Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects.

Analysis of environmental DNA (eDNA) enables indirect detection of species without the need to directly observe and sample them. For biosecurity and invasion biology, eDNA-based methods are useful to address biological invasions at all phases, from detecting arrivals to confirming eradication of past invasions. We conducted a systematic review of the literature and found that in biosecurity and invasion biology, eDNA has primarily been used to detect new incursions and monitor spread in marine and freshwater ecosystems, with much slower uptake in terrestrial ecosystems, reflecting a broader trend common to the usage of eDNA tools. In terrestrial ecosystems, eDNA research has mostly focussed on the use of eDNA metabarcoding to characterise biodiversity, rather than targeting biosecurity threats or non-native populations. We discuss how eDNA-based methods are being applied to terrestrial ecosystems for biosecurity and managing non-native populations at each phase of the invasion continuum: transport, introduction, establishment, and spread; across different management options: containment, control, and eradication; and for detecting the impact of non-native organisms. Finally, we address some of the current technical issues and caveats of eDNA-based methods, particularly for terrestrial ecosystems, and how these might be solved. As eDNA-based methods improve, they will play an increasingly important role in the early detection and adaptive management of biological invasions, and the implementation of effective biosecurity controls.

Antimicrobial stewardship hindered by inadequate biosecurity and biosafety practices, and inappropriate antibiotics usage in poultry farms of Nepal-A pilot study.

Nepal's poultry industry has experienced remarkable growth in the last decade, but farm biosafety and biosecurity measures are often overlooked by farmers. As a result, farms often suffer from sporadic and regular outbreaks of many diseases, impacting production and creating public health challenges. Poor management practices, including overuse of antibiotics for prophylaxis and therapeutics, can enhance the spread of poultry diseases by propagating antimicrobial resistance (AMR) that is threatening poultry and human health. We assessed biosafety, biosecurity risks and AMR stewardship in sixteen poultry farms located in four districts: Ramechhap, Nuwakot, Sindhupalchowk, and Kavre. Risk assessment and AMR stewardship evaluation questionnaires were administered to formulate biosafety and biosecurity compliance matrix (BBCM). Risk assessment checklist assessed facility operations, personnel and standard operating procedures, water supply, cleaning and maintenance, rodent/pest control and record keeping. Oral and cloacal samples from the poultry were collected, pooled, and screened for eight poultry pathogens using Polymerase Chain Reaction (PCR) tests. Based on BBCM, we identified the highest BBCM score of 67% obtained by Sindhupalchowk farm 4 and the lowest of 12% by Kavre farm 3. Most of the farms (61.6%) followed general poultry farming practices, only half had clean and well-maintained farms. Lowest scores were obtained for personnel safety standard (42.4%) and rodent control (3.1%). At least one of the screened pathogens were detected in all farms. Mycoplasma gallisepticum was the most common pathogen detected in all but three farms, followed by Mycoplasma synoviae. More than half of the farmers considered AMR a threat, over 26% of them used antibiotics as a preventive measure and 81% did not consider withdrawal period for antibiotics prior to processing of their meat products. Additionally, antibiotics classified as "Watch" and "Restrict" by the WHO were frequently used by the farmers to treat bacterial infections in their farms.

Optimal allocation of resources among general and species-specific tools for plant pest biosecurity surveillance.

This paper proposes a surveillance model for plant pests that can optimally allocate resources among survey tools with varying properties. While some survey tools are highly specific for the detection of a single pest species, others are more generalized. There is considerable variation in the cost and sensitivity of these tools, but there are no guidelines or frameworks for identifying which tools are most cost-effective when used in surveillance programs that target the detection of newly invaded populations. To address this gap, we applied our model to design a trapping surveillance program in New Zealand for bark- and wood-boring insects, some of the most serious forest pests worldwide. Our findings show that exclusively utilizing generalized traps (GTs) proves to be highly cost-effective across a wide range of scenarios, particularly when they are capable of capturing all pest species. Implementing surveillance programs that only employ specialized traps (ST) is cost-effective only when these traps can detect highly damaging pests. However, even in such cases, they significantly lag in cost-effectiveness compared to GT-only programs due to their restricted coverage. When both GTs and STs are used in an integrated surveillance program, the total expected cost (TEC) generally diminishes when compared to programs relying on a single type of trap. However, this relative reduction in TEC is only marginally larger than that achieved with GT-only programs, as long as highly damaging species can be detected by GTs. The proportion of STs among the optimal required traps fluctuates based on several factors, including the relative pricing of GTs and STs, pest arrival rates, potential damage, and, more prominently, the coverage capacity of GTs. Our analysis suggests that deploying GTs extensively across landscapes appears to be more cost-effective in areas with either very high or very low levels of relative risk density, potential damage, and arrival rate. Finally, STs are less likely to be required when the pests that are detected by those tools have a higher likelihood of successful eradication because delaying detection becomes less costly for these species.

Contribution of herd management, biosecurity, and environmental factors to the risk of bovine tuberculosis in a historically low prevalence region.

Eradication of bovine tuberculosis (bTB) in certain historically low-prevalence regions remains elusive. A complete characterisation of the husbandry practices, biosecurity, and environment where farms are located is crucial to implement targeted in-farm risk mitigation protocols. Here, a detailed survey performed in 94 dairy cattle farms located in Navarra, a low-prevalence region of Spain between 2016 and 2020 was carried out. Data on 73 biosecurity, farm-, and environmental-level factors potentially associated with the risk of bTB occurrence were evaluated using an ordinal logistic regression model: farms were classified based on their prevalence index, a score linked to each farm to account for the severity and recurrence of bTB cases: 22.3% of the farms had a score of 1, 21.3% a score of 2, 26.6% a score of ≥ 3, and 29.8% were negative herds. A statistically significant association between a higher prevalence index and the frequency of badger sightings along with the lease of pastures to sheep during Winter was identified. Farms that detected badgers on a monthly to daily basis in the surroundings and those that leased pastures for sheep flocks during Winter were four [odds ratio, 95% CI (4.3; 1.1-17.5)] and three (3.1; 1.0-9.9) times more likely to have the highest prevalence index, respectively (predicted probabilityprevalence index≥3 = 0.7; 95% CI 0.3-0.9). Conversely, farms that used a vehicle to transport animals from holdings to pastures were less likely (0.1; <0.1-0.3) to present higher levels of prevalence index compared with farms that used none (on foot). Results suggested that the combined effect of farm- and environmental-level risk factors identified here may be hampering disease eradication in Navarra, highlighting the need to implement targeted protocols on farms and grazing plots. An increased awareness of monitoring sheep and wildlife in direct or indirect contact with cattle herds in historically low bTB prevalence areas should be raised.

Biosecurity implementation on large-scale poultry farms in Europe: A qualitative interview study with farmers.

Biosecurity is an essential tool for rearing healthy animals. Biosecurity measures (BMs) are well known in poultry production, but it is difficult to assess actual implementation on farms. The aims of this qualitative study were (1) to provide an overview of biosecurity implementation according to poultry farmers in Europe; and (2) to better understand the reported reasons and potential obstacles for not implementing the measures. In seven European Union Member States, 192 farmers (118 under contract with a company and 68 independents) working in seven different categories of poultry production were interviewed on 62 BMs to determine the frequency of implementation and the reasons for non-implementation. Most of the replies (n = 7791) concerning BM implementation were reported by the farmers as "always" implemented (81%), statistically higher for breeders (87%) and layers (82%) and lower for independent farms versus farms under contract with a company (79.5% and 82.5%, respectively). Regardless the poultry production category, the most frequently implemented BMs declared by the farmers were daily surveillance of birds, rodent control and feed storage protection. Standard hygiene practices were also mentioned as high-implementation measures for most production categories, with some deficiencies, such as rendering tank disinfection after each collection and, for meat poultry, disinfection of the feed silo and bacterial control of house cleaning and disinfection between each cycle. The entry of vehicles and individuals onto poultry farms, especially during critical points of eggs collection for breeders and layers, as well as the presence of other animals, such as the "all in/all out" practice, particularly in layers and ducks, were also reported as the least commonly practiced measures. The main reasons for not implementing the measures (n = 1683 replies) were low awareness and poor knowledge of the expected benefits of biosecurity ("no known advantages" 14%, and "not useful" 12%), the lack of training ("not enough training" 5% and "advice" 7%), lack of time (19%), and financial aspects (17%). Despite the good overall biosecurity mentioned by the farmers, these findings highlight certain deficiencies, suggesting room for improvement and the need for targeted and tailored support of poultry farmers in Europe.

Characterization of biosecurity practices among cattle transport drivers in Spain.

Transmission of pathogens between farms via animal transport vehicles is a potential concern; however, the available information on driver routines and biosecurity measures implemented during transport is limited. Given the above, the aim of this study was to describe and characterize the prevailing practices and biosecurity measures adopted by cattle transport drivers in Spain. Eighty-two drivers were surveyed via face-to-face or remotely. The survey included questions on general characteristics of the drivers (type of journeys and vehicles) together with biosecurity practices implemented during cattle transport and vehicle hygiene practices. Results showed that several risky practices are performed quite frequently such as visiting different premises with different levels of risk (e.g., breeder and fattening farms); entering the farm premises to load/unload animals, passing by several farms to load and unload animals, or not always cleaning and disinfecting the vehicle between travels, among others. To explore similarities among the drivers and identify groups sharing specific practices, hierarchical clustering on principal components (HCPC) was computed on the results of multiple correspondence analysis (MCA). The first three MCA dimensions (out of 13) were retained in the agglomerative clustering and four different clusters were identified. Clusters 1 and Cluster 4 accounted for 39.5% and 29.6% of respondents, respectively. The clusters were mainly differentiated by practices in the loading/unloading of cattle, such as the frequency of contact with animals remaining on the farm, and the frequency of the vehicle's disinfection between farms. Cluster 2 and Cluster 3 were of similar size, about 15% of respondents each. Cluster 2 consisted of drivers who mainly made journeys to slaughterhouse, while drivers in Cluster 3 were characterised by the use of working clothes and boots. Based on these findings, it is advisable to increase awareness on the role that animal transport can have in the spread of pathogens between cattle farms and the importance of biosecurity in preventing such transmission. There is also a need to support animal transport professionals in such task, not only through the development of initiatives to increase awareness, but also through the investment in improving cleaning and disinfection facilities and to consider the economic cost associated with some practices to not compromise the economic viability of the sector.

Gaps and inconsistencies in the current knowledge and implementation of biosafety and biosecurity practices for rickettsial pathogens.

INTRODUCTION: Rickettsia spp. and Orientia spp. are the causes of neglected infections that can lead to severe febrile and systemic illnesses in humans. Implementing proper biosafety practices when handling these pathogens is crucial to ensure a safe and sustainable work environment. It is essential to assess the current knowledge and identify any potential gaps to develop effective measures that minimise the risk of exposure to these pathogens. By doing so, we can establish a comprehensive framework that promotes safety, mitigates hazards, and safeguards the well-being of personnel and the surrounding community. METHODS AND RESULTS: This review aimed to synthesise and determine the evidence base for biosafety precautions for Rickettsia spp. and Orientia spp. pathogens. Enhancing our understanding of the relative infectious risk associated with different strains of Rickettsia and Orientia spp. requires identifying the infectious dose of these pathogens that can cause human disease. The application of risk groups for Rickettsia and Orientia spp. is inconsistent across jurisdictions. There is also incomplete evidence regarding decontamination methods for these pathogens. With regards to Orientia spp. most of the available information is derived from experiments conducted with Rickettsia spp. CONCLUSIONS: Rickettsia and Orientia spp. are neglected diseases, as demonstrated by the lack of evidence-based and specific biosafety information about these pathogens. In the case of Orientia spp., most of the available information is derived from Rickettsia spp., which may not be appropriate and overstate the risks of working with this pathogen. The advent of effective antibiotic therapy and a better understanding of the true hazards and risks associated with pathogen manipulation should inform decisions, allowing a sustainable and safe work environment.

Biosecurity, health and disease management practices among the dairy farms in five districts of Bangladesh.

Herd health management is a planned program to optimize health, welfare, and production of dairy cows. A cross-sectional study focused on herd health management of dairy farms, was carried out to assess the biosecurity, health, and disease management practices with associated socio-demographic factors. A structured questionnaire with closed- and open-ended questions was employed for farmers' interviews to acquire information on dairy farms. Data were collected from randomly selected 205 dairy farms in five districts (Dhaka-Savar, Mymensingh, Gazipur, Rangpur, and Sirajganj) of Bangladesh. Overall, 1.5% farms had "good", 17% had "moderate" and 81.5% had "poor" levels of biosecurity, health and disease management practices (BHDMP). Analysis of variance revealed that mean BHDMP scores were significantly (p < 0.05) higher in farms of Rangpur (27.6 ± 0.8) and Gazipur (26.7 ± 0.6) than those of the other three districts. Educational status had a significant effect on BHDMP scores. The farms owned by graduated farmers had the highest mean BHDMP score (30.4 ± 1.1) while the farms operated by illiterate farmers had the lowest BHDMP score (20.4 ± 0.4). Multiple linear regression analysis also revealed that educational status (secondary to post-graduation), training experience, area of study (Rangpur district), and herd size were significantly associated with BHDMP score of the farms. The findings lay a basis for improving dairy farms' biosecurity, health and disease management practices, which further envisage the adoption and implementation of herd health management programs.

Improvements in swine herd biosecurity reduce the incidence risk of porcine reproductive and respiratory syndrome virus in breeding herds in the Midwestern United States.

OBJECTIVE: Porcine reproductive and respiratory syndrome (PRRS) is a significant disease of swine. The purpose of this study was to determine whether application of a comprehensive, science-based approach to breeding herd biosecurity, known as next-generation biosecurity (NGB), could reduce PRRS incidence risk across a large commercial production company. ANIMALS: Pigs (381,404 sows across 76 breeding herds). METHODS: From 2009 to 2020, the annual incidence risk of PRRS in sow farms managed by the same company averaged 33%, ranging from 20% to 50%. To measure the effect of NGB on PRRS incidence risk, a retrospective cohort study was conducted from July 1, 2021, to June 30, 2023, across breeding herds managed by the same company. During the analysis, 2 groups of herds emerged: those that implemented protocols for all phases of NGB (NGB COMPLETE), and those that implemented all described protocols of biosecurity except for air filtration (NGB INCOMPLETE). RESULTS: During the 2-year assessment period, 56 breeding herds were classified as NGB COMPLETE, while 20 herds were NGB INCOMPLETE. The PRRS incidence risk in NGB COMPLETE herds was 8.9% as compared to 40.0% in NGB INCOMPLETE herds. From disease year 1 (July 1, 2021, to June 30, 2022) and disease year 2 (July 1, 2022, to June 30, 2023), system-wide PRRS incidence risk was 8.6% and 9.2%, respectively. The association between NGB status and PRRS incidence risk for the 2-year period was statistically significant at a P value of .006. CLINICAL RELEVANCE: Results of the present report provided evidence that improvements in biosecurity result in lower PRRS incidence risk under large-scale commercial swine production conditions.

Capacity and needs assessment of veterinary services in Vietnam in biosecurity, biosafety and One Health.

The Asia-Pacific region is recognised as an epicentre of emerging infectious diseases (EIDs), of which 75% are zoonotic in nature. Vietnam is recognised as a potential hotspot for zoonotic EIDs. There is a growing recognition that progress towards global health security requires greater focus on collaboration between the human health and animal health sectors to control diseases at their animal source and prevent against human health impacts. Assessment of veterinary epidemiology capacity in Vietnam is paramount to strengthening the health security of Asia-Pacific. This study aims to evaluate the national capacity and needs of veterinary services in Vietnam in biosecurity, biosafety and One Health. A cross-sectional, convergent mixed-methods study was conducted between November 2020 and April 2021. An online questionnaire was administered to government-employed field veterinarians. Descriptive analyses and logistic regression models were performed using survey responses to understand capacity in the field. Semi-structured interviews were also conducted with stakeholders in veterinary services including government, academia, research institutes, non-profit and international organisations. Coding and thematic analysis using a deductive approach was used for data collected from interviews to contextualise findings from the survey and understand institutional capacity. In total, 178 field veterinarians completed the online survey and 25 stakeholders were interviewed. The majority of participants had reported receiving training in biosecurity and biosafety, including use of personal protective equipment. Most respondents reported practicing good biosecurity measures (92%) and good biosafety measures (88%). Physical and socioeconomic barriers to practicing biosecurity were reported to be prevalent for smallholder farmers, which may suggest a gap in the capacity of veterinary services to provide cost-effective and practical biosecurity strategies. Seventy five percent of participants had never or rarely participated in One Health approaches in the field in the last 12 months and 69% reported further training as a high priority. There was a knowledge gap reported amongst district and commune-level veterinary staff about the need for, and awareness of multisectoral collaboration. Respondents that completed postgraduate qualifications in epidemiology or Field Epidemiology Training Programs (adjusted OR: 3.06; 95% CI: 1.01, 9.23, p = 0.046) and had longer job tenure between 10-12 years (OR: 10.38; 95% CI: 3.06, 35.15, p = <0.001) were more likely to have higher levels of experience in One Health. This study identified gaps in knowledge, attitudes and adoption of practices related to biosecurity, biosafety and One Health specifically in lower-level or less experienced veterinary staff without further training opportunities in epidemiology. These findings enable prioritisation of training, policy, and planning activities to further enhance the national capacity of veterinary services in Vietnam.

Protein design meets biosecurity.

The power and accuracy of computational protein design have been increasing rapidly with the incorporation of artificial intelligence (AI) approaches. This promises to transform biotechnology, enabling advances across sustainability and medicine. DNA synthesis plays a critical role in materializing designed proteins. However, as with all major revolutionary changes, this technology is vulnerable to misuse and the production of dangerous biological agents. To enable the full benefits of this revolution while mitigating risks that may emerge, all synthetic gene sequence and synthesis data should be collected and stored in repositories that are only queried in emergencies to ensure that protein design proceeds in a safe, secure, and trustworthy manner.

Global change and adaptive biosecurity: managing current and emerging Aleurocanthus woglumi threats to Europe.

Global climate changes undermine the effectiveness of 'set and forget' phytosanitary regulations. Uncertainties in future greenhouse gas emission profiles render it impossible to accurately forecast future climate, thus limiting the ability to make long-term biosecurity policy decisions. Agile adaptive biosecurity frameworks are necessary to address these climatic uncertainties and to effectively manage current and emerging threats. This paper provides opinions on these issues and presents a case study focusing on the threats posed by Aleurocanthus woglumi (citrus blackfly) to Europe. It delves into the biology of the species, its preferred hosts, and how climate change could affect its spread. Utilizing a bioclimatic niche model, the paper estimates the potential distribution of A. woglumi in Europe under recent historical and medium-term future conditions, revealing a potential expansion of its range into higher elevations and more northern regions by the year 2050. The main aim is to leverage the results to showcase the system's sensitivity to likely emission scenarios, essentially stress-testing for potential emerging threats to biosecurity policies and phytosanitary regulations. The results underscore the significance of considering global change factors in pest risk assessment and phytosanitary regulations for effective risk mitigation. Consequently, adaptive biosecurity measures are essential, encompassing horizon scanning, enhanced targeted surveillance, periodic updates of risk assessments, and adjustments to regulations. For instance, biosecurity risk management could involve establishing a set of trigger conditions to prompt updates of risk assessments, such as identifying a zone where the confirmed establishment of a pest signifies a significant change in the pest risk profile. For jurisdictions containing areas modeled as being climatically suitable under historical climates or future climate scenarios, we caution against importing untreated host materials from regions that are likely to become suitable habitats for A. woglumi in the future. Moreover, it is important to consider both present and future climate change scenarios when making decisions to effectively address the threats posed by invasive species. In the case of highly impactful invasives, investing in preemptive biological control measures may prove to be a prudent choice.

Assessment of fungal contamination and biosecurity risk factors in duck-breeding farms in South Korea.

Fungi are pathogens that infect all types of poultry and farmers, leading to economic losses in poultry production. Fungi can be isolated from environmental samples and are ubiquitous in the air. This study aimed to evaluate fungal contamination in domestic duck farm environments and analyze biosecurity risk factors associated with fungal infection incidence to assess the vulnerability of the farms to fungal infection. The average fungal concentration was 203 colony-forming units (CFU)/m3 in the air and 365 × 103 CFU/m2 in the wall surface samples. Sixteen fungal genera were recovered from air and wall surface samples from 19 duck-breeding farms, Aspergillus being the most frequently isolated (air: 43.2%; wall surface: 40%). Eleven additional fungal genera (Acrophialophora, Byssochlamys, Fusarium, Lichtheimia, Paecilomyces, Penicillium, Polycephalomyces, Rhizomucor, Scopulariopsis, Talaromyces, and Thermoascus) were isolated from air samples. Also, 8 additional fungal genera (Chaetomium, Lichtheimia, Penicillium, Petriella, Rhizomucor, Rhizopus, Talaromyces, and Trichosporon) were isolated from wall surface samples. The characteristics of the poultry farms (geographic region, stocking density, breeding house type, affiliate, duck age, and season) and fungal concentrations in the air and wall surface samples were analyzed to evaluate the biosecurity risk of the farms. Fungal infections were significantly affected by high stocking density (>2 ducks/m2), duck age (18-25 wk and >60 wk), and high fungal concentration in the wall surface samples (>300 × 103 CFU/m2).

The application of biosecurity practices for preventing avian influenza in North-Eastern Italy turkey farms: An analysis of the point of view and perception of farmers.

INTRODUCTION: Italian and international outbreaks of highly pathogenic avian influenza (HPAI), particularly in densely populated poultry areas (DPPAs), have increased over the past few decades. These emerging risks, which endanger both human and animal health and the entire poultry industry, can be effectively limited by biosecurity measures implemented at human-animal food chain interfaces. Some problems, however, persist in the application of these measures on the part of poultry farmers, prompting the need to explore those aspects and causes that limit their implementation. MATERIAL AND METHODS: A qualitative approach was selected for the study and a semi-structured interview technique was applied to collect data among turkey farmers (n = 29) working in the north-east of Italy. The aim of this technique was to gather data on farms in order to understand the biosecurity practices adopted and the reasons for and impediments to farmer implementation, or lack thereof. This article presents and discusses the main data collected. RESULTS: The study revealed that farmers were familiar with the biosecurity measures necessary to contain avian influenza (AI) and other poultry diseases; personal disinfection and animal isolation practices were particularly prominent. Based on the reported procedures, managerial, economic, and psychosocial factors were among the barriers behind the failure to implement biosecurity measures. These obstacles were variously intertwined and associated with the different action settings. In particular management factors, such as lack of time to apply the rules and difficulties contingent on the farm's structural characteristics, mediate the application of biosecurity measures. In terms of communication channels, the company, particularly its technicians, proved to be the primary source of information for farmers in case of emergencies, as well as the primary source of information on the application of biosecurity measures. However, other sources of information were indicated, such as word of mouth among farmers or other non-institutional figures (relatives and acquaintances). CONCLUSIONS: What emerged, was the need to improve not only the biosecurity management skills, but also to implement forms of cooperation among the various key stakeholders in the poultry sector. The information presented in this pilot study needs to be discussed among competent authorities, public and company veterinarians, company technicians, and farmers. Furthermore, this information will help in participatory co-planning of risk prevention and communication strategies to implement a long-term, sustainable, effective approach to address future epidemic emergencies.

Status, evaluation, and influencing factors of biosecurity levels in pig farms in China.

BACKGROUND: Animal diseases have always been a serious threat to livestock breeding, and the establishment of a biosecurity barrier is important for disease prevention and control. Based on the investigations conducted in seven provinces located farms, this study aimed to explore the current biosecurity levels of farms in China, construct a biosecurity evaluation system, calculate the biosecurity levels of farms using the rank sum ratio comprehensive evaluation method, and develop an empirical analysis of the factors influencing biosecurity levels. RESULTS: The results show that the greater the cost of biosecurity invested, the greater the level of biosecurity. Male farmers, educational attainment and participation in technical training had a significant positive effect on biosecurity levels. In addition, biosecurity levels first decreased and then increased as the scale of farming increased. The study also found that the more people in the household engaged in farming, the higher the biosecurity level of the farm. And farms that joined cooperatives had higher levels of biosecurity. CONCLUSION: The rank sum ratio method can evaluate the index system, so as to obtain a comprehensive index RSR value that can be compared, and the operation steps are simple and effective. By taking measures such as improving the comprehensive quality of farmers and increasing the investment in human, material and financial resources for biosecurity, the biosecurity level of farms can be effectively improved and animal diseases can be effectively prevented and controlled.