Molecular characterisation of Giardia duodenalis from human and companion animal sources in the United Kingdom using an improved triosephosphate isomerase molecular marker.

Giardia duodenalis is a protozoan parasite known for its ability to cause gastrointestinal disease in human and non-human mammals. In the UK, the full impact of this parasite has yet to be fully explored, due to the limited testing which has been undertaken in humans and the low-resolution assemblage-typing methods currently available. Rather than being primarily a travel-associated condition, a recent study has highlighted that an endemic Giardia cycle is present in the UK, although the source of human disease is unclear in the majority of cases. This study focussed on the improvement of one of the commonly used assemblage-typing assays, a nested topoisomerase phosphate (tpi) PCR, to increase the amplification success rate across both human and companion animal samples. After comparing published primers to full Giardia reference genomes, this marker protocol was optimised and then deployed to test a substantial number of human (n â€‹= â€‹79) and companion animal (n â€‹= â€‹174) samples to gain an insight into the molecular epidemiology of Giardia in the UK. One assemblage A1 and eleven assemblage A2 genotypes were detected in humans, along with and 25 assemblage B genotypes. Assemblage A1 genotypes, known to be human-infective, were found in three feline and one canine sample, while one feline sample contained assemblage A2. Additionally, four feline samples contained assemblage B, which is recognised as potentially human-infective. This study demonstrates the presence of potentially human-infective Giardia genotypes circulating in the companion animal population, notably with 17.4% (8/46) of feline-derived Giardia strains being potentially zoonotic. Using a modified tpi-based genotyping assay, this work highlights the potential for domestic pets to be involved in the endemic transmission of giardiasis in the UK and underlines the need for appropriate hygiene measures to be observed when interacting with both symptomatic and asymptomatic animals. It also serves to underline the requirement for further studies to assess the zoonotic risk of Giardia associated with companion animals in high-income countries.

FAIR data pipeline: provenance-driven data management for traceable scientific workflows.

Modern epidemiological analyses to understand and combat the spread of disease depend critically on access to, and use of, data. Rapidly evolving data, such as data streams changing during a disease outbreak, are particularly challenging. Data management is further complicated by data being imprecisely identified when used. Public trust in policy decisions resulting from such analyses is easily damaged and is often low, with cynicism arising where claims of 'following the science' are made without accompanying evidence. Tracing the provenance of such decisions back through open software to primary data would clarify this evidence, enhancing the transparency of the decision-making process. Here, we demonstrate a Findable, Accessible, Interoperable and Reusable (FAIR) data pipeline. Although developed during the COVID-19 pandemic, it allows easy annotation of any data as they are consumed by analyses, or conversely traces the provenance of scientific outputs back through the analytical or modelling source code to primary data. Such a tool provides a mechanism for the public, and fellow scientists, to better assess scientific evidence by inspecting its provenance, while allowing scientists to support policymakers in openly justifying their decisions. We believe that such tools should be promoted for use across all areas of policy-facing research. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

A scoping review of risk factors and transmission routes associated with human giardiasis outbreaks in high-income settings.

The flagellated pathogen Giardia duodenalis is one of the leading causes of parasitic gastrointestinal illness worldwide. In many higher income countries, such as the United Kingdom, the disease is often perceived as being travel-related, likely leading to the under-reporting of sporadic cases and outbreaks. A summary of the literature describing outbreaks and risk factors in higher income countries is necessary to improve our understanding of this pathogen and identify existing knowledge gaps. Initial literature searches were carried out in September 2016 and updated at regular intervals until November 2021, using appropriate search terms in Medline, Embase and PubMed databases. A total of 75 papers met the inclusion criteria, revealing that the consumption of contaminated water and contact with young children of diaper-wearing age were the most common transmission routes leading to outbreaks of giardiasis. Of the ten studies where food was primarily associated with outbreaks, food handlers accounted for eight of these. Another reported transmission route was direct contact with fecal material, which was reported in six studies as the primary transmission route. Travel-associated giardiasis was considered the sole transmission route in two studies, whereas multiple transmission routes contributed to giardiasis outbreaks in eleven studies. The evidence around zoonotic transmission was less clear and hampered by the lack of robust and regularly applied parasite molecular typing techniques. This literature review summarizes the findings of Giardia outbreak investigations and epidemiological studies in high-income countries. Transmission routes are identified and discussed to highlight the associated risk factors. These data also indicate gaps in our current knowledge that include the need for robust, in-depth molecular studies and have underscored the importance of water as a transmission route for Giardia cysts. These future molecular studies will improve our understanding of Giardia epidemiology and transmission pathways in higher income countries to prevent spread of this significantly under-reported pathogen.

EPIC, Scottish Government's Centre of Expertise in Animal Disease Outbreaks: A Model for Provision of Risk-Based Evidence to Policy.

EPIC, Scottish Government's Centre of Expertise on Animal Disease Outbreaks, offers a successful and innovative model for provision of scientific advice and analysis to policy-makers in Scotland. In this paper, we describe EPIC's remit and operations, and reflect on three case studies which illustrate how the Centre of Expertise Model provides risk-based evidence through rapid access to emergency advice and analyses, estimating disease risks and improving disease detection, assessing different disease control options, and improving future risk resilience. The successes and challenges faced by EPIC and its members offer useful lessons for animal health researchers and authorities, working in contingency planning for animal health security in other countries.

Between roost contact is essential for maintenance of European bat lyssavirus type-2 in Myotis daubentonii bat reservoir: 'The Swarming Hypothesis'.

Many high-consequence human and animal pathogens persist in wildlife reservoirs. An understanding of the dynamics of these pathogens in their reservoir hosts is crucial to inform the risk of spill-over events, yet our understanding of these dynamics is frequently insufficient. Viral persistence in a wild bat population was investigated by combining empirical data and in-silico analyses to test hypotheses on mechanisms for viral persistence. A fatal zoonotic virus, European Bat lyssavirus type 2 (EBLV-2), in Daubenton's bats (Myotis daubentonii) was used as a model system. A total of 1839 M. daubentonii were sampled for evidence of virus exposure and excretion during a prospective nine year serial cross-sectional survey. Multivariable statistical models demonstrated age-related differences in seroprevalence, with significant variation in seropositivity over time and among roosts. An Approximate Bayesian Computation approach was used to model the infection dynamics incorporating the known host ecology. The results demonstrate that EBLV-2 is endemic in the study population, and suggest that mixing between roosts during seasonal swarming events is necessary to maintain EBLV-2 in the population. These findings contribute to understanding how bat viruses can persist despite low prevalence of infection, and why infection is constrained to certain bat species in multispecies roosts and ecosystems.

Hair nicotine concentration of cats with gastrointestinal lymphoma and unaffected control cases.

BACKGROUND: A previous study showed an association between owner-reported exposure to environmental tobacco smoke (ETS) and lymphoma in cats. This study aimed to investigate the association between ETS exposure and gastrointestinal lymphoma in cats, using hair nicotine concentration (HNC) as a biomarker. METHODS: This was a prospective, multi-centre, case-control study. Gastrointestinal lymphoma was diagnosed on cytology or histopathology. Hair samples were obtained from 35 cats with gastrointestinal lymphoma and 32 controls. Nicotine was extracted from hair by sonification in methanol followed by hydrophilic interaction chromatography with mass spectrometry. Non-parametric tests were used. RESULTS: The median HNC of the gastrointestinal lymphoma and control groups was not significantly different (0.030 ng/mg and 0.029 ng/mg, respectively, p=0.46). When the HNC of all 67 cats was rank ordered and divided into quartiles, there was no significant difference in the proportion of lymphoma cases or controls within these groups (p=0.63). The percentage of cats with an HNC≥0.1 ng/mg was higher for the lymphoma group (22.9%) than the control group (15.6%) but failed to reach significance (p=0.45). CONCLUSION: A significant association was not identified between HNC (a biomarker for ETS) and gastrointestinal lymphoma in cats; however, an association may exist and further studies are therefore required.

The Risk of Foot and Mouth Disease Transmission Posed by Public Access to the Countryside During an Outbreak.

During the 2001 UK FMD outbreak, local authorities restricted rural access to try to prevent further disease spread by people and animals, which had major socio-economic consequences for rural communities. This study describes the results of qualitative veterinary risk assessments to assess the likelihood of different recreational activities causing new outbreaks of foot and mouth disease, as part of contingency planning for future outbreaks. For most activities, the likelihood of causing new outbreaks of foot and mouth disease is considered to vary from very low to medium depending on the control zone (which is based on distance to the nearest infected premises), assuming compliance with specified mitigation strategies. The likelihood of new outbreaks associated with hunting, shooting, stalking, and equestrian activities is considered to be greater. There are areas of significant uncertainty associated with data paucity, particularly regarding the likelihood of transmission via fomites. This study provides scientific evidence to underpin refinement of rural access management plans and inform decision-making in future disease outbreaks.

Development of a New Scale to Measure Ambiguity Tolerance in Veterinary Students.

The ability to cope with ambiguity and feelings of uncertainty is an essential part of professional practice. Research with physicians has identified that intolerance of ambiguity or uncertainty is linked to stress, and some authors have hypothesized that there could be an association between intolerance of ambiguity and burnout. We describe the adaptation of the TAMSAD (Tolerance of Ambiguity in Medical Students and Doctors) scale for use with veterinary students. Exploratory factor analysis supports a uni-dimensional structure for the Ambiguity tolerance construct. Although internal reliability of the 29-item TAMSAD scale is reasonable (α=.50), an alternative 27-item scale (drawn from the original 41 items used to develop TAMSAD) shows higher internal reliability for veterinary students (α=.67). We conclude that there is good evidence to support the validity of this latter TAVS (Tolerance of Ambiguity in Veterinary Students) scale to study ambiguity tolerance in veterinary students.

Detection of Rare Antimicrobial Resistance Profiles by Active and Passive Surveillance Approaches.

Antimicrobial resistance (AMR) surveillance systems are generally not specifically designed to detect emerging resistances and usually focus primarily on resistance to individual drugs. Evaluating the diversity of resistance, using ecological metrics, allows the assessment of sampling protocols with regard to the detection of rare phenotypes, comprising combinations of resistances. Surveillance data of phenotypic AMR of Canadian poultry Salmonella Heidelberg and swine Salmonella Typhimurium var. 5- were used to contrast active (representative isolates derived from healthy animals) and passive (diagnostic isolates) surveillance and assess their suitability for detecting emerging resistance patterns. Although in both datasets the prevalences of resistance to individual antimicrobials were not significantly different between the two surveillance systems, analysis of the diversity of entire resistance phenotypes demonstrated that passive surveillance of diagnostic isolates detected more unique phenotypes. Whilst the most appropriate surveillance method will depend on the relevant objectives, under the conditions of this study, passive surveillance of diagnostic isolates was more effective for the detection of rare and therefore potentially emerging resistance phenotypes.

Risk factors for epistaxis in jump racing in Great Britain (2001-2009).

The aim of this study was to evaluate risk factors associated with developing epistaxis in jump racing in Great Britain (GB). A retrospective analysis of records from horses running in all hurdle and steeplechase races in GB between 2001 and 2009 identified diagnoses of epistaxis whilst still at the racecourse. Data were used from 603 starts resulting in epistaxis (event) and 169,065 starts resulting in no epistaxis (non-event) in hurdle racing, and from 550 event starts and 102,344 non-event starts in steeplechase racing. Two multivariable logistic regression models to evaluate risk factors associated with epistaxis were produced. The potential effect of clustering of data (within horse, horse dam, horse sire, trainer, jockey, course, race and race meet) on the associations between risk factors and epistaxis was examined using mixed-effects models. Multiple factors associated with increased risk of epistaxis were identified. Those identified in both types of jump racing included running on firmer ground; horses with >75% of career starts in flat racing and a previous episode of epistaxis recorded during racing. Risk factors identified only in hurdle racing included racing in the spring and increased age at first race; and those identified only in steeplechase racing included running in a claiming race and more starts in the previous 3-6 months. The risk factors identified provide important information about the risk of developing epistaxis. Multiple avenues for further investigation are highlighted, including unmeasured variables at the level of the racecourse. The results of this study can be used to guide the development of interventions to minimise the risk of epistaxis in jump racing.

Contrasting clinical outcomes in two cohorts of cats naturally infected with feline immunodeficiency virus (FIV).

Despite over 25 years of feline immunodeficiency virus (FIV) research, relatively little is known about the longitudinal course of FIV infection following natural infection. In contrast to published reports of experimental infections using lethal strains of the virus, clinical signs of naturally acquired FIV infection can be mild or inapparent, rather than life-threatening. In this prospective, longitudinal controlled study, based in Chicago, IL (n=17) and Memphis, TN (n=27), we investigated two cohorts of privately owned, naturally infected cats kept under different housing conditions. Cats in the Chicago cohort (Group 1) were kept in households of ≤2 cats, while the Memphis cohort (Group 2) comprised part of a large multi-cat household of over 60 cats kept indoors only, with unrestricted access to one another. The majority of cats from Group 1 did not display clinical signs consistent with immunodeficiency during the 22-month observation period. In contrast, the outcome of infection in Group 2 was dramatically different; 17/27 (63%) of cats lost a median of 51.3% of their bodyweight (P<0.0005) and died during the study period, with lymphoma being the most common cause of mortality. Although the decrease in CD4+ T cell count between enrolment and terminal disease was significant (P=0.0017), the CD4:CD8 ratio at the time of enrolment did not reliably distinguish FIV-positive cats classified as 'healthy' and 'not healthy' at either cohort. FIV load at enrolment was significantly lower in Group 1 than in Group 2 (P<0.0001), but there were no significant differences at enrolment between healthy and not healthy cats at either group. In conclusion, the results of this study suggest that management and housing conditions impact on disease progression and survival times of FIV-positive cats.

Estimates of genetic parameters of distal limb fracture and superficial digital flexor tendon injury in UK Thoroughbred racehorses.

A retrospective cohort study of distal limb fracture and superficial digital flexor tendon (SDFT) injury in Thoroughbred racehorses was conducted using health records generated by the British Horseracing Authority (BHA) between 2000 and 2010. After excluding records of horses that had both flat and jump racing starts, repeated records were reduced to a single binary record per horse (n = 66,507, 2982 sires), and the heritability of each condition was estimated using residual maximum likelihood (REML) with animal logistic regression models. Similarly, the heritability of each condition was estimated for the flat racing and jump racing populations separately. Bivariate mixed models were used to generate estimates of genetic correlations between SDFT injury and distal limb fracture. The heritability of distal limb fracture ranged from 0.21 to 0.37. The heritability of SDFT injury ranged from 0.31 to 0.34. SDFT injury and distal limb fracture were positively genetically correlated. These findings suggest that reductions in the risk of the conditions studied could be attempted using targeted breeding strategies.

E. coli O157 on Scottish cattle farms: evidence of local spread and persistence using repeat cross-sectional data.

BACKGROUND: Escherichia coli (E. coli) O157 is a virulent zoonotic strain of enterohaemorrhagic E. coli. In Scotland (1998-2008) the annual reported rate of human infection is 4.4 per 100,000 population which is consistently higher than other regions of the UK and abroad. Cattle are the primary reservoir. Thus understanding infection dynamics in cattle is paramount to reducing human infections.A large database was created for farms sampled in two cross-sectional surveys carried out in Scotland (1998-2004). A statistical model was generated to identify risk factors for the presence of E. coli O157 on farms. Specific hypotheses were tested regarding the presence of E. coli O157 on local farms and the farms previous status. Pulsed-field gel electrophoresis (PFGE) profiles were further examined to ascertain whether local spread or persistence of strains could be inferred. RESULTS: The presence of an E. coli O157 positive local farm (average distance: 5.96 km) in the Highlands, North East and South West, farm size and the number of cattle moved onto the farm 8 weeks prior to sampling were significant risk factors for the presence of E. coli O157 on farms. Previous status of a farm was not a significant predictor of current status (p = 0.398). Farms within the same sampling cluster were significantly more likely to be the same PFGE type (p < 0.001), implicating spread of strains between local farms. Isolates with identical PFGE types were observed to persist across the two surveys, including 3 that were identified on the same farm, suggesting an environmental reservoir. PFGE types that were persistent were more likely to have been observed in human clinical infections in Scotland (p < 0.001) from the same time frame. CONCLUSIONS: The results of this study demonstrate the spread of E. coli O157 between local farms and highlight the potential link between persistent cattle strains and human clinical infections in Scotland. This novel insight into the epidemiology of Scottish E. coli O157 paves the way for future research into the mechanisms of transmission which should help with the design of control measures to reduce E. coli O157 from livestock-related sources.

Dynamics of bovine intramammary infections due to coagulase-negative staphylococci on four farms.

The objectives of this study were to compare the impact of different coagulase-negative species (CNS) on udder health measured in terms of individual quarter milk somatic cell count (SCC) and duration of intramammary infection, and to get some insight into most likely routes of infection for different CNS species. This longitudinal observational study was performed on four farms that were sampled at 4-week intervals for a total of 12 visits each. Quarters infected with CNS were followed through time with milk samples being submitted for bacteriological culture and SCC determination. PCR amplification of the internal transcribed spacer region and sequencing of the sodA and rpoB genes were used for species allocation. Pulsed-field gel electrophoresis (PFGE) was performed to assess strain identity. The percentage of quarters affected per farm varied between 6 and 35%, with the most frequently isolated CNS species being Staphylococcus epidermidis, followed by Staph. simulans, Staph. chromogenes and Staph. haemolyticus. It was possible to follow 111 intramammary infections due to CNS through time. Duration of infection had a mean of 188 d and was not significantly different between CNS species. Geometric mean quarter SCC overall was 132 000 cells/ml and was also not significantly different between CNS species. Despite the possibility of a different epidemiology of infection, the impact in terms of udder health seems to be similar for different CNS species.

Systems approaches to animal disease surveillance and resource allocation: methodological frameworks for behavioral analysis.

While demands for animal disease surveillance systems are growing, there has been little applied research that has examined the interactions between resource allocation, cost-effectiveness, and behavioral considerations of actors throughout the livestock supply chain in a surveillance system context. These interactions are important as feedbacks between surveillance decisions and disease evolution may be modulated by their contextual drivers, influencing the cost-effectiveness of a given surveillance system. This paper identifies a number of key behavioral aspects involved in animal health surveillance systems and reviews some novel methodologies for their analysis. A generic framework for analysis is discussed, with exemplar results provided to demonstrate the utility of such an approach in guiding better disease control and surveillance decisions.

An online survey of horse-owners in Great Britain.

BACKGROUND: Contingency planning for potential equine infectious disease outbreaks relies on accurate information on horse location and movements to estimate the risk of dissemination of disease(s). An online questionnaire was used to obtain unique information linking owner and horse location to characteristics of horse movements within and outwith Great Britain (GB). RESULTS: This online survey yielded a strong response, providing more than four times the target number of respondents (1000 target respondents) living in all parts of GB. Key demographic findings of this study indicated that horses which were kept on livery yards and riding schools were likely to be found in urban environments, some distance away from the owner's home and vaccinated against influenza and herpes virus. Survey respondents were likely to travel greater than 10 miles to attend activities such as eventing or endurance but were also likely to travel and return home within a single day (58.6%, 2063/3522). This may affect the geographical extent and speed of disease spread, if large numbers of people from disparate parts of the country are attending the same event and the disease agent is highly infectious or virulent. The greatest risk for disease introduction and spread may be represented by a small proportion of people who import or travel internationally with their horses. These respondents were likely to have foreign horse passports, which were not necessarily recorded in the National Equine Database (NED), making the location of these horses untraceable. CONCLUSIONS: These results illustrate the difficulties which exist with national GB horse traceability despite the existence of the NED and the horse passport system. This study also demonstrates that an online approach could be adopted to obtain important demographic data on GB horse owners on a more routine and frequent basis to inform decisions or policy pertaining to equine disease control. This represents a reasonable alternative to collection of GB horse location and movement data given that the NED no longer exists and there is no immediate plan to replace it.

Preliminary genetic analyses of important musculoskeletal conditions of Thoroughbred racehorses in Hong Kong.

A retrospective cohort study of important musculoskeletal conditions of Thoroughbred racehorses was conducted using health records generated over a 15 year period (n=5062, 1296 sires). The prevalence of each condition in the study population was: fracture, 13%; osteoarthritis, 10%; suspensory ligament injury, 10%; and tendon injury, 19%. Linear and logistic sire and animal regression models were built to describe the binary occurrence of these musculoskeletal conditions, and to evaluate the significance of possible environmental risk factors. The heritability of each condition was estimated using residual maximum likelihood (REML). Bivariate mixed models were used to generate estimates of genetic correlations between each pair of conditions. Heritability estimates of fracture, osteoarthritis, suspensory ligament and tendon injury were small to moderate (range: 0.01-0.20). Fracture was found to be positively genetically correlated with both osteoarthritis and suspensory ligament injury. These results suggest that there is a significant genetic component involved in the risk of the studied conditions. Due to positive genetic correlations, a reduction in prevalence of one of the correlated conditions may effect a reduction in risk of the other condition.

Direct RT-PCR from serum enables fast and cost-effective phylogenetic analysis of bovine viral diarrhoea virus.

Studies of the molecular epidemiology of viral diseases are dependent on the analysis of large numbers of samples from infected individuals, and the assembly of relevant sequence databases are a prerequisite to investigate chains of infection. As part of research in support of the Scottish BVDV eradication campaign, we have established a direct RT-PCR method for the high throughput amplification and analysis of the informative 5'-untranslated region of the BVDV genome. Heat-treatment followed by a one-step RT-PCR, performed in 96-well plates, produced sufficient material for sequence analysis from 0.5 µl of serum or plasma. Of 93 samples assayed, only five failed to give full sequence data for the region amplified and these were subsequently successfully analysed in single tube format reactions. This approach improved the speed of analysis, reduced costs, operator time and the potential for contamination, and may allow analysis of samples for which volumes are too low for conventional RNA isolation. It also has the potential for wider application in both human and animal disease research in which high throughput and low cost would increase the size of datasets that can be obtained.

Effect of breed, age, weight and gender on radiographic renal size in the dog.

In the adult dog, kidney length has been reported as 2.98 ± 0.44 times the length of L2 on ventrodorsal views and 2.79 ± 0.46 times the length of L2 on lateral radiographs. Our aim was to test the hypothesis that the suggested maximum normal left kidney size is too high, and to evaluate the effect of breed type, gender, weight and age of the dog on kidney size. Abdominal radiographs of 200 dogs with no evidence of concurrent disease that might have an effect on renal size were included in the study. The mean ratio of kidney length to the second lumbar vertebra length was similar to previous reports. For the right lateral view it measured 2.98 ± 0.60 and for the ventrodorsal view 3.02 ± 0.66. Significant differences of this ratio between skull type were present, especially between brachycephalic and dolichocephalic dogs. On the right lateral view brachycephalic dogs had the highest median LK/L2 ratio of 3.1 (3.20 ± 0.40), whereas for dolichocephalic dogs it was 2.8 (2.82 ± 0.50), and for mesaticephalic dogs it was 2.97 (3.01 ± 0.6). A ratio >3.5 was found only in mesaticephalic dogs on the ventrodorsal view. There was a significant difference in the LK/L2 ratio between small (≤10kg) and large breed dogs (>30kg) where small dogs had a significantly higher LK/L2 ratio. There was no statistically significant relation between this ratio and age or gender. The previously reported ratios for kidney size seem valid, but because skull type has an impact on the LK/L2 ratio, a single normal ratio should not be used for all dogs.