Pathogens detected
We detected Anaplasma and Rickettsia bacteria, BabesiaTheileriaHepatozoon protozoa, and CCHF virus (Figure 2) in ticks and lice collected from 13 LMs and 13 SHs across the three sampled counties (Table 2). Out of the 333 pools tested (Supplementary Table 2), one Rh. decoloratus and one Rhipicephalus sp. were positive for CCHF virus (deposited GenBank accessions MN267048, MN267049) (0.62% estimated true prevalence). These ticks were removed from cattle at two SHs. The CCHF virus isolates identified fall into the genotype II clade, which includes isolates from Uganda and the Democratic Republic of Congo (DRC) (Figure 3). Their nucleotide sequence identity was highest (98.6%) to the Nakiwogo (GenBank accession KX013483) strain isolated from Uganda (Simpson et al., 1967).
Eighty-two out of 96 pools of Am. variegatum, three pools of Rh. decoloratus, four pools of Rhipicephalus sp., one pool of Rh. appendiculatus, one pool of Am. gemma, and one pool of H. suis were positive for R. africae (deposited GenBank accessions MN294740-MN294749) (Table 2). These R. africae-positive ectoparasites were removed from cattle, sheep, goats and pigs. Two of the R. africae sequences from this study were identical to those previously detected in Am. variegatum ticks in Asembo in Kenya (GenBank accession KF660534) and another to a strain detected in a patient diagnosed with African tick bite fever in Tanzania (unpublished; GenBank accession KU721071). Rickettsia africae variants in this study were characterised by base substitutions in several positions and possessed a four-base insertion that is absent from most Kenyan isolates (Supplementary Figure 2).
We detected A. platys (deposited GenBank accessions MN266939-MN266941) in five pools of Rh. decoloratus, two pools of Rhipicephalus sp., and three pools of Rh. appendiculatus, all obtained from cattle (Supplementary Table 3). Anaplasma marginale (deposited GenBank accessions MN266931-MN266935) was detected in four pools of Rh. decoloratus and two pools of Rhipicephalus sp. Anaplasma ovis (deposited GenBank accessions MN266936-MN266938) was detected in two pools of Rh. decoloratus, three pools of Rhipicephalus sp., and one pool of Rh. evertsi from goats and cattle.
Only one Rhipicephalus sp. tick pool was positive for T. parva (GenBank accession MN294730) (Table 2). Twelve out of 108 pools of Rh. decoloratus were positive for Theileria mutans (deposited GenBank accessions MN294725-MN294729), while two pools were positive for Theileria taurotragi (deposited GenBank accessions MN294731-MN294732). In Rhipicephalus sp., six pools were positive for T. mutans, three for T. taurotragi, and one for Theileria velifera (deposited GenBank accessions MN294733-MN294734). Theileria mutans was also detected in one Rh. appendiculatus and one A. variegatum pool. All Theileria spp. positive ticks were removed from cattle (Supplementary Table 3). We detected Babesia caballi (deposited GenBank accessions MN294721-MN294723) exclusively in eight Am. variegatum tick pools. Single pools each of Rh. decoloratusRh. appendiculatus, and Am. variegatum were positive for Babesia bigemina (deposited GenBank accession MN294720)One pool of Rh. decoloratus was positive for Hepatozoon canis (deposited GenBank accession MN294724). The phylogenetic relationships of the apicomplexan parasite sequences identified in this study with homologous pathogen sequences are shown in Figure 4.
In addition to these pathogens, we detected Coxiella endosymbionts (deposited GenBank accessions MN262071-MN262076, MN266922-MN266928, MN266946-MN266948), which are phylogenetically close to, but distinct from, Coxiella burnetii, the pathogen responsible for Q fever, in all the genera of ticks except in Haemaphysalis. The Coxiella endosymbionts characterised in this study fell into the group B and C clades of previously detected tick Coxiella endosymbionts of ticks (Figure 5).
No DNA/RNA of the pathogens evaluated in this study was detected in the flea specimens. All of the 33 selected associated livestock blood samples were negative for R. africae and CCHF virus. Thirty-one of these blood samples were from animals (28 cattle and three pigs) from which R. africae positive Am. variegatum ticks were collected, while the other two were from the cattle from which the two CCHF virus-positive Rhipicephalus spp. were obtained.