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Table 5 Allelic profiles of the 33 Francisella isolates used in the study.

From: Multiple-locus, variable number of tandem repeat analysis (MLVA) of the fish-pathogen Francisella noatunensis

Allelic profile

Strain name

Fnn-VNTR1

Fnn-VNTR2

Fnn-VNTR3

Fnn-VNTR4

Fnn-VNTR5

Fnn-VNTR6

Fnn-VNTR7

 

F. noatunensis ssp. Noatunensis

 

FnnUA2660A

NA

392nt - 33r

212nt - 10r

335nt - 14br

285nt - 2r

307nt - 12hr

405nt - 2ir

I

FnnR-001 -04 (GM2212) T

211nt - 7r

217nt - 8r

212nt - 10r

311nt - 10r

312nt - 5r

301nt - 10er

435nt - 5r

I

FnnR-002 - 06

211nt - 7r

217nt -8r

212nt - 10r

311nt - 10r

312nt - 5r

301nt - 10er

435nt - 5r

I

FnnR-004 - 06

211nt - 7r

217nt - 8r

212nt - 10r

311nt - 10r

312nt - 5r

301nt - 10er

435nt - 5r

I

FnnR-017 - 05

211nt - 7r

217nt - 8r

212nt - 10r

311nt - 10r

312nt - 5r

301nt - 10er

435nt - 5r

I

FnnMR-005 - 06

211nt - 7r

217nt - 8r

212nt - 10r

311nt - 10r

312nt - 5r

301nt - 10er

435nt - 5r

I

FnnMR-011 - 07

211nt - 7r

217nt -8r

212nt - 10r

311nt - 10r

312nt - 5r

301nt - 10er

435nt - 5r

I

FnnSF-012 - 07

211nt - 7r

217nt - 8r

212nt - 10r

311nt - 10r

312nt - 5r

301nt - 10er

435nt - 5r

I

FnnMR-013 - 07

211nt - 7r

217nt - 8r

212nt - 10r

311nt - 10r

312nt - 5r

301nt - 10er

435nt - 5r

II

FnnR-003 - 06W

211nt - 7r

217nt - 8r

207nt - 9r

311nt - 10r

312nt - 5r

301nt - 10er

435nt - 5r

II

FnnN-006 - 06

211nt - 7r

217nt - 8r

207nt - 9r

311nt - 10r

312nt - 5r

301nt - 10er

435nt- 5r

III

FnnH-007 - 06 F

219nt - 8r

259nt - 14r

202nt - 8r

341nt - 15r

312nt - 5r

301nt - 10er

430nt - 4r

III

NCIMB 14265T

219nt - 8r

259nt - 14r

202nt - 8r

341nt - 15r

312nt - 5r

301nt - 10er

430nt - 4r

III

FnnH-014 - 06F

219nt - 8r

259nt - 14r

202nt - 8r

341nt - 15r

312nt - 5r

301nt - 10er

430nt - 4r

III

FnnSF-018 - 09

219nt - 8r

259nt- 14r

202nt - 8r

341nt - 15r

312nt - 5r

301nt - 10er

430nt- 4r

III

FnnSF-019 - 09

219nt - 8r

259nt - 14r

202nt - 8r

341nt - 15r

312nt - 5r

301nt - 10er

430nt - 4r

 

FnnH-008 - 06W

195nt - 5r

217nt - 8r

202nt - 8r

311nt - 10r

312nt - 5r

301nt - 10er

435nt - 5r

 

FnnMR-015 - 08F

195nt - 5r

259nt - 14r

197nt - 7r

437nt - 31r

312nt - 5r

301nt - 10er

435nt - 5r

 

FnnH-016 - 08F

219nt - 8r

287nt - 18r

197nt - 7r

359nt - 18r

312nt- 5r

295nt - 8er

435nt - 5r

 

FnnAA-009 - 07W

211nt - 7r

294nt - 19r

197nt - 7r

347nt - 16r

312nt - 5r

301nt - 10er

435nt - 5r

 

FnnVA-010 - 07W

211nt - 7r

308nt - 21r

197nt - 7r

329nt - 13r

312nt - 5r

301nt - 10er

435nt - 5r

 

FnnH-020 - 09

195nt - 5r

280nt - 17r

207nt - 9r

437nt - 31r

312nt - 5r

301nt - 10er

435nt - 5r

 

F. noatunensis ssp. orientalis

 

FnoJ-001 - 02 (Ehime-1)

195nt - 5r

217nt - 8r

NA

317nt - 11dr

285nt - 2r

301nt - 10fr

405nt - 2ir

 

FnoI-002 - 04 1368

211nt - 7r

392nt - 33r

212nt - 10r

365nt - 19dr

285nt - 2r

301nt - 10fr

404nt - 1.8r

 

FnoI-003 - 05 1436

211nt - 7r

217nt - 8r

212nt - 10r

329nt - 13dr

285nt - 2r

301nt - 10fr

404nt - 1.8r

 

FnoI-004 - 07 2070

211nt - 7r

217nt - 8r

212nt- 10r

371nt - 20dr

285nt - 2r

301nt - 10fr

404nt - 1.8r

 

F. philomiragia

 

FpDSM7535T

NA

175nt - 2.8br

182nt - 4c

401nt - 25dr

NA

301nt - 10gr

404nt - 1.8r

 

FpCCUG19701

NA

175nt - 2.8br

NA

395nt - 24dr

NA

301nt - 10gr

405nt - 2r

 

FpCCUG13404

NA

175nt - 2.8br

NA

311nt - 10dr

NA

301nt - 10gr

404nt - 1.8r

 

FpCCUG12603

NA

175nt - 2.8br

NA

407nt - 26dr

NA

301nt - 10gr

425nt - 3r

 

Fp1951

NA

175nt - 2.8ar

NA

443nt - 32r

NA

301nt - 10gr

404nt - 1.8r

 

Fp080107 -I

NA

Na

NA

431nt - 30dr

NA

301nt - 10gr

405nt - 2r

 

Fp080107 -II

NA

175nt - 2.8ar

NA

257nt - 1ar

NA

301nt - 10gr

404nt - 1.8r

  1. Identical allelic profiles are assigned Greek numerals I-III. Allelic profiles are presented as number of nucleotides in repeat marker (nt) and numbers of repeats (r). Identical profiles occur for several isolates from cod culturing, profile I (FnnR-001-04 to FnnMR-013-07), profile II (FnnR-003-06W and FnnN-006-06) and profile III (FnnH-007-06 to FnnSF-019-09)
  2. Isolated in ChileA, Isolated from broodfishF, type strainT, W = wild caught, NA = Not Amplified with primer sets
  3. Heterogeneous repeats with Single Nucleotide Polymorphism (snp), noted as nucleotide number in repeat sequence (nt) and at repeat of occurrence (r); a = snp G-A nt1 r1 r3 b = snp. G-A nt1 r3, c = snp G-A nt3 r4, d = snp T-C nt1 from r2, e = 2 snp C-T nt1 r4 r6, f = 2 snp C-T nt1 r5 r7, g = 2 snp C-T nt1 r6 r8, h = 2 snp C-T nt1 r8 r10, i = snp T-C nt4 r1