCGTTGATTTAT	168	152	176	8	144–240	0.85
BRU344_5bp_110bp_3u	Bruce17	2	100	TTTTCACAGGGCATGTTCTCAG	CGCGTTTCGATTGTGGAAAATA	125	110	115	6	110–135	0.79
BRU339_8bp_146bp_5u	Bruce18**	2	87	TATGTTAGGGCAATAGGGCAGT	GATGGTTGAGAGCATTGTGAAG	138	146	154	6	130–170	0.82
BRU324_6bp_163bp_18u	Bruce19	2	59	GACGACCCGGACCATGTCT	ACTTCACCGTAACGTCGTGGAT	169	163	184	7	76–190	0.79
BRU329_8bp_148bp_7u	Bruce20 or TR4	2	100	AATACTGGGTCCAGTCCGATG	AGCGCAGCGACCATATTCT	100	148	124	ND	ND	ND
BRU329_8bp_148bp_6u	Bruce21**	2	68	CTCATGCGCAACCAAAACA	GATCTCGTGGTCGATAATCTCATT	175	148	164	3	148–175	0.57
BRU322_8bp_158bp_6u	Bruce22 or TR1	2	98	GATGAAGACGGCTATCGACTG	TAGGGGAGTATGTTTTGGTTGC	150	158	134	10	125–214	0.9
56 tandem repeats with a predicted different length in 2/3 genomes:
vntr ^a	alias name ^a	Chr	% ^b	upper primer	lower primer	b.suis ^c	b.mel ^c	b.abor ^c	nb of different alleles ^e	min-max bp ^f	*HGDI* ^g
BRU1990_9bp_152bp_1u	Bruce23	1	88	ATCAGCGAGTCGAAGGTCAGTT	TTCGACTATGCCAATCCAGATG	161	152	161	2	152–161	0.26
BRU1940_8bp_146bp_8u	Bruce24 or TR5	1	100	AGGGGAGTATGTTTTTGGTTGC	GCTACAAGATCGAAGTGCTCCA	146	146	106	10	106–217	0.88
BRU1915_8bp_215bp_2u	Bruce25 or TR3	1	100	GGGAGTATGTTTTGGTTGCACA	CTATTTCGTCCTGCCATTCGAC	239	215	239	8	215–736	0.9
BRU1704_12bp_189bp_5u	Bruce26	1	68	TCTTCATCCTGCGAGATCATGT	ATTCGTGATCGGGGTGATGAT	162	189	189	2	162–189	0.5
BRU1609_8bp_170bp_6u	Bruce27	1	76	TCGACGTCGTCTGACATTTTCT	GGGAGTAAGGCAGTAGGGGAAT	170	170	162	3	162–178	0.61
BRU1599_11bp_147bp_4u	Bruce28	1	95	TATCTTCCACGGCCATGAATC	GGCAGGATCGGCGTATAGATAA	136	147	136	2	136–147	0.1
BRU1528_15bp_132bp_3u	Bruce29	1	81	TTGCGTTATTGATTGTCAGCAC	GCTGTGGCTCGTCTATGTGG	132	132	117	2	117–132	0.47
BRU1505_8bp_151bp_6u	Bruce30 or TR2**	1	96	TGACCGCAAAACCATATCCTTC	TATGTGCAGAGCTTCATGTTCG	127	151	151	5	119–151	0.7
BRU1475_18bp_120bp_1u	Bruce31	1	100	GCTGAATCTTTTCCGCATCCT	GGAATCTCTGCACTGACAAAGC	138	120	120	2	120–138	0.51
BRU1424_8bp_106bp_5u	Bruce32	1	88	AGGTTTCCGGCGATAATGG	TCGGGATGCGCTCTAGAATATC	106	106	98	3	98–114	0.6
BRU1413_15bp_158bp_4u	Bruce33	1	81	GATGGAGCTTGGTTCCTGCTT	GCATGATCCGTTTTCTTCTCAA	143	158	143	3	128–158	0.5
BRU1409_18bp_83bp_2u	Bruce34	1	84	GCGATCGAAGGAAATATCGAG	CGCTGCCGGGATGTGAAC	101	83	101	2	83–101	0.26
BRU1282_10bp_136bp_4u	Bruce35	1	91	TGCGATAACAGGTGTACCCAAG	GACGGCAGCCATGCTGAT	116	136	116	3	116–136	0.27
BRU1234_15bp_157bp_4u	Bruce36	1	76	TAAGGCTCTTGCGTTTGTATCG	TGCGTATCTTCAGACTGGCAAT	142	157	142	2	142–157	0.38
BRU1176_21bp_124bp_2u	Bruce37	1	95	CCAAGCGTATCATCGATCTGTC	TCGGACGCAGATTGTTTCTATC	103	124	123	2	103–124	0.51
BRU1116_18bp_108bp_2u	Bruce38	1	100	CTGAATTGGGAGGAGGAACCAG	AGCTGAACGACCTTGGCATCT	126	108	108	2	108–126	ND
BRU1112_15bp_164bp_7u	Bruce39	1	66	GAAGGTCTCGAAGGAAGAGCTG	CCATCCATATTGATCGTCAGGA	164	164	146	2	146–164	0.51
BRU1048_15bp_94bp_2u	Bruce40	1	85	AAAAGAAGGGTTTCCCCATACC	GGAAAGGACAGCTTCGAGTACC	109	94	109	3	94–109	0.34
BRU1030_13bp_94bp_1u	Bruce41	1	100	TTATGTCACCGCTGACGAATTT	CTCATTATGGACCCGGTCTTTC	107	94	107	2	94–107	0.1
BRU424_125bp_539bp_4u	Bruce42*	1	96	CATCGCCTCAACTATACCGTCA	ACCGCAAAATTTACGCATCG	538	539	289	5	164–789	0.75
BRU379_12bp_182bp_2u	Bruce43*	1	69	TCTCAAGCCCGATATGGAGAAT	TATTTTCCGCCTGCCCATAAAC	170	182	182	3	170–194	0.55
BRU256_12bp_110bp_3u	Bruce44	1	96	GGCGCAAGATCGGAATGC	AGGCAGGTGCTGATTCTCCT	110	110	122	1	110	0
BRU233_18bp_151bp_3u	Bruce45*	1	70	ATCCTTGCCTCTCCCTACCAG	CGGGTAAATATCAATGGCTTGG	187	151	151	4	133–187	0.65
BRU217_15bp_256bp_4u	Bruce46	1	81	AAAAGCTTCCGAACCAAGTGTC	GGAGCTGGTTGAGCGTTATTTC	256	256	241	2	241–256	0.5
BRU149_15bp_116bp_2u	Bruce47	1	90	CTGCCAAGGGCGAGATAAAC	CATCGTTCTGATCTTCGTGACC	131	116	131	2	116–131	0.26
BRU131_29bp_131bp_2u	Bruce48	1	95	TATAAGTCCAGCCCATGACAGG	GCGGAATATCTGGATGGGATAC	131	131	160	2	131–160	0.51
BRU112_13bp_266bp_2u	Bruce49	1	97	AACCTCGGTCTATGATGCAACC	ACGCAGGGTTAGGTTTCTCAAA	279	266	265	2	266–279	0.52
BRU80_12bp_162bp_3u	Bruce50	1	75	GCAGAACCTGATGAACAACCTG	ATTTTCTGGTCGAGATCGAAGG	174	162	174	2	162–174	0.26
BRU80_15bp_74bp_2u	Bruce51	1	90	TGACATGATGCAGAAAATGCAG	GTCCCTTGCCGCCTTTCAT	74	74	89	2	74–89	0.47
BRU50_15bp_185bp_3u	Bruce52	1	95	CAATGAACCAGATCAGCTTTCG	CGCCATGGTTTCAATATCACC	170	185	170	2	170–185	0.26
BRU50_30bp_110bp_1u	Bruce53	1	70	CGGTTATGGTGTGGAGCAACT	CTTCCAGCGGGCTTTCAG	140	110	110	2	110–140	0.52
BRU28_13bp_150bp_1u	Bruce54	1	100	CCGATCACAGACACAACAACTTC	GCGAAAAGGGAGCAGACATTAT	163	150	163	2	150–163	0.26
BRU2066_40bp_273bp_3u	Bruce55*	1	80	TCAGGCTGTTTCGTCATGTCTT	AATCTGGCGTTCGAGTTGTTCT	234	273	273	5	194–354	0.69
BRU2028_12bp_135bp_4u	Bruce56	1	79	TTGGTCGTTAGAACAAGAGTGG	CTGAACCTGTTCCGTCAAATCA	135	135	123	2	123–135	0.38
BRU69_9bp_301bp_4u	Bruce57	2	90	ATGGGAGCCTATTTCGCTTACA	GGCGGTAGAATGGATAGCTCAC	292	301	292	3	283–301	0.19
BRU33_24bp_98bp_1u	Bruce58	2	82	CATCCTGCTTGGTGTTCTTTTG	GATGGTCGTCACCAAGTCCAG	122	98	122	2	98–122	0.32
BRU33_9bp_256bp_7u	Bruce59	2	78	CGTATCATCCGGCAATGGT	CTTTCTCTTTGTCGTGGGCTTC	265	256	256	2	256–265	0.38
BRU24_12bp_279bp_3u	Bruce60	2	90	AGCAAATGAATATGTCGCGTTG	TTCACCCCGATATCGATGAAT	267	279	279	2	267–279	0.38
BRU22_12bp_162bp_5u	Bruce61	2	75	CCTAATTTCGCCATTCGGTAAC	TTGCGGATTTTCCGAATAGAAC	162	162	150	2	150–162	0.5
BRU979_18bp_140bp_3u	Bruce62	2	85	CTGACGCAGGGAAGCTTTGT	GAAAGAATGGTGAGCAGCAAGA	155	140	155	2	140–155	0.26
BRU833_15bp_145bp_3u	Bruce63	2	77	AGGGTGACATTTGTTGGAGTCA	GTGGACAGACCCATGGTAAACG	160	145	145	2	145–160	0.51
BRU832_14bp_104bp_1u	Bruce64	2	93	GAGACGACGCTTGAGGTTTTTC	CTTCCGGCGCTTCTTTCTTAT	118	104	118	2	104–118	0.26
BRU824_41bp_182bp_2u	Bruce65	2	94	CGCTCTAGGCATAGCTGTTGTG	GTCCAGCCGATAACCTTGCTAT	143	182	143	1	142	0
BRU652_17bp_91bp_1u	Bruce66	2	100	ATATCCATGCGGGAAGGAAGAT	TATGCAGTGGGCATTCTCTACG	108	91	91	2	91–108	0.32
BRU609_31bp_155bp_2u	Bruce67	2	68	GCACCAGTGCGAGAAAATAGTG	AATTTTCCTTCGCGACTCCTTT	124	155	155	2	124–155	0.52
BRU564_18bp_111bp_3u	Bruce68	2	79	GACAACGATCCGCAGAAAGG	GTCAATGCCCTGATCGGTATC	111	111	93	2	93–111	0.47
BRU488_57bp_181bp_1u	Bruce69	2	100	CGATGACAGAGCAAGACCGTTA	TTGACCGATAATTCTGCAATGG	181	181	238	1	181	0
BRU339_21bp_146bp_2u	Bruce70	2	74	GAGTAAGGCGAATAGGGGGAAC	AACTCTTCTTCCGCGACAACAC	146	146	162	2	146–162	0.51
BRU337_12bp_394bp_3u	Bruce71	2	79	GAAGACGGCTATCGACTGGTCT	ACAAGCTCTATTCGCCTTACGC	370	394	370	ND	ND	ND
BRU322_8bp_230bp_8u	Bruce72	2	66	GAAGACGGCTATCGACTGGTCT	GTTTCAATGAAGGCGAGGTGAG	206	230	206	10	198–294	0.87
BRU285_28bp_178bp_3u	Bruce73	2	86	GTGGAAGGCGTTGTCATTCTG	ATCGGTCATGGTCTATCCTTCC	178	178	150	2	150–178	0.51
BRU275_8bp_147bp_6u	Bruce74	2	85	GGATGAGGATTGAGGGCTTTT	ACGCAGACGATTTAACAAAGCA	139	147	139	4	131–155	0.63
BRU250_19bp_82bp_2u	Bruce75	2	100	AGGACTATCAGGTGCGTGACAA	AAGGAAGACGTCGCTGAAAGAC	82	82	101	2	82–10	0.52
BRU181_14bp_122bp_2u	Bruce78	2	87	CTAACAAATGACGGCAGAGTGC	TTGAACGCAAGCTTATCCAAAA	136	122	136	2	122–136	0.32
BRU163_12bp_141bp_4u	Bruce79	2	65	TCCTGTTGAACGCAAGCTAATG	ATACTTCAGGCGGGGAGGAC	153	141	153	ND	ND	ND
BRU542_12bp_178bp_4u	Bruce80	2	87	CGAGGAATGTCAGGAAGATCAC	ACACAGACGCCAAAAGACAAA	166	178	166	2	166–178	0.18

* markers constituting MLVA-15 ; the 8 non-octamers (*) are panel 1, the 7 octamers (**) are panel 2
^a naming nomenclature includes repeat unit size, PCR product size in strain 16M, corresponding repeat copy number, and common name;
^b internal repeat homogeneity ; ^c expected PCR product size in each of the three sequenced genomes, Brucella suis 1330, B. melitensis 16M, B. abortus 9–941;
^d number of alleles observed in the 21 strains ; ^e observed size range ; ^f HGDI : Hunter-Gaston diversity index ; ND, not determined

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