A molecular assessment of Ostertagia leptospicularis and Spiculopteragia asymmetrica among wild fallow deer in Northern Ireland and implications for false detection of livestock-associated species.

Background: Wild deer populations utilizing livestock grazing areas risk cross-species transmission of gastrointestinal nematode parasites (GINs), including GINs with anthelmintic resistance (AR) traits. Wild deer have been shown to carry problematic GIN species such as Haemonchus contortus and Trichostrongylus species in the UK, but the presence of livestock GINs in Northern Ireland deer populations is unknown. Also, is it not known whether AR traits exist among GINs of deer such as Ostertagia leptospicularis and Spiculopteragia asymmetrica in pastureland where anthelmintics are heavily used.

Estimation of the Prevalence of Antimicrobial Resistance in Badgers () and Foxes () in Northern Ireland.

Antimicrobial resistant (AMR) bacteria can be shared between humans and animals, through food, water, and the environment. Wild animals are not only potential reservoirs of AMR, but are also sentinels mirroring the presence of AMR zoonotic bacteria in the environment. In Northern Ireland, little is known about levels of AMR in bacteria in wildlife, thus the current study aimed to estimate the prevalence of AMR bacteria in wildlife using wildlife species from two ongoing surveys as a proxy.

Bovine tuberculosis breakdown duration in cattle herds: an investigation of herd, host, pathogen and wildlife risk factors.

Background: Despite rigorous controls placed on herds which disclose test positive cattle to bovine tuberculosis, caused by the infection of , many herds in Northern Ireland (NI) experience prolonged breakdowns. These herds represent a considerable administrative and financial burden to the State and farming community.

Methods: A retrospective observational study was conducted to better understand the factors associated with breakdown duration, which was modelled using both negative binomial and ordinal regression approaches.

Trends in serovars and antimicrobial resistance in pigs and poultry in Northern Ireland between 1997 and 2016.

Background: In the EU, salmonellosis is the second most commonly reported zoonosis. This pattern is reflected in Northern Ireland. Historically, foodborne salmonellosis has largely been attributed to the consumption of poultry products, and as such a number of legislative measures have been introduced by the EC.

Characteristics of Northern Irish cattle herds without bovine tuberculosis infection.

Background: Despite ongoing eradication efforts, bovine tuberculosis (bTB) is endemic in cattle herds in Northern Ireland (NI). This disease has serious implications for the economy, farming and animal welfare. Previous research identified a population of herds which have remained free from bTB infection for 10 years (2004-2014).

Spatiotemporal analysis of prolonged and recurrent bovine tuberculosis breakdowns in Northern Irish cattle herds reveals a new infection hotspot.

Despite a state-led eradication programme, bovine tuberculosis (bTB) remains endemic in Northern Ireland (NI). Of particular concern are "chronic" prolonged and recurrent bTB breakdowns, which represent significant financial and administrative burdens. However, little is known regarding the spatiotemporal distribution of chronic breakdowns in NI.

Liver fluke (Fasciola hepatica) co-infection with bovine tuberculosis (bTB) in cattle: A retrospective animal-level assessment of bTB risk in dairy and beef cattle.

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, remains a persistent problem for cattle industries in endemic countries. The frequency, quality, and performance of tests, and the presence of wildlife reservoirs, have been identified as impediments to eradication. Recently, exposure to helminth infection (Fasciola hepatica) has been associated negatively with the disclosure of bTB.

Bayesian latent class estimation of sensitivity and specificity parameters of diagnostic tests for bovine tuberculosis in chronically infected herds in Northern Ireland.

In the European Union, the recommended ante-mortem diagnostic methods for bovine tuberculosis (bTB) include the single intradermal cervical comparative tuberculin (SICCT) test and the interferon-gamma (IFN-γ) test as an ancillary test. The SICCT test has a moderate sensitivity (Se) and high specificity (Sp), while the IFN-γ test has good Se, but a lower Sp than the SICCT test. A retrospective Bayesian latent class analysis was conducted on 71,185 cattle from 806 herds chronically infected with bTB distributed across Northern Ireland (NI) to estimate the Se and Sp of the common ante-mortem tests and meat inspection.

Key actors in driving behavioural change in relation to on-farm biosecurity; a Northern Ireland perspective.

Background: Agriculture and farming are valued contributors to local economy in Northern Ireland (NI). There is limited knowledge about farmers' behaviours and attitudes towards disease biosecurity measures. As part of a larger project, a scenario-based workshop with key stakeholders was organised by the Agri-Food and Biosciences Institute (AFBI)-NI in December 2015.

Assessment of concurrent infection with bovine viral diarrhoea virus (BVDV) and Mycobacterium bovis: A herd-level risk factor analysis from Northern Ireland.

Bovine viral diarrhoea virus (BVDV) is a significant pathogen of cattle, leading to severe economic and animal-welfare impacts. Furthermore, the pathogen has been associated with impacting the progression or spread of other pathogens (e.g.

Livestock-Associated Methicillin Resistant (LA-MRSA) Clonal Complex (CC) 398 Isolated from UK Animals belong to European Lineages.

In recent years, there has been an increase in the number of livestock-associated methicillin resistant (LA-MRSA) clonal complex (CC) 398 recovered from isolated animals in the UK. To determine possible origins of 12 LA-MRSA CC398 isolates collected after screening more than a thousand animal isolates from the UK between 2013 and 2015, whole genome sequences (WGS) of CC398 European, including UK, and non-European isolates from diverse animal hosts were compared. Phylogenetic reconstruction applied to WGS data to assess genetic relatedness of all 89 isolates, clustered the 12 UK CC398 LA-MRSA within the European sub-lineages, although on different nodes; implicating multiple independent incursions into the UK, as opposed to a single introduction followed by clonal expansion.

Risk factors for failure to detect bovine tuberculosis in cattle from infected herds across Northern Ireland (2004-2010).

Correctly identifying animals that are truly infected with a pathogen using ante-mortem tests is the cornerstone of any disease eradication programme. Failure to identify all infected animals will impede the progress towards controlling and eradicating disease and may also have unforeseen consequences when specific prevention measures are in place to avoid animal-to-animal transmission. In the case of bovine tuberculosis (bTB), the screening ante-mortem test, the Single Comparative Intradermal Tuberculin Test (SCITT), can exhibit moderate sensitivity which can result in a "hidden burden" of infection residing within the population.

Liver fluke (Fasciola hepatica) infection in cattle in Northern Ireland: a large-scale epidemiological investigation utilising surveillance data.

Background: Liver fluke (Fasciola hepatica) is a widespread parasite of ruminants which can have significant economic impact on cattle production. Fluke infection status at the animal-level is captured during meat inspection of all animals processed for human consumption within Northern Ireland. These national datasets have not been analysed to assess their utility in uncovering patterns in fluke infection at animal- and herd-levels in Northern Ireland.

First report of lukM-positive livestock-associated methicillin-resistant Staphylococcus aureus CC30 from fattening pigs in Northern Ireland.

The increasing number of reports of livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) world-wide attests to the public health concern surrounding this pathogen in animal husbandry and in-contact humans. In Europe, LA-MRSA CC398 is predominant and generally regarded as being of low virulence for animals. Herein we report the recovery of a lineage of LA-MRSA, belonging to CC30, from three pigs in Northern Ireland and which encodes a marker of virulence (lukM and lukF-P83) restricted to animal-associated clones of S.

Should they stay, or should they go? Relative future risk of bovine tuberculosis for interferon-gamma test-positive cattle left on farms.

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is a serious infectious disease that remains an ongoing concern for cattle farming worldwide. Tuberculin skin-tests are often used to identify infected animals (reactors) during test-and-cull programs, however, due to relatively poor sensitivity, additional tests can be implemented in parallel. For example, in Northern Ireland interferon-gamma (IFN-g) testing is used in high-risk herds.

Isolation of a novel Campylobacter jejuni clone associated with the bank vole, Myodes glareolus.

Campylobacter jejuni can be isolated from different animal hosts. Various studies have used multilocus sequence typing to look for associations between particular clones of C. jejuni and specific hosts.

Risk factors for the occurrence of Escherichia coli virulence genes eae, stx1 and stx2 in wild bird populations.

Shiga toxin-producing Escherichia coli (STEC) can cause serious disease in human beings. Ruminants are considered to be the main reservoir of human STEC infections. However, STEC have also been isolated from other domestic animals, wild mammals and birds.

Molecular epidemiology and characterization of Campylobacter spp. isolated from wild bird populations in northern England.

Campylobacter infections have been reported at prevalences ranging from 2 to 50% in a range of wild bird species, although there have been few studies that have investigated the molecular epidemiology of Campylobacter spp. Consequently, whether wild birds are a source of infection in humans or domestic livestock or are mainly recipients of domestic animal strains and whether separate cycles of infection occur remain unknown. To address these questions, serial cross-sectional surveys of wild bird populations in northern England were carried out over a 2-year period.