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

Parasite co-infections and their impact on survival of indigenous cattle

In natural populations, individuals may be infected with multiple distinct pathogens at a time. These pathogens may act independently or interact with each other and the host through various mechanisms, with resultant varying outcomes on host health and survival. To study effects of pathogens and their interactions on host survival, we followed 548 zebu cattle during their first year of life, determining their infection and clinical status every 5 weeks. Using a combination of clinical signs observed before death, laboratory diagnostic test results, gross-lesions on post-mortem examination, histo-pathology results and survival analysis statistical techniques, cause-specific aetiology for each death case were determined, and effect of co-infections in observed mortality patterns. East Coast fever (ECF) caused by protozoan parasite Theileria parva and haemonchosis were the most important diseases associated with calf mortality, together accounting for over half (52%) of all deaths due to infectious diseases. Co-infection with Trypanosoma species increased the hazard for ECF death by 6 times (1.4–25; 95% CI). In addition, the hazard for ECF death was increased in the presence of Strongyle eggs, and this was burden dependent. An increase by 1000 Strongyle eggs per gram of faeces count was associated with a 1.5 times (1.4–1.6; 95% CI) increase in the hazard for ECF mortality. Deaths due to haemonchosis were burden dependent, with a 70% increase in hazard for death for every increase in strongyle eggs per gram count of 1000. These findings have important implications for disease control strategies, suggesting a need to consider co-infections in epidemiological studies as opposed to singlepathogen focus, and benefits of an integrated approach to helminths and East Coast fever disease control.The Wellcome Trust (grant No. 079445)http://www.plosone.orgam201

Design and descriptive epidemiology of the Infectious Diseases of East African Livestock (IDEAL) project, a longitudinal calf cohort study in western Kenya

BACKGROUND: There is a widely recognised lack of baseline epidemiological data on the dynamics and impacts of infectious cattle diseases in east Africa. The Infectious Diseases of East African Livestock (IDEAL) project is an epidemiological study of cattle health in western Kenya with the aim of providing baseline epidemiological data, investigating the impact of different infections on key responses such as growth, mortality and morbidity, the additive and/or multiplicative effects of co-infections, and the influence of management and genetic factors. A longitudinal cohort study of newborn calves was conducted in western Kenya between 2007-2009. Calves were randomly selected from all those reported in a 2 stage clustered sampling strategy. Calves were recruited between 3 and 7 days old. A team of veterinarians and animal health assistants carried out 5-weekly, clinical and postmortem visits. Blood and tissue samples were collected in association with all visits and screened using a range of laboratory based diagnostic methods for over 100 different pathogens or infectious exposures. RESULTS: The study followed the 548 calves over the first 51 weeks of life or until death and when they were reported clinically ill. The cohort experienced a high all cause mortality rate of 16% with at least 13% of these due to infectious diseases. Only 307 (6%) of routine visits were classified as clinical episodes, with a further 216 reported by farmers. 54% of calves reached one year without a reported clinical episode. Mortality was mainly to east coast fever, haemonchosis, and heartwater. Over 50 pathogens were detected in this population with exposure to a further 6 viruses and bacteria. CONCLUSION: The IDEAL study has demonstrated that it is possible to mount population based longitudinal animal studies. The results quantify for the first time in an animal population the high diversity of pathogens a population may have to deal with and the levels of co-infections with key pathogens such as Theileria parva. This study highlights the need to develop new systems based approaches to study pathogens in their natural settings to understand the impacts of co-infections on clinical outcomes and to develop new evidence based interventions that are relevant

Genomic diversity of East African shorthorn Zebu of western Kenya

Indigenous zebu cattle in Kenya are predominant across the country owing to their tropical adapted physiology. These breeds have been embraced by most small-scale farmers, who are the drivers of the low-input sustainable agricultural sector within the country. Though autosomal microsatellites revealed ancient taurine and zebu admixture in East African sh0l1horn zebu (EASZ) cattle, the extent of this admixture and the effect of modern European taurine introgression through indiscriminate breed improvement programmes in these populations remains unclear. The population structure and ancestral origin of the EASZ a pre-requisite to genome-wide association studies has also not been documented yet. In this study, 548 East African shorthorn zebu (EASZ) calves were randomly sampled from 20 sub-locations across 4 agro-ecological zones in Western Kenya and monitored from bi11h to I year of age, with no veterinary intervention allowed. Data included reports of calf clinical episodes, post-mortem examination and selected sets of phenotypic parameters associated with infectious parasitic disease (Packed Cell Volume (PCV), parasiteamia load and body weight). Phenotypic data also included detailed information on coat color, coat patterns, hair texture, calf body stature measures, horn size, hump size and dewlap size. A total of 460 calves survived the one year period follow-up and diseases challenges, while 88 died across the one year period, succumbing to various infectious and non-infectious causes. The leading cause of death at 38% was attributed to East Coast Fever (ECF) infections. The main objectives of the study were to : (i) Evaluate the informativeness of the Illumina® BovineSNP50 beadchip, a genetic tool primarily developed for European commercial breed, on an indigenous African cattle population, (ii) unravel the genetic architecture and origin of EASZ of Western Kenya and (iii) identify imprints of genetic selection through phenotype-genotype associations. Out of the 56,947 SNPs genotyped using the IIIumina® BovineSNP50 beadchip, 55,777 were successfully mapped on the University of Maryland genome assembly (3 .0) 1 and only 6,151 failed the quality control criteria. An average genome spacing of 46 kbp was observed with less than 5% of the gaps between informative SNPs being larger than 100 kbp. The ancestral origin of the study cohort was established, with 83%, 15% and 2% of the genetic background being of Asiatic zebu, African taurine and European taurine ancestry respectively. Most importantly, we identified the main taurine ancestral source as African and established the degrees of admixture within this indigenous breed. In addition, a North-South genetic cline in the amount of European taurine introgression was observed \ ) I I VI with two localized hotspots in the Northern and central studied regions. The dissemination of the European blood was attributed to rampant breed improvement programmes and animal markets as main entry points. A three-tier categorization associated with the amount of European taurine introgression was revealed, namely pure (:S 1.56%), moderate (> 1.56 - < 12.5%) and substantial (~ 12.5%). Excluding the moderate and substantial calf categories, revealed an EASZ population that was genetically homogenous with closer genetic relatedness been observed within sub-locations than between sub-locations. However, genetic differentiation, between sub-locations was not significant and the population may be considered as "panmictic" for the purpose of genetic mapping. The effective population size (N) analysis, revealed a short stint of increasing population size but was generally characterized by a major population decline over-time. A rich diversity of coat colours and patterns was observed across the study site with a characteristic spatial distribution of some ofthese phenotypic traits. Significant SNPs were identified within or neighbouring genomic loci that control for selected non-disease (coat color) and disease traits (survival). Our findings provide valuable new insights in the understanding of the genetic landscape, genetic admixture and demographic history of an African indigenous breed. The genotype-phenotype association outcomes call for fU11her analysis aiming to unravel the genotype control of adaptations using more " powerful" approaches (e .g. High Density SNPs genotyping or next generation sequencing). We advocate for an urgent move towards understanding these unique adaptations of African indigenous cattle breeds before the ultimate loss of these ecologically important traits to unsustainable economic traits via indiscriminate crossbreeding.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

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

The development of sensitive surveillance technologies using PCR-based detection ofmicrobial DNA, such as the reverse line blot assay, can facilitate the gathering of epidemi-ological information on tick-borne diseases, which continue to hamper the productivityof livestock in many parts of Africa and elsewhere. We have employed a reverse line blotassay to detect the prevalence of tick-borne parasites in an intensively studied cohort ofindigenous calves in western Kenya. The calves were recruited close to birth and monitoredfor the presence of infectious disease for up to 51 weeks. The final visit samples from 453calves which survived for the study period were analyzed by RLB. The results indicated highprevalences of Theileria mutans (71.6%), T. velifera (62.8%), Anaplasma sp. Omatjenne (42.7%),A. bovis (39.9%), Theileria sp. (sable) (32.7%), T. parva (12.9%) and T. taurotragi (8.5%), withminor occurrences of eight other haemoparasites. The unexpectedly low prevalence of thepathogenic species Ehrlichia ruminantium was confirmed by a species-specific PCR targetingthe pCS20 gene region. Coinfection analyses of the seven most prevalent haemoparasitesindicated that they were present as coinfections in over 90% of the cases. The analysesrevealed significant associations between several of the Theileria parasites, in particular T.velifera with Theileria sp. sable and T. mutans, and T. parva with T. taurotragi. There was verylittle coinfection of the two most common Anaplasma species, although they were com-monly detected as coinfections with the Theileria parasites. The comparison of reverse line∗Wellcome Trust (grant no. 079445) through the Infectious Diseases of East African Livestock (IDEAL) project and the Institute of Tropical Medicine (ITM) through the University of Pretoria.http://www.elsevier.com/locate/vetparhb201

Map of Western Kenya showing the 4 agro-ecological zones and the 20 study sub-locations (in red).

<p>The study area comprised sub-locations falling within a 45 km radius from Busia town where the IDEAL project laboratory was located.</p

Plot of time to death for ECF and haemonchus deaths, the two main causes of calf mortality causing 33 and 10 deaths respectively.

<p>More than 80% of ECF deaths were observed in calves below 6 months of age, whereas most deaths attributed to haemonchosis were in calves older than 6 months.</p

List of covariates tested for their relationship with mortality due to ECF and haemonchosis.

<p>For infectious factors, the diagnostic tests (in bold) used are recorded against pathogens identified.</p

Results of significant predictors of haemonchosis deaths.

<p>Results of significant predictors of haemonchosis deaths.</p

Map showing number of deaths attributable to haemonchosis by sub-location.

<p>In total, 10 of 88 deaths were attributed to haemonchosis.</p