Molecular characterization of Coxiella burnetii isolates by infrequent restriction site-PCR and MLVA typing

Arricau-Bouvery, Nathalie; Hauck, Yolande; Bejaoui, Awatef; Frangoulidis, Dimitrios; Bodier, Christelle C; Souriau, Armel; Meyer, Hermann; Neubauer, Heinrich; Rodolakis, Annie; Vergnaud, Gilles

doi:10.1186/1471-2180-6-38

BMC Microbiology

Table 3 MLVA loci and properties.

From: Molecular characterization of Coxiella burnetii isolates by infrequent restriction site-PCR and MLVA typing

	Locus name	alias^a	% matches	% G+C content	Primer sequence	Estimated size range (bp)	Unit number^a,b	No. of alleles^a	HGDI
Panel 1 markers (minisatellites, repeat unit above 9 base-pairs)	Cbu0033_ms01_16bp_4U_198bp		77	35	L: GGCTCATTCAATTTTAGCTTCG R: AACGTGGGGAAGTTTGTTATTT	182–198	3–4	2	0,47
	Cbu0448_ms03_12bp_7U_229bp		81	18	L: TTGTCGATAAATCGGGAAACTT R: CACTGGGAAAAGGAGAAAAAGA	217–229	6–7	2	0,46
	Cbu0988_ms07_126bp_8U_1112bp		69	6	L: CTCTTAGCCATCGCTTACCACT R: AACGAAAATTGGTTTGCATTTT	734–1112	5–8	4	0,42
	Cbu1316_ms12_126bp_8U_1074bp		74	12	L: GAAAATTGGTTTGCGCTCTG R: CCTTCTCCCAAGAAGTTTAGCC	570–1200	4, 7–9	4	0,67
	Cbu1941_ms20_18bp_15U_402bp		76	6	L: CTGAAACCAGTCTTCCCTCAAC R: CTTTATCTTGGCCTCGCCCTTC	384–528	14–15, 18–19, 22	6	0,7
	Cbu1963_ms21_12bp_6U_210bp		75	42	L: AGCATCTGCCTTCTCAAGTTTC R: TGGGAGGTAGAAGAAAAGATGG	210–222	5–6	2	0,37
	Cbu1980_ms22_11bp_6U_246bp		66	9	L: GGGGTTTGAACATAGCAATACC R: CAATATCTCTTTCTCCCGCATT	246–257	6–7	2	0,28
	Cbu0831_ms26_9bp_4U_127bp	Cox3	94	99	L: AGAATCAAACCTGCAAAACCTT R: TTGATTATTTTGACTTCGCTGGT	109–244	2, 4–5, 11, 13–14, 17 (2,4,13,14,16,18)^c	6	0,73
	Cbu1351_ms30_18bp_6U_215bp		63	81	L: ATTTCCTCGACATCAACGTCTT R: AGTCGATTTGGAAACGGATAAA	197–215	5–6	2	0,42
	Cbu1941_ms36_9bp_4U_447bp		80	59	L: GAAACCAGTCTTCCCTCAACAG R: ATAACCGTCATCGTCACCTTCT	474–601	7,15,17,21	4	0,55
Panel 2 markers (microsatellites, 6 or 7 bp repeat units)	Cbu0197_ms23_7bp_8U_157bp	Cox6	90	51	L: GGACAAAAATCAATAGCCCGTA R:GAAAACAGAGTTGTGTGGCTTC	122–157	3,5,8 (3,5–6,8)^c	4	0,67
	Cbu0259_ms24_7bp_27U_344bp	Cox4^d	94	46	L: ATGAAGAAAGGATGGAGGGACT R: GATAGCCTGGACAGAGGACAGT	204–344	7–13,27 (6,9,12,27)^c	8	0,79
	Cbu0838_ms27_6bp_4U_276bp	Cox2	90	99	L: TTTTGAGTAAAGGCAACCCAAT R: CAAACGTCGCACTAACTCTACG	264–282	2–5 (2–4)^c	4	0,73
	Cbu0839_ms28_6bp_6U_276bp	Cox5	94	83	L: TAGCAAAGAAATGTGAGGATCG R: ATTGAGCGAGAGAATCCGAATA	258–288	3–8 (3–7)^c	6	0,74
	Cbu1418_ms31_7bp_5U_182bp	Cox7	89	41	L: GGGCATCTAATCGAGATAATGG R: TTTGAGAAAATTTTGGGTGCTT	161–182	2–5 (idem)^c	4	0,51
	Cbu1435_ms33_7bp_9U_262bp		87	50	L: TAGGCAGAGGACAGAGGACAGT R: ATGGATTTAGCCAGCGATAAAA	227–1600	4,6–9	6	0,75
	Cbu1471_ms34_6bp_5U_210bp	Cox1	100	99	L: TGACTATCAGCGACTCGAAGAA R: TCGTGCGTTAGTGTGCTTATCT	192–252	2–5,7–12 (2,3,5,10)^c	10	0,86

^a previously described loci (and corresponding data) is indicated; ^b an uninterrupted allele range is indicated by a '-'; ^c allele size range reported by [48]; ^d Cox4 was initially reported as a 21 bp tandem repeat [48], however we observe a 7 bp repeat unit based variation, in agreement with [46]

Back to article page

ISSN: 1471-2180

Contact us

General enquiries: journalsubmissions@springernature.com