Animal and Plant Health Agency

Emerging infectious diseases are of major concern to animal and human health. Recent emergence of high pathogenicity avian influenza virus (HPAIV) (H5N1 clade 2.3.4.4b) led to substantial global mortality across a range of host species. Co-occurring species showed marked differences in mortality, generating an urgent need for better epidemiological understanding within affected populations. We therefore tested for antibodies, indicative of previous exposure and recovery, and for active viral infection in apparently healthy individuals (n = 350) across five co-occurring seabird species on the Isle of May, Scotland, during 2023, following H5N1 HPAIV associated mortality in the preceding summer. Antibody prevalence to AIV subtypes varied substantially between species, ranging from 1.1% in European shags (Gulosus aristotelis) (to H5) to 78.7% in black-legged kittiwakes (Rissa tridactyla) (to H16 or both H13 and H16), and between 31 and 41% for three auk species (H5, H16 or both). At least 20.4% of auks had antibodies to an as yet unidentified subtype, suggesting further subtypes circulating in the population. We found low levels of active, but asymptomatic, AIV infection in individuals (1.6–4.5%), but excluded this as H5N1. Our results emphasise the importance of testing healthy individuals to understand the prevalence of co-circulating AIV subtypes in wild populations, and the potential for future reassortment events which could alter virus behaviour and impact.

Background Bovine tuberculosis (TB) is a burden to cattle farming in Great Britain. Poor biosecurity has been identified as contributing to the epidemic. Methods We conducted a systematic review of epidemiological studies published in the scientific literature between 1921 and 2024 that measured the association between farm biosecurity and cattle TB. Eligible studies controlled for confounding factors and reported statistically significant association/s between biosecurity and TB ( p < 0.05) and/or an effect ratio/s of more than 3. Biosecurity uptake in England was assessed using official Disease Report Forms (DRFs) from 4074 TB incidents occurring in 2018 and 2019. Results Thirty‐three papers with 116 effect estimates met the inclusion criteria and were grouped according to a five‐point biosecurity plan. There was consistent evidence for TB risk being reduced by reducing contact with neighbouring herds and preventing cattle at higher TB risk from entering herds. The evidence for the effectiveness of measures for reducing contact between badgers and cattle was inconsistent. The DRF data showed a low uptake of biosecurity to reduce contact between badgers and cattle. Limitations All the studies identified were retrospective. Biosecurity was measured using different instruments, for example, questionnaires. Conclusions There is analytical epidemiological evidence supporting guidance for improving biosecurity, but there are some limitations. Further research is needed to identify the most effective wildlife‐focused measures.

Salmonella spp. and hepatitis E virus (HEV) are significant foodborne zoonotic pathogens that impact the health of livestock, farmers, and the general public. This study aimed to identify biosecurity measures (BSMs) against these pathogens on swine farms in Europe, the United States, and Canada. Overall, 1,529 articles from three scientific databases were screened manually and with the artificial intelligence (AI) tool ASReview. We identified 54 BSMs from 32 articles, primarily focused on Salmonella spp. control. Amongst the extracted BSMs, only five measures for Salmonella spp. control, namely, ‘acidification of feed’, ‘acidification of drinking water’, ‘rodent control’, ‘all-in and all-out production’, and ‘disinfection’ had sufficient observations to conduct a meta-analysis. Of these five, acidification and rodent control were found to be protective measures, that is, their summary odds ratios in the corresponding meta-analyses were lower than 1, indicating lower odds of Salmonella spp. presence on farms which implemented these BSM compared to farms which did not implement them (odds ratio [OR] around 0.25). All-in and all-out production showed a non-significant protective effect (OR = 0.71), while disinfection showed a statistically non-significant lack of association between disinfection and the presence of Salmonella spp. on the farm (OR = 1.03). For HEV, no meta-analysis could be performed. According to multiple articles, two BSMs were significantly associated with a lower risk of HEV presence, namely, disinfecting vehicles (OR = 0.30) and quarantining pigs before introducing them on the farm (OR = 0.48). A risk of bias assessment for each included article revealed a high risk in the majority of the articles, mainly due to selection and performance bias. This emphasises the lack of standardised, high-quality study designs and robust empirical evidence linking BSM implementation to pathogen reduction. The limited data available for meta-analysis, coupled with the high risk of bias (RoB) in the literature, highlights the urgent need for more substantial evidence on the effectiveness of BSMs in mitigating the transmission and spread of zoonotic pathogens, such as Salmonella spp. and HEV on pig farms.

Atypical scrapie (AS) is a transmissible spongiform encephalopathy (TSE) that affects sheep and goats. Low within-flock incidence suggests that AS is not transmissible between animals, and testing of all animals that exit positive flocks for two years following detection (i.e., intensified monitoring) used to be carried out in the EU to provide data to test this. This intensified monitoring stopped in 2021 but continues in Great Britain (GB). The aim of this study was to predict the number of AS cases missed if this monitoring were also stopped in GB, using a combination of statistical and transmission modelling. The number of AS cases estimated to be missed if the intensified monitoring was stopped was low relative to the number of AS cases detected in other active surveillance streams (e.g., fallen stock and abattoir surveys), at approximately 1 case every 3 years (0.34 per year, 95% CI: 0.18–0.54) compared to 10 per year (95% CI: 4–17) in the active surveillance stream. This suggests that stopping the intensive monitoring of AS would have relatively little impact on AS surveillance and on the power of the available AS data to infer whether AS is contagious.

Babesia divergens, a major cause of bovine babesiosis with zoonotic potential, was analyzed through genomes Bdiv23B and Bdiv24B following Illumina sequencing of DNA extracted from PCR-positive cattle blood. The genomes comprised 3888 and 4032 predicted coding sequences, respectively, comparable to the reference genome, Rouen 1987, highlighting genomic consistency across isolates.

This work was performed to generate the data needed to set epidemiological cut-off values for minimal inhibitory concentrations (MICs) of 10 antimicrobial agents against Vibrio parahaemolyticus determined using standardised broth microdilution protocols. Eight laboratories performed broth microdilution tests with incubation at 35°C for 16 to 20 h, and 7 also performed tests on the same isolates with incubation at 28°C for 24 to 28 h. Data were analysed by the ECOFFinder and normalised resistance interpretation algorithms. The cut-off values calculated for ceftazidime, florfenicol and trimethoprim/sulfamethoxazole, 1, 1 and 0.25/4.75 µg ml ⁻¹ , respectively, were the same when calculated from data obtained at both temperatures. The cut-off values calculated from data obtained at 35°C and from data obtained at 28°C were 0.25 and 0.5 µg ml ⁻¹ for enrofloxacin, 2 and 4 µg ml ⁻¹ for gentamicin, 0.5 and 1 µg ml ⁻¹ for oxolinic acid and 2 and 1 µg ml ⁻¹ for oxytetracycline, respectively. The influence of incubation temperature on MIC values was investigated by comparing MICs obtained at 35 and 28°C for a specific antimicrobial agent with a particular isolate by an individual laboratory. Results showed that 56% of 1473 of these paired MIC values were identical, while 38% differed from one another by not more than 1 dilution step. The data generated in this work will be submitted to the Clinical and Laboratory Standards Institute for consideration in their setting of internationally agreed epidemiological cut-off values for V. parahaemolyticus that are essential for interpreting antimicrobial susceptibility testing data of this species.

The European hedgehog ( Erinaceus europaeus) is a protected species of conservation concern in the UK. In recent years, there have been multiple incidents of fatal encephalitis in captive hedgehogs in wildlife rescue centers associated with the molecular detection of a hedgehog arterivirus (HhAV-1). However, it remains unclear whether the virus is the causative agent of the central nervous system (CNS) lesions. In a retrospective investigation using postmortem material from 7 captive hedgehogs with neurological disease, and a single hedgehog with previously identified meningoencephalitis, histologic examination was conducted in tandem with viral RNA in situ hybridization (ISH) to appraise tissue distribution of HhAV-1 and the colocalization with histologic lesions. ISH revealed multicellular tropism of HhAV-1 involving monocyte-macrophage and vascular endothelial cells, with viral RNA detected in multiple organs, likely due to endotheliotropism and viremia. In the CNS, encephalomyelitis was mild whilst viral RNA was abundant and widely distributed, particularly in the microglial population and localized to areas with glial nodules. Splenic lymphoid depletion was generally mild but was moderate to severe in 2 septicemic animals. Brain samples from 13 control hedgehogs, found dead in the wild due to predation/trauma, were also screened for HhAV-1, of which 8 tested positive by real-time reverse transcription polymerase chain reaction (RT-PCR) with a low viral load. No CNS lesions or ISH labeling was observed in 2 of these control hedgehogs that could be examined histologically. Combined, these findings indicate that HhAV-1 infections in captive hedgehogs in English wildlife rescue centers may be associated with histopathologic alterations and clinical neurological disease.

Epidemiological and eradication trial evidence indicates that Helicobacter pylori, a major causative factor in peptic ulcer and gastric cancer, is a driver of the hypokinesia of Parkinson’s disease (PD). Psychological (cognitive impairment, depression and anxiety) and gastrointestinal (peptic ulceration and constipation) PD features can precede the symptomatic onset of motor features by decades. We hypothesise that the non-H. pylori Helicobacters (NHPH), which have farm, companion and wild animals as their main hosts, can have a role in PD aetiopathogenesis. In those occupationally at risk of NHPH infection, we address whether there is increased mortality with PD, or depression or suicide. Our systematic review gave evidence that occupational exposure to animals/their products is associated with excess mortality with PD. Indeed, whilst livestock farming increased the risk, crop farming decreased it. Moreover, excess mortality from non-Hodgkin lymphoma in livestock farmers is compatible with NHPH being causal. Our scoping review showed that farmers, veterinarians and abattoir workers have an increased risk of depression and suicide; whether their depression is associated with being down the pathway to PD and/or the presence of Helicobacter infection needs investigation. Regarding Helicobacter species specificity, the link between the presence of NHPH in gastric biopsy and PD was described using a ureA polymerase chain reaction (PCR) assay, targeting the most-commonly named NHPH, H. suis. We describe its redesign and optimisation as a probe-based PCR, confirming the exclusion of H. pylori but not H. suis specificity (additionally identifying 6 species of a 22-NHPH-species panel). The exploration of the zoonotic hypothesis requires a non-invasive pan-Helicobacter PCR screen, allowing the detection and molecular grouping of Helicobacter species.

Background This retrospective cohort study evaluated 584 cattle caesarean sections (C‐sections) performed at a first opinion practice in Southwest England between 2015 and 2021. Methods Outcomes were recorded contemporaneously, and procedures were followed up after 14 days. Results Thirty‐one dams died within 14 days of undergoing a C‐section (94.7% survival rate). Dam parity and purpose did not significantly impact mortality. Dams were at 2.7 times greater odds of dying within 14 days if they delivered a stillborn calf ( p < 0.05, 95% confidence interval [CI] = 1.20‒6.13), and at 2.9 times greater odds of dying within 14 days if they were recumbent for some, or all, of the C‐section ( p < 0.05, 95% CI = 1.02‒8.2). Among the 428 procedures where calf outcomes were recorded, 32.9% ( n = 141) were stillborn, reflecting previous studies reporting perinatal mortality. Uterine torsion was anecdotally listed as the reason for operating in 34 cases, and 58.1% ( n = 18) of these C‐sections resulted in a dead calf. Limitations Despite the large number of cases studied, all C‐sections were carried out by a single veterinary practice. Individual operator(s) and farms were not recorded and could be undetected confounding variables. Conclusion This study's results provide much needed relevant benchmarking for completing in‐house practice audit cycles, ensuring improved clinical governance and outcomes.

Background: The international gold standard for avian influenza virus (AIV) diagnosis is virus isolation (VI) in specific pathogen-free embryonated chicken eggs (ECEs). AIV isolation typically involves a 6-day turnaround, during which premises under suspicion for notifiable AIV infection are held under restriction regardless of molecular diagnoses, often with significant welfare implications. Methods: A reduction in time for negation by VI was investigated following experimental inoculation of AIV from known-positive original clinical material into ECEs. VI data derived from more than 600 case investigations from epizootics of high-pathogenicity AIV (HPAIV) in Great Britain since 2016 and from low-pathogenicity AIV (LPAIV) cases in Great Britain since 2014 were examined to support a reduction in test timing using alternative regimens. Results: HPAIVs were isolated during the first passage, and for LPAIV VI, the second passage could be reduced to 2 days. Power analysis showed that the benefit of reducing the number of days outweighed the risk of missing a positive isolate. Limitations: Limited data were available from experimental inoculations. Conclusion: This truncated methodology, which enables an earlier release of restrictions, may substantially ease the economic implications of restriction. It could also reduce bird welfare implications and improve international standards without loss of test performance.

Methodologies for source attribution (SA) of foodborne illnesses comprise a rapidly expanding suite of techniques for estimating the most important source or sources of human infection. Recently, the increasing availability of whole genome sequencing (WGS) data for a wide range of bacterial strains has led to the development of novel SA methods. These techniques utilize the unique features of bacterial genomes adapted to different host types and hence offer increased resolution of the outputs. Comparative studies of different SA techniques reliant on WGS data are currently lacking. Here, we critically assessed and compared the outputs of three SA methods: a supervised classification random forest machine learning algorithm (RandomForest), an Accessory genes-Based Source Attribution method (AB_SA), and a Bayesian frequency matching method (Bayesian). Each technique was applied to the WGS data of a panel of 902 reservoir host and human monophasic and biphasic Salmonella enterica subsp. enterica serovar Typhimurium isolates sampled in the British Isles (BI) and Denmark from 2012 to 2016. Additionally, for RandomForest and Bayesian, we explored whether utilization of accessory genome features as model inputs improved attribution accuracy of these methods over using the core genome derived features only. Results indicated that this was the case for RandomForest, but for Bayesian the overall attribution estimates varied little regardless of the inclusion or not of the accessory genome features. All three methods attributed the vast majority of human isolates to the Pigs primary source class, which was expected given the known high relative prevalence rates in pigs, and hence routes of infection into the human population, of monophasic and biphasic S. Typhimurium in the BI and Denmark. The accuracy of AB_SA was lower than of RandomForest when attributing the primary source classes to the 120 animal test set isolates with known primary sources. A major advantage of both AB_SA and Bayesian was a much faster execution time as compared to RandomForest. Overall, the SA method comparison presented in this study describes the strengths and weaknesses of each of the three methods applied to attributing potential monophasic and biphasic S. Typhimurium animal sources to human infections that could be valuable when deciding which SA methodology would be the most applicable to foodborne disease outbreak scenarios involving monophasic and biphasic S. Typhimurium.

Between 2013 and 2016, the A/H1N1pdm09 component of the live attenuated influenza vaccine (LAIV) produced instances of lower-than-expected vaccine effectiveness. Standard pre-clinical ferret models, using a human-like vaccine dose and focusing on antigenic match to circulating wildtype (wt) strains, were unable to predict these fluctuations. By optimising the vaccine dose and utilising clinically relevant endpoints, we aimed to develop a ferret efficacy model able to reproduce clinical observations. Ferrets were intranasally vaccinated with 4 Log10 FFU/animal (1000-fold reduction compared to clinical dose) of seven historical LAIV formulations with known (19–90%) H1N1 vaccine efficacy or effectiveness (VE). Following homologous H1N1 wt virus challenge, protection was assessed based on primary endpoints of wt virus shedding in the upper respiratory tract and the development of fever. LAIV formulations with high (82–90%) H1N1 VE provided significant protection from wt challenge, while formulations with reduced (19–32%) VE tended not to provide significant protection. The strongest correlation observed was between reduction in wt shedding and VE (R² = 0.75). Conversely, serum immunogenicity following vaccination was not a reliable indicator of protection (R² = 0.37). This demonstrated that, by optimisation of the vaccine dose and the use of non-serological, clinically relevant protection endpoints, the ferret model could successfully translate clinical H1N1 LAIV VE data.

Tick-borne diseases pose a growing threat to human and animal health in Europe, with tick-borne encephalitis virus (TBEV) and Crimean-Congo haemorrhagic fever virus (CCHFV), vectored by Ixodes ricinus and Hyalomma marginatum , respectively, emerging as primary public health concerns. The ability of ticks to transmit pathogens to multiple hosts and maintain infections across life stages makes them highly efficient vectors. However, many aspects of tick ecology and vectorial capacity remain understudied. This review examines key factors contributing to the vectorial competence of European ticks and their associated viruses. We first explore the influence of climate change on vector and disease ecology, using TBEV and CCHFV as case studies. We then analyse the role of the tick antiviral response in shaping vector competence. By integrating these elements, this review aims to enhance our understanding of tick-borne viral diseases and support the development of public health strategies, particularly through the One Health framework, to mitigate their impact in Europe.

Background Brucellosis remains a significant health and economic challenge for livestock and humans globally. Despite its public health implications, the factors driving the endemic persistence of Brucella at the human-livestock interface in Tanzania remain poorly elucidated. This study aimed to identify the seroprevalence of Brucella infection in livestock and humans within a ranching system and determine associated risk factors for disease endemicity. Methods A cross-sectional sero-epidemiological study was conducted in 2023 in Tanzania’s Karagwe District, involving 725 livestock (cattle, goats, sheep) from 10 herds and 112 humans from associated camps. Seroprevalence was assessed using competitive ELISA while epidemiological data were collected via questionnaires. Generalized Linear Models and Contrast Analysis were used to identify risk factors for infection. Results Overall seroprevalence was 34% in livestock and 41% in humans. Goats exhibited the highest prevalence (69.2%), while cattle had the lowest (22.6%). Mixed-species herds (Odds Ratio, OR = 2.96, CI [1.90–4.60]) and small ruminants-only herds (OR = 6.54, CI [3.65–11.72]) showed a significantly higher risk of seropositivity compared to cattle-only herds. Older cattle (OR = 5.23, CI [2.70–10.10]) and lactating females (OR = 2.87, CI [1.78–4.63]) represented significant risks for brucellosis in livestock. In humans, close contact with animals (OR = 7.20, CI [1.97–36.31]) and handling animals during parturition or aborted fetuses (OR = 2.37, CI [1.01–5.58]) were significant risk factors. Notably, no spatial association was found in seroprevalence between herds and nearby human communities. Conclusion The lack of spatial correlation between livestock and human seroprevalence suggests complex transmission dynamics, potentially involving endemic circulation in livestock and human infections from multiple sources of exposure to livestock. This study highlights the need for comprehensive zoonotic risk education and targeted intervention strategies. Further research is crucial to elucidate transmission pathways and improve Brucella infection control. This includes developing robust methods for identifying infective species and implementing effective strategies to mitigate Brucella infection in endemic regions.

Background Antimicrobial resistance (AMR) is a global threat. Monitoring using an integrated One Health approach is essential to detect changes in AMR occurrence. Aim We aimed to detect AMR genes in pathogenic and commensal Escherichia coli collected 2013–2020 within monitoring programmes and research from food animals, food (fresh retail raw meat) and humans in six European countries, to compare vertical and horizontal transmission. Methods We whole genome sequenced (WGS) 3,745 E. coli isolates , detected AMR genes using ResFinder and performed phylogenetic analysis to determine isolate relatedness and transmission. A BLASTn-based bioinformatic method compared draft IncI1 genomes to conserved plasmid references from Europe. Results Resistance genes to medically important antimicrobials (MIA) such as extended-spectrum cephalosporins (ESC) were widespread but predicted resistance to MIAs authorised for human use (carbapenem, tigecycline) was detected only in two human and three cattle isolates. Phylogenetic analysis clustered E. coli according to phylogroups; commensal animal isolates showed greater diversity than those from human patients. Only 18 vertical animal-food and human-animal transmission events of E. coli clones were detected. However, IncI1 plasmids from different sources and/or countries carrying resistance to ESCs were conserved and widely distributed, although these variants were rarely detected in human pathogens. Conclusion Using WGS we demonstrated AMR is driven vertically and horizontally. Human clinical isolates were more closely related, but their IncI1 plasmids were more diverse, while animal or food isolates were less similar with more conserved IncI1 plasmids. These differences likely arose from variations in selective pressure, influencing AMR evolution and transmission.

Adults and immatures of Aedes epactius were collected in July and December 2022 at sites of high elevation in the states of Chihuahua (2300 masl) and Zacatecas (2182 and 2595 masl), Mexico, respectively. Mosquitoes were identified morphologically and sequenced for a DNA barcode of the cytochrome c oxidase I (COX1). This is the first distributional record of Ae. epactius in Zacatecas and provides evidence of the highest altitude in the Americas, including Mexico. The geographical distribution of Ae. epactius in Mexico was reviewed, and the COX1 analysis, using phylogenetic Bayesian analysis to confirm species identification, was performed.

Disinfectants are essential for biosecurity, preventing the persistence and spread of zoonotic pathogens on farms and subsequent human infections. In this study, transcriptomics and genomics were utilised to assess the effect of disinfectant exposure on pathogenic Escherichia coli. The exposure of E. coli O157:H7 to sub-optimal concentrations of commonly used farm disinfectants elicited changes in both the transcriptome and genome. The transcriptomics identified upregulation of >300 genes and downregulation of >100 genes with functions, which included stress response, metabolism, transcription, transportation, membrane-associated and virulence genes. The phage shock protein (psp) operon was highly upregulated in response to a quaternary ammonium compound (QAC)-containing disinfectant, which has not previously been associated with a response to chemical stress. Disinfectant-adapted isolates generated by exposure to sub-lethal disinfectants levels demonstrated resistance to several common antibiotics and decreased sensitivity to biocides. Whole genome sequencing of the mutant strains indicated that they had acquired mutations in the genes associated with the upregulation of the multiple antibiotic resistance (MAR) efflux system (lon protease and marR) and topoisomerase genes (gyrA and gyrB). The disinfectant-adapted isolates also exhibited increased expression of transcription, respiration and several pH stress response genes localised in the “acid fitness island.” This study demonstrated that sub-optimal disinfectant concentrations allow E. coli O157:H7 to adapt and survive disinfection and develop antibiotic resistance. These changes could have implications for disease treatment and elimination on farms. Although E. coli O157:H7 and farm disinfectants were the focus of this study, we believe these findings are also applicable to other settings, including hospitals.