Table 2.
Microorganisms amplified in this study
| Microorganisms | Target gene |
Amblyomma variegatum (2: 5N, 1M)a |
Hyalomma truncatum (3: 1M, 5F)a |
Rhipicephalus decoloratus (16: 24M, 83F)a |
Rhipicephalus duttoni (2: 1M, 2F)a |
Rhipicephalus evertsi mimeticus (1: 1F)a |
Rhipicephalus sp. (1: 1 M)a |
|---|---|---|---|---|---|---|---|
| Rickettsia spp. | ompA |
R. africae (100;CP001612) 2 (5N, 1M) |
R. aeschlimannii (100;HQ335157) 3 (1M, 5F) |
R. africae (100; CP001612) 1 (9M) |
– | – | – |
| Anaplasma/Neoehrlichia/Ehrlichia spp. | groESL | – | – |
Ehrlichia spp. (100; MW054557) 6 (44F) |
– | – | – |
| Ehrlichia spp. | gltA | NP | NP |
Ehrlichia spp. (96.9–97.0; KX987353)b 6(44F) |
NP | NP | NP |
| 16S rRNAc | NP | NP |
Ehrlichia sp. (99.9; AF497581) 1 (9F)d |
NP | NP | NP | |
| Borrelia spp. | flaB | – | – | – | – | – | – |
| glpQ | – | – | – | – | – | – | |
| Coxiella burnetii | IS1111 | – | – | – | – | – | – |
| Coxiella/Francisella spp. | rpoB |
Coxiella spp. (98.9–99.2; KP985305) 2 (5N, 1M) |
SNC |
Coxiella spp. (100; KP985329) 16 (24M,38F) |
Coxiella sp. (95.9; KP985337) 2 (1M, 2F) |
Coxiella sp. (99.1; KP985331) 1 (1F) |
Coxiella sp. (97.8;KP985337) 1 (1M) |
| groEL |
Coxiella spp. (99.5; KP985486) 2 (5N, 1M) |
Francisella sp. 1 (4F) |
Coxiella spp. (100; KP985510) 16 (24M, 38H) |
Coxiella sp. (97.3; KY678195) 2 (1M, 2F) |
Coxiella sp. (98.2; KY678195) 1 (1F) |
Coxiella sp. (98.3;CP011126) 1 (1M) |
|
| 16S rRNAc | NP |
Francisella sp. (99.6; AB001522) 1 (4F)f |
Coxiella sp. (99.4; JQ480818) 1 (5H)d |
NP | NP | NP | |
| Spiroplasma spp. | rpoB | – | – |
Spiroplasma spp. (99.4; KP967687)g 3 (24M) |
– | – | – |
| 16S rRNA | NP | NP |
Spiroplasma spp. (98.7–100; KP967685)h 3 (24M) |
NP | NP | NP | |
| Theileria spp./Babesia spp. | 18S rRNA |
Babesia spp. (91.4; AB734390) 2 (5N, 1M) |
– |
B. bigemina (100; KF606863) 2 (10F) |
– | – | – |
| Babesia spp. | ITS 1 |
Babesia spp. (70.9; LK391709) 2 (5N, 1M) |
NP |
B. bigemina (98.8–100; EF458251)h 2 (10H) |
NP | NP | NP |
| ITS 2 |
Babesia spp. (74.7; EF186914) 2 (5N, 1M) |
NP |
B. bigemina (99.5; EF458266) 2 (10F) |
NP | NP | NP |
Data show the species names and the highest identity with public sequences (%; GenBank accession number) followed by the number of pools in which the microorganisms have been detected and, in brackets, the number of ticks from each pool
N: nymphs; M: males; F: females; SNC: sequences not conclusive; NP: not performed
aNumbers in brackets indicate (number of pools: number of ticks and developmental stage); btwo genetic variants were identified; cpan-bacterial PCR assay; dPCR assay performed to four samples, but because this is a pan-bacterial PCR assay (Additional file 1:Table S1), the bacterium was only amplified from one sample; ewith 87.6% and 65% query cover, this genotype reached 98.2% and 98.7% identity with Francisella sp. detected in soft and hard ticks, respectively (MW287617 and KY678032); fwith 92% query cover, this genotype reached 99.8% identity with Francisella sp. amplified from Hyalomma truncatum (JF290387); gwith 42% query cover, the sequences are identical to available Spiroplasma sequences from Rhipicephalus decoloratus (MK267083-4), but also to those detected in other Rhipicephalus and Ixodes species (MK267073-7, MK267082, MK267085); hNucleotide sequences show several ambiguous bases