Comparison of the sensitivity, specificity, correlation and inter-assay agreement of eight diagnostic in vitro assays for the detection of African swine fever virus.

With the recent spread of African swine fever (ASF) in Europe, Asia and the Caribbean region, after being endemic for decades in Africa, PCR-based commercial kits and various master mixes are increasingly being used in addition to the Office International des Epizooties-recommended protocol from King et al. (World Organization for Animal Health). Often, the availability and cost of commercial kits or master mixes can be a limiting factor for diagnostic laboratories, in addition to the requirements for transportation and storage of temperature-sensitive reagents in remote areas. In such cases, alternatives should be ready to maximize surveillance and mining of ASF. To evaluate alternatives, we tested five commercial quantitative real-time PCR (qPCR) master mixes from Applied Biosystems, Bio-Rad, Biotechrabbit, Promega and Qiagen using the same primers and probe mix derived from the King et al.'s protocol for the sensitivity, specificity, correlation and inter-assay agreement. We further included three ad hoc molecular diagnostic kits (VetMax™ African Swine Fever Virus Detection Kit [Applied Biosystems], ID Gene African Swine Fever Duplex [ID-Vet] and Virotype ASF PCR Kit [Qiagen/Indical]). The limit of detection (LOD) was assessed for each assay. The comparative study panel comprised 83 archived DNA samples from ASF virus (ASFV) clinical samples, belonging to five different genotypes from outbreaks in 16 countries in Asia and Africa. The analytical specificity was assessed against a panel of swine pathogens. The LOD ranged from 13 to 41 gene copies per reaction; VetMax ™ African Swine Fever Virus Detection Kit from Applied Biosystems exhibited the lowest detection limit (13 gene copies per reaction) and iQ Supermix from Bio-Rad the highest detection limit (41 gene copies per reaction). Cq values obtained from the lowest dilution, in which all replicates (n = 25) could still be amplified (50 gene copies per reaction), were not significantly different between kits using Kruskal-Wallis test. Inter-assay agreement was assessed using statistical test Fleiss-Kappa and was shown to be excellent in all cases. Agreement using statistical test Bland-Altman was good for samples with Cq values <25 and moderate for Cq values >25. We conclude that all the assays evaluated in this study can be used for the routine detection of ASFV.

A systematic approach toward progressive improvement of national antimicrobial resistance surveillance systems in food and agriculture sectors.

The first Food and Agriculture Organization of the United Nations (FAO) Action Plan on antimicrobial resistance (AMR), published in 2016, identified the need to develop capacity for AMR surveillance and monitoring in food and agriculture sectors. As part of this effort, FAO has developed the "Assessment Tool for Laboratories and AMR Surveillance Systems" (FAO-ATLASS) to assist countries in systematically assessing their AMR surveillance system in food and agriculture. FAO-ATLASS includes two different modules for surveillance and laboratory assessment. Each module includes two questionnaires that collect either qualitative or semi-quantitative data to describe and score the performance of national AMR surveillance system data production network, data collection and analysis, governance, communication and overall sustainability in a standardized manner. Based on information captured in the questionnaire by trained assessors (1) tables and figures describing the outputs of the surveillance system are automatically generated (2) a Progressive Improvement Pathway (PIP) stage, ranging from "1-limited" to "5-sustainable", is assigned to each laboratory assessed in the country, each area of the surveillance system and also to the overarching national AMR surveillance system. FAO-ATLASS allows national authorities to implement a strategic stepwise approach to improving their AMR surveillance systems via the FAO-ATLASS PIP system and provides an evidence base for actions and advocacy. The implementation of FAO-ATLASS at regional and global levels can contribute to harmonize and better coordinate strategies aimed at implementing an integrated AMR surveillance system under the One Health approach.

Informing resilience building: FAO's Surveillance Evaluation Tool (SET) Biothreat Detection Module will help assess national capacities to detect agro-terrorism and agro-crime.

Attacks using animal pathogens can have devastating socioeconomic, public health and national security consequences. The livestock sector has some inherent vulnerabilities which put it at risk to the deliberate or accidental spread of disease. The growing concern of countries about the risks of agro-terrorism and agro-crime has led to efforts to prepare against potential attacks. One recent international effort is the launch of a joint OIE, FAO and INTERPOL project in 2019 to build resilience against agro-terrorism and agro-crime targeting animal health with the financial support of the Weapons Threat Reduction Programme of Global Affairs Canada. Given the importance of strong animal health surveillance systems for the early and effective response to agro-terrorism and agro-crime, the project will use the FAO Surveillance Evaluation Tool (SET) and its new Biothreat Detection Module to evaluate beneficiary countries' capacities to detect criminal or terrorist animal health events. This paper presents the development of the new SET Biothreat Detection Module and how it will be used to evaluate surveillance for agro-terrorism and agro-crime animal disease threats. The module will be piloted in early 2021 and, once finalized, will be used by beneficiary countries of the joint OIE-FAO-INTERPOL project. Results from evaluations using SET and its Biothreat Detection Module are expected to provide a baseline from which countries can build targeted capacity for animal disease surveillance including early detection and investigation of potential terrorist or criminal events involving zoonotic and non-zoonotic animal pathogens.

Dog rabies control in West and Central Africa: A review.

Rabies is a neglected but preventable zoonotic disease that predominantly affects the most vulnerable populations living in remote rural areas of resource-limited countries. To date, every country on the African mainland is considered endemic for dog-mediated rabies with an estimated 21'500 human rabies deaths occurring each year. In 2018, the United Against Rabies collaboration launched the Global Strategic Plan to end human deaths from dog-mediated rabies by 2030. The epidemiology of rabies from most Western and Central African countries remains poorly defined, making it difficult to assess the overall rabies situation and progress towards the 2030 goal. In this review, we attempt to provide an overview of the current rabies situation in 22 West and Central African countries based on published scientific literature and information obtained from rabies focal points. To this end, information was collected on i) established surveillance, ii) diagnostic capacity, iii) post-exposure prophylaxis (PEP) availability and coverage, iv) dog population estimates, v) dog vaccination campaigns, vi) animal and human health communication (One Health), vii) molecular studies, viii) Knowledge, Attitude and Practices (KAP), ix) cost estimates and x) national control strategies. Although rabies is a notifiable disease in the majority of the studied countries, national surveillance systems do not adequately capture the disease. A general lack of rabies diagnostic capacity has an additional negative impact on rabies surveillance and attempts to estimate rabies burden. Recurrent shortages of human rabies vaccine are reported by all of the countries, with vaccine availability usually limited to major urban centers but no country has yet adopted the new WHO-recommended 1-week intradermal vaccination regimen. Most countries carry out subsidized mass dog vaccination campaigns on World Rabies Day. Such activities are indispensable to keep rabies in the public consciousness but are not of the scale and intensity that is required to eliminate rabies from the dog population. Countries will need to scale up the intensity of their campaigns, if they are to progress towards the 2030 goal. But more than half of the countries do not yet have reliable figures on their dog populations. Only two countries reached stage 2 on the Stepwise Approach towards Rabies Elimination ladder - indicating that their national governments have truly prioritized rabies elimination and are thus providing the necessary support and political buy-in required to achieve success. In summary, the sub-region of West and Central Africa seems to be divided into countries which have accepted the challenge to eliminate rabies with governments committed to pushing forward rabies elimination, while other countries have achieved some progress, but elimination efforts remain stuck due to lacking government commitment and financial constraints. The possibility to meet the 2030 goal without international solidarity is low, because more than two-thirds of the countries rank in the low human development group (HDI ≤ 152). Leading countries should act as role models, sharing their experiences and capacities so that no country is left behind. Unified and with international support it is possible to reach the common goal of zero human rabies deaths by 2030.

A Tool for Assessment of Animal Health Laboratory Safety and Biosecurity: The Safety Module of the Food and Agriculture Organization's Laboratory Mapping Tool.

The Laboratory Management Tool (LMT) is a standardized spreadsheet-based assessment tool developed to help support national, regional, and global efforts to maintain an effective network of animal health and veterinary public health laboratories. The safety and biosecurity module of the LMT (LMT-S) includes 98 measures covering administrative, operational, engineering, and personal protective equipment practices used to provide laboratory safety and biosecurity. Performance aspects of laboratory infrastructure and technical compliance considered fundamental for ensuring that a laboratory is able to appropriately function in a safe and biosecure manner are systematically queried and scored for compliance on a four-point scale providing for a semi-quantitative assessment. Data collected is used to generate graphs and tables mapping levels of compliance with international standards and good practices, as well as for documenting progress over time. The LMT-S was employed by trained auditors in 34 laboratories located in 19 countries between 2015 and 2017. The tool is intended to help standardize animal health laboratory assessments, document compliance with recognized laboratory safety and biosecurity measures, serve as a self-help and training tool, and assist global laboratory development efforts by providing an accurate measurement of laboratory safety and biosecurity at local, national, and regional levels.

FAO/INFOODS food composition database for biodiversity.

Nutrient content can vary as much between different varieties of the same foods, as they do among different foods. Knowledge of varietal differences can therefore mean the difference between nutrient adequacy and inadequacy. The FAO/INFOODS food composition database for biodiversity has been developed with analytical data for foods described at the level of variety, cultivar and breed, and for underutilized and wild foods. It contains 6411 food entries and values for 451 components together with the bibliographic references and other information. The database is in MS Excel format and can be downloaded free-of-charge from the INFOODS website http://www.fao.org/infoods/biodiversity/index_en.stm. It is intended to annually publish new editions, making these data available for national and regional food composition databases. This database could be used to raise the awareness, promote and investigate food biodiversity and help to better estimate nutrient intakes.

Enterocyte metabolism during early adaptation after extensive intestinal resection in a rat model.

OBJECTIVE: A better knowledge of intestinal adaptation after resection is required to improve the nutritional support that is given to patients. The aim of this study was to understand the metabolic changes underlying early adaptation after massive intestinal resection. METHODS: Rats were assigned to either 80% intestinal resection or transection. All animals received the same intragastric nutrition. On day 8, plasma glutamine turnover was measured. Substrate use was determined on isolated enterocytes that were incubated in the presence of D-[U-(14)C] glucose (2 mmol/L), L-[U-(14)C] glutamine (2 mmol/L), L-[U-(14)C] arginine (1 mmol/L), or L-[1-(14)C] ornithine (1 mmol/L). RESULTS: Plasma glutamine turnover was similar in both groups. The rate of enterocyte glutamine use was significantly increased in the resection group, although the maximal glutaminase activity was unchanged. Glutathione generation was enhanced 3-fold in remnant intestine as compared with transected intestine (P <.05). L-ornithine decarboxylation was increased markedly in resected animals (P <.05), without any detectable change of maximal ornithine decarboxylase activity. CONCLUSION: The early phase of intestinal adaptation after resection induces changes in enterocyte glutamine and ornithine metabolism that may be related, in part, to increased de novo polyamine synthesis. This observation suggests that a supplementation of artificial nutrition by nutrients that lead to the generation of trophic agents may be of potential interest.

Adaptative increase of ornithine production and decrease of ammonia metabolism in rat colonocytes after hyperproteic diet ingestion.

Chronic high-protein consumption leads to increased concentrations of NH(4)(+)/NH(3) in the colon lumen. We asked whether this increase has consequences on colonic epithelial cell metabolism. Rats were fed isocaloric diets containing 20 (P20) or 58% (P58) casein as the protein source for 7 days. NH(4)(+)/NH(3) concentration in the colonic lumen and in the colonic vein blood as well as ammonia metabolism by isolated surface colonic epithelial cells was determined. After 2 days of consumption of the P58 diet, marked increases of luminal and colonic vein blood NH(4)(+)/NH(3) concentrations were recorded when compared with the values obtained in the P20 group. Colonocytes recovered from the P58 group were characterized at that time and thereafter by an increased capacity for l-ornithine and urea production through arginase (P < 0.05). l-Ornithine was mostly used in the presence of NH(4)Cl for the synthesis of the metabolic end product l-citrulline. After 7 days of the P58 diet consumption, however, the ammonia metabolism into l-citrulline was found lower (P < 0.01) when compared with the values measured in the colonocytes recovered from the P20 group despite any decrease in the related enzymatic activities (i.e., carbamoyl-phosphate synthetase I and ornithine carbamoyl transferase). This decrease was found to coincide with a return of blood NH(4)(+)/NH(3) concentration in colonic portal blood to values close to the one recorded in the P20 group. In response to increased NH(4)(+)/NH(3) concentration in the colon, the increased capacity of the colonocytes to synthesize l-ornithine is likely to correspond to an elevated l-ornithine requirement for the elimination of excessive blood ammonia in the liver urea cycle. Moreover, in the presence of NH(4)Cl, colonocytes diminished their synthesis capacity of l-citrulline from l-ornithine, allowing a lower cellular utilization of this latter amino acid. These results are discussed in relationship with an adaptative process that would be related to both interorgan metabolism and to the role of the colonic epithelium as a first line of defense toward luminal NH(4)(+)/NH(3) concentrations.

Inhibition of human colon carcinoma cell growth by ammonia: a non-cytotoxic process associated with polyamine synthesis reduction.

Ammonia, produced by bacterial degradation of unabsorbed and endogenous nitrogenous compounds, is found to be present at millimolar concentrations in the colon lumen. From in vivo animal experiments, this metabolite has been shown to alter colonic epithelial cell morphology and to increase compensatory cell proliferation when present in excess. In this in vitro study, using the human colon adenocarcinoma HT-29 Glc(-/+) cell line treated with increasing doses of NH(4)Cl, we found that 20 mM NH(4)Cl, a concentration close to that found in the large intestine lumen, was able to increase the volume of vacuolar lysosomes and to repress HT-29 Glc(-/+) cell proliferation. This growth-inhibitory effect was not correlated with decrease of cell viability, with modification of cell differentiation and change of the cell distribution in the different cell cycle phases, thus indicating a proportional slowdown in all cell cycle phases. In contrast to what is found in healthy colonocytes, ammonia was not metabolized by HT-29 cells into carbamoyl-phosphate (carbamoyl-P) and citrulline, indicating that ammonia was likely acting on cells by itself. This agent was shown to markedly reduce cellular ornithine decarboxylase (ODC) activity resulting in a threefold decrease in the capacity of HT-29 cells to synthetize polyamines, these latter metabolites being strictly necessary for cell growth. The unexpected finding that ammonia is acting as an antimitotic agent against tumoral HT-29 colonic cells may be related to the inability of these cells to metabolize this compound.