EPPO ontology: a semantic-driven approach for plant and pest codes representation.

The agricultural industry and regulatory organizations define strategies and build tools and products for plant protection against pests. To identify different plants and their related pests and avoid inconsistencies between such organizations, an agreed and shared classification is necessary. In this regard, the European and Mediterranean Plant Protection Organization (EPPO) has been working on defining and maintaining a harmonized coding system (EPPO codes). EPPO codes are an easy way of referring to a specific organism by means of short 5 or 6 letter codes instead of long scientific names or ambiguous common names. EPPO codes are freely available in different formats through the EPPO Global Database platform and are implemented as a worldwide standard and used among scientists and experts in both industry and regulatory organizations. One of the large companies that adopted such codes is BASF, which uses them mainly in research and development to build their crop protection and seeds products. However, extracting the information is limited by fixed API calls or files that require additional processing steps. Facing these issues makes it difficult to use the available information flexibly, infer new data connections, or enrich it with external data sources. To overcome such limitations, BASF has developed an internal EPPO ontology to represent the list of codes provided by the EPPO Global Database as well as the regulatory categorization and relationship among them. This paper presents the development process of this ontology along with its enrichment process, which allows the reuse of relevant information available in an external knowledge source such as the NCBI Taxon. In addition, this paper describes the use and adoption of the EPPO ontology within the BASF's Agricultural Solutions division and the lessons learned during this work.

Biosafety and Biosecurity in Containment: A Regulatory Overview.

When biosafety for contained use is addressed in international fora and discussions, often the topic is limited to working with genetically modified organisms (GMOs) in facilities such as laboratories, animal facilities, and greenhouses. However, the scope of biosafety in containment encompasses many other types of biological materials, such as human, animal and plant pathogens, nucleic acids, proteins, human samples, animals or plants, or by-products thereof, and overlaps often with the topic of biosecurity. This is also reflected in the regulations that apply for activities with biological materials in contained facilities. The common denominator of these regulations is the focus on protection of people and environment, while applying the key principles of risk assessment and risk management. This review provides an overview of regulatory frameworks for biosafety and biosecurity in containment around the globe, as well as points out overlap with other regulatory frameworks, such as the Nagoya Protocol, or Plant and Animal Health regulations.

Use of ovotransferrin as an antimicrobial in turkeys naturally infected with Chlamydia psittaci, avian metapneumovirus and Ornithobacterium rhinotracheale.

Respiratory pathogens are difficult to control in large-scale turkey production. This report describes a clinical trial of antimicrobial ovoTF aerosol on a large Belgian turkey farm. ovoTF was administered to reduce Chlamydia psittaci (C. psittaci) infections and to study the impact of this action on the occurrence of Ornithobacterium rhinotracheale (O. rhinotracheale) and avian metapneumovirus (aMPV) infections. Two subsequent broods were included; (i) a control brood receiving no ovoTF and (ii) an ovoTF brood receiving ovoTF aerosol (5mg/animal) at the age of 2 weeks, continuing daily for 12 days. Twenty-four one-day-old toms of the control and ovoTF brood were tagged and monitored for 15 weeks. The control brood experienced two periods of respiratory disease, the first (2-3 weeks of age) due to C. psittaci and the second (8-17 weeks of age) in the presence of C. psittaci, O. rhinotracheale and maybe aMPV. Extensive antibiotic treatment was needed in 2, 8 and 9 week-old toms. In the ovoTF brood, toms stayed healthy until the age of 9 weeks, whereafter respiratory disease occurred in the presence of C. psittaci, O rhinotracheale and aMPV. OvoTF administration: (i) reduced the amount of C. psittaci in the air as demonstrated by bioaerosol monitoring, (ii) prevented respiratory disease during the first half of the brood period, (iii) was associated with 46% reduction of mortality, and (iv) reduced the antibiotic cost. Our results justify additional clinical trials to explore the use of this innovative antimicrobial strategy for poultry.

Multi locus sequence typing of Chlamydia reveals an association between Chlamydia psittaci genotypes and host species.

Chlamydia comprises a group of obligate intracellular bacterial parasites responsible for a variety of diseases in humans and animals, including several zoonoses. Chlamydia trachomatis causes diseases such as trachoma, urogenital infection and lymphogranuloma venereum with severe morbidity. Chlamydia pneumoniae is a common cause of community-acquired respiratory tract infections. Chlamydia psittaci, causing zoonotic pneumonia in humans, is usually hosted by birds, while Chlamydia abortus, causing abortion and fetal death in mammals, including humans, is mainly hosted by goats and sheep. We used multi-locus sequence typing to asses the population structure of Chlamydia. In total, 132 Chlamydia isolates were analyzed, including 60 C. trachomatis, 18 C. pneumoniae, 16 C. abortus, 34 C. psittaci and one of each of C. pecorum, C. caviae, C. muridarum and C. felis. Cluster analyses utilizing the Neighbour-Joining algorithm with the maximum composite likelihood model of concatenated sequences of 7 housekeeping fragments showed that C. psittaci 84/2334 isolated from a parrot grouped together with the C. abortus isolates from goats and sheep. Cluster analyses of the individual alleles showed that in all instances C. psittaci 84/2334 formed one group with C. abortus. Moving 84/2334 from the C. psittaci group to the C. abortus group resulted in a significant increase in the number of fixed differences and elimination of the number of shared mutations between C. psittaci and C. abortus. C. psittaci M56 from a muskrat branched separately from the main group of C. psittaci isolates. C. psittaci genotypes appeared to be associated with host species. The phylogenetic tree of C. psittaci did not follow that of its host bird species, suggesting host species jumps. In conclusion, we report for the first time an association between C. psittaci genotypes with host species.

Digital titration: automated image acquisition and analysis of load and growth of Chlamydophila psittaci.

Traditionally, the amount of infective chlamydiae in a given sample is determined by inoculating dilution series into cell cultures and physically counting chlamydial inclusions. This approach is time consuming, tedious, and error prone, mainly when dealing with high titers. Therefore, this paper describes a largely automated technique that was developed to standardize the determination of chlamydial load in vitro. Cells are fixed at 36 h post-inoculation and bacteria visualized using standard immunological detection methods. Consequently, for 81 microscopic fields, an image is recorded at the interpolated focal plane. These images are then automatically processed using an ImageJ plugin and the obtained results are imported into Excel to determine the number of inclusion forming units per mL in the sample. The main advantage of this technique is that no or minimal sample dilution is required, thus minimizing dilution errors. In addition, this technique was employed during the early, middle and late growth stages of the chlamydial developmental cycle and results correlated well (P < 0.01) with 16S rRNA values from previous experiments, thereby proving its suitability to follow chlamydial growth in vitro. The method described is highly suitable for high throughput titration of cell culture inoculated samples and assessment of possible antichlamydial effects of novel compounds throughout the chlamydial growth cycle.

Simultaneous zoonotic transmission of Chlamydophila psittaci genotypes D, F and E/B to a veterinary scientist.

Two groups of five 1-day-old conventional turkeys were housed in negative pressure stables to become experimentally infected with Avian Metapneumovirus (aMPV) and Ornithobacterium rhinotracheale (ORT) at the age of 3 weeks. However, during the first 2 weeks, turkeys started to show respiratory disease characterized by rhinitis and dyspnoea. Routine bacterial and viral diagnoses remained negative. Therefore, pharyngeal swabs from the turkeys and from the veterinary scientist handling the animals were examined for the presence of Chlamydophila (C.) psittaci by using a combination of cell culture, nested PCR and ompA genotype-specific quantitative real-time PCR, as well as by serology. Results revealed simultaneous transmission of C. psittaci outer membrane protein A (ompA) genotypes D, F and E/B from infected turkeys to the veterinary scientist.

Evaluation of the prophylactic use of ovotransferrin against chlamydiosis in SPF turkeys.

Chlamydophila (C.) psittaci infections are highly prevalent in turkeys and the economical and public health importance of these infections has been recognized since 1950. As there are no vaccines, antibiotic treatment (tetracylines, enrofloxacine) is often needed to allow marketing of poultry. In this study, we explored the use of ovotransferrin (ovoTF), a natural anti-microbial protein, in preventing an experimental C. psittaci infection in specific pathogen free (SPF) turkeys. Turkeys were treated with aerosolized ovoTF prior to the infection. Groups 1 and 2 received a single dose of 10 and 5 mg ovoTF per turkey, respectively. Group 3 received a daily dose of 5mg ovoTF per turkey during 12 days. Group 4 served as untreated, infected control group. Turkeys were aerosol infected using 10(6) TCID(50) of the virulent C. psittaci serovar/genotype D strain 92/1293. Birds were monitored (clinical signs, bacterial excretion) during 12 subsequent days before being necropsied. At necropsy, pathology and C. psittaci replication in various tissues was examined. A single dose of 10mg ovoTF and a repeated daily dose of 5mg ovoTF could not prevent the birds from becoming infected with C. psittaci, but they significantly reduced the outcome of the infection. A single dose of 5mg ovoTF had no influence on the outcome of the infection as compared to the non-treated infected controls. Our results demonstrate the anti-chlamydial effect of ovoTF in vivo and present a base for further research on practical applications of ovoTF on turkey farms.