A5001914734- Mycobacterium research and diagnosis
- Tuberculosis Research and Epidemiology
- Genomics and Phylogenetic Studies
- Microbial infections and disease research
- Animal Disease Management and Epidemiology
- Evolution and Genetic Dynamics
- Bacteriophages and microbial interactions
- Ginseng Biological Effects and Applications
- COVID-19 epidemiological studies
- Parasite Biology and Host Interactions
- Helminth infection and control
- Parasites and Host Interactions
- RNA and protein synthesis mechanisms
- Climate Change and Health Impacts
- Climate Change and Geoengineering
- Zoonotic diseases and public health
- Climate Change, Adaptation, Migration
- Genetic diversity and population structure
Foreign, Commonwealth & Development Office
2021-2023
Foreign and Commonwealth Office
2021-2023
University College Dublin
2018-2022
Office for National Statistics
2020-2021
University of Glasgow
2017
Quantifying pathogen transmission in multi-host systems is difficult, as exemplified bovine tuberculosis (bTB) systems, but crucial for control. The agent of bTB, Mycobacterium bovis, persists cattle populations worldwide, often where potential wildlife reservoirs exist. However, the relative contribution different host species to bTB persistence generally unknown. In Britain, role badgers infection highly contentious, despite decades research and control efforts. We applied Bayesian...
Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing means to determine the relative importance inter- and intra-species host for disease persistence. We sequenced an exceptional data set 619 Mycobacterium bovis isolates from badgers cattle in 100 km 2 bTB ‘hotspot’ Northern Ireland. Historical...
Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is an important livestock disease raising public health and economic concerns around the world. In New Zealand, a number of wildlife species are implicated in spread persistence bTB cattle populations, most notably brushtail possum (Trichosurus vulpecula). Whole Genome Sequenced (WGS) M. bovis isolates sourced from infected across Zealand were analysed. Bayesian phylogenetic analyses conducted to estimate substitution rate sampled...
A homoplasy is a nucleotide identity resulting from process other than inheritance common ancestor. Importantly, by distorting the ancestral relationships between sequences, homoplasies can change structure of phylogeny. Homoplasies emerge naturally, especially under high selection pressures and/or mutation rates, or be created during generation and processing sequencing data. Identification critical, both to understand their influence on analyses phylogenetic data allow an investigation...
Livestock movements are an important mechanism of infectious disease transmission. Where these well recorded, network analysis tools have been used to successfully identify system properties, highlight vulnerabilities transmission, and inform targeted surveillance control. Here we the main uses properties in understanding livestock epidemiology discuss statistical approaches infer characteristics from biased or fragmented datasets. We use a 'hurdle model' approach that predicts (i)...
Abstract The role of wildlife in the persistence and spread livestock diseases is difficult to quantify control. These difficulties are exacerbated when several species potentially involved. Bovine tuberculosis (bTB), caused by Mycobacterium bovis , has experienced an ecological shift Michigan, with spillover from cattle leading endemically infected white‐tailed deer (deer) population. It substantial implications for health well‐being both incurs a significant economic cost industry...
The ability to DNA fingerprint Mycobacterium bovis isolates helped define the role of wildlife in persistence bovine tuberculosis New Zealand. fingerprinting results currently help guide control measures and also aid tracing source infections that result from movement livestock. During last 5 years we have developed distinguish Zealand (NZ) M. by comparing sequences whole genome sequenced (WGS) samples. WGS provides much higher resolution than our other established typing methods greatly...
Control of bovine tuberculosis (bTB), caused by Mycobacterium bovis, in the Republic Ireland costs €84 million each year. Badgers are recognized as being a wildlife source for M. bovis infection cattle. Deer thought to act spillover hosts infection; however, population density is an important driver shifting their epidemiological role, and deer populations across country have been increasing range. County Wicklow represents one specific area with high that has had consistently bTB prevalence...
Abstract Understanding how emergent pathogens successfully establish themselves and persist in previously unaffected populations is a crucial problem disease ecology, with important implications for management. In multi‐host pathogen systems this particularly difficult, as the importance of each host species to transmission often poorly characterised, epidemiology complex. Opportunities observe analyse such scenarios are few. Here, we exploit unique dataset combining densely collected data...
Abstract New ideas for diagnostics in clinical parasitology are needed to overcome some of the difficulties experienced widespread adoption detection methods gastrointestinal parasites livestock. Here we provide an initial evaluation performance a newly developed automated device (Telenostic) identify and quantify parasitic elements fecal samples. This study compared Telenostic with McMaster Mini-FLOTAC counting strongyle eggs sample. Three bovine samples were examined, triplicate, on each...
We describe application of whole genome sequencing (WGS) to a collection 197 Mycobacterium avium subsp paratuberculosis (MAP) isolates gathered from 122 cattle herds across 27 counties the island Ireland. compare WGS MAP diversity quantified using mycobacterial interspersed random unit - variable number tandem repeats (MIRU-VNTR). While MIRU-VNTR showed only two major types, could split into eight groups. also found six corresponding INMV 13, novel type for Evidence dispersal Ireland via...
Abstract Background Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Pathogen whole genome sequencing can improve the resolution of epidemiological tracing. We sequenced an exceptional data set 619 Mycobacterium bovis isolates from badgers and cattle in 100km 2 bTB ‘hotspot’. Historical molecular subtyping permitted targeting pathogen lineage, whose long-term persistence provided opportunity to study epidemiology detail. To assess whether badger...
Abstract Established methods for whole-genome-sequencing (WGS) technology allow the detection of single-nucleotide polymorphisms (SNPs) in pathogen genomes sourced from host samples. The information obtained can be used to track pathogen’s evolution time and potentially identify ‘who-infected-whom’ with unprecedented accuracy. Successful include ‘phylodynamic approaches’ that integrate evolutionary epidemiological data. However, they are typically computationally intensive, require extensive...
Mycobacterium bovis AF2122/97 is the reference strain for bovine tuberculosis bacillus. Here we report an update to M. genome annotation reflect 616 new protein identifications that replace many of old hypothetical coding sequences and proteins unknown function in genome. These changes integrate information from functional assignments orthologous H37Rv We have also added 69 additional gene names.
Abstract Understanding how an emergent pathogen successfully establishes itself and persists in a previously unaffected population is crucial problem disease ecology. In multi-host systems this particularly difficult, as the importance of each host species to transmission often poorly characterised, epidemiology complex. Opportunities observe analyse such scenarios are few. Here, we exploit unique dataset combining densely-collected data on epidemiological evolutionary characteristics...
Abstract Established methods for whole-genome-sequencing (WGS) technology allow the detection of single-nucleotide polymorphisms (SNPs) in pathogen genomes sourced from host samples. The information obtained can be used to track pathogen’s evolution time and potentially identify ‘who-infected-whom’ with unprecedented accuracy. Successful include ‘phylodynamic approaches’ that integrate evolutionary epidemiological data. However, they are typically computationally intensive, require extensive...
Introduction Bovine tuberculosis (bTB) is an epidemiologically complex disease affecting both cattle and badgers in the UK Ireland. Traditional molecular typing schemes have been used to characterise spatial structure of pathogen relationship M. bovis derived from sympatric animals. However, these methods lack resolution describe transmission dynamics at farm level or inform on extent which hosts contribute. Whole genome sequencing can improve epidemiology investigations this epi-system....
Abstract Mycobacterium bovis AF2122/97 is the reference strain for bovine tuberculosis bacillus. We here report an update to M. genome annotation reflect 616 new protein identifications which replace many of old hypothetical coding sequences and proteins unknown function in genome. These changes integrate information from functional assignments orthologous H37Rv have also added 69 additional gene names.
Mycobacterium avium subspecies paratuberculosis (MAP) causes Johne’s Disease (JD), a chronic enteritis, in cattle. Whole genome sequencing (WGS) has been applied to many pathogen systems, where its unprecedented resolution greatly enhanced our understanding of the molecular epidemiology transmission. However, WGS seen limited application MAP; transmission dynamics MAP will inform control JD. We report first study into Ireland. DNA was extracted from 167 isolates sourced cattle across...