Table 3 PCR/Real time PCR/LAMP primers (and probes) used for detection/characterisation of Francisella spp.
From: Francisella infections in farmed and wild aquatic organisms
Specific for | Target gene or region | Amplicon size | Primer sequence (5' - 3') | Probe sequence (Real time PCR) | Reference |
|---|---|---|---|---|---|
F. noatunensis subsp. noatunensis + subsp. orientalis | 16S rRNA | 101 bp | FcF50 aac-gac-tgt-taa-tac-cgc-ata-ata-tct-g | Fc50-probe gtg-gcc-ttt-gtg-ctg-c | Ottem et al. [51] |
| Â | Â | Â | FcR50 cct-tac-cct-acc-aac-tag-cta-atc-ca | Â | Â |
F. noatunensis subsp. noatunensis + F. philomiragia | FopA | 85 bp | FopAF ggt-gcg-aac-atg-act-att-ggt-tat | FopA-probe ttt-gca-gtt-cag-tat-aac | Ottem et al. [51] |
| Â | Â | Â | FopAR aac-ctg-caa-ata-ctc-tac-cca-cta-act | Â | Â |
F. noatunensis subsp. orientalis | iglC | 88 bp | iglC forward ggg-cgt-atc-taa-gga-tgg-tat-gag | iglC probe atc-tat-tga-tgg-gct-cac-aac-ttc-aca-a | Soto et al. [68] |
| Â | Â | Â | iglC reverse agc-aca-gca-tac-agg-caa-gct-a | Â | Â |
Francisella-like | 16S rRNA | 286 bp | FLB16S180f gcg-gat-taa-agg-tgg-cct-ttg-c | n.a. | Hsieh et al. [42] |
| Â | Â | Â | FLB16S465r cct-gca-agc-tat-taa-ctc-aca-gg | Â | Â |
Francisella spp. | 16S rRNA | 1113 bp | F5 cct-ttt-tga-gtt-tcg-ctc-c | n.a. | Forsmann et al. [64] |
| Â | Â | Â | F11 tac-cag-ttg-gaa-acg-act-gt | Â | Â |
Francisella spp. | 16S rRNA | ~1170 bp | Fr153F0.1 gcc-cat-ttg-agg-ggg-ata-cc | n.a. | Barns et al. [11] |
| Â | Â | Â | Fr1281R0.1 gga-cta-aga-gta-cct-ttt-tga-gt | Â | Â |
F. noatunensis subsp. noatunensis | groEL | Multiple bands | Primer set 4 (LAMP) F3 ggt-gct-caa-ata-gtt-aaa-gaa-gt | n.a. | Caipang et al. [69] |
| Â | Â | Â | B3 gta-ccc-act-tgc-tcg-ata-g | Â | Â |
| Â | Â | Â | FIP ttc-tgt-aag-taa-cgc-ttg-agc-taa-ttt-tt c-tgc-tga-tgt-agc-agg-tg | Â | Â |
| Â | Â | Â | BIP aac-agg-tat-tga-taa-ggc-tgc-tgt-ttt-tct-gaa-caa-ggc-tta-gaa-agt | Â | Â |