Table 1.
List of primer/probe sets constituting the BioMark system, with the positive controls used for their validation (new designs mainly). *: Design from Michelet et al., 2014 [18]. **: include all the controls belonging to the genus described in the table and targeted by specific design. Plasmids used as control are recombinant PBluescript IISK+ containing the target gene.
| Microorganisms | Target | Design Name | Sequence (5′ à 3′) | Length (bp) | Controls |
|---|---|---|---|---|---|
| Rickettsia spp. | gltA | Rick_spp_gltA_F | GTCGCAAATGTTCACGGTACTT | 78 | **, Culture of R. slovaca |
| Rick_spp_gltA_R | TCTTCGTGCATTTCTTTCCATTG | ||||
| Rick_spp_gltA_P | TGCAATAGCAAGAACCGTAGGCTGGATG | ||||
| Rickettsia massiliae * | ITS | Ri_ma_ITS_F | GTTATTGCATCACTAATGTTATACTG | 128 | Culture |
| Ri_ma_ITS_R | GTTAATGTTGTTGCACGACTCAA | ||||
| Ri_ma_ITS_P | TAGCCCCGCCACGATATCTAGCAAAAA | ||||
| Rickettsia rickettsii * | ITS | Ri_ri_ITS_F | TCTACTCACAAAGTTATCAGGTTAA | 124 | Plasmid |
| Ri_ri_ITS_R | CCTACGATACTCAGCAAAATAATTT | ||||
| Ri_ri_ITS_P | TCGCTGGATATCGTTGCAGGACTACAG | ||||
| Rickettsia conorii | sca1 | Ri_co_sca1_F | GTAGATGCTTCATAGAATACTGC | 88 | Infected Rhipicephalus sanguineus s.l. |
| Ri_co_sca1_R | CCAAATTTAGTCTACCTTGTGATC | ||||
| Ri_co_sca1_P | TCCTCCTGACGTATTAAAAGAAGCTGAAGCT | ||||
| Rickettsia africae | sca1 | Ri_af_sca1_F | GATACGACAAGTACCTCGCAG | 122 | Culture |
| Ri_af_sca1_R | GGATTATATACTTTAGGTTCGTTAG | ||||
| Ri_af_sca1_P | CAGATAGGAACAGTAATTGTAACGGAACCAG | ||||
| Rickettsia felis | orfB | Ri_fel_orfB_F | ACCCTTTTCGTAACGCTTTGC | 163 | Culture |
| Ri_fel_orfB_R | TATACTTAATGCTGGGCTAAACC | ||||
| Ri_fel_orfB_P | AGGGAAACCTGGACTCCATATTCAAAAGAG | ||||
| Rickettsia typhi | ompB | Ri_typ_ompB_F | CAGGTCATGGTATTACTGCTCA | 133 | Culture |
| Ri_typ_ompB_R | GCAGCAGTAAAGTCTATTGATCC | ||||
| Ri_typ_ompB_P | ACAAGCTGCTACTACAAAAAGTGCTCAAAATG | ||||
| Rickettsia prowazekii | gltA | Ri_pro_gltA_F | CAAGTATCGGTAAAGATGTAATCG | 151 | Plasmid |
| Ri_pro_gltA_R | TATCCTCGATACCATAATATGCC | ||||
| Ri_pro_gltA_P | ATATAAGTAGGGTATCTGCGGAAGCCGAT | ||||
| Borrelia spp. * | 23S rRNA | Bo_bu_sl_23S_F | GAGTCTTAAAAGGGCGATTTAGT | 73 | **, Culture of B. afzelii, B. garinii, B. valaisiana, B. lusitaniae, B. recurrentis |
| Bo_bu_sl-23S_R | CTTCAGCCTGGCCATAAATAG | ||||
| Bo_bu_sl_23S_P | TAGATGTGGTAGACCCGAAGCCGAGT | ||||
| Borrelia burgdorferi sensu stricto | glpA | Bo_bu_glpA_F | GCAATTACAAGGGGGTATAAAGC | 206 | Culture |
| Bo_bu_glpA_R | GGCGTGATAAGTGCACATTCG | ||||
| Bo_bu_glpA_P | TTAATTAAACGGGGTGCATTCTTCTCAAGAATG | ||||
| Borrelia anserina | fla | Bor_ans_fla_F | GGAGCACAACAAGAGGGAG | 76 | Plasmid |
| Bor_ans_fla_R | TTGGAGAATTAACCCCACCTG | ||||
| Bor_ans_fla_P | TGCAAGCAACTCCAGCTCCAGTAGCT | ||||
| Borrelia lonestari | glpQ | Bor_lon_glpQ_F | GATCCAGAACTTGATACAACCAC | 99 | Infected Amblyomma americanum |
| Bor_lon_glpQ_R | TTCATCTAGTGAGAAGTCAGTAG | ||||
| Bor_lon_glpQ_P | AGTAATATCGTCCGTCTTCCCTAGCTCG | ||||
| Borrelia parkeri | gyrB | Bor_par_gyrB_F | GCAAAACGATTCAAAGTGAGTCC | 184 | Culture |
| Bor_par_gyrB_R | CTCATTGCCTTTAAGAAACCACTT | ||||
| Bor_par_gyrB_P | TTAAAACCAGCAACATGAGTTCCTCCTTCTC | ||||
| Borrelia bissettii * | rpoB | Bo_bi_rpoB_F | GCAACCAGTCAGCTTTCACAG | 118 | Plasmid |
| Bo_bi_rpoB_R | CAAATCCTGCCCTATCCCTTG | ||||
| Bo_bi_rpoB_P | AAAGTCCTCCCGGCCCAAGAGCATTAA | ||||
| Borrelia theileri | glpQ | Bo_th_glpQ_F | GTGCTAACAAAGGACAATATTCC | 213 | Plasmid |
| Bo_th_glpQ_R | GGTTAGTGGAAAACGGTTAGGAT | ||||
| Bo_th_glpQ_P | TATTATAATTCACGAGCCAGAGCTTGACAC | ||||
| Bartonella spp. | ssrA | Bart_spp_ssrA_F | CGTTATCGGGCTAAATGAGTAG | 118 | **, Culture of B. quintana |
| Bart_spp_ssrA_R | ACCCCGCTTAAACCTGCGA | ||||
| Bart_spp_ssrA_P | TTGCAAATGACAACTATGCGGAAGCACGTC | ||||
| Bartonella barcilliformis * | rpoB | Ba_ba_rpoB_F | GAAGAGTTTGTAGTTTGTCGTCA | 105 | Culture |
| Ba_ba_rpoB_R | AGCAGCTACAGAAACCAACTG | ||||
| Ba_ba_rpoB_P | TGCAGGTGAAGTTTTGATGGTGCCACG | ||||
| Bartonella henselae | ribC | Bar_he_ribC_F | GGGATGCGATTTAATAGTTCTAC | 116 | Culture |
| Bar_he_ribC_R | CGCTTGTTGTTTTGATCCTCG | ||||
| Bar_he_ribC_P | ACGTTATAGTAGCGAAAACTTAGAAATTGGTGC | ||||
| Bartonella vinsonii subsp. berkhoffii | ITS | Bar_vin_ITS_F | GGAATTGCTTAACCCACTGTTG | 141 | Culture |
| Bar_vin_ITS_R | CCTTATTGATTTAGATCTGATGGG | ||||
| Bar_vin_ITS_P2 | AGAAACTCCCGCCTTTATGAGAGAAATCTCT | ||||
| Coxiella burnetii and Coxiella-like * | Icd | Co_bu_icd_F | AGGCCCGTCCGTTATTTTACG | 74 | Culture |
| Co_bu_icd_R | CGGAAAATCACCATATTCACCTT | ||||
| Co_bu_icd_P | TTCAGGCGTTTTGACCGGGCTTGGC | ||||
| IS1111 | Co_bu_IS111_F | TGGAGGAGCGAACCATTGGT | 86 | Culture | |
| Co_bu_IS111_R | CATACGGTTTGACGTGCTGC | ||||
| Co_bu_IS111_P | ATCGGACGTTTATGGGGATGGGTATCC | ||||
| Francisella tularensis and Francisella-like endosymbionts * | tul4 | Fr_tu_tul4_F | ACCCACAAGGAAGTGTAAGATTA | 76 | Culture |
| Fr_tu_tul4_R | GTAATTGGGAAGCTTGTATCATG | ||||
| Fr_tu_tul4_P | AATGGCAGGCTCCAGAAGGTTCTAAGT | ||||
| fopA | Fr_tu_fopA_F | GGCAAATCTAGCAGGTCAAGC | 91 | Culture | |
| Fr_tu_fopA_R | CAACACTTGCTTGAACATTTCTAG | ||||
| Fr_tu_fopA_P | AACAGGTGCTTGGGATGTGGGTGGTG | ||||
| Anaplasma spp. | 16S rRNA | Ana_spp_16S_F | CTTAGGGTTGTAAAACTCTTTCAG | 160 | ** |
| Ana_spp_16S_R | CTTTAACTTACCAAACCGCCTAC | ||||
| Ana_spp_16S_P | ATGCCCTTTACGCCCAATAATTCCGAACA | ||||
| Anaplasma marginale * | msp1b | An_ma_msp1_F | CAGGCTTCAAGCGTACAGTG | 85 | Experimentally infected bovine blood sample |
| An_ma_msp1_R | GATATCTGTGCCTGGCCTTC | ||||
| An_ma_msp1_P | ATGAAAGCCTGGAGATGTTAGACCGAG | ||||
| Anaplasma phagocytophilum * | msp2 | An_ph_msp2_F | GCTATGGAAGGCAGTGTTGG | 77 | Infected Ixodes spp. tick |
| An_ph_msp2_R | GTCTTGAAGCGCTCGTAACC | ||||
| An_ph_msp2_P | AATCTCAAGCTCAACCCTGGCACCAC | ||||
| Anaplasma platys * | groEL | An_pla_groEL_F | TTCTGCCGATCCTTGAAAACG | 75 | Infected canine blood sample |
| An_pla_groEL_R | CTTCTCCTTCTACATCCTCAG | ||||
| An_pla_groEL_P | TTGCTAGATCCGGCAGGCCTCTGC | ||||
| Anaplasma bovis * | groEL | An_bo_groEL_F | GGGAGATAGTACACATCCTTG | 73 | Plasmid |
| An_bo_groEL_R | CTGATAGCTACAGTTAAGCCC | ||||
| An_bo_groEL_P | AGGTGCTGTTGGATGTACTGCTGGACC | ||||
| Anaplasma ovis * | msp4 | An_ov_msp4_F | TCATTCGACATGCGTGAGTCA | 92 | Plasmid |
| An_ov_msp4_r | TTTGCTGGCGCACTCACATC | ||||
| An_ov_msp4_P | AGCAGAGAGACCTCGTATGTTAGAGGC | ||||
| Ehrlichia spp. * | 16S rRNA | Neo_mik_16S_F | GCAACGCGAAAAACCTTACCA | 98 | ** |
| Neo_mik_16S_R | AGCCATGCAGCACCTGTGT | ||||
| Neo_mik_16S_P | AAGGTCCAGCCAAACTGACTCTTCCG | ||||
| Ehrlichia canis | gltA | Eh_ca_gltA_F | GACCAAGCAGTTGATAAAGATGG | 136 | Culture |
| Eh_ca_gltA_R | CACTATAAGACAATCCATGATTAGG | ||||
| Eh_ca_gltA_P | ATTAAAACATCCTAAGATAGCAGTGGCTAAGG | ||||
| Ehrlichia chaffeensis * | dsb | Eh_ch_dsb_F | TATTGCTAATTACCCTCAAAAAGTC | 117 | Infected Amblyomma americanum |
| Eh_ch_dsb_R | GAGCTATCCTCAAGTTCAGATTT | ||||
| Eh_ch_dsb_P | ATTGACCTCCTAACTAGAGGGCAAGCA | ||||
| Ehrlichia ewingii * | dsb | Eh_ew_dsb_F | CAATACTTGGAGAAGCATCATTG | 111 | Infected Amblyomma americanum |
| Eh_ew_dsb_R | TTGCTTATGGCTTAATGCTGCAT | ||||
| Eh_ew_dsb_P | AAAGCAGTACGTGCAGCATTGGCTGTA | ||||
| Ehrlichia ruminantium | gltA | Eh_ru_gltA_F | CCAGAAAACTGATGGTGAGTTAG | 116 | Culture |
| Eh_ru_gltA_R | AGCCTACATCAGCTTGAATGAAG | ||||
| Eh_ru_gltA_P | AGTGTAAACTTGCTGTTGCTAAGGTAGCATG | ||||
| Panola Mountain Ehrlichia | gltA | Eh_PME_gltA_F | GCTAGTTATGAGTTAGAATGTAAAC | 121 | Infected Amblyomma americanum |
| Eh_PME_gltA_R | TACTATAGGATAATCTTGAATCAGC | ||||
| Eh_PME_gltA_P | TTGCTATCGCTAAAATTCCAAGTATGATTGCG | ||||
| Neoehrlichia mikurensis * | groEL | Neo_mik_groEL_F | AGAGACATCATTCGCATTTTGGA | 96 | Infected rodent blood sample |
| Neo_mik_groEL_R | TTCCGGTGTACCATAAGGCTT | ||||
| Neo_mik_groEL_P | AGATGCTGTTGGATGTACTGCTGGACC | ||||
| Aegyptianella pullorum | groEL | Ae_pul_groEL_F | AGCCAGTATTATCGCTCAAGG | 168 | Plasmid |
| Ae_pul_groEL_R | GCCTCACGTGCCTTCATAAC | ||||
| Ae_pul_groEL_P | TGCTTCTCAGTGTAACGACAGGGTTGG | ||||
| Apicomplexa | 18S rRNA | Apic_18S_F | TGAACGAGGAATGCCTAGTATG | 104 | **, Infected canine blood sample, with B. canis rossi, B. canis canis; Culture of B. divergens, T. lestoquari, T. annulata |
| Apic_18S_R | CACCGGATCACTCGATCGG | ||||
| Apic_18S_S | TAGGAGCGACGGGCGGTGTGTAC | ||||
| Babesia canis vogeli * | hsp70 | Ba_vo_hsp70_F | TCACTGTGCCTGCGTACTTC | 87 | Infected canine blood sample |
| Ba_vo_hsp70_R | TGATACGCATGACGTTGAGAC | ||||
| Ba_vo_hsp70_P | AACGACTCCCAGCGCCAGGCCAC | ||||
| Babesia ovis * | 18S rRNA | Ba_ov_18S_F | TCTGTGATGCCCTTAGATGTC | 92 | Plasmid |
| Ba_ov_18S_R | GCTGGTTACCCGCGCCTT | ||||
| Ba_ov_18S_P | TCGGAGCGGGGTCAACTCGATGCAT | ||||
| Babesia bigemina * | 18S rRNA | Ba_big_RNA18S_F | ATTCCGTTAACGAACGAGACC | 99 | Plasmid |
| Ba_big_RNA18S_R | TTCCCCCACGCTTGAAGCA | ||||
| Ba_big_RNA18S_P | CAGGAGTCCCTCTAAGAAGCAAACGAG | ||||
| Babesia gibsoni | Rap1 | Ba_gib_rap1_F | CTCTTGCTCATCATCTTTTCGG | 130 | Plasmid |
| Ba_gib_rap1_R | TCAGCGTATCCATCCATTATATG | ||||
| Ba_gib_rap1_S | TTTAATGCGTGCTACGTTGTACTTCCCAAAG | ||||
| Babesia caballi * | Rap1 | Ba_cab_rap1_F | GTTGTTCGGCTGGGGCATC | 94 | Plasmid |
| Ba_cab_rap1_R | CAGGCGACTGACGCTGTGT | ||||
| Ba_cab_rap1_P | TCTGTCCCGATGTCAAGGGGCAGGT | ||||
| Babesia bovis * | CCTeta | Ba_bo_CCTeta_F | GCCAAGTAGTGGTAGACTGTA | 100 | Plasmid |
| Ba_bo_CCTeta_R | GCTCCGTCATTGGTTATGGTA | ||||
| Ba_bo_CCTeta_P | TAAAGACAACACTGGGTCCGCGTGG | ||||
| Babesia duncani * | ITS2 | Ba_du_ITS_F | ATTTCCGTTTGCGAGAGTTGC | 87 | Plasmid |
| Ba_du_ITS_R | AGGAAGCATCAAGTCATAACAAC | ||||
| Ba_du_ITS_P | AACAAGAGGCCCCGAGATCAAGGCAA | ||||
| Babesia microti * | CCTeta | Bab_mi_CCTeta_F | ACAATGGATTTTCCCCAGCAAAA | 145 | Culture |
| Bab_mi_CCTeta_R | GCGACATTTCGGCAACTTATATA | ||||
| Bab_mi_CCTeta_P | TACTCTGGTGCAATGAGCGTATGGGTA | ||||
| Theileria parva * | 18S rRNA | Th_pa_18S_F | GAGTATCAATTGGAGGGCAAG | 173 | Culture |
| Th_pa_18S_R | CAGACAAAGCGAACTCCGTC | ||||
| Th_pa_18S_P | AAATAAGCCACATGCAGAGACCCCGAA | ||||
| Theileria mutans | ITS | The_mu_ITS_F | CCTTATTAGGGGCTACCGTG | 119 | Plasmid |
| The_mu_ITS_R | GTTTCAAATTTGAAGTAACCAAGTG | ||||
| The_mu_ITS_P | ATCCGTGAAAAACGTGCCAAACTGGTTAC | ||||
| Theileria velifera | 18S rRNA | The_ve_18S_F | TGTGGCTTATCTGGGTTCGC | 151 | Plasmid |
| The_ve_18S_R | CCATTACTTTGGTACCTAAAACC | ||||
| The_ve_18S_P | TTGCGTTCCCGGTGTTTTACTTTGAGAAAG | ||||
| Theileria equi | ema1 | Th_eq_ema1_F4 | CGGCAAGAAGCACACCTTC | 167 | Plasmid |
| Th_eq_ema1_R4 | TGCCATCGCCCTTGTAGAG | ||||
| Th_eq_ema1_P4 | AAGGCTCCAGGCAAGCGCGTCCT | ||||
| Cytauxzoon felis | ITS2 | Cy_fel_ITS2_F | AAGATCCGAACGGAGTGAGG | 119 | Plasmid |
| Cy_fel_ITS2_R | GTAGTCTCACCCAATTTCAGG | ||||
| Cy_fel_ITS2_S | AAGTGTGGGATGTACCGACGTGTGAG | ||||
| Hepatozoon spp. | 18S rRNA | Hepa_spp_18S_F | ATTGGCTTACCGTGGCAGTG | 175 | ** |
| Hepa_spp_18S_R | AAAGCATTTTAACTGCCTTGTATTG | ||||
| Hepa_spp_18S_S | ACGGTTAACGGGGGATTAGGGTTCGAT | ||||
| Hepatozoon canis | 18S rRNA | He_can_18S_F | TTCTAACAGTTTGAGAGAGGTAG | 221 | Infected canine blood sample |
| He_can_18S_R | AGCAGACCGGTTACTTTTAGC | ||||
| He_can_18S_S | AGAACTTCAACTACGAGCTTTTTAACTGCAAC | ||||
| Hepatozoon americanum | 18S rRNA | He_ame_18S_F2 | GGTATCATTTTGGTGTGTTTTTAAC | 159 | Plasmid |
| He_ame_18S_R2 | CTTATTATTCCATGCTCCAGTATTC | ||||
| He_ame_18S_P2 | AAAAGCGTAAAAGCCTGCTAAAAACACTCTAC | ||||
| Leishmania spp. | hsp70 | Leish_spp_hsp70_F | CGACCTGTTCCGCAGCAC | 78 | ** and culture of L. martiniquensis |
| Leish_spp_hsp70_R | TCGTGCACGGAGCGCTTG | ||||
| Leish_spp_hsp70_S | TCCATCTTCGCGTCCTGCAGCACG | ||||
| Leishmania infantum | ITS | Le_inf_ITS_F | CGCACCGCCTATACAAAAGC | 103 | Culture |
| Le_inf_ITS_R | GTTATGTGAGCCGTTATCCAC | ||||
| Le_inf_ITS_S | ACACGCACCCACCCCGCCAAAAAC | ||||
| Rangelia vitalii | 18S rRNA | Ra_vit_18S_F | TAACCGTGCTAATTGTAGGGC | 92 | Plasmid |
| Ra_vit_18S_R | GAATCACCAAACCAAATGGAGG | ||||
| Ra_vit_18S_S | TAATACACGTTCGAGGGCGCGTTTTGC | ||||
| Tick spp. | 16S rRNA | Tick_spp_16S_F | AAATACTCTAGGGATAACAGCGT | 99 | ** |
| Tick_spp_16S_R | TCTTCATCAAACAAGTATCCTAATC | ||||
| Tick_spp_16S_P | CAACATCGAGGTCGCAAACCATTTTGTCTA | ||||
| Amblyomma variegatum | ITS2 | Amb_var_ITS2_F | GCCAGCCTCTGAAGTGACG | 117 | Tick extract (Guadeloupe) |
| Amb_var_ITS2_R | TTCTGCGGTTTAAGCGACGC | ||||
| Amb_var_ITS2_P | TCTTGCCACTCGACCCGTGCCTC | ||||
| Rhipicephalus microplus | ITS2 | Rhi_mic_ITS2_F | GCTTAAGGCGTTCTCGTCG | 144 | Tick extract (Galapagos Islands) |
| Rhi_mic_ITS2_R | CAAGGGCAGCCACGCAG | ||||
| Rhi_mic_ITS2_P | TAGTCCGCCGTCGGTCTAAGTGCTTC | ||||
| Rhipicephalus sanguineus sensu lato | ITS2 | Rhi_san_ITS2_F | TTGAACGCTACGGCAAAGCG | 110 | Tick extract (France) |
| Rhi_san_ITS2_R | CCATCACCTCGGTGCAGTC | ||||
| Rhi_san_ITS2_P | ACAAGGGCCGCTCGAAAGGCGAGA |