The interplay between host and pathogen genetics in the increasing incidence of bovine tuberculosis

Bovine TB is a chronic disease of animals caused by infection with the slow-growing, obligate intracellular bacterium Mycobacterium bovis. This highly-adapted and ‘successful’ pathogen has a world-wide distribution and in several countries bovine TB remains a major, costly infectious disease of cattle and other domesticated, feral and wild animal populations. Bovine TB is an OIE (World Organisation for Animal Health) listed (formerly List B) disease. Bovine TB affects cattle health, impacts negatively on profitability and trade and can decimate years of genetic improvement towards desirable production traits. It also impacts negatively on the welfare of affected farming families. Despite sustained and costly implementation of eradication programmes since the 1950s bovine TB has not been eradicated from either the United Kingdom (UK) or Ireland. Indeed, there has been a sustained and largely unexplained increase over the last 25 years in parts of the UK. Consequently, bovine TB is the most complex and difficult multi-species endemic disease currently facing government, the veterinary profession and the farming industry in the UK and Ireland.
Previous studies and observations in other animals had suggested that animals were likely to differ in their susceptibility to bovine TB and that at least a proportion of the TB risk had a genetic component and was effectively a genetic trait, amenable to improvement through genetic selection. In order to estimate the relative risk posed by individual proven sires this project required the generation of a new data-set, compiled from two existing retrospective data-sets: individual animal histories controlled by the competent authority (DARDNI) and industry-controlled performance and pedigree data (HUK). These data facilitated the estimation of TB diagnostic test performance (i.e. sensitivity and specificity) by means of advanced statistical modelling techniques (latent class analyses), which required no ‘gold standard’ diagnostic test. The sensitivity (Se) of the eradication programme TB skin test was estimated at 0.56 and the Se of abattoir TB inspection was estimated at 0.25. These estimates are significantly below the accepted test Se for these measures, which was estimated by gold standard methods, which tend to over-estimate. They indicate that a significant proportion of infected cattle evade detection at individual tests. Both tests were highly specific (Sp=0.99). Consequently, the true prevalence of TB in NI cattle was estimated at 1.7-fold the current estimate, indicating that substantial cattle TB was not being diagnosed effectively, reducing the effectiveness of current control strategies.
The most significant work-package involved the design and execution of a large genetic epidemiology study – a case-control designed genome-wide association study (GWAS). The study set out to classify (phenotype) NI Holstein-Friesians based on their TB life histories and to identify TB case and TB control animals for the GWAS. TB cases were defined as confirmed culture-positive cows, mostly TB test reactors. TB control animals were matched to TB case animals to control for confounders and maximise the probability that both TB cases and TB controls had equal exposure to pathogen. DNA samples from TB cases and controls were genotyped using the Illumina bovineHD SNP array (~770,000 SNP genotypes per animal). The GWAS data were quality control analysed using bioinformatics approaches, and then subjected to state-of-the-art genetic analyses to detect SNPs significantly associated with the TB susceptibility phenotype. The GWAS produced a number of significant SNP associations with TB susceptibility, which have been mapped to genome regions. Biochemical pathway and network analyses should identify those genetic regions that are significant in the TB host-pathogen interaction and may provide important new leads on TB diagnosis and vaccinology.
The GWAS data were also interrogated to provide an estimate of the heritable component to TB susceptibility risk (genomic heritability). This was estimated at 0.23, in line with previous estimates from Irish and GB data. This heritability of TB susceptibility is inherently exploitable via selective breeding, including marker-assisted and genomic selection techniques. The direct route to exploitation of the heritability estimate is via sire relative TB risk estimates, i.e. estimated breeding values (EBVs) based on the above heritability value. These EBVs could become a breeding index and part of the estimated breeding index for pedigree cattle; plans are in progress for this information to be made available to farmers through collaborations with SAC and DairyCo. In principle, it should be possible to identify and deploy low- or lower-risk sires and avoid high risk sires in high-prevalence areas. Encouragingly, no significantly negative associations were detected between the reduced TB susceptibility phenotype and other desirable production traits. The GWAS results hold promise for marker assisted and genomic selection. The PIs continue to engage with industry and competent authorities to exploit the project findings. 

Scientists from the Roslin Institute at the University of Edinburgh, the Agri-Food and Biosciences Institute (AFBI) and Queen’s University (QUB) in Belfast have found important new evidence of genetic differences between cattle in their resistance to bovine TB. Bovine tuberculosis (bTB) caused by the bacterium Mycobacterium bovis is an endemic disease of major economic importance in UK cattle populations. Despite sixty years of control, the UK has not reached TB-free status, indicating a need for alternative strategies. The study involved comparing the genetic makeup of a large number of Holstein-Friesian cattle that had TB with matched herd-mates that did not have TB. Using the latest genomic techniques the researchers were able to analyse each individual animal at over 700 thousand genetic markers, generating more than a billion pieces of genetic information. These findings have identified a number of genetic markers which associate with an increased risk of cattle acquiring TB. Further analysis should help to better understand how cattle respond to TB infection, and provide new leads to improve diagnosis. Previous work in AFBI has shown that multiple TB strains exist in the Northern Ireland cattle population. This new genetic analysis suggests that susceptibility to TB may also be influenced by the strain of TB encountered. Following further research and validation, host genetics can play an important complementary role in control strategies. This study illustrates the value of scientific collaboration and the integration of both basic and applied research. Genetic selection for increased resistance to TB could complement and enhance existing control efforts.

• Identification and location of significant SNP associations with TB susceptibility through a case-control genome-wide association study (GWAS) in Northern Ireland Holstein-Friesian cattle. A greater number of case-control samples than initially planned (~1300) were genotyped on the Illumina bovineHD SNP array (consisting of 770,000 SNPs). Thus we achieved approximately 100 fold greater genetic marker information than initially planned.
• An estimate of the host genetic component that influences TB risk (genomic heritability = 0.23). Having controlled for environmental confounders, TB strains did not appear to differ significantly in their detectability or transmissibility.
• Estimates of TB skin test and TB abattoir inspection sensitivities (Se= 0.56 and 0.25, respectively). Specificity was high for both tests (Sp=0.99). Consequently, true prevalence was estimated at 1.7-fold the current surveillance estimate.