Pathogens detected
We detected Anaplasma and Rickettsia bacteria, Babesia, Theileria, Hepatozoon 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patient diagnosed with African tick bite fever in Tanzania (unpublished;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. decoloratus, Rh. 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.