The epidemiology of tick-borne haemoparasites as determined by the reverse line blot hybridization assay in an intensively studied cohort of calves in western Kenya

Molecular Investigation of Tick-Borne Haemoparasites Isolated from Indigenous Zebu Cattle in the Tanga Region, Tanzania

Tick-borne diseases (TBDs) are a major hindrance to livestock production in pastoral communities of Africa. Although information on tick-borne infections is necessary for setting up control measures, this information is limited in the pastoral communities of Tanzania. Therefore, this study aimed to provide an overview of the tick-borne infections in the indigenous cattle of Tanzania. A total of 250 blood samples were collected from the indigenous zebu cattle in the Tanga region, Tanzania. Then, we conducted a molecular survey using the polymerase chain reaction (PCR) and gene sequencing to detect and identify the selected tick-borne pathogens. The PCR was conducted using assays, based on Theileria spp. (18S rRNA), Theileria parva (p104), Theileria mutans and T. taurotragi (V4 region of the 18S rRNA), Babesia bigemina (RAP-1a), B. bovis (SBP-2), Anaplasma marginale (heat shock protein groEL) and Ehrlichia ruminantium (pCS20). The PCR screening revealed an overall infection rate of (120/250, 48%) for T. mutans, (64/250, 25.6%) for T. parva, (52/250, 20.8%) for T. taurotragi, (33/250, 13.2%) for B. bigemina and (81/250, 32.4%) for A. marginale. Co-infections of up to four pathogens were revealed in 44.8% of the cattle samples. A sequence analysis indicated that T. parva p104 and A. marginale groEL genes were conserved among the sampled animals with sequence identity values of 98.92−100% and 99.88−100%, respectively. Moreover, the B. bigemina RAP-1a gene and the V4 region of the 18S rRNA of T. mutans genes were diverse among the sampled cattle, indicating the sequence identity values of 99.27−100% and 22.45−60.77%, respectively. The phylogenetic analyses revealed that the T. parva (p104) and A. marginale (groEL) gene sequences of this study were clustered in the same clade. In contrast, the B. bigemina (RAP-1a) and the T. mutans V4 region of the 18S rRNA gene sequences appeared in the different clades. This study provides important basement data for understanding the epidemiology of tick-borne diseases and will serve as a scientific basis for planning future control strategies in the study area.

Molecular survey of Babesia parasites in Kenya: first detailed report on occurrence of Babesia bovis in cattle

BACKGROUND

Among protozoan parasites in the genus Babesia, Babesia bigemina is endemic and widespread in the East African region while the status of the more pathogenic Babesia bovis remains unclear despite the presence of the tick vector, Rhipicephalus microplus, which transmits both species. Recent studies have confirmed the occurrence of R. microplus in coastal Kenya, and although B. bovis DNA has previously been detected in cattle blood in Kenya, no surveillance has been done to establish its prevalence. This study therefore investigated the occurrence of B. bovis in cattle in Kwale County, Kenya, where R. microplus is present in large numbers.

METHODS

A species-specific multiplex TaqMan real-time PCR assay targeting two Babesia bovis genes, 18S ribosomal RNA and mitochondrially-encoded cytochrome b and B. bigemina cytochrome b gene was used to screen 506 cattle blood DNA samples collected from Kwale County for presence of Babesia parasite DNA. A sub-set of 29 B. bovis real-time PCR-positive samples were further amplified using a B. bovis-specific spherical body protein-4 (SBP-4) nested PCR and the resulting products sequenced to confirm the presence of B. bovis.

RESULTS

A total of 131 animals (25.8%) were found to have bovine babesiosis based on real-time PCR. Twenty-four SBP4 nucleotide sequences obtained matched to B. bovis with a similarity of 97-100%. Of 131 infected animals, 87 (17.2%) were positive for B. bovis while 70 (13.8%) had B. bigemina and 26 (5.1%) were observed to be co-infected with both Babesia species. A total of 61 animals (12.1%) were found to be infected with B. bovis parasites only, while 44 animals (8.7%) had B. bigemina only. Babesia bovis and B. bigemina infections were detected in the three Kwale sub-counties.

CONCLUSION

These findings reveal high prevalence of pathogenic B. bovis in a Kenyan area cutting across a busy transboundary livestock trade route with neighbouring Tanzania. The Babesia multiplex real-time PCR assay used in this study is specific and can detect and differentiate the two Babesia species and should be used for routine B. bovis surveillance to monitor the spread and establishment of the pathogen in other African countries where B. bigemina is endemic. Moreover, these findings highlight the threat of fatal babesiosis caused by B. bovis, whose endemic status is yet to be established. GRAPHICAL ABTRACT.

Molecular prevalence and risk factors associated with tick-borne pathogens in cattle in western Kenya

Background

Tick-borne pathogens (TBPs) are of global importance, especially in sub-Saharan Africa where they represent a major constraint to livestock production. Their association with human disease is also increasingly recognized, signalling their zoonotic importance. It is therefore crucial to investigate TBPs prevalence in livestock populations and the factors associated with their presence. We set out to identify TBPs present in cattle and to determine associated risk factors in western Kenya, where smallholder livestock production is important for subsistence and market-driven income.

Results

Tick-borne pathogen infections in blood samples collected from cattle at livestock markets and slaughterhouses between May 2017 and January 2019 were identified by high-resolution melting analysis and sequencing of PCR products of genus-specific primers. Of the 422 cattle sampled, 30.1% (127/422) were infected with at least one TBP, while 8.8% (37/422) had dual infections. Anaplasma spp. (19.7%) were the most prevalent, followed by Theileria (12.3%), Ehrlichia (6.6%), and Babesia (0.2%) spp. Sequence analysis of the TBPs revealed them to be Anaplasma platys-like organisms (13.5%), Theileria velifera (7.4%), Anaplasma marginale (4.9%), Theileria mutans (3.1%), Theileria parva (1.6%), and Babesia bigemina (0.2%). Ehrlichia ruminantium, Rickettsia spp., and arboviruses were not detected. Exotic breeds of cattle were more likely to be infected with A. marginale compared to local breeds (OR: 7.99, 95% CI: 3.04–22.02, p <  0.001). Presence of ticks was a significant predictor for Anaplasma spp. (OR: 2.18, 95% CI: 1.32–3.69, p = 0.003) and Ehrlichia spp. (OR: 2.79, 95% CI: 1.22–7.23, p = 0.022) infection. Cattle sampled at slaughterhouses were more likely to be positive for Anaplasma spp. (OR: 1.64, 95% CI: 1.01–2.70, p = 0.048) and A. marginale (OR: 3.84, 95% CI: 1.43–12.21, p = 0.012), compared to those sampled at livestock markets.

Conclusion

This study reports TBP prevalence and associated risk factors in western Kenya, factors which are key to informing surveillance and control measures.

Survey of Ticks and Tick-Borne Rickettsial and Protozoan Pathogens in Eswatini

Ticks are widespread parasites of vertebrates and major vectors of pathogens to humans, domestic animals, and wildlife. In southern Africa, numerous tick species transmit diseases of economic and health importance. This study aimed to describe the occurrence of ticks and tick-borne pathogens in multiple land-use types and the possible role of ticks in the transmission of pathogen species. Using molecular techniques, we screened 1716 ticks for infection by rickettsial bacteria and protozoans. To characterize pathogen identity, we sequenced multiple loci from positive samples and analyzed sequences within a phylogenetic framework. Across the seven tick species collected as nymphs or adults, we detected Rickettsia, Anaplasma, Ehrlichia, Babesia, Hepatozoon, and Theileira species. We found that some tick species and tick-borne pathogens differed according to land use. For example, we found a higher density of Haemaphysalis elliptica and higher prevalence of Rickettsia in H. elliptica collected from savanna grasses used for livestock grazing near human settlements than savanna grasses in conservation areas. These findings highlight the importance of comprehensive surveillance to achieve a full understanding of the diversity and ecology of the tick-borne pathogens that can infect humans, domestic animals, and wildlife.

Molecular detection and characterisation of protozoan and rickettsial pathogens in ticks from cattle in the pastoral area of Karamoja, Uganda

Ticks and tick-borne diseases (TBDs) significantly affect cattle production and the livelihoods of communities in pastoralist areas. Data on protozoan and rickettsial pathogens in ticks infesting cattle in Uganda is scanty; while it is an indicator of the likelihood of disease transmission and occurrence. A cross-sectional study was conducted amongst cattle in the Karamoja Region, northeastern Uganda, from July through September 2017, to determine the tick species diversity, identify protozoan and rickettsial pathogens in the ticks, and characterise pathogenic species by sequence and phylogenetic analyses. About 50 % of the ticks detected from each predilection site on each animal were collected from 100 purposively-selected cattle from 20 randomly-selected herds. Twelve tick species belonging to the genera Amblyomma, Rhipicephalus and Hyalomma were identified, the most abundant being Amblyomma lepidum (93.9 %), followed by Amblyomma variegatum (2.0 %) and Rhipicephalus evertsi evertsi (1.0 %). Tick species that have not been reported in recent studies amongst cattle in Uganda were found, namely Rhipicephalus pravus, Rhipicephalus praetextatus and Rhipicephalus turanicus. The ticks were grouped into 40 pools, by species and location, and the reverse line blot (RLB) hybridisation assay was used to detect pathogens from the ticks. The most frequently detected tick-borne parasites were Theileria mutans, Theileria velifera and Theileria parva, each observed in 25 % (10/40) of the tick pools. Tick-borne pathogens, namely Babesia rossi, Babesia microti and Theileria sp. (sable) that are not common to, or not known to infect, cattle were identified from ticks. The gene encoding Ehrlichia ruminantium pCS20 region, the Ehrlichia and Anaplasma 16S rRNA gene, and T. parva p67 sporozoite antigen gene were amplified, cloned and sequenced. Seven novel E. ruminantium pCS20 variants were identified, and these grouped into two separate clusters with sequences from other parts of Africa and Asia. The T. parva p67 sequences were of the allele type 1, and parasites possessing this allele type are commonly associated with East Coast fever in eastern Africa. Analysis of the Ehrlichia and Anaplasma 16S rRNA gene sequences showed that they were closely related to Rickettsia africae and to a new Ehrlichia species variant recently found in China. Our R. africae 16S rRNA sequences grouped with R. africae isolates from Nigeria, Egypt and Benin. The information on tick species diversity and pathogens in the various tick species provides an indicator of potential transmission amongst cattle populations, and to humans, and can be useful to estimate disease risk and in control strategies.

Development of a Multiplex PCR and Magnetic DNA Capture Assay for Detecting Six Species Pathogens of the Genera Anaplasma and Ehrlichia in Canine, Bovine, Caprine and Ovine Blood Samples from Grenada, West Indies

Infections with tick-borne pathogens belonging to Anaplasma/Ehrlichia in various vertebrate hosts are a persistent problem resulting in nonspecific clinical signs during early infection. Diagnosis of single and multi-infections with these pathogens, causing diseases in companion/agricultural animals and people, remains a challenge. Traditional methods of diagnosis, such as microscopy and serology, have low sensitivity and specificity. Polymerase chain reaction (PCR) assays are widely used to detect early-phase infections, since these have high sensitivity and specificity. We report the development and validation of an assay involving PCR followed by magnetic capture method using species-specific oligonucleotides to detect six Anaplasma/Ehrlichia species pathogens in canine, bovine, caprine, and ovine blood samples. Overall, the assay application to 455 samples detected 30.1% (137/455) positives for one or more out of six screened pathogens. Single-pathogen infections were observed in 94.9% (130/137) of the positive samples, while co-infections were detected in 5.1% (7/137). Anaplasma marginale infection in cattle had the highest detection rate (34.4%), followed by canines positive for Anaplasma platys (16.4%) and Ehrlichia canis (13.9%). The assay aided in documenting the first molecular evidence for A. marginale in cattle and small ruminants and Ehrlichia chaffeensis and Ehrlichia ewingii in dogs in the Caribbean island of Grenada.

Unique Mitochondrial Single Nucleotide Polymorphisms Demonstrate Resolution Potential to Discriminate Theileria parva Vaccine and Buffalo-Derived Strains

Distinct pathogenic and epidemiological features underlie different Theileria parva strains resulting in different clinical manifestations of East Coast Fever and Corridor Disease in susceptible cattle. Unclear delineation of these strains limits the control of these diseases in endemic areas. Hence, an accurate characterization of strains can improve the treatment and prevention approaches as well as investigate their origin. Here, we describe a set of single nucleotide polymorphisms (SNPs) based on 13 near-complete mitogenomes of T. parva strains originating from East and Southern Africa, including the live vaccine stock strains. We identified 11 SNPs that are non-preferentially distributed within the coding and non-coding regions, all of which are synonymous except for two within the cytochrome b gene of buffalo-derived strains. Our analysis ascertains haplotype-specific mutations that segregate the different vaccine and the buffalo-derived strains except T. parva-Muguga and Serengeti-transformed strains suggesting a shared lineage between the latter two vaccine strains. Phylogenetic analyses including the mitogenomes of other Theileria species: T. annulata, T. taurotragi, and T. lestoquardi, with the latter two sequenced in this study for the first time, were congruent with nuclear-encoded genes. Importantly, we describe seven T. parva haplotypes characterized by synonymous SNPs and parsimony-informative characters with the other three transforming species mitogenomes. We anticipate that tracking T. parva mitochondrial haplotypes from this study will provide insight into the parasite’s epidemiological dynamics and underpin current control efforts.

Tick-borne pathogens, including Crimean-Congo haemorrhagic fever virus, at livestock markets and slaughterhouses in western Kenya

Vectors of emerging infectious diseases have expanded their distributional ranges in recent decades due to increased global travel, trade connectivity and climate change. Transboundary range shifts, arising from the continuous movement of humans and livestock across borders, are of particular disease control concern. Several tick-borne diseases are known to circulate between eastern Uganda and the western counties of Kenya, with one fatal case of Crimean-Congo haemorrhagic fever (CCHF) reported in 2000 in western Kenya. Recent reports of CCHF in Uganda have highlighted the risk of cross-border disease translocation and the importance of establishing inter-epidemic, early warning systems to detect possible outbreaks. We therefore carried out surveillance of tick-borne zoonotic pathogens at livestock markets and slaughterhouses in three counties of western Kenya that neighbour Uganda. Ticks and other ectoparasites were collected from livestock and identified using morphological keys. The two most frequently sampled tick species were Rhipicephalus decoloratus (35%) and Amblyomma variegatum (30%); Ctenocephalides felis fleas and Haematopinus suis lice were also present. In total, 486 ticks, lice and fleas were screened for pathogen presence using established molecular workflows incorporating high-resolution melting analysis and identified through sequencing of PCR products. We detected CCHF virus in Rh. decoloratus and Rhipicephalus sp. cattle ticks, and 82 of 96 pools of Am. variegatum were positive for Rickettsia africae. Apicomplexan protozoa and bacteria of veterinary importance, such as Theileria parva, Babesia bigemina and Anaplasma marginale, were primarily detected in rhipicephaline ticks. Our findings show the presence of several pathogens of public health and veterinary importance in ticks from livestock at livestock markets and slaughterhouses in western Kenya. Confirmation of CCHF virus, a Nairovirus that causes haemorrhagic fever with a high case fatality rate in humans, highlights the risk of under-diagnosed zoonotic diseases and calls for continuous surveillance and the development of preventative measures.

Anaplasma and Theileria Pathogens in Cattle of Lambwe Valley, Kenya: A Case for Pro-Active Surveillance in the Wildlife-Livestock Interface

Tick-borne pathogens (TBPs) are major constraints to livestock production and a threat to public health in Africa. This cross-sectional study investigated the risk of infection with TBPs in cattle of Lambwe Valley, Kenya. Blood samples of 680 zebu cattle from 95 herds in six geospatial clusters within 5 km of Ruma National Park were screened for bacterial and protozoan TBPs by high-resolution melting analysis and sequencing of PCR products. We detected Anaplasma bovis (17.4%), Anaplasma platys (16.9%), Anaplasma marginale (0.6%), Theileria velifera (40%), and Theileria mutans (25.7%), as well as an Anaplasma sp. (11.6%) that matched recently reported Anaplasma sp. sequences from Ethiopia. Babesia, Rickettsia, and Ehrlichia spp. were not detected. The animal and herd-level prevalences for TBPs were 78.5% (95% confidence intervals (CI): 75.3, 81.5) and 95.8% (95% CI: 91.8, 99.8), respectively. About 31.6% of cattle were co-infected with 13 combinations of TBPs. The prevalence of TBPs differed between clusters and age, but the risk of infection was not associated with sex, herd size, or the distance of homesteads from Ruma. This study adds insight into the epidemiology of TBPs around Ruma and highlights the need for proactive surveillance of TBPs in livestock–wildlife interfaces.

Molecular detection and characterization of tick-borne haemoparasites among cattle on Zanzibar Island, Tanzania

Tick-borne diseases (TBDs) are serious constraints to livestock production in Tanzania and other tropical and subtropical countries and impact the livelihoods of resource-poor farming communities in the region. In Tanzania, detailed studies on tick-borne pathogens (TBPs) in cattle using sensitive molecular detection methods are scarce. The objective of this study was to investigate the occurrence and species composition of bovine TBPs in cattle kept in Zanzibar Island. A total of 236 blood samples were randomly collected in cattle population in June and July 2019. We used polymerase chain reaction (PCR) and gene sequencing to detect and identify pathogens. PCR screening of all 236 samples revealed that 64.5% of animals were infected by TBPs, including Theileria parva (34.3%), T. mutans (38.1%), T. taurotragi (30.9%), Anaplasma marginale (10.2%), Babesia bigemina (5.1%), T. velifera (3.4%) and B. bovis (2.1%). Overall a total of 86 animals (36.4%) were co-infected with up to five pathogens including T. parva, T. mutans, T. taurotragi, A. marginale and B. bigemina. The pathogens mostly involved in the co-infection were T. parva, T. taurotragi and T. mutans. Sequence analysis indicated that T. parva p104 and B. bigemina RAP1a genes are diverse among the sampled animals in Zanzibar Island, with 99.64%-100% and 99.51%-100% nucleotide sequence identity value respectively. In contrast, the A. marginale MSP-5, T. mutans 18S rRNA V4 region and B. bovis SBP-2 genes are conserved, with 100%, 99.05%-100% and 99.66%-100% nucleotide sequence identity values respectively. The phylogenetic analyses revealed that T. parva p104 and B. bigemina RAP1a gene sequences showed significant differences of genotypes, as they appear in different clades. Meanwhile, A. marginale MSP-5, T. mutans 18S rRNA V4 region and B. bovis SBP-2 gene sequences appear in the same clade with other sequences extracted from the NCBI GenBank. The epidemiological findings revealed in this study will provide important information on tick-borne diseases in Tanzania and will be used as scientific basis for planning future control strategies.

Molecular prevalence of emerging Anaplasma and Ehrlichia pathogens in apparently healthy dairy cattle in peri-urban Nairobi, Kenya

Background

Anaplasma and Ehrlichia species are tick-borne pathogens of both veterinary and public health importance. The current status of these pathogens, including emerging species such as Ehrlichia minasensis and Anaplasma platys, infecting cattle in Kenya, remain unclear, mainly because of limitation in the diagnostic techniques. Therefore, we investigated the Anaplasma and Ehrlichia species infecting dairy cattle in Nairobi, Kenya using molecular methods.

Results

A total of 306 whole blood samples were collected from apparently healthy dairy cattle. Whole blood DNA was extracted and tested for presence of Anaplasma and Ehrlichia DNA through amplification and sequencing of the 16S rDNA gene. Sequence identity was confirmed using BLASTn analysis while phylogenetic reconstruction was performed to determine the genetic relationship between the Kenyan isolates and other annotated genotypes available in GenBank. Anaplasma and Ehrlichia species were detected in 19.9 and 3.3% of all the samples analyzed, respectively. BLASTn analysis of the sequences against non-redundant GenBank nucleotide database revealed infections with A. platys (44.8%), A. marginale (31%) and A. bovis (13.8%). All four sequenced Ehrlichia spp. were similar to Ehrlichia minasensis. Nucleotide polymorphism was observed for A. platys, A. bovis and E. minasensis. The Anaplasma species clustered in four distinct phylogenetic clades including A. marginale, A. platys, A. bovis and some unidentified Anaplasma spp. The Kenyan Ehrlichia minasensis clustered in the same clade with isolates from America and Australia but distant from E. ruminantium.

Conclusion

This study provides the first report of infection of dairy cattle in Kenya with A. platys and E. minasensis, which are emerging pathogens. We conclude that cattle in peri-urban Nairobi are infected with various species of Anaplasma and E. minasensis. To understand the extent of these infections in other parts of the country, large-scale screening studies as well as vector identification is necessary to inform strategic control.

Molecular evidence confirms occurrence of Rhipicephalus microplus Clade A in Kenya and sub-Saharan Africa

Background

The tick vector Rhipicephalus microplus which transmits Babesia spp. and rickettsial pathogens has not been reported in Kenya since 1998. More recently, the pathogenic Babesia bovis has been detected in cattle blood DNA. The status of R. microplus in Kenya remains unknown. This study employed morphological and molecular tools to characterize R. microplus originating from Kenya and assess the genetic relationships between Kenyan and other African R. microplus genotypes.

Methods

Ticks were collected in south-eastern Kenya (Kwale County) from cattle and characterized to investigate the existence of R. microplus. Genetic and phylogenetic relationships between the Kenyan and other annotated R. microplus reference sequences was investigated by analysis of the cytochrome c oxidase subunit 1 (cox1) gene. To further characterize Kenyan ticks, we generated low coverage whole genome sequences of two R. microplus, one R. decoloratus and R. appendiculatus. A B. bovis specific TaqMan probe qPCR assay was used to detect B. bovis in gDNA from R. microplus ticks.

Results

Occurrence of R. microplus was confirmed in Kwale County, Kenya. The Kenyan R. microplus cox1 sequences showed very high pairwise identities (> 99%) and clustered very closely with reference African R. microplus sequences. We found a low genetic variation and lack of geographical sub-structuring among the African cox1 sequences of R. microplus. Four complete mitochondrial (mt) genomes for two R. microplus, one R. decoloratus and one R. appendiculatus were assembled from next generation sequence data. The mitochondrial genome sequences of the two Kenyan R. microplus ticks clustered closely with reference genome sequences from Brazil, USA, Cambodia and India forming R. microplus Clade A. No B. bovis was detected in the Kwale R. microplus DNA.

Conclusions

These findings confirm the presence of R. microplus in Kenya and suggest that R. microplus Clade A is prevalent in cattle in sub-Saharan Africa. These and other recent findings of widespread occurrence of R. microplus in Africa provide a strong justification for urgent surveillance to determine and monitor the spread of R. microplus and vector competence of Boophilus ticks for B. bovis in Africa, with the ultimate goal of strategic control.

First detection of Theileria parva in cattle from Cameroon in the absence of the main tick vector Rhipicephalus appendiculatus

A major risk factor for the spread of livestock diseases and their vectors is the uncontrolled transboundary movement of live animals for trade and grazing. Such movements constrain effective control of tick-transmitted pathogens, including Theileria parva. Only limited studies have been undertaken to identify ticks and tick-borne diseases (TTBDs) affecting cattle in central African countries, including Cameroon. We hereby report the collection of baseline data on the prevalence of T. parva in Cameroon through a countrywide cross-sectional survey, conducted in 2016, involving collection of blood samples from cattle from 63 sites across the five agro-ecological zones (AEZs) of the country. ELISA-based surveillance of infected cattle was performed on 479 randomly selected samples and revealed specific antibodies to T. parva in 22.7% and T. mutans in 41.1% of cattle. Screening of 1,340 representative DNA samples for the presence of T. parva identified 25 (1.86%) positives using a p104 antigen gene-based nested PCR assay. The positives were distributed across agro-ecological zones I, II, III and V. None of the p104 positive cattle exhibited clinical symptoms of East Coast fever (ECF). Using reverse line blot (RLB), 58 (4.3%) and 1,139 (85%) of the samples reacted with the T. parva and T. mutans oligonucleotide probes, respectively. This represents the first report of T. parva from Cameroon. Surprisingly, no Rhipicephalus appendiculatus ticks, the main vector of T. parva, were identified in a parallel study involving comprehensive morphological and molecular survey of tick species present in the country. Only two of the 25 p104 positive cattle were PCR-positive for the CD8+ T-cell target schizont-expressed antigen gene Tp1. Cloning and sequencing of Tp1 amplicons revealed sequence identity with the reference T. parva Muguga. This new finding raises serious concerns of a potential spread of ECF into the central African region.

IDEAL, the Infectious Diseases of East African Livestock project open access database and biobank

The Infectious Diseases of East African Livestock (IDEAL) project was a longitudinal cohort study of calf health which was conducted in Western Kenya between 2007–2010. A total of 548 East African shorthorn zebu calves were recruited at birth and followed at least every 5 weeks during the first year of life. Comprehensive clinical and epidemiological data, blood and tissue samples were collected at every visit. These samples were screened for over 100 different pathogens or infectious exposures, using a range of diagnostic methods. This manuscript describes this comprehensive dataset and bio-repository, and how to access it through a single online site (http://data.ctlgh.org/ideal/). This provides extensive filtering and searching capabilities. These data are useful to illustrate outcomes of multiple infections on health, investigate patterns of morbidity and mortality due to parasite infections, and to study genotypic determinants of immunity and disease.

Measurement(s)	Health • disease • genotype • Phenotypic variability
Technology Type(s)	Examination • single-nucleotide polymorphism analysis
Sample Characteristic - Organism	Bos indicus
Sample Characteristic - Environment	farm
Sample Characteristic - Location	Kenya

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12459737

Upscaling the Surveillance of Tick-borne Pathogens in the French Caribbean Islands

Despite the high burden of vector-borne disease in (sub)tropical areas, few information are available regarding the diversity of tick and tick-borne pathogens circulating in the Caribbean. Management and control of vector-borne disease require actual epidemiological data to better assess and anticipate the risk of (re)emergence of tick-borne diseases in the region. To simplify and reduce the costs of such large-scale surveys, we implemented a high-throughput microfluidic real-time PCR system suitable for the screening of the main bacterial and parasitic genera involved in tick-borne disease and potentially circulating in the area. We used the new screening tool to perform an exploratory epidemiological study on 132 adult specimens of Amblyomma variegatum and 446 of Rhipicephalus microplus collected in Guadeloupe and Martinique. Not only the system was able to detect the main pathogens of the area-Ehrlichia ruminantium, Rickettsia africae, Anaplasma marginale, Babesia bigemina and Babesia bovis-but the system also provided evidence of unsuspected microorganisms in Caribbean ticks, belonging to the Anaplasma, Ehrlichia, Borrelia and Leishmania genera. Our study demonstrated how high-throughput microfluidic real-time PCR technology can assist large-scale epidemiological studies, providing a rapid overview of tick-borne pathogen and microorganism diversity, and opening up new research perspectives for the epidemiology of tick-borne pathogens.

Investigations into the carrier-state of Theileria sp. (buffalo) in cattle

The Theileria are apicomplexan parasites transmitted by ticks to vertebrate hosts. Most Theileria species exhibit some form of host or vector specificity, since under endemic conditions only a limited number of tick species act as vectors and not all vertebrate hosts are able to maintain a persistent carrier state. Data for Theileria sp. (buffalo) suggest host specificity for African buffalo (Syncerus caffer). However, T. sp. (buffalo) infections in cattle co-grazing with African buffalo have been reported in Kenya and schizonts were cultured from these infected cattle, raising questions regarding host specificity. A Corridor disease outbreak in 2013 on a ranch in South Africa where cattle co-grazed with Theileria parva and T. sp. (buffalo) infected buffalo presented the opportunity to investigate the possible carrier-state of T. sp. (buffalo) in cattle using real-time PCR analysis. Almost all buffalo (n = 19, 95%) were infected with T. sp. (buffalo) and showed CP values (22-20) indicative of high parasitemia similar to that observed for buffalo in endemic areas. Conversely, only ~14-27% cattle (n = 69, 100, 96) were positive with CP values (31-40) suggesting low parasitemia and a carrier state epidemiology different from African buffalo. Long term monitoring of T. sp. (buffalo) positive cattle showed that most cattle lost their parasitemia or presented fluctuating parasitemia around the PCR assay detection limit. A single splenectomized animal showed a persistent carrier state. The general trends and epidemiology observed in cattle infected with T. sp. (buffalo) are similar to that seen for buffalo-adapted T. parva, for which a defined carrier state in cattle has not yet been proven. The study suggests that cattle may be infected by T. sp. (buffalo) but are not definitive hosts that play an important part in the epidemiology of this parasite.

Pentaplex PCR assay for rapid differential detection of Babesia bigemina, Theileria annulata, Anaplasma marginale and Trypanosoma evansi in cattle

A multiplex PCR (mPCR) assay for simultaneous detection and differentiation of four major haemoparasites in crossbred cattle was established using parasite specific genomic DNA and four sets of primer pairs targeting AMA-1, Tams1, MSP5 and VSG genes of Babesia bigemina, Theileria annulata, Anaplasma marginale and Trypanosoma evansi generating precise amplicons of 448, 156, 382 and 110 bp, respectively. An internal amplification control, 202 bp bovine β-casein gene fragment, was simultaneously amplified with four target genes to avoid false-negative results. The sensitivity of mPCR was 3.44 × 10², 5.9 × 10³, 2.88 × 10² and 3.3 × 10³ copies for B. bigemina, T. annulata, A. marginale and T. evansi, respectively. mPCR of cattle clinical samples (n = 516), suspected for haemoparasites, revealed single haemoparasitic infection in 279 (54.06%) cases, whereas mixed infection was recorded in 54 (10.46%) samples. In clinical samples, coinfection with T. annulata and A. marginale was the most common. The findings of mPCR were consistent with uniplex PCR under field conditions except for subtle variations in A. marginale infection. Overall, the mPCR assay represents an economical, reproducible and robust diagnostic tool for concurrent detection of cattle haemoparasites and large scale epidemiological studies.

Prevalence and risk factors associated with Ehrlichia infections in smallholder dairy cattle in Nairobi City County, Kenya

BACKGROUND AND AIM

Ehrlichiosis caused by Ehrlichia ruminantium is a tick-borne disease of great economic importance in cattle production worldwide. Despite its economic impact, limited knowledge is available on its epidemiology in Africa, including Kenya. Suspected cases of E. ruminantium infections have been reported in the recent past to the University of Nairobi's Veterinary Hospital, prompting the need to investigate their possible re-emergence. Therefore, this study was aimed at determining the prevalence of E. ruminantium among smallholder dairy cattle in Nairobi City County and to assess potential risk factors. This knowledge may guide the development of appropriate control strategies of ehrlichiosis, subsequently reducing associated losses.

MATERIALS AND METHODS

A total of 107 smallholder dairy farms from Nairobi City County were recruited for the study. Blood samples were collected from 314 apparently healthy dairy cattle, and Giemsa-stained blood smears were screened under the microscope for Ehrlichia species. A commercial antigen enzyme-linked immunosorbent assay (ELISA) kit was then used to confirm the presence of the infections in serum samples. A pre-tested questionnaire was used to collect data on management practices that may be potential risk factors. A univariate and mixed-effects logistic regression was then used to determine significant risk factors.

RESULTS

On microscopy, 79.3% (249/314) of the sampled animals had Ehrlichia-like inclusion bodies in white blood cells, though only 18.6% (95% confidence interval [CI] 14.2-23.0) of these were confirmed to be E. ruminantium on ELISA. A farm-level prevalence of 35.5% (95% CI 27.0-45.3) was reported. Female-headed households (p=0.013), farms in Langata region (p=0.027), cleaning of cowsheds fortnightly (p=0.019), and roofing of cowshed (p=0.022) were factors significantly associated with E. ruminantium infections.

CONCLUSION

There is a relatively high prevalence of E. ruminantium infections in apparently healthy cattle in smallholder dairy farms in this area, warranting control measures. It is critical to improve animal welfare-related factors, such as cowshed cleaning and roofing, as well as the strategic location of farms, especially, since reservoirs may reduce infection levels in the farms, in relation to wildlife. However, since Ehrlichia-like inclusion bodies other than those of E. ruminantium were observed in this study, there is a need to investigate further these factors and the possibility of other Ehrlichia species infecting cattle in the study area.

The host-specificity of Theileria sp. (sable) and Theileria sp. (sable-like) in African Bovidae and detection of novel Theileria in antelope and giraffe

Tick-borne diseases caused by Theileria are of economic importance in domestic and wildlife ruminants. The majority of Theileria infects a limited number of host species, supporting the concept of host specificity. However, some Theileria seem to be generalists challenging the host specificity paradigm, such as Theileria sp. (sable) reported from various vertebrate hosts, including African buffalo, cattle, dogs and different antelope species. We tested the hypothesis that T. sp. (sable) uses Bovidae as hosts in general using a real-time polymerase chain reaction assay specific for T. sp. (sable) and a closely related genotype: T. sp. (sable-like). Various antelope species from the Tragelaphini (black wildebeest, blesbuck, blue wildebeest, gemsbuck, sable and waterbuck) tested positive for either T. sp. (sable) or T. sp. (sable-like). However, no African buffalo (n = 238) or cattle (n = 428) sampled in the current study tested positive, suggesting that these latter species are not carrier hosts. The results were confirmed using next-generation sequencing which also indicated at least 13 new genotypes or species found in various antelope and giraffes. Genotypes were found in single host species or in evolutionarily related hosts, suggesting that host specificity in Theileria may be a lineage specific phenomenon likely associated with tick-host-parasite co-evolution.

First Molecular Evidence of Anaplasma bovis and Anaplasma phagocytophilum in Bovine from Central Punjab, Pakistan

Obligate intracellular bacteria belonging to the genus Anaplasma spp. are responsible for causing a hemolytic disease called anaplasmosis in animals, as well as in humans. This study was aimed at the molecular identification and genetic analysis of responsible causative agents of anaplasmosis beyond those already reported. A survey was performed during July and August 2018 in the Jhang District, Punjab, Pakistan. Four hundred and fifty blood samples from asymptomatic, tick-infested cattle were collected on FTA cards and tested for the Anaplasma spp. presence using nested-polymerase chain reaction (PCR) methods. The 16S ribosomal RNA gene sequences generated from the positive samples were used for genetic analysis of Anaplasma spp. The nested-PCR results showed the presence of two Anaplasma spp. with an overall prevalence rate of 10.44%, where the prevalence of A. bovis and A. phagocytophilum was 7.78% and 2.66%, respectively. The study portrayed new molecular data on the prevalence of Anaplasma spp. in the studied cattle population, indicating a potential threat to the human population as well.

Prevalence of hemoprotozoan parasites in small ruminants along a human-livestock-wildlife interface in western Uganda

Small ruminants are important to community livelihood in developing countries; however information on the role of hemoprotozoan parasites is scanty. The objective of the study was to determine hemoprotozoan parasitic prevalence in western Uganda and identify major areas associated with these infections. This was a cross sectional study conducted at the edge of Budongo Conservation Forest in Masindi district of western Uganda in which 712 small ruminants were sampled. Blood from the jugular vein was collected from caprines and ovines and placed in an EDTA tube, and transported to the laboratory for examination. Thin and thick smears were prepared and examined by microscopy for hemoprotozoan parasites, and DNA was extracted and examined by PCR for Trypanosoma spp. A total of 13 villages in Budongo sub-county were surveyed and the study showed that caprines were the major small ruminants of importance to the community. Prevalence of hemoprotozoan parasites was as follows; anaplasmosis (3.65%) > theileriosis (0.45%) > trypanosomiasis (0.15%) and babesiosis (0%) by microscopy. Infections were found in the young with the exception of Anaplasma spp. while coinfections of anaplasmosis and theileriosis were high. Molecular analysis showed an overall trypanosome prevalence of 9.27% (PCR), mainly due to Trypanosoma brucei and T. congolense forest. Villages with trypanosomiasis were found in lowlands and swamps. The current trypanosomiasis prevalence in small ruminants of Uganda was 10 times greater than that previously reported showing that the disease burden has increased overtime within Uganda. A prevalence of 0.14% (95% CI: 0.00, 0.78) for the SRA gene showed that small ruminants would be important reservoirs of infection to humans. Hemoprotozoan parasites are a threat to community livelihood in developing countries and the role of molecular diagnostic techniques in disease monitoring was re-emphasized by this study. Information on primary hosts involved in the propagation of hemoprotozoan parasites in Uganda would help streamline prospective disease surveillance and control efforts.

Development of multiplex PCR assay for concurrent detection of tick borne haemoparasitic infections in bovines

This study describes development and evaluation of a multiplex PCR assay for simultaneous detection of Theileria annulata, Babesia bigemina and Anaplasma marginale infections in bovines. The assay was developed using parasites specific genomic DNA and three sets of PCR primers targeting the Tams1, 18S rRNA and 16S rRNA genes of T. annulata, B. bigemina and A. marginale, respectively. Blood samples collected from a total of 461 bovines, suspected for haemoparasitic infections, were examined microscopically to record the status of infection and simultaneously, genomic DNA extracted from these blood samples were utilized for the optimization and validation of multiplex PCR assay. Microscopic examination of blood samples revealed presence of single and multiple species of haemoparasites in 25.8% and 2.4% samples, respectively. Results of multiplex PCR revealed the presence of single haemoparasitic species infection in 159 cases (34.5%), whereas mixed infection was recorded in 82 (17.8%) samples. Occurrence of individual species infection detected by mPCR in the study was 26.03% (120/461) for T. annulata, 3.25% (15/461) for B. bigemina and 5.20% (24/461) for A. marginale. The detection limit of multiplex PCR assay was at the template dilutions of 10-6, 10-6 and 10-4, which corresponded to 0.1 pg, 0.1 pg and 10.0 pg of DNA for T. annulata, A. marginale, and B. bigemina, respectively. Based on the high diagnostic sensitivity and throughput, multiplex PCR assay developed in the present study could be exploited as a tool to conduct large-scale epidemiological survey for tick-borne haemoparasitic infection of bovines.

Cross-Genera PCR Amplification of DNA from Apicomplexan Parasites

BACKGROUND

The discovery of an unexpected genetic sequence raised doubts about the specificity of a primer pair targeting Babesia spp. and Theileria spp. This study aimed to check the specificity of this primer pair.

METHODS

Conventional end-point PCR and real-time PCR protocols using primers targeting the 18S rRNA gene V4 hypervariable region of Babesia spp. and Theileria spp. were tested for potential cross-genera amplification using DNA from a palette of parasitic protists and pathogenic bacteria as a template. These investigations took place at the Ludwig Maximilian University of Munich (Germany) in 2010 as part of the EDEN project.

RESULTS

Successful amplification was obtained with DNA from five apicomplexan genera: Babesia, Theileria, Hepatozoon, Toxoplasma, and Hammondia. No amplicons were obtained when DNA from Leishmania infantum or bacteria within the genera Borrelia, Leptospira or Anaplasma was used as a template.

CONCLUSION

This cross-genera amplification ability is useful for the quick exclusion of many parasite species from PCR negative diagnostic samples. Accurate species identification from PCR positive samples requires genetic sequencing of the amplicon.

Molecular epidemiology of Babesia species, Theileria parva, and Anaplasma marginale infecting cattle and the tick control malpractices in Central and Eastern Uganda

East Coast fever, babesiosis, and anaplasmosis are the major tick-borne diseases affecting cattle productivity in Uganda. The emergence of acaricide-resistant ticks is suspected to have caused a rise in hemoparasites. This study sought to detect and characterize hemoparasites among farms in acaricide-failure hotspots of central as compared to the acaricide-failure naïve areas in Eastern Uganda. Nested PCR assays were performed to determine the prevalences of Babesia bovis, Babesia bigemina, Theileria parva, and Anaplasma marginale in cattle blood samples sourced from randomly selected farms. Randomly selected isolates were sequenced to determine the genetic diversity of the parasites using the following marker genes: B. bovis spherical body protein 4, B. bigemina rhoptry-associated protein 1a, T. parva 104 kDa microneme-rhoptry antigen, and A. marginale major surface protein 5. Furthermore, partially and fully engorged adult ticks were collected for taxonomy, and tick-control practices were assessed using a semi-structured questionnaire. The prevalences of B. bigemina, T. parva, and A. marginale in cattle were 17.2, 65.1, and 22.0%, and 10.0, 26.5, and 3% in the central and eastern region, respectively. Whilst, B. bovis was not detected in the farms involved. The sequences for B. bigemina, T. parva, and A. marginale from the central region showed 99% identity with those from the eastern region. Of the 548 ticks collected, 319, 147, 76, and 6 were Rhipicephalus (Boophilus) decoloratus, Rhipicephalus appendiculatus, Amblyomma variegatum, and Rhipicephalus evertsi evertsi, respectively. The Rhipicephalus ticks were more abundant in the central region, whereas A. variegatum ticks were more abundant in the eastern region. Tick control malpractices were found in both Central and Eastern Uganda, and 42 of the 56 surveyed farms lacked appropriate restraining facilities and so they utilized either ropes or a 'boma' (enclosure). In summary, B. bigemina, T. parva, A. marginale and their co-infections were more prevalent in the central than eastern region; even though, tick control malpractices were observed in both regions. Therefore, an urgent tick and TBD control strategy is needed.

Molecular Detection of Tick-Borne Pathogen Diversities in Ticks from Livestock and Reptiles along the Shores and Adjacent Islands of Lake Victoria and Lake Baringo, Kenya

Although diverse tick-borne pathogens (TBPs) are endemic to East Africa, with recognized impact on human and livestock health, their diversity and specific interactions with tick and vertebrate host species remain poorly understood in the region. In particular, the role of reptiles in TBP epidemiology remains unknown, despite having been implicated with TBPs of livestock among exported tortoises and lizards. Understanding TBP ecologies, and the potential role of common reptiles, is critical for the development of targeted transmission control strategies for these neglected tropical disease agents. During the wet months (April-May; October-December) of 2012-2013, we surveyed TBP diversity among 4,126 ticks parasitizing livestock and reptiles at homesteads along the shores and islands of Lake Baringo and Lake Victoria in Kenya, regions endemic to diverse neglected tick-borne diseases. After morphological identification of 13 distinct Rhipicephalus, Amblyomma, and Hyalomma tick species, ticks were pooled (≤8 individuals) by species, host, sampling site, and collection date into 585 tick pools. By supplementing previously established molecular assays for TBP detection with high-resolution melting analysis of PCR products before sequencing, we identified high frequencies of potential disease agents of ehrlichiosis (12.48% Ehrlichia ruminantium, 9.06% Ehrlichia canis), anaplasmosis (6.32% Anaplasma ovis, 14.36% Anaplasma platys, and 3.08% Anaplasma bovis,), and rickettsiosis (6.15% Rickettsia africae, 2.22% Rickettsia aeschlimannii, 4.27% Rickettsia rhipicephali, and 4.95% Rickettsia spp.), as well as Paracoccus sp. and apicomplexan hemoparasites (0.51% Theileria sp., 2.56% Hepatozoon fitzsimonsi, and 1.37% Babesia caballi) among tick pools. Notably, we identified E. ruminantium in both Amblyomma and Rhipicephalus pools of ticks sampled from livestock in both study areas as well as in Amblyomma falsomarmoreum (66.7%) and Amblyomma nuttalli (100%) sampled from tortoises and Amblyomma sparsum (63.6%) sampled in both cattle and tortoises at Lake Baringo. Similarly, we identified E. canis in rhipicephaline ticks sampled from livestock and dogs in both regions and Amblyomma latum (75%) sampled from monitor lizards at Lake Victoria. These novel tick-host-pathogen interactions have implications on the risk of disease transmission to humans and domestic animals and highlight the complexity of TBP ecologies, which may include reptiles as reservoir species, in sub-Saharan Africa.

Limited sharing of tick-borne hemoparasites between sympatric wild and domestic ungulates

Tick-borne hemoparasites (TBHs) are a group of pathogens of concern in animal management because they are associated with a diversity of hosts, including both wild and domestic species. However, little is known about how frequently TBHs are shared across the wildlife-livestock interface in natural settings. Here, we compared the TBHs of wild Grant's gazelle (Nanger granti) and domestic sheep (Ovis aries) in a region of Kenya where these species extensively overlap. Blood samples collected from each species were screened for piroplasm and rickettsial TBHs by PCR-based amplification of 18S/16S ribosomal DNA, respectively. Overall, 99% of gazelle and 66% of sheep were positive for Babesia/Theileria, and 32% of gazelle and 47% sheep were positive for Anaplasma/Ehrlichia. Sequencing a subset of positive samples revealed infections of Theileria and Anaplasma. Sequences sorted into seven phylogenetically distinct genotypes-two Theileria, and five Anaplasma. With the exception of a putatively novel Anaplasma lineage from Grant's gazelle, these genotypes appeared to be divergent forms of previously described species, including T. ovis, A. ovis, A. bovis, and A. platys. Only one genotype, which clustered within the A. platys clade, contained sequences from both gazelle and sheep. This suggests that despite niche, habitat, and phylogenetic overlap, the majority of circulating tick-borne diseases may not be shared between these two focal species.

Molecular investigation of tick-borne haemoparasite infections among transhumant zebu cattle in Karamoja Region, Uganda

Tick-borne diseases (TBDs) are a major constraint to cattle production in pastoral areas in Africa. Although information on tick-borne infections is important to prioritise control approaches, it is limited for transhumant zebu cattle in Karamoja, Uganda. We conducted a study to determine the occurrence and level of tick-borne infections among cattle in Karamoja Region. A total of 240 cattle were selected for blood collection using systematic sampling in 20 randomly-selected herds in two districts. The hypervariable V4 region of the 18S rRNA gene for Theileria/Babesia and the V1 region of the 16S rRNA gene for Ehrlichia/Anaplasma were amplified and hybridised to genus- and species-specific oligonucleotide probes on a reverse line blot (RLB) membrane. A duplex quantitative real-time polymerase chain reaction (qPCR) assay based on msp1β and groEL genes was used for the detection of Anaplasma marginale and A. centrale, while monoplex qPCR assays were used for the detection of Ehrlichia ruminantium (226bp fragment of the pCS20 region) and Theileria parva (18S rRNA gene). The RLB hybridisation assay demonstrated the presence of tick-borne haemoparasites in all but one sample (99.6%), mostly as mixed infections (97.5%). The most frequently detected species were Theileria mutans (88.3%, 95% confidence interval: 84.6-91.7%), A. marginale (73.8%: 68.3-78.8%), Theileria velifera (71.3%: 65.8-76.7%) and Anaplasma sp. Omatjenne (63.3%: 57.5-68.8%). Other virulent pathogens, namely Babesia bigemina (5.0%) and T. parva (2.9%), were also detected with RLB, but not E. ruminantium. The proportions of qPCR positive samples were 82.9% (A. marginale), 12.1% (A. centrale), 3.3% (T. parva), and 1.7% (E. ruminantium). The full-length 18S rRNA genes from 6 out of 47 samples that were positive on RLB for the Babesia genus-specific probe and not for any of the Babesia species-specific probes were amplified, cloned and sequenced. The sequences were used to construct phylogenetic trees. Variations (5 to 9 nucleotides) in the 18S rRNA gene sequences of B. bigemina were identified, when compared with B. bigemina sequences from other parts of the world. Three nucleotide differences in the B. bigemina probe region may explain the failure of the RLB hybridisation assay to detect B. bigemina in some samples. T. mutans and B. bigemina sequences grouped in separate clades from previously published sequences. In conclusion, this study demonstrated high and widespread occurrence, and sequence variation of tick-borne haemoparasites among cattle in the pastoral area of Karamoja, which is useful for diagnosis and control of TBDs.

Tick-borne pathogens of zoonotic and veterinary importance in Nigerian cattle

BACKGROUND

Ticks and tick-borne diseases undermine cattle fitness and productivity in the whole of sub-Saharan Africa, including Nigeria. In this West African country, cattle are challenged by numerous tick species, especially during the wet season. Consequently, several TBDs are known to be endemic in Nigerian cattle, including anaplasmosis, babesiosis, cowdriosis and theilerioris (by Theileria mutans and Theileria velifera). To date, all investigations on cattle TBDs in Nigeria have been based on cytological examinations and/or on serological methods. This study aimed to ascertain the occurrence of tick-borne pathogens of veterinary and zoonotic importance in cattle in Nigeria using molecular approaches.

METHODS

In October 2008, 704 whole blood samples were collected from indigenous cattle in the Plateau State, Nigeria. Analysis for tick-borne pathogens was conducted by means of PCR-based reverse line blotting (RLB) and sequencing targeting a panel of five genera of microorganisms (i.e. Babesia, Theileria, Anaplasma, Ehrlichia and Rickettsia spp.).

RESULTS

In total, 561/704 (82.6%) animals were found infected, with 465 (69.6%) of them being infected by two or more microorganisms, with up to 77 possible combinations of pathogens detected. Theileria mutans was the most prevalent microorganism (66.3%), followed by Theileria velifera (52.4%), Theileria taurotragi (39.5%), Anaplasma marginale (39.1%), Anaplasma sp. (Omatjenne) (34.7%), Babesia bigemina (7.9%), Anaplasma centrale (6.3%), Anaplasma platys (3.9%), Rickettsia massiliae (3.5%), Babesia bovis (2.0%) and Ehrlichia ruminantium (1.1%). Calves were found significantly less infected than juvenile and adult cattle.

CONCLUSIONS

This study provides updated, molecular-based information on cattle TBDs in Nigeria. The molecular approach employed allowed the diagnosis of numerous positive cases including carrier statuses, multiple infections and novel pathogen detections within the indigenous cattle population. Moreover, the RLB method here described enabled the detection of veterinary agents not only pertaining to bovine health, including also those of zoonotic importance. The high prevalence recorded for T. mutans, T. velifera, A. marginale, T. taurotragi and Anaplasma sp. (Omatjenne), suggests they may be endemically established in Nigeria, whereas the lower prevalence recorded for other microorganisms (i.e. A. centrale and B. bovis) highlights a less stable epidemiological scenario, requiring further investigations.

Investigating the diversity of the 18S SSU rRNA hyper-variable region of Theileria in cattle and Cape buffalo (Syncerus caffer) from southern Africa using a next generation sequencing approach

Molecular classification and systematics of the Theileria is based on the analysis of the 18S rRNA gene. Reverse line blot or conventional sequencing approaches have disadvantages in the study of 18S rRNA diversity and a next-generation 454 sequencing approach was investigated. The 18S rRNA gene was amplified using RLB primers coupled to 96 unique sequence identifiers (MIDs). Theileria positive samples from African buffalo (672) and cattle (480) from southern Africa were combined in batches of 96 and sequenced using the GS Junior 454 sequencer to produce 825711 informative sequences. Sequences were extracted based on MIDs and analysed to identify Theileria genotypes. Genotypes observed in buffalo and cattle were confirmed in the current study, while no new genotypes were discovered. Genotypes showed specific geographic distributions, most probably linked with vector distributions. Host specificity of buffalo and cattle specific genotypes were confirmed and prevalence data as well as relative parasitemia trends indicate preference for different hosts. Mixed infections are common with African buffalo carrying more genotypes compared to cattle. Associative or exclusion co-infection profiles were observed between genotypes that may have implications for speciation and systematics: specifically that more Theileria species may exist in cattle and buffalo than currently recognized. Analysis of primers used for Theileria parva diagnostics indicate that no new genotypes will be amplified by the current primer sets confirming their specificity. T. parva SNP variants that occur in the 18S rRNA hypervariable region were confirmed. A next generation sequencing approach is useful in obtaining comprehensive knowledge regarding 18S rRNA diversity and prevalence for the Theileria, allowing for the assessment of systematics and diagnostic assays based on the 18S gene.

Alpha proteobacteria of genusAnaplasma(Rickettsiales: Anaplasmataceae): Epidemiology and characteristics ofAnaplasmaspecies related to veterinary and public health importance

TheAnaplasmaspecies are important globally distributed tick-transmitted bacteria of veterinary and public health importance. These pathogens, cause anaplasmosis in domestic and wild animal species including humans.Rhipicephalus, Ixodes, DermacentorandAmblyommagenera of ticks are the important vectors ofAnaplasma.Acute anaplasmosis is usually diagnosed upon blood smear examination followed by antibodies and nucleic acid detection. All age groups are susceptible but prevalence increases with age. Serological cross-reactivity is one of the important issues amongAnaplasmaspecies. They co-exist and concurrent infections occur in animals and ticks in same geographic area. These are closely related bacteria and share various common attributes which should be considered while developing vaccines and diagnostic assays. Movement of susceptible animals from non-endemic to endemic regions is the major risk factor of bovine/ovine anaplasmosis and tick-borne fever. Tetracyclines are currently available drugs for clearance of infection and treatment in humans and animals. Worldwide vaccine is not yet available. Identification, elimination of reservoirs, vector control (chemical and biological), endemic stability, habitat modification, rearing of tick resistant breeds, chemotherapy and tick vaccination are major control measures of animal anaplasmosis. Identification of reservoirs and minimizing the high-risk tick exposure activities are important control strategies for human granulocytic anaplasmosis.

Molecular detection and characterization of Babesia bovis, Babesia bigemina, Theileria species and Anaplasma marginale isolated from cattle in Kenya

Background

Infections with Babesia bovis, Babesia bigemina, Theileria species and Anaplasma marginale are endemic in Kenya yet there is a lack of adequate information on their genotypes. This study established the genetic diversities of the above tick-borne hemoparasites infecting cattle in Kenya.

Methods

Nested PCR and sequencing were used to determine the prevalence and genetic diversity of the above parasites in 192 cattle blood samples collected from Ngong and Machakos farms. B. bovis spherical body protein 4, B. bigemina rhoptry-associated protein 1a, A. marginale major surface protein 5, Theileria spp. 18S rRNA, T. parva p104 and T. orientalis major piroplasm surface protein were used as the marker genes.

Results

B. bovis, B. bigemina, T. parva, T. velifera, T. taurotragi, T. mutans and A. marginale were prevalent in both farms, whereas T. ovis, Theileria sp. (buffalo) and T. orientalis were found only in Ngong farm. Co-infections were observed in more than 50 % of positive samples in both farms. Babesia parasites and A. marginale sequences were highly conserved while T. parva and T. orientalis were polymorphic. Cattle-derived T. parva was detected in Machakos farm. However, cattle and buffalo–derived Theileria were detected in Ngong farm suggesting interactions between cattle and wild buffaloes. Generally, the pathogens detected in Kenya were genetically related to the other African isolates but different from the isolates in other continents.

Conclusions

The current findings reaffirm the endemicity and co-infection of cattle with tick-borne hemoparasites, and the role of wildlife in pathogens transmission and population genetics in Kenya.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-015-1106-9) contains supplementary material, which is available to authorized users.

The African buffalo parasite Theileria. sp. (buffalo) can infect and immortalize cattle leukocytes and encodes divergent orthologues of Theileria parva antigen genes

African Cape buffalo (Syncerus caffer) is the wildlife reservoir of multiple species within the apicomplexan protozoan genus Theileria, including Theileria parva which causes East coast fever in cattle. A parasite, which has not yet been formally named, known as Theileria sp. (buffalo) has been recognized as a potentially distinct species based on rDNA sequence, since 1993. We demonstrate using reverse line blot (RLB) and sequencing of 18S rDNA genes, that in an area where buffalo and cattle co-graze and there is a heavy tick challenge, T. sp. (buffalo) can frequently be isolated in culture from cattle leukocytes. We also show that T. sp. (buffalo), which is genetically very closely related to T. parva, according to 18s rDNA sequence, has a conserved orthologue of the polymorphic immunodominant molecule (PIM) that forms the basis of the diagnostic ELISA used for T. parva serological detection. Closely related orthologues of several CD8 T cell target antigen genes are also shared with T. parva. By contrast, orthologues of the T. parva p104 and the p67 sporozoite surface antigens could not be amplified by PCR from T. sp. (buffalo), using conserved primers designed from the corresponding T. parva sequences. Collectively the data re-emphasise doubts regarding the value of rDNA sequence data alone for defining apicomplexan species in the absence of additional data. ‘Deep 454 pyrosequencing’ of DNA from two Theileria sporozoite stabilates prepared from Rhipicephalus appendiculatus ticks fed on buffalo failed to detect T. sp. (buffalo). This strongly suggests that R. appendiculatus may not be a vector for T. sp. (buffalo). Collectively, the data provides further evidence that T. sp. (buffalo). is a distinct species from T. parva.

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Theileria sp. (buffalo) can infect and immortalize cattle leukocytes.

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Antigen genes of T. sp. (buffalo) vary in level of identity to those of T. parva

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The tick that transmits T. sp. (buffalo) to cattle is not Rhipicephalus appendiculatus

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18s rDNA sequence information alone is insufficient to define species of Theileria