Bovine tuberculosis in a multi-host system in Northern Ireland: spatial distribution, molecular epidemiology and rapid diagnosis

Bovine tuberculosis (bTB) has a complex epidemiology and a wide range of host species. United Kingdom and Ireland are one of the examples where control of bovine tuberculosis (bTB) is complex and very desirable for the farming and economy sectors. Despite the increasing implementation of control measures, such as rigorous farms surveillance, control of animal movements, testing of individual animals, and effective contact tracing are implemented for reducing the bTB spread on a national scale as the prevalence of the disease in cattle herds remains high (9.95% in 2021) (DAERA, 2021). The presence of a wildlife reservoir, the Eurasian badger Meles meles and its possible role in bTB persistence and spread in cattle species make bTB epidemiology very complex. Test-and-vaccinate or remove (TVR) wildlife intervention study was implemented in years 2014-2018 to control bTB levels in badgers and prevent disease transmission to livestock in Northern Ireland. Chapter 1 included literature review about bovine tuberculosis, its pathogenesis and diagnosis in animals, summary of previous research in the field of detection and molecular epidemiology as well as recent control system of bTB in Great Britain and Northern Ireland. This Chapter also covered recent issues and research gaps in relation to bTB laboratory diagnosis tests and epidemiology and thesis outline. Chapter 2 focused on Mycobacterium bovis spatial and molecular analysis of data from 1248 cattle and badger individuals within the TVR region (100 km2 and 2 km buffer zone) south eastern area in Northern Ireland with high bTB prevalence and high badger density (DAERA, 2018a). The study aimed to estimate the association between the spatial distribution of M. bovis multiple locus variable number of tandem repeats analysis (MLVA) types found in cattle and in badgers in the TVR area. Kernel density estimates of the shared MLVA types between cattle and badgers were evaluated to understand the spatial structure of the data. Contours in 95% density levels were estimated to demonstrate the spatial overlap of the main MLVA types, for each of the major strains. Two spatial models were built to assess the spatial distribution associations of M. bovis MLVA types in relationship to badger-cattle and cattle-badger transmissions. Thirty-seven MLVA types were found in cattle (n=31) and badger (n=6) species, with four of them (004, 006, 122 and 297) shared between two host species. Genotype 006 was identified as the most frequent and represented >51% M. bovis isolates; it was indicated as a founder MLVA type for other genotypes using goeBURST algorithm. Strong association between spatial distribution of MLVA types in cattle and badgers was identified using kernel discriminant analysis (KDA). Combining whole genome sequence (WGS) data analysis with the associated epidemiological metadata provided an opportunity for a thorough genomic epidemiological analysis of M. bovis transmission in the TVR area. These results were shown in Chapter 3 of current PhD thesis and aimed to explain the relative importance of within and between species transmissions for bTB persistence. In total 619 M. bovis isolates collected between years 1986 and 2018 from cattle and badgers were sequenced. From this dataset, previously studied endemic clade (MLVA 006 genotype) comprising of 302 isolates was used to study bTB transmission dynamics using Bayesian coalescent-based methods, Discrete Ancestral Trait Mapping (DATM) approach to reconstruct ancestral states of M. bovis collected from cattle and badgers, and outbreaker2 software to reconstruct M. bovis transmission tree and outbreak reconstruction (Campbell et al., 2018). Estimated M. bovis substitution rate (mean 0.36-0.37 substitutions per genome per year) and most recent common ancestor (1970-1980s) was similar with other studies for bTB genomic epidemiology (Crispell et al., 2019, Salvador et al., 2019). Results obtained from the transmission trees reconstruction demonstrated high levels of between cattle transmissions and transmissions from cattle to badgers, and within badgers. The evidence of inter-species was also demonstrated in reconstructed phylogenetic trees. Overall, the results of this chapter showed that genetic and genomic M. bovis data obtained from historical isolates and the TVR intervention study can provide exceptional resolution for the genomic epidemiology of bTB, shedding light into the role of livestock and wildlife in the transmission of M. bovis in the region. In Chapter 4, I developed a molecular bacterial load assay for rapid quantification of M. bovis directly from infected animals’ tissues collected in Northern Ireland. Molecular bacterial load assay is currently used as a research method to monitor anti-TB therapy for human tuberculosis and quantifies M. tuberculosis bacterial load decline in response to treatment. I optimised this laboratory protocol on bTBfree bovine tissues spiked with M. bovis BCG and evaluated the performance of MBLA for bTB detection. This demonstrated that MBLA assay is efficient for bTB diagnostics in animal tissues. MBLA identifying Mycobacterium tuberculosis complex (MTBC) specific ribosomal RNA can quantify viable M. bovis in animal tissues with the range of concentrations between 1.59E+09 CFU/ml to 1.68E+02 CFU/ml. MBLA was then applied for the analysis of 214 culture-positive bTB infected bovine tissue samples. Using MBLA, M. bovis was detected in 90% of cases and bacterial loads were reliably quantified in 73% of positive samples. Work with hazard group 3 highly contagious bacilli as M. bovis, requires the use of facilities with higher biosafety level (containment level 3, CL3) that are not always available in diagnostic and research laboratories. Therefore, I conducted heat inactivation experiments to quantify M. bovis BCG using both 16S rRNA and DNA to determine the possibility of working with infected tissues outside a CL3 laboratory, i.e. in a CL2 laboratory after inactivation. This showed that infected samples can be used for RNA-based techniques such as MBLA after heat killing of bacilli without any impact on mycobacterial load in clinical specimens. To enable the MBLA to be used in the field, I also tested the stability of M. bovis BCG RNA at room temperature for up to one month. I demonstrated that if tested RNA samples were stored and transported at room temperature within at least one month, it would not affect the quantification of mycobacteria. The results of the MBLA assay in Chapter 4 used for the infected bovine tissue samples collected within the TVR study area suggested that this molecular technique can be used as diagnostic method for rapid (results obtained within the same day as sample collection as opposed to weeks of culture testing) and sensitive detection of bovine tuberculosis directly in animal tissue samples. Overall, these findings aided to our understanding of bTB transmission within cattle and badgers in an endemic area and offered tools for rapid molecular identification of M. bovis in this setting. The discussion of these results was presented in Chapter 5

Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland

Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra-species host transmission for disease persistence. We sequenced an exceptional data set of 619 Mycobacterium bovis isolates from badgers and cattle in a 100 km2 bTB 'hotspot' in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area. Birth death models and TransPhylo analyses indicated that cattle were likely driving the local epidemic, with transmission from cattle to badgers being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution of M. bovis genetic diversity, suggesting that badger-to-badger transmission is not playing a major role in transmission dynamics. Our data were consistent with badgers playing a smaller role in transmission of M. bovis infection in this study site, compared to cattle. We hypothesize, however, that this minor role may still be important for persistence. Comparison to other areas suggests that M. bovis transmission dynamics are likely to be context dependent, with the role of wildlife being difficult to generalize.ISSN:2057-585

Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland

Publication history: Accepted - 29 March 2023; Published - 25 May 2023.Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra-species host transmission for disease persistence. We sequenced an exceptional data set of 619 Mycobacterium bovis isolates from badgers and cattle in a 100 km2 bTB 'hotspot' in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area. Birth death models and TransPhylo analyses indicated that cattle were likely driving the local epidemic, with transmission from cattle to badgers being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution of M. bovis genetic diversity, suggesting that badger-to-badger transmission is not playing a major role in transmission dynamics. Our data were consistent with badgers playing a smaller role in transmission of M. bovis infection in this study site, compared to cattle. We hypothesize, however, that this minor role may still be important for persistence. Comparison to other areas suggests that M. bovis transmission dynamics are likely to be context dependent, with the role of wildlife being difficult to generalize.This work was funded by the Department of Agriculture, Environment and Rural Affairs for Northern Ireland (DAERA-NI) through its Evidence and Innovation programme – project no. 15/3/07. Additional funding was provided by the UK’s Biotechnology and Biological Sciences Research Council (BBSRC) – grant numbers BB/P0105598 and BB/M01262X. A. A. is supported by a Bolashak International Scholarship

The subsystems design of methods for solving a problem of non-stationary waves propagation in solid bodies

In this paper is considered the design of information subsystem of method bicharacteristics, and also their numerical solution and computer visualization. The bicharacteristics method is one of the most convenient methods for software creating. This information subsystem combines the results of the solutions of practical tasks in the dynamics of a homogeneous elastic media, with the aim of creating digital collections for use in calculations of building constructions in engineering practice and also in problems of mechanical engineering and in general for researches in respective industries

Salt Intrusion in Gatun Lake

The expansion of the Panama Canal is adding another lock lane to the canal, allowing passage of larger ships. Increases in the number of transits and the size of the locks may displace more salt from the oceans into the freshwater lake, Gatun Lake, which is a drinking water source for Panama City. This project evaluated future salinity levels in Gatun Lake. Water quality and hydrometeorological data were input into a predictive hydrodynamic software package to project salinity levels in the lake after the new lock system is completed. Modeling results showed that salinity levels are expected to remain in the freshwater range. In the event that the lake becomes brackish, the team designed a water treatment plant using electrodialysis reversal for salt removal and UV light disinfection

Bus Emissions and Their Impact on Disadvantaged Communities

This project addresses franchised bus emissions and their impact on disadvantaged communities in Hong Kong. Using interviews, literature reviews, and data analysis, it was found that franchised bus emissions contribute significantly to roadside pollution on main roads in Hong Kong. A modified Social Deprivation Index (mSDI) was also designed, and analysis of this showed a statistically significant (p < 0.05) relationship between high roadside air pollution and social deprivation in the districts of Wan Chai, Central/Western, and Yau Tsim Mong

Communicative Method of Teaching of Foreign Language: Nature and Specificity

The article discusses the relevance and nature of the communicative method of teaching of foreign language in modern pedagogy. Analysis of modern techniques and methods known in the history shows that certain aspects of communicativeness present the methodology more clearly, making the trend of methodological science and practice of education development obligatory. Communicative method refers to the category of comprehensive concepts, so communicativeness should be shown in its relation to all major aspects of the educational process. It will help to determine the content of the principles of the communicative method, and, therefore, formulate them. In this situation specific approach aims to study the specific language principles and mechanisms of interaction between the significance of different linguistic means, lexical, grammatical, syntactical, involved in the construction of statement, i.e. determine specific language conditions and means that ultimately define the convey of a meaning

Structural Characteristics of Rosa Iliensis Chrshan. under Conditions of the Floodplains of the Rivers Ili and Sharyn

The article provides brief geobotanical characteristics of plant communities of three populations of R. iliensis Chrshan. found in the floodplains of the Ili and Sharyn rivers, as well as presents the morpho-anatomical structure of vegetative organs (stem and leaf) of the species under study. R. iliensis Chrshan. is undoubtedly a rare, endangered species of the flora of Kazakhstan. Its distribution area is shrinking from year to year as a result of the anthropogenic pressure on the environment. The biometric indicators of vegetative organs in the samples collected from populations 1 and 2 were approximately the same. The indicators of the samples collected from population 3 differed substantially. This is a completely natural process, since there are substantial differences in the climatic conditions of the upper and lower parts of the basin where the Ili River flows: a sharp increase in temperature and a decrease in precipitation from high to low hypsometric levels of the basin. Moreover, there is a gradual aridization of the territory from east to west. Naturally, this entails a change in both soil and vegetation cover as well as leaves its mark on the morpho-anatomical structure of vegetative organs. With this in mind, the authors recommend continuous monitoring of the state of the populations at the three sites where R. iliensis Chrshan. was found

Comparative Anatomical and Morphological Study of Three Populations of Salvia aethiopis L. Growing in the Southern Balkhash Region

The manuscript presents the results of morpho-anatomical structure of vegetative organs of Salvia aethiopis L. S.aethiopis L. is a promising medicinal plant of flora of Kazakhstan, which is able to grow under certain soil and climatic conditions. According to its anatomical and morphological features, S.aethiopis L. is a drought-resistant plant that does not tolerate excess moisture. The aim of the study was to investigate the morpho-anatomical structure of S.aethiopis L. plants growing in three different populations of the South Balkhash region of the country. As a result of the study of the morpho-anatomical structure of vegetative organs of the studied plants, the following features of xeromorphic structure of S.aethiopis L. were noted: strong pubescence of all above-ground parts of plants by simple, globular and glandular hairs, well expressed cuticle with small spinules, presence of cuticular thickening of guard cells, large number of stomatal apparatus on lower epidermis. A comparative analysis of the structure of plants of three different populations showed that in the stem of plants of population № 1 the primary cortex and the diameter of the central cylinder are more pronounced in comparison with plants growing in populations № 2 and № 3, which is due to the growing conditions of these populations. In plants of population № 1, an increase in the thickness of the leaf blade as well as inclusions of essential oils, which are localized in single or paired essential oil passages, were noted. In plants of populations № 1 and № 2, the more essential oil passages were observed. The studied plants of population № 1 have the most pronounced thickness of the primary bark than plants of populations № 2 and № 3. The revealed changes in the morpho-anatomical structure of plants are associated with the influence of various environmental and anthropogenic factors depending on the location of the studied plants