Coinfections in East African Shorthorn Zebu

The Infectious Diseases of East African Livestock (IDEAL) project followed 548 East African Shorthorn Zebu (EASZ) calves in Western Kenya for the first year of life and monitored the sequelae of infections by multiple parasites. More than 50 different parasites were identified during this time. The IDEAL project also gathered environmental information about the farm and collected phenotypic data on the calf and its dam. Calves were also genotyped for 55,777 single nucleotide polymorphisms (SNPs). Recent research has looked at coinfection in rodents and humans but not in indigenous cattle. Here I investigate the evidence for coinfection in EASZ and study the associations occurring between coinfecting parasites. In addition, I examine the genetic and phenotypic factors which predispose an individual to infection with multiple parasites. Using information gathered by the IDEAL project, my thesis consists of the following chapters. An investigation of the nature of concurrent associations and of lagged effects between different parasites. Using the parasites Theileria spp., Coccidia spp., Strongyloides spp., strongyles and Calicophoron spp. I show that the patterns of association between different parasites are complex: there is evidence for both positive and negative associations. For example, infection with Strongyloides spp. increased the risk of strongyle infection. Conversely, in other cases, being infected with one parasite decreased the calf’s risk of infection with another parasite: for example, infection with Strongyloides spp. decreased the risk of infection with Calicophoron spp. A study of the relationship between different respiratory viruses and their effect upon the host. I confirm that positive associations exist between Infectious Bovine Rhinotracheitis (IBR), Bovine Viral Diarrhoea Virus (BVDV) and Bovine Parainfluenza Virus Type 3 (PIV3) in a previously unstudied setting; being seropositive for any one of these three viruses means that an individual is more likely to be seropositive for the other two viruses than expected by chance. Being seropositive for IBR, BVDV or PIV3 did not affect the average daily weight gain of the calf, nor did PIV3 and BVDV serostatus have an effect on the calf ever experiencing a clinical episode. However, IBR seropositive calves were less likely to experience a clinical episode of some form, suggestive of some protective aspect of IBR. An examination of the sources of variation in faecal strongyle egg counts (EPG), and their association with body weight, host genetics and a suite of haematological measures. Using estimates of relatedness derived from the SNP data, I established that strongyle EPG has a genetic basis in EASZ, with a heritability of 23.9% (S.E. = 11.8%) and showed a consistently strong negative association between strongyle infection and the haematological parameters white blood cell count, red blood cell count, total serum protein and absolute eosinophil count. Furthermore, calf body weight at 1 week old was a significant predictor of strongyle EPG at 16-51 weeks, with smaller calves being predisposed to a higher strongyle EPG later in life. A genome-wide association study (GWAS) to investigate if there is a genetic predisposition to East Coast Fever (ECF) death and a genetic basis to the packed cell volume at the time of seroconversion to Theileria parva (PCVTP). I found no robust evidence for a relationship between genotyped single nucleotide polymorphisms (SNPs) and ECF death or PCVTP. The effect of sample size upon GWAS and significance thresholds was investigated further through simulations. I conclude that the small number of cases influences the probability of association between a SNP and the phenotypic trait. Smaller case numbers produce more artifactual associations with SNPs, an effect not fully compensated for by the standard Bonferroni correction, suggesting that an empirical significance threshold should be used to directly account for sample size. The results of this thesis provide an understanding of the associations occurring between different parasites, and of their causes and consequences. I discuss the results in the context of their implications for disease control strategies, suggesting the benefits of an integrated approach to control worm and T. parva alongside the possible genetic selection for parasite resistance and supplementary feeding of lightweight individuals to improve the health of EASZ

The impact of variation in reporting practices on the validity of recommended birdstrike risk assessment processes for aerodromes

AbstractBirdstrikes are a major hazard to aviation; costing millions of pounds a year in damage and delays, as well as occasional hull losses and loss of life. The numbers and species of birds on and around airfields therefore need to be managed. To aid this process, airport staff often use risk assessments to identify which bird species cause the greatest risk and use the outcome to target their bird control effort. To this end, a number of national and international regulators, airports and other organisations recommend, or use, a derivation of a risk assessment process first published in 2006. This was developed using the UK Civil Aviation Authority's birdstrike database, employing data collected between 1976 and 1996. The risk assessment process relies on using the proportion of reported strikes that cause damage to the aircraft as a proxy for the likely severity of the outcome of strike incidents, so any change in the relative level of reporting of damaging and non-damaging strikes may significantly bias the results. The implementation of mandatory birdstrike reporting by the UK CAA in 2004 led to a significant increase in the number of strikes reported. If this involved a disproportionate increase in the number of non-damaging compared to damaging incidents reported, it may have impacted on the accuracy of the risk assessment process. This paper examines how differential reporting of damaging and non-damaging strikes can impact on the risk assessment process. It shows that changes in reporting practices since the original risk assessment was developed have impacted on the apparent birdstrike risk at UK airports, giving a false impression of increasing risk over the period. It makes recommendations for how the process can be better adapted to cope with such changes in the future, and how it should be modified for use in countries with different reporting regimes to that in the UK

Results from a study of the effect of enhanced cleaning and disinfection on Salmonella prevalence in finisher pig building

Salmonella is the second most commonly reported zoonotic gastrointestinal pathogen in the European Union. Although the majority of foodborne outbreaks have been linked to the consumption of eggs and egg products (44.0%), a substantial proportion originate from pork and pork products (9.3%). Biosecurity measures correctly implemented on farm are important to reducing Salmonella carriage in live pigs and consequently the number of Salmonella contaminated carcasses entering the food chain

Fertility control for managing free-roaming feral cattle in Hong Kong

Human-wildlife conflicts are increasing worldwide. For instance, growing numbers of free-roaming feral cattle in Hong Kong are causing traffic accidents and damaging crops. Public antipathy towards lethal methods to manage wildlife has promoted research into alternative options, such as fertility control. The aims of this study were to assess the potential side effects and effectiveness of the injectable immunocontraceptive vaccine GonaCon on free-roaming feral cattle in Hong Kong. Sixty female cattle were captured and randomly assigned to treatment or control groups. Treatment animals were administered one dose of GonaCon, followed by a booster dose 3–6 months later. Control animals were administered an equivalent dose of a saline solution. The side effects of GonaCon were assessed by monitoring injection site, body condition and body weight at vaccination, at the booster stage and one year after initial vaccination. At the same times, blood samples were collected to quantify antibodies to the vaccine and to assess pregnancy status. GonaCon did not affect the body weight or body condition of cattle and had no adverse side effects such as injection site reactions, limping or abnormal behaviour. GonaCon did not appear to interrupt ongoing pregnancies but reduced fertility significantly: the proportion of pregnant animals in the GonaCon-treated group decreased from 76% at initial vaccination to 6% one year after vaccination, compared to 67% and 57% respectively in the control group. There was no difference between antibody titres at the booster stage or one year post vaccination, suggesting the booster dose maintained antibody levels. This study confirmed that GonaCon is safe and effective in inducing infertility in feral cattle, with a booster dose critical for maintaining infertility

Temporal, spatial and household dynamics of Typhoid fever in Kasese district, Uganda

<div><p>Typhoid fever affects 21 million people globally, 1% of whom succumb to the disease. The social, economic and public health consequences of this disease disproportionately affect people in Africa and Asia. In order to design context specific prevention strategies, we need to holistically characterise outbreaks in these settings. In this study, we used retrospective data (2013–2016) at national and district level to characterise temporal and spatial dynamics of Typhoid fever outbreaks using time series and spatial analysis. We then selected cases matched with controls to investigate household socio-economic drivers using a conditional logistic regression model, and also developed a Typhoid fever outbreak-forecasting framework. The incidence rate of Typhoid fever at national and district level was ~ 160 and 60 cases per 100,000 persons per year, respectively, predominantly in urban areas. In Kasese district, Bwera sub-county registered the highest incidence rate, followed by Kisinga, Kitholhu and Nyakiyumbu sub-counties. The male-female case ratio at district level was at 1.68 and outbreaks occurred between the 20^th and 40^th week (May and October) each year following by seven weeks of precipitation. Our forecasting framework predicted outbreaks better at the district level rather than national. We identified a temporal window associated with Typhoid fever outbreaks in Kasese district, which is preceded by precipitation, flooding and displacement of people. We also observed that areas with high incidence of Typhoid fever also had high environmental contamination with limited water treatment. Taken together with the forecasting framework, this knowledge can inform the development of specific control and preparedness strategies at district and national level.</p></div

Genetic diversity of Cameroon cattle and a putative genomic map for resistance to bovine tuberculosis

Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurization of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies have demonstrated that breeding European taurine cattle, such as Holsteins for increased resistance to bTB is feasible. The utility of such an approach is still unknown for African cattle populations. This study aims to assess genetic variation in bTB resistance and the underlying genomic architecture of cattle in Cameroon. We conducted a cross-sectional study of 2,346 slaughter cattle in Cameroon. Retropharyngeal lymph node samples were collected and cultured on Lowenstein Jensen media and the BACTEC MGIT 960 system, and M. bovis was identified using the Hain® Genotype kits. A total of 153 cattle were positive for M. bovis and were archived along with a random selection of negative samples. In this study, we genotyped archived samples from 212 cattle. Their genomic diversity was characterized using PCA, hierarchical clustering and admixture analysis. We assessed genetic variation in bTB resistance using heritability analysis and compared quantitative trait loci. Previous research on this study population have shown that Fulani cattle are more susceptible to bTB than mixed breeds. However, here we show that these apparent phenotypic differences in breeds are not reflected by clear genomic differences. At the genetic level, both the Fulani and mixed cattle show similar patterns of admixture with evidence of both taurine and indicine ancestry. There was little European taurine introgression within the studied population. Hierarchical clustering showed clusters of cattle that differed in their susceptibility to bTB. Our findings allude to bTB resistance being polygenic in nature. This study highlights the potential for genetic control of bTB in Africa and the need for further research into the genetics of bTB resistance within African cattle populations