Veterinary clinical biosecurity is key to preventing infectious diseases in animal clinics, particularly when there is high patient turnover, a mix of species, close contact among animals, or immunocompromised patients that raise the risk of hospital-associated infections (HAIs). This review outlines a practical, evidence-based approach designed to address biohazards, including zoonotic pathogens, and inherent risk factors that elevate HAI incidence in veterinary healthcare settings. It further outlines the principles and components of clinical biosecurity, i.e., bio-exclusion, bio-containment, and procedural hygiene, necessary to establish a robust infection control framework. A suite of actionable strategies is delineated, ranging from rigorous hand hygiene ('Clean hands, strong defense!') and proper cleaning and disinfection protocols to the integration of biosecurity measures with Hazard Analysis and Critical Control Points (HACCP) principles and a continuous Plan-Do-Check-Act (PDCA) cycle for quality improvement. Further, this review emphasizes the importance of regular audits and systematic quantitative monitoring to ensure adherence to biosecurity protocols, recommending practical tools such as compliance scoring systems and standardized checklist evaluations. The integration of artificial intelligence (AI)-based tools for predictive analytics and real-time pathogen surveillance, is proposed to enhance early outbreak detection and emergency response effectiveness. Additionally, tailored biosecurity protocols are detailed for implementation in resource-limited veterinary practices, providing specific, achievable strategies for diverse operational environments. By merging rigorous scientific principles with practical applications, this review delivers actionable, evidence-based guidelines to effectively mitigate HAIs, thereby improving animal welfare and safeguarding public health.

Fluoroquinolone (FQ) resistance has a major impact on human and animal health by complicating treatment of infections. In Belgium, the use of FQ in the agricultural chain is restricted, but high levels of resistance have nevertheless been observed. The spread of resistant strains and their genomic resistance determinants throughout the poultry production chain remain poorly understood. This study investigated the role of the parental flocks and hatchery in the spread of FQ resistance towards broiler farms. Samples were collected from four parental farms and corresponding hatcheries in Belgium. E. coli and FQ-resistant E.coli isolates were recovered from the samples using non-selective and FQ-selective media. Isolates were identified using MALDI-TOF mass spectrometry. A selection of 79 isolates were analyzed using whole genome sequencing (WGS) to determine antimicrobial resistance and to identify phylogenetically related isolates. FQ-resistant E. coli were detected in the faeces of the parent stock on all four farms, with 70.3% of all E. coli positive samples showing FQ resistance. No FQ-resistant E. coli were detected in the egg samples. All environmental samples from the sorting belt of the hatcheries carried FQ resistant E. coli. Of the sampled day-old chicks at the hatchery, 3 out of 4 batches were positive. The WGS analysis could not identify any genomic links between isolates from parent stock and the day-old chicks. Additionally, WGS revealed high genomic diversity among the collected strains, with 13 different sequence types and a wide range of genomic AMR determinants. In conclusion, our findings highlight the complexity of FQ resistance transmission in broiler production. The presence of FQ-resistant E. coli in the hatchery and their spread among day-old chicks stress the need for critical interventions at multiple stages, which should include enhanced, batch-level cleaning and disinfection protocols in hatcheries, and minimizing antimicrobial usage across the whole broiler production chain.

African swine fever (ASF) poses a serious economic threat to European pig production, with no vaccines or treatments available. This study consolidates the scattered economic evidence on ASF costs and biosecurity expenditure and applies a benefit-cost framework to assess whether prevention-focused investment is a sound economic strategy relative to outbreak response. A structured literature search across PubMed/MEDLINE, Web of Science, ScienceDirect, CAB Abstracts and EconLit (January 1990–December 2025) screened 1,247 records, of which 34 were retained to parameterise an illustrative expected-value benefit-cost analysis, with all costs converted to 2025 EUR. For a 122-sow reference farm, preventive biosecurity was estimated at €125,750 infrastructure plus €22,051 annual operating costs (€12.37 per pig), whereas an outbreak imposed farm-level losses of approximately €838,000, exceeding 830% of annual profits (€101,000). European simulations for larger industrialised herds suggested per-herd direct costs of €0.9–1.2 million, while government-funded control reached €28.4 million even for a geographically limited wild boar outbreak with no domestic pig infections, alongside export losses from trade bans. At base-case assumptions (10% outbreak probability, 50% prevention effectiveness), the farm-level benefit-cost ratio was 1.21:1, rising to 2.42:1 at 20% probability; the break-even threshold was 41.3% prevention effectiveness. Because farm-level analysis captures only part of total costs—indirect trade losses may reach 29 times direct control costs—the sector-wide case for prevention is substantially stronger. Despite considerable uncertainty, the evidence consistently favours prevention over reactive approaches, suggesting policy should prioritise biosecurity investment, particularly for vulnerable small-scale producers facing the highest per-unit costs and greatest outbreak risk.

Downtime, also known as an animal avoidance period, refers to a 24-72 h period during which individuals who have had contact with one animal species avoid subsequent contact with other susceptible species. This scoping review critically evaluated the effectiveness of downtime as a biosecurity measure. Peer-reviewed studies were identified and analysed using three electronic databases (Pubmed, Web of Science and Scopus). Two experimental studies directly evaluated downtime, nine additional articles examined human nasal carriage of pathogens after exposure to infected animals and seven articles evaluated the effectiveness of hygiene-based biosecurity measures targeting indirect mechanical pathogen transmission via humans (n = 14 unique articles in total; topical overlap noted where studies contributed to multiple categories). No evidence indicated an added benefit of downtime over other, more evidence-based measures such as hand hygiene, changing of clothes and boots and showering. While certain studies were able to identify the nasal carriage of pathogens, only one study indicated possible consequent transmission to naïve animals. This limited and species-specific evidence base reveals a critical gap between policy recommendations and scientific support for downtime. Based on these results, no clear benefit or necessity of downtime over other measures have been identified, other than its ability to deter unnecessary visitors, but these do not outweigh the impracticalities associated with an 'animal avoidance period'. Resources and policy efforts should therefore shift from enforcing downtime toward ensuring and verifying adherence to fundamental hygiene measures.

BACKGROUND: Livestock production accounts for nearly half of all agricultural output globally, but the long-term sustainability of the sector is threatened by a range of infectious diseases. Endemic diseases lead to a wide range of production losses and animal welfare issues, while transboundary and epidemic diseases can lead to widespread deaths, the implementation of stringent control measures, and a disruption of trade. Zoonotic diseases further threaten human health. It is therefore critical that livestock diseases are effectively controlled. When implementing disease control strategies and biosecurity measures, it is important to understand stakeholders’ views, particularly regarding which diseases should be prioritised. METHODS: The current study aims to develop our understanding of veterinarians’ views regarding infectious diseases in livestock across Belgium, Ireland, Hungary, Romania, and Sweden through an online survey. The survey examines veterinarians’ perception of the risk posed by infectious livestock diseases based on a three-part score comprising of: the perceived likelihood of an outbreak occurring; the impact of an outbreak; and the ease of controlling an outbreak. Veterinarians’ awareness of given diseases was also assessed. RESULTS: We report a high degree of variation in the perception of risk for livestock diseases across both the livestock production sectors examined, and countries. The transboundary diseases African swine fever, foot and mouth disease and avian influenza were seen as posing a high risk overall, however, bluetongue, lumpy skin disease, peste des petits ruminants, and sheep and goat pox showed a highly regional variation. Endemic diseases were often seen as posing a higher risk than transboundary diseases in many countries. We further identified several awareness gaps, particularly related to zoonotic diseases such as Hepatitis E, Campylobacter and Salmonella Dublin. CONCLUSIONS: Perception of risk for both transboundary and endemic diseases show a high degree of variation at the national level, often reflecting differences in the importance of production sectors by country. Critical awareness gaps for both transboundary, and zoonotic, diseases require further investigation.

Background: Raw-meat-based diets (RMBDs) for companion animals have gained popularity but may serve as vehicles for antimicrobial-resistant (AMR) bacteria, posing risks to animal and public health. This study investigated the occurrence and risk factors of AMR in indicator bacteria (Escherichia coli, Enterococcus faecalis, Enterococcus faecium) and Campylobacter spp. from commercial RMBD products. Methods: In 2023, 50 RMBD samples were collected in Belgium, representing 21 brands from five countries. After both selective and non-selective isolation and MALDI-TOF identification, antimicrobial susceptibility testing of the isolates was performed using broth microdilution. Results: From non-selective media, E. coli was found in 45 samples (90.0%), E. faecalis in 31 samples (62.0%), E. faecium in 23 samples (46.0%), and Campylobacter spp. in 3 samples (6.0%). Among these, one E. faecalis strain with acquired resistance to vancomycin and daptomycin was isolated. Multidrug resistance (MDR) was identified in 17 isolates from 15 samples (30.0%), including 14 MDR E. coli, 1 MDR E. faecalis, and 2 MDR E. faecium. From selective media, presumptive ESBL/AmpC-producing E. coli were detected in 17 samples (34.0%), and 5 E. faecium from linezolid-supplemented media were confirmed by the broth microdilution method. Samples from Belgian origin showed significantly higher E. faecium prevalence (76.5%) compared to Dutch samples (21.4%) (OR = 11.9, p < 0.001). Minor livestock sources were associated with increased MDR risk (OR = 5.52, p = 0.016). Conclusions: Commercial RMBDs in Belgium exhibit widespread bacterial contamination with concerning AMR patterns. These findings highlight the need for improved production standards in the RMBD industry and the need to raise awareness in pet owners.

Background Biosecurity is essential for preventing the introduction and spread of infectious diseases in livestock production. Despite the well-established benefits of biosecurity, the implementation remains inconsistent across production systems. Objective This study reviewed studies on biosecurity-supporting measures, focusing on training, coaching, and sensor technologies, and incorporated findings from a farmer survey on availability and accessibility of biosecurity-supporting measures. Methods A scoping review of 29 peer-reviewed studies was conducted following PRISMA‑ScR guidelines. Information about the availability of relevant biosecurity-supporting measures was collected between October 2023 and May 2024 on 390 farms across 11 different animal species–production system combinations in seven European countries. Results Training and coaching were the most frequently studied biosecurity-supporting measures, whereas sensor technologies received less attention. Coaching and training were associated with improved biosecurity scores, reduced antimicrobial use, and increased farmer engagement. Sensor technologies showed potential for monitoring compliance but raised ethical and practical concerns. Survey results indicated that although many farmers considered themselves well informed, notable gaps remained, particularly in extensive and small-scale systems, in terms of engagement with available information sources and the adoption of supporting measures. Hygiene protocols were the most widely implemented measure, whereas sensors were the least used. Conclusion Overall, personalised and ongoing support, particularly through coaching and training, can improve the implementation of biosecurity practices. However, differences in access to and adoption of supporting measures across systems highlight the need for tailored strategies. Combining conventional approaches with modern technologies and actively involving relevant stakeholders can help strengthen biosecurity across farming contexts.

Background/Objectives: Methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP) represent important antimicrobial resistance threats related to companion animals, which can directly or indirectly lead to adverse health effects in humans and animals living in close contact. Characterizing the phenotypic resistance of MRSA and MRSP to a panel of antimicrobials relevant to both veterinary and human medicine is crucial within a “One Health” framework. Methods: In this study, a total of 79 presumptive MRSA isolates (34 from cats, 45 from dogs) and 110 presumptive MRSP isolates (105 from dogs, 5 from cats) from clinical cases were analysed. Real-time PCR was used to detect the presence of mecA and mecC genes, and susceptibility testing was performed using the Sensititre EUST2 panel. Results: Most of the isolates (88.9%, 168/189) were positive for the mecA gene, while a minority (1.1%, 2/189) were mecC-positive (2 MRSA, 1 dog, 1 cat). MRSP isolates exhibited acquired resistance to a broader range of antibiotics compared to MRSA strains. Furthermore, several isolates demonstrated acquired resistance to antibiotics considered critically important for human medicine. Resistance to vancomycin was found in an MRSP isolate from a dog, and resistance to linezolid in an MRSP isolate from a cat. This study reveals that 83.3% (30/36) of MRSA isolates from dogs and 89.3% (25/28) from cats were multidrug-resistant organisms, while MRSP isolates exhibited multidrug resistance in 99% (101/102) of cases for dogs and 100% (4/4) for cats. Conclusions: The extremely high level of multidrug resistance, with some isolates resistant to critically important antibiotics used in human medicine, highlight the importance of monitoring antimicrobial susceptibility in MRSA and MRSP isolates collected from cats and dogs in a One Health perspective.

Between 2006 and 2010, northwestern Europe experienced its first significant bluetongue virus (BTV) outbreak, driven by the spread of BTV-8, which had major repercussions on the European livestock sector. While BTV-3 was first identified in Europe in Italy in 2017, a new introduction of the virus was reported in 2023, in the Netherlands, and subsequently spread rapidly across the continent. A limited number of BTV-3 outbreaks were notified in Belgium in 2023, leading to the loss of its BTV-free status. In the following year, 2024, the virus spread throughout the country in a short time period. This study describes the impact of BTV-3 circulation in Belgium in 2024, detailing both its geographic spread and the associated increase in mortality, reduced births recorded, and decline in milk production among ruminants. Furthermore, preliminary results on the effectiveness of field vaccination and maternal immunity transfer are presented, as well as critical gaps that hinder the development of a robust, evidence-based management strategy. As the epidemiological situation is expected to become more complex in the future, due to the co-circulation of multiple BTV serotypes and other Culicoides-borne diseases, such as EHDV, effective collaboration and communication among stakeholders and international authorities will be crucial for implementing measures to mitigate the spread of these diseases.

Biosecurity is the basis for animal disease prevention and a key factor in achieving a sustainable poultry production, particularly in Pakistan's rapidly expanding broiler industry. However, the extent of on-farm biosecurity implementation remains largely unquantified, making it essential to conduct an objective assessment to guide targeted interventions. To address this gap, this study evaluated biosecurity practices on 100 conventional broiler farms in Punjab, Pakistan, using the Biocheck.UGent scoring tool. The resulting biosecurity scores were then analyzed in relation to key farm management practices and antimicrobial use (AMU). Biosecurity practices varied across farms with overall scores ranging from 30 % to 75 % (mean: 49 %). External biosecurity was weaker (27 %-76 %, mean: 44 %) than internal biosecurity (34 %-83 %, mean: 55 %). Highly implemented external measures included farm location (scores 73 %) and infrastructure (scores 72 %), while manure and carcass removal (scores 9 %) were poorly implemented. Internal biosecurity showed strengths in disease management (scores 76 %) but weaknesses in cleaning and disinfection (scores 47 %). Overall biosecurity scores correlated positively with farm manager experience (ρ = 0.39, p = 0.01) and farm size (ρ = 0.21, p = 0.04), indicating stronger biosecurity on farms with experienced personnel and larger teams. A negative correlation was found between AMU and overall biosecurity (r = -0.20, p = 0.04), external biosecurity (r = -0.20, p = 0.04), and internal biosecurity (r = -0.15, p = 0.12), suggesting that in farms with better biosecurity less antimicrobials are used. These findings highlight that biosecurity in Pakistan's broiler sector requires major improvements, particularly in areas such as manure and carcass disposal, cleaning and disinfection, and depopulation of broilers. Strengthening these specific measures will help enhance farm productivity, improve disease prevention, and reduce reliance on antimicrobials.

BACKGROUND:Antimicrobial resistance poses a global health threat, driven by antimicrobial use (AMU). In veterinary medicine, antibiotics are being prescribed in both livestock and companion animals. Therefore, promoting responsible AMU across both sectors is essential. METHODS:This qualitative study explored the determinants of antibiotic prescribing among Belgian veterinarians using focus groups and thematic analysis. RESULTS:Forty-two veterinarians specialised in companion animals, poultry, pigs or cattle participated in eight focus groups. Six themes were identified: (i) diagnostic assessments as the basis for antibiotic decision making, (ii) evaluating therapeutic options, (iii) the veterinarian's role in decision making, (iv) client characteristics, (v) initiatives promoting responsible AMU, and (vi) veterinarian-client communication. Antibiotic prescribing involves complex decision making, mainly guided by clinical expertise. Veterinarians value guidelines, but prioritise therapeutic autonomy. A shift from routine AMU to preventive care was found, especially among livestock veterinarians, while companion animal veterinarians are still adopting this mindset. Despite progress, challenges remain, including client expectations, prescribing habits and limited awareness. LIMITATIONS:Although data saturation was not confirmed for pig and poultry, broader themes reached saturation, reinforcing the relevance of the findings. CONCLUSION:This study provides a framework for enhancing antimicrobial stewardship in both livestock and companion animals.

Fluoroquinolones (FQ) are critically important antimicrobials. When broilers are treated with FQs, residues of these compounds can accumulate in their feathers, posing potential risks if feathers are repurposed, such as for use in animal feed. The aim of this study was to determine the residue depletion profiles of enrofloxacin (ENR) and its metabolite ciprofloxacin (CIP) in broiler parent stock feathers by using a sensitive UHPLC-MS/MS method. The total antibiotic residue concentration was determined. An experimental study was conducted with a treatment group and a control group. In the treatment group, fifty broiler parent stock were administered ENR for three consecutive days at 22.5 weeks of age, with four individual feathers analysed per animal at different timepoints after administration. After 15 weeks, all animals had ENR and CIP concentrations above the limit of quantification (LOQ) of 5 ng/g feather. ENR concentrations remained relatively stable throughout the observation period. For CIP, an initial rapid decline in concentration was observed, followed by a steady-state phase. Additionally, CIP concentrations were considerably lower than those of ENR. For both ENR and CIP the within-animal variance in residue levels was higher than the variability in mean residue levels across different animals sampled at the same timepoint. In conclusion, ENR and CIP demonstrate high stability in broiler parent stock feathers and can be detected for at least 15 weeks post-treatment. These findings highlight the persisting nature of FQ residues in feathers, underscoring the need for caution when considering the reuse of feathers in agricultural or industrial applications to prevent the development of antimicrobial resistance.

Cleaning and disinfection (C&D) procedures are essential components of farm biosecurity, aiming to reduce microbial load and eliminate the pathogenic microorganisms in livestock farms facilities. This review examines the various methods used to assess the effectiveness of both cleaning and disinfection, exploring their strengths, limitations, and optimal-use scenarios. For cleaning evaluation, common methods include basic visual inspections, ultraviolet (UV) fluorescence, adenosine triphosphate (ATP) bioluminescence, rapid protein tests (RPT), redox potential, and microbiological swabbing. However, visual inspections and UV fluorescence alone provide only qualitative insights. ATP offers quantitative data, though the accuracy can be influenced by the presence of detergents or disinfectants, requiring careful calibration. Additionally, ATP and RPT testing demands standardization to ensure consistent results. A new promising redox method is fast and more accurate, however still has limited field applicability. Microbiological methods, while highly accurate in detecting microbial contamination, are resource-intensive and therefore not in frequent use for routine evaluation of the cleaning procedures. For assessment of disinfection procedures microbiological tests such as colony-forming unit counts on agar plates, as well as the use of selective media for target microbes or hygiene indicator organisms are more appropriate than non-microbiological tests as they offer direct evidence of microbial elimination. However, these methods can be labor-intensive and time-consuming. Molecular methods can be powerful tools in detecting hard-to-culture organisms, however, are more expensive and require specialized equipment. Given these challenges, our study recommends a comprehensive C&D evaluation protocol, incorporating multiple methods tailored to the farm’s specific biosecurity needs and epidemiological context. This integrated approach improves the reliability and efficiency of C&D monitoring, ensuring robust hygiene management in farm settings.

Dynamic modelling of infectious diseases of importance to livestock production is a valuable tool for policy and decision makers. Mathematical and simulation models play an essential role in understanding complex systems, but parameterising these models can be challenging, especially in data-sparse environments. When parameters are unable to be estimated from epidemiological or experimental data, a time-consuming and labour-intensive literature review-to identify suitable literature-informed values-is often necessary. In service of this, here we present PARAMETRA, a parameter database for 20 pathogens of livestock, envisaged as an open-source collaborative tool for the research community to aid in the development of future transmission models of livestock pathogens. Pathogens included in the database so far were selected using a disease prioritisation exercise. Parameters of interest were selected by experts with a strong background in epidemiology and mathematical modelling. We populated the database with over 2000 individual values, covering a wide range of different parameters including transmission rates, diagnostic test efficacies, pathogen survival on surfaces, and the farm and regional level prevalences of selected diseases. Finally, we present an initial illustrative analysis of the database contents and the associated metadata of studies included. One of the principal conclusions we can draw from the data available is that in many cases research is reactive, rather than proactive, with research only tending to focus on specific diseases after outbreaks have already occurred, as is the case for African swine fever for example. This has important implications for future research moving to a more proactive approach for experimental and epidemiological studies based on observations of gaps in the data, and high-risk diseases. This publication represents the first step in development for the PARAMETRA database, which will be updated and expanded in the coming years.

Introduction:Antimicrobial resistance is an alarming public health problem, and comprehensive surveillance across environments is required to reduce its impact. Phenotypic testing and whole-genome sequencing of isolates are efficient, but culture-free approaches like metagenomic sequencing potentially allow for broader investigation of resistance gene occurrence, evolution and spread. However, technical challenges such as difficulties in associating antimicrobial resistance genes with their bacterial hosts and the collapse of strain-level variation during metagenome assembly, hinder its implementation. Methods:To illustrate how these challenges can be overcome, we applied Oxford Nanopore Technologies long-read metagenomic sequencing and novel bioinformatic methods to a case study focused on fluoroquinolone resistance in chicken fecal samples. Results:We demonstrate plasmid-host linking based on detecting common DNA methylation signatures. Additionally, we use new bioinformatic approaches for strain haplotyping, enabling phylogenomic comparison and uncovering fluoroquinolone resistance determining point mutations in metagenomic datasets. Discussion:We leverage long-read sequencing, including DNA methylation profiling and strain-level haplotyping, to identify antimicrobial resistance gene hosts, link plasmids to their bacterial carriers, and detect resistance-associated point mutations. Although some limitations remain, our work demonstrates how these improvements in metagenomic sequencing can enhance antimicrobial resistance surveillance.

Bats are a known means of insect control in various agricultural settings. In this study, the use of local bats was suggested as sustainable pest control after problems with stinging invertebrates on an outdoor pig farm. However, contact between bats and livestock may bring the potential risk of pathogen transmission as bats are hosts of many pathogens. In this study, the occurrence of pathogens in feces of Myotis emarginatus was investigated, using nanopore sequencing via PathoSense and light microscopic parasitological examination. Additionally, the literature on the fecal biome of Western European bats is reviewed to assess the potential risks for pigs. Apart from opportunistically pathogenic Escherichia coli and rotavirus A, no relevant pathogens were identified during fecal examination. This finding differs from the reports in the literature where adenoviruses, rabies, Pasteurella spp. and Yersinia spp. etc. have been described as pathogenic risks. This study is a first step in estimating pathogenic risks, but further research on the pathogenic reservoir of these bats is necessary.

In een enquête afgenomen bij dierenartsen afgestudeerd aan de Universiteit Gent werd gepeild naar hun arbeidssituatie en de kwaliteit van de opleiding. Hiervoor werden vier cohorten van dierenartsen gecontacteerd die afstudeerden tussen 2003 en 2023. Uit 889 ingevulde enquêtes (35,3 % van de afgestudeerde dierenartsen in de geselecteerde jaren) werd onder andere duidelijk dat dierenartsen die afgestudeerd zijn in Gent zelden werkloos zijn. Ze werken gemiddeld 42,8 uur per week en zijn behoorlijk tevreden over de invulling van hun job en de verloning. Eenenzeventig procent van de respondenten werkt in de praktijk en de overgrote meerderheid hiervan (89%) werkt in een groepspraktijk. Dierenartsen met de Belgische nationaliteit hebben voornamelijk een zelfstandigenstatuut, terwijl dierenartsen met de Nederlandse nationaliteit voornamelijk in loondienst werken. Er wordt ook een stijgende trend naar specialisatie en doorgedreven postacademische vorming waargenomen. Deze studie levert voor de vierde maal op rij verrassend positieve resultaten op die ingaan tegen de soms negatieve pers die het dierenartsenberoep krijgt.

IntroductionSustained resistance against fluoroquinolones (FQ), without the use of FQ in broilers, raises important questions about other possible factors contributing to the persistence in farms. Therefore, the current study investigates the prevalence of FQ non-susceptibility in Escherichia coli on broiler farms and examines the roles of day-old chicks, the farm environment, and the antimicrobial use (AMU) in the dynamics of the within-flock spread.MethodsOn 29 Belgian broiler farms, AMU was monitored, while environmental and day-old chick intestinal samples (day 0) were collected before their arrival. On days 3 and 36 of the production round, 30 cloacal swabs were taken per farm. In all samples, total E. coli and FQ non susceptible E. coli isolates were quantified by non-selective and FQ selective isolation. A selection of the isolates was analyzed using whole-genome sequencing to characterize their resistance and virulence-associated determinants and to investigate their phylogenetic relatedness using core-genome multi-locus sequence typing (cgMLST) and whole-genome single-nucleotide polymorphism (SNP) analysis.ResultsBefore entering the stable, day-old chicks carried FQ non-susceptible E. coli on 79.3% of the farms, while FQ non-susceptible E. coli were found in 48.3% of the sampled environments. According to cgMLST, identical FQ non-susceptible isolates were found on day 0 and 36, suggesting that FQ non-susceptible isolates present in the environment at the start of a production round or in day-old chicks, can remain present until slaughter, even when no FQs were used. Total AMU was positively correlated with the proportion of FQ non-susceptible E. coli [r = 0.42, 95% CI (0.06, 0.68), p = 0.03], often also multidrug-resistant, at the end of the production cycle.ConclusionThe continued presence of FQ non-susceptible E. coli in broiler farms is likely the result of both a historical contamination at the farm level and a continuous influx along the production chain. AMU contributes to the continued presence of FQ non-susceptible E. coli in broiler farms, but accounted for only a small proportion of the variability in FQ non-susceptibility in currently investigated farms. The role of certain virulence-associated genes in the persistence of FQ non-susceptible E. coli in broiler farms deserves more in-depth research.

Backyard poultry farming is common in rural areas worldwide, especially in low- and middle-income countries, where approximately 80 % of rural households are involved. Effective biosecurity assessments are essential to prevent diseases and therefore, this study aimed to develop a risk-based weighted scoring system to evaluate biosecurity levels in backyard poultry households in low- and middle-income countries (LMICs), as well as to describe its use in Bangladesh. A questionnaire was drafted with input from backyard poultry experts, followed by weights were attributed to the answers to obtain a weighted and risk-based questionnaire where scores represent the level of biosecurity measures. A score of 0 indicates absence of biosecurity measures, while 100 implies optimal biosecurity. The questionnaire was pretested with 20 households in Savar, Dhaka. Subsequently, 384 households were randomly selected from six districts in Bangladesh, based on the poultry population and consistent backyard poultry rearing. The scoring system is freely available online at https://biocheckgent.com/en/. External biosecurity (50 questions) was assessed in the following subcategories: purchase of eggs or day-old chicks, purchase of laying hens, depopulation and transport of poultry and poultry products, feed and water supply, visitors and farm personnel, manure and carcass removal, infrastructure and biological vectors of the farm, location of the farm. Internal biosecurity (13 questions) was subdivided in disease management and cleaning and disinfection. The average biosecurity scores for the external and internal categories were 30.3 % and 32.4 %, respectively. The two highest mean external biosecurity scores were obtained for depopulation and transport of poultry and poultry products (mean= 56.0 %) and manure and carcass removal (mean = 37.5 %) while the lowest means score was obtained for the category visitors and farm workers (mean = 12.4 %). In the internal biosecurity category, cleaning and disinfection had the highest mean score (34.1 %). Besides backyard production, small-scale commercial broiler production was present in 7 % of the visited households and the biosecurity score in these households was on average higher compared to those without commercial farming. This study reveals sub-optimal levels of biosecurity among backyard poultry in Bangladesh, as evaluated through the Biocheck.UGent scoring tool which has shown to be valuable for addressing biosecurity challenges in backyard production in low- and middle-income countries. The observed biosecurity gaps expose the poultry system to considerable risks of introduction and spread of infectious diseases.