The population and landscape genetics of the European badger (Meles meles) in Ireland

Publication history: Accepted - 27 July 2018; Published - 12 September 2018.The population genetic structure of free-ranging species is expected to reflect landscape-level effects. Quantifying the role of these factors and their relative contribution often has important implications for wildlife management. The population genetics of the European badger (Meles meles) have received considerable attention, not least because the species acts as a potential wildlife reservoir for bovine tuberculosis (bTB) in Britain and Ireland. Herein, we detail the most comprehensive population and landscape genetic study of the badger in Ireland to date—comprised of 454 Irish badger samples, genotyped at 14 microsatellite loci. Bayesian and multivariate clustering methods demonstrated continuous clinal variation across the island, with potentially distinct differentiation observed in Northern Ireland. Landscape genetic analyses identified geographic distance and elevation as the primary drivers of genetic differentiation, in keeping with badgers exhibiting high levels of philopatry. Other factors hypothesized to affect gene flow, including earth worm habitat suitability, land cover type, and the River Shannon, had little to no detectable effect. By providing a more accurate picture of badger population structure and the factors effecting it, these data can guide current efforts to manage the species in Ireland and to better understand its role in bTB.DAFM - Department of Food Agriculture and the Marine, Republic of Ireland; Department of Agriculture Environment and Rural Affairs for Northern Ireland (DAERA-NI

Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis

Mycobacterium bovis is the causal agent of bovine tuberculosis, one of the most important diseases currently facing the UK cattle industry. Here, we use high-density whole genome sequencing (WGS) in a defined sub-population of M. bovis in 145 cattle across 66 herd breakdowns to gain insights into local spread and persistence. We show that despite low divergence among isolates, WGS can in principle expose contributions of under-sampled host populations to M. bovis transmission. However, we demonstrate that in our data such a signal is due to molecular type switching, which had been previously undocumented for M. bovis. Isolates from farms with a known history of direct cattle movement between them did not show a statistical signal of higher genetic similarity. Despite an overall signal of genetic isolation by distance, genetic distances also showed no apparent relationship with spatial distance among affected farms over distances <5 km. Using simulations, we find that even over the brief evolutionary timescale covered by our data, Bayesian phylogeographic approaches are feasible. Applying such approaches showed that M. bovis dispersal in this system is heterogeneous but slow overall, averaging 2 km/year. These results confirm that widespread application of WGS to M. bovis will bring novel and important insights into the dynamics of M. bovis spread and persistence, but that the current questions most pertinent to control will be best addressed using approaches that more directly integrate WGS with additional epidemiological data

Development of a skin test for bovine tuberculosis for differentiating infected from vaccinated animals

The tuberculin skin test has been used for the diagnosis of bovine and human tuberculosis (TB) for over a hundred years. However, the specificity of the test is compromised by vaccination with the Mycobacterium bovis-derived vaccine strain bacille Calmette-Guérin (BCG). Since current promising vaccines against bovine TB are based on heterologous prime-boost combinations that include BCG, there is a need for diagnostic tests for differentiating infected from vaccinated animals (DIVA). The application of antigens such as ESAT-6 and CFP-10 for DIVA has so far been realized largely through their application in the blood-based gamma interferon release assay. In the current study, we have reassessed the potential of such antigens as skin test reagents for DIVA in cattle. A cocktail of the Mycobacterium tuberculosis complex recombinant protein antigens ESAT-6, CFP-10, MPB70, and MPB83 elicited delayed-type hypersensitivity (DTH) skin test responses in 78% of naturally infected tuberculin-positive cattle. Importantly, this cocktail induced no skin responses in BCG-vaccinated cattle despite them being sensitized for strong tuberculin responses. Further optimization of skin test antigen combinations identified that the inclusion of Rv3615c (Mb3645c) enhanced skin test sensitivity in naturally infected cattle without compromising specificity. In addition, we demonstrate for the first time the utility of synthetic peptides as promising skin test antigens for bovine TB for DIVA. Our data provide a promising basis for the future development of skin tests for DIVA with practical relevance for TB diagnosis in both veterinary and clinical settings

Supplementary Data 1 (badger genotypes)

Genotypes of 454 Irish badgers (Meles meles) at 14 microsatellite loci

Molecular Epidemiology of <i>Brucella abortus</i> in Northern Ireland—1991 to 2012

<div><p>Background</p><p>Brucellosis is the most common bacterial zoonoses worldwide. Bovine brucellosis caused by <i>Brucella abortus</i> has far reaching animal health and economic impacts at both the local and national levels. Alongside traditional veterinary epidemiology, the use of molecular typing has recently been applied to inform on bacterial population structure and identify epidemiologically-linked cases of infection. Multi-locus variable number tandem repeat VNTR analysis (MLVA) was used to investigate the molecular epidemiology of a well-characterised <i>Brucella abortus</i> epidemic in Northern Ireland involving 387 herds between 1991 and 2012.</p><p>Results</p><p>MLVA identified 98 unique <i>B</i>. <i>abortus</i> genotypes from disclosing isolates in the 387 herds involved in the epidemic. Clustering algorithms revealed the relatedness of many of these genotypes. Combined with epidemiological information on chronology of infection and geographic location, these genotype data helped to identify 7 clonal complexes which underpinned the outbreak over the defined period. Hyper-variability of some VNTR loci both within herds and individual animals led to detection of multiple genotypes associated with single outbreaks. However with dense sampling, these genotypes could still be associated with specific clonal complexes thereby permitting inference of epidemiological links. MLVA- based epidemiological monitoring data were congruent with an independent classical veterinary epidemiology study carried out in the same territory.</p><p>Conclusions</p><p>MLVA is a useful tool in ongoing disease surveillance of <i>B</i>. <i>abortus</i> outbreaks, especially when combined with accurate epidemiological information on disease tracings, geographical clustering of cases and chronology of infection.</p></div

eBurst Minimum Spanning Trees of 98 disclosing isolate MLVA11 genotypes.

<p>Clonal Complex designation based on genotype similarity and epidemiological information indicated. Blue nodes indicate putative founder genotypes for a complete cluster. Yellow nodes indicate putative founders of sub clusters within larger clusters. Node size is related to frequency of observance of a specific genotype. Lines connecting node pairs are indicative of single locus variation.</p

Individual and 11 VNTR combined loci discrimination indices (DI) 95% confidence intervals and number of loci observed in study meta population and sub-populations.

<p>* indicates a locus not included in the originally described VNTR21 scheme [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136721#pone.0136721.ref004" target="_blank">4</a>]but taken from the panel described by Le Fleche <i>et al</i> 2006 characterising 80 repetitive loci [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136721#pone.0136721.ref020" target="_blank">20</a>].</p><p>Individual and 11 VNTR combined loci discrimination indices (DI) 95% confidence intervals and number of loci observed in study meta population and sub-populations.</p

<i>Brucella abortus</i> confirmed herd incidence in Northern Ireland 1991–2012.

<p><a href="http://www.dardni.gov.uk/index/statistics/animal-disease-statistics/statistics-brucellosis.htm" target="_blank">http://www.dardni.gov.uk/index/statistics/animal-disease-statistics/statistics-brucellosis.htm</a></p

Dendrogram of 98 1^st isolate genotypes.

<p>Strain genotype and clonal complex assignation indicated.</p