Vingt-huit organisations internationales viennent de s'associer pour mieux lutter contre les maladies du manioc en Afrique. Le réseau PACSUN (Pan-African Cassava Surveillance Network) ainsi formé ambitionne de prévenir une éventuelle catastrophe alimentaire puisque, sur le continent, le manioc est de plus en plus central dans la subsistance des populations.
During the French President's State visit to Ivory Coast on 17 July, CIRAD and the Centre national de recherche agronomique (CNRA) signed a new general cooperation agreement. The signing marks the resumption of CIRAD's scientific cooperation activities in Ivory Coast, following a period of political unrest in the country. Other agreements with Ivorian research and higher education establishments, professional bodies and funding agencies look set to follow.
A l’occasion de la visite d’Etat du président de la république Française en Côte d’Ivoire le 17 juillet dernier, le Cirad et le Centre national de recherche agronomique (CNRA) viennent de signer un nouvel accord-cadre de coopération. Cette signature symbolise la relance des activités de coopération scientifique du Cirad en Côte d’Ivoire, après la période de troubles politiques qu’a connu le pays. D’autres rapprochements, avec les partenaires ivoiriens de la recherche et de l’enseignement supérieur, des filières professionnelles et des agences de financement, devraient suivre.
5e symposium international "Farming Systems Design" organisé par la European Society for Agronomy et Agropolis International dont le Cirad est membre.
Issue de la fusion des unités Systèmes de culture annuels (SCA) et Système et ingéniérie agronomique (Sia), cette nouvelle unité de recherche du Cirad propose un large éventail de compétences mises au service de l'intensification écologique en réponse à la demande sociétale et aux besoins du développement. Retrouvez, sur le site Internet ur-aida.cirad.fr, l'actualité et les activités de l’unité de recherche.
By the end of the century, food security will be affected by several factors: population growth, climate change, economic unequalities, natural resource shortages, etc. This issue is therefore a major challenge for research, which is why CIRAD and INRA have joined forces to conduct joint, long-term programmes framed by a metaprogramme. The two organizations will be addressing novel issues, at the interface between between more conventional lines of research in this field. The metaprogramme, called GloFoodS (Transitions to Global Food Security), was launched in Montpellier in June 2014.
The current report discusses the process in which a methods comparison study in the National Animal Health Laboratory Network is performed. Specific details are provided for designing and analyzing studies intended to evaluate analytical sensitivity, efficiency, analytical specificity, cross-contamination, repeatability, operator variability, and to compare the performance of methods using diagnostic samples. As an example, a case study is presented comparing the performance of a candidate reverse transcription polymerase chain reaction (RT-PCR) chemistry to the current RT-PCR chemistry in use when the assay was originally validated. The present study revealed that, for all of the validation factors evaluated, the candidate method performed at least as well and generally better than the current method. The candidate method was, therefore, deemed fit for the original intended purpose of the current method and rendered acceptable for use. A discussion of the case study is intended to further motivate consideration of the study designs chosen.
Streptococcus spp. were recovered from diseased tilapia in Thailand during 2009–2010 (n = 33), and were also continually collected from environmental samples (sediment and water) from tilapia farms for 9 months in 2011 (n = 25). The relative percent recovery of streptococci from environmental samples was 13–67%. All streptococcal isolates were identified as S. agalactiae (group B streptococci [GBS]) by a species-specific polymerase chain reaction. In molecular characterization assays, 4 genotypic categories comprised of 1) molecular serotypes, 2) the infB allele, 3) virulence gene profiling patterns (cylE, hylB, scpB, lmb, cspA, dltA, fbsA, fbsB, bibA, gap, and pili backbone–encoded genes), and 4) randomly amplified polymorphic DNA (RAPD) fingerprinting patterns, were used to describe the genotypic diversity of the GBS isolates. There was only 1 isolate identified as molecular serotype III, while the others were serotype Ia. Most GBS serotype Ia isolates had an identical infB allele and virulence gene profiling patterns, but a large diversity was established by RAPD analysis with diversity tending to be geographically dependent. Experimental infection of Nile tilapia (Oreochromis niloticus) revealed that the GBS serotype III isolate was nonpathogenic in the fish, while all 5 serotype Ia isolates (3 fish and 2 environmental isolates) were pathogenic, with a median lethal dose of 6.25–7.56 log10 colony-forming units. In conclusion, GBS isolates from tilapia farms in Thailand showed a large genetic diversity, which was associated with the geographical origins of the bacteria.
A multiplex amplification refractory mutation system reverse transcription polymerase chain reaction (ARMS RT-PCR) was developed for the differential diagnosis of Feline leukemia virus (FeLV) vaccine and wild-type strains based on a point mutation between the vaccine strain (S) and the wild-type strain (T) located in the p27 gene. This system was further upgraded to obtain a real-time ARMS RT-PCR (ARMS qRT-PCR) with a high-resolution melt analysis (HRMA) platform. The genotyping of various strains of FeLV was determined by comparing the HRMA curves with the defined wild-type FeLV (strain TW1), and the results were expressed as a percentage confidence. The detection limits of ARMS RT-PCR and ARMS qRT-PCR combined with HRMA were 100 and 1 copies of transcribed FeLV RNA per 0.5 ml of sample, respectively. No false-positive results were obtained with 6 unrelated pathogens and 1 feline cell line. Twelve FeLV Taiwan strains were correctly identified using ARMS qRT-PCR combined with HRMA. The genotypes of the strains matched the defined FeLV wild-type strain genotype with at least 91.17% confidence. A higher degree of sequence polymorphism was found throughout the p27 gene compared with the long terminal repeat region. In conclusion, the current study describes the phylogenetic relationship of the FeLV Taiwan strains and demonstrates that the developed ARMS RT-PCR assay is able to be used to detect the replication of a vaccine strain that has not been properly inactivated, thus acting as a safety check for the quality of FeLV vaccines.
Brucella species infect a wide range of hosts with a broad spectrum of clinical manifestations. In mammals, one of the most significant consequences of Brucella infection is reproductive failure. There is evidence of Brucella exposure in many species of marine mammals, but the outcome of infection is often challenging to determine. The eastern Pacific stock of northern fur seals (NFSs, Callorhinus ursinus) has declined significantly, spawning research into potential causes for this trend, including investigation into reproductive health. The objective of the current study was to determine if NFSs on St. Paul Island, Alaska have evidence of Brucella exposure or infection. Archived DNA extracted from placentas (n = 119) and serum (n = 40) samples were available for testing by insertion sequence (IS) 711 polymerase chain reaction (PCR) and the Brucella microagglutination test (BMAT), respectively. As well, placental tissue was available for histologic examination. Six (5%) placentas were positive by PCR, and a single animal had severe placentitis. Multilocus variable number tandem repeat analysis profiles were highly clustered and closely related to other Brucella pinnipedialis isolates. A single animal was positive on BMAT, and 12 animals had titers within the borderline range; 1 borderline animal was positive by PCR on serum. The findings suggest that NFSs on the Pribilof Islands are exposed to Brucella and that the organism has the ability to cause severe placental disease. Given the population trend of the NFS, and the zoonotic nature of this pathogen, further investigation into the epidemiology of this disease is recommended.
Intraparenchymal spinal cord tumors in the cat are rarely reported and often as single case reports. In the current study, the clinical, magnetic resonance imaging (MRI), histologic, and immunohistochemical features of 7 cases of intraparenchymal spinal cord tumors in the cat are described. All cats were domestic breed, ranged from 4 to 12 years of age (median 8 years), and included spayed females (5/7) and neutered males (2/7). The duration of clinical signs ranged from 2 weeks to 3 months. MRI revealed lesions that were hyperintense on T2-weighted images with variable contrast enhancement. All 7 tumors had histologic features consistent with glial origin: 3 were astrocytic (gemistocytic or fibrous), and 2 were oligoastrocytic. Single cases of oligodendroglioma and gliomatosis cerebri were also present in the study. Glial fibrillary acidic protein immunoreactivity was robust in the tumors that were predominately astrocytic, and the gliomatosis cerebri case had extensive BLA.36 and Iba1 immunoreactivity. Ki-67 immunoreactivity was variable and most abundant in the case of malignant oligoastrocytoma. The majority of peritumoral lymphocytes were CD3 positive. The current study expands upon the known reports of spinal cord neoplasia in the cat, confirms a caudal cervical segment predilection, and includes a report of gliomatosis cerebri in the spinal cord of a cat.
Biliverdin is an intermediate of heme degradation with an established role in veterinary clinical diagnostics of liver-related diseases. The need for chromatographic assays has so far prevented its wider use in diagnostic laboratories. The current report describes a simple, fast, high-throughput, and inexpensive assay, based on the interaction of biliverdin with infrared fluorescent protein (iRFP) that yields functional protein exhibiting infrared fluorescence. The assay is linear in the range of 0–10 µmol/l of biliverdin, has a limit of detection of 0.02 μmol/l, and has a limit of quantification of 0.03 µmol/l. The assay is accurate with relative error less than 0.15, and precise, with coefficient of variation less than 5% in the concentration range of 2–9 µmol/l of biliverdin. More than 95% of biliverdin was recovered from biological samples by simple dimethyl sulfoxide extraction. There was almost no interference by hemin, although bilirubin caused an increase in the biliverdin concentration, probably due to spontaneous oxidation of bilirubin to biliverdin. The newly developed biliverdin assay is appropriate for reliable quantification of large numbers of samples in veterinary medicine.
Diagnosis of equine hyperinsulinemia requires an accurate method for quantification of equine insulin concentrations. The objectives of the current study were to compare 2 commercially available techniques for measurement of equine insulin, the radioimmunoassay (RIA) and chemiluminescent immunoassay (CIA). Recovery was poor for both assays, but worse for the CIA. Serial dilution of a high endogenous insulin sample yielded better linearity for the RIA (r 2 = 0.99, P < 0.001) than the CIA (r 2 = 0.92, P = 0.009). Bland–Altman analysis indicated that the CIA was, on average, 91 pmol/l higher than the RIA, with wide limits of agreement (95% limits of agreement: –508 to 691 pmol/l). These findings suggest that results between the assays should not be considered interchangeable.
Analysis of rumen contents is helpful in solving poisoning cases when ingestion of a toxic substance by cattle or other ruminant animals is suspected. The most common technique employs extraction of the sample with organic solvent followed by clean-up method(s) before analysis with gas chromatography–mass spectrometry equipped with a library of mass spectra to help identify unknowns. A rapid method using magnesium sulfate, primary secondary amine, and C18 sorbents following principles of QuEChERS to clean up rumen contents samples is reported herein. The method was validated to analyze fortified bovine rumen contents to detect commonly found organophosphorus pesticides, carbamates, and several other compounds such as atropine, 4-aminopyridine, caffeine, scopolamine, 3-chloro-4-methylaniline, strychnine, metaldehyde, and metronidazole. For each compound, the ratio of 2 ions from the mass spectrum was monitored in fortified rumen contents. The ion ratio of fortified sample was compared with the ion ratio of standard sample spectrum and was found to be within 20%, with the exception of aldicarb and 4-aminopyridine with ion ratio of 26% and 29%, respectively. Usefulness of the method was demonstrated by not only analyzing bovine rumen contents but also canine and avian gastrointestinal contents submitted for organic chemical screening.
The effect of fixation and storage conditions on the performance of polymerase chain reaction (PCR) assays for Babesia odocoilei were examined using 3 different primer sets targeting the eukaryotic 18S ribosomal RNA gene, with variably sized products of 1,723 base pairs (bp), 483 bp, and 306 bp. All primer sets performed well on fresh-frozen tissue, and storage for 1 year at –20°C did not affect PCR performance. Formalin fixation markedly affected the amplicon length that could be amplified. However, DNA was successfully amplified after storage in formalin for 2 months using the primer set with a 483-bp product, and up to 6 months using the primer set with a 306-bp product. The latter primer set successfully differentiated B. odocoilei and Babesia microti DNA; however, further evaluation is required to confirm its specificity. Treatment of tissues with formic acid, at concentrations typically used to denature prions, degraded the DNA and made it unsuitable for PCR testing.
Autosomal-dominant polycystic kidney disease (ADPKD) is the most prevalent inherited genetic disease of cats, predominantly affecting Persian and Persian-related cats. A point mutation (C->A transversion) in exon 29 of the PKD1 gene causes ADPKD, and is the specific molecular target for genetic diagnosis in cats. The current study describes a newly developed touchdown polymerase chain reaction (PCR) to detect this single point mutation, using 2 primers specific for the mutant allele, adapted from an existing multiplex amplification refractory mutation system (ARMS PCR). Furthermore, correlations between the clinical outcomes of tested animals and the results of the genetic test were investigated. A total of 334 cats were tested, 188 from the Veterinary Hospital of Small Animals at the University of Brasilia, and 146 from an anti-rabies vaccine campaign of the Federal District. A total prevalence of 9% was evident among the samples, with 33% of the Persian cats testing positive, and 7% of the Brazilian long- and shorthaired cats testing positive. Prevalence was not correlated with gender or hemogram. Positive animals exhibited hyperglobulinemia (P = 0.02). This research demonstrated that the mutation does not only occur in Persian and Persian-related cats, and that a touchdown PCR can be used to diagnose ADPKD.
In the current study, molecular, biological, and antigenic analyses were performed to characterize Border disease virus (BDV) strain FNK2012-1 isolated from a pig in 2012 in Japan. The complete genome comprises 12,327 nucleotides (nt), including a large open reading frame of 11,685 nt. Phylogenetic analysis revealed that FNK2012-1 was clustered into BDV genotype 1 with ovine strains. FNK2012-1 grew in porcine, bovine, and ovine primary cells and cell lines, but grew better in bovine and ovine cells than in porcine cells. Specific pathogen–free pigs inoculated with FNK2012-1 did not show any clinical signs. Noninoculated contact control pigs also did not show clinical signs and did not seroconvert. The results suggest that FNK2012-1 may be of ruminant origin and is poorly adapted to pigs. Such observations can provide important insights into evidence for infection and transmission of BDV, which may be of ruminant origin, among pigs.
Bluetongue is a potentially fatal arboviral disease of domestic and wild ruminants that is characterized by widespread edema and tissue necrosis. Bluetongue virus (BTV) serotypes 10, 11, 13, and 17 occur throughout much of the United States, whereas serotype 2 (BTV-2) was previously only detected in the southeastern United States. Since 1998, 10 other BTV serotypes have also been isolated from ruminants in the southeastern United States. In 2010, BTV-2 was identified in California for the first time, and preliminary sequence analysis indicated that the virus isolate was closely related to BTV strains circulating in the southeastern United States. In the current study, the whole genome sequence of the California strain of BTV-2 was compared with those of other BTV-2 strains in the Americas. The results of the analysis suggest co-circulation of genetically distinct viruses in the southeastern United States, and further suggest that the 2010 western isolate is closely related to southeastern strains of BTV. Although it remains uncertain as to how this novel virus was translocated to California, the findings of the current study underscore the need for ongoing surveillance of this economically important livestock disease.
Ehrlichia canis is the most common cause of monocytotropic ehrlichiosis in dogs around the world. The purpose of the present study was to validate a new automated fluorescence system (Accuplex4™ BioCD system; Antech Diagnostics, Lake Success, New York) to detect antibodies against the E. canis immunodominant glycoprotein 36 (gp36). Sera and blood samples (ethylenediamine tetra-acetic acid) were collected from mixed sex beagles (n = 8) on days 0, 3, 7, 10, 14, 17, 21, 28, 42, 49, 56, 63, 70, 77, 84, and 98 after intravenous inoculation with culture-derived E. canis. Sera were assayed using the Accuplex4 BioCD system (Accuplex4), an E. canis indirect fluorescent antibody test (IFAT), and a commercially available kit. A complete blood cell count and a proprietary E. canis polymerase chain reaction (PCR) were performed on each blood sample. On the day thrombocytopenia was first detected for each dog, E. canis DNA was amplified from blood of all dogs. At those times, E. canis antibodies were detected in 7 of 8 dogs by the Accuplex4, 1 of 8 dogs by the commercial kit, and 4 of 8 dogs by IFAT. Ehrlichia canis DNA was amplified from blood before seroconversion in any antibody assay for 6 dogs. Antibodies against gp36 were detected by Accuplex4 within 3 days of PCR-positive test results and were detected up to 25 days sooner than the commercial kit. After starting doxycycline treatment, E. canis DNA was no longer amplified by PCR assay, but serum antibodies remained detectable by all assays.
An epidemiological survey for Canine parvovirus 2 (CPV-2) and Canine coronavirus (CCoV) was conducted in Albania. A total of 57 fecal samples were collected from diarrheic dogs in the District of Tirana during 2011–2013. The molecular assays detected 53 and 31 CPV- and CCoV-positive specimens, respectively, with mixed CPV–CCoV infections diagnosed in 28 dogs. The most frequently detected CPV type was 2a, whereas IIa was the predominant CCoV subtype. A better comprehension of the CPV–CCoV epidemiology in eastern European countries will help to assess the most appropriate vaccination strategies to prevent disease due to infections with these widespread agents of acute gastroenteritis in the dog.
In late January 2013, 10 nonpregnant Lacaune dairy ewes raised under extensive husbandry management on a farm in Rio de Janeiro, Brazil, presented with the general clinical signs of lethargy, hyporexia, edema of the face, hyperemia of the exposed parts of the skin, mouth lesions, pyrexia, and lameness. Additionally, 2 pregnant ewes died suddenly after the onset of respiratory signs. The complete blood counts and biochemistry analyses showed neutrophilic leukocytosis with monocytosis and reactive lymphocytes, normocytic normochromic anemia and increased aspartate aminotransferase levels. Postmortem examination revealed erosions on the lingual mucosa, bilateral submandibular ganglia infarctions, yellow foamy fluid accumulation in the trachea and bronchial bifurcation, pulmonary congestion, and edema associated with hemorrhagic lesions on the pulmonary artery and heart. The clinical and pathological findings were suggestive of bluetongue. For a molecular and virological diagnosis, tissue samples were analyzed by Bluetongue virus–specific real-time reverse transcription polymerase chain reaction (qRT-PCR), and viral isolation was performed in embryonated chicken eggs. For viral typing, positive tissue and egg-isolated samples were analyzed by qRT-PCR using primers and probes specific for the structural VP2 gene in genome segment 2 of all 26 serotypes. There are still no contingency plans for responding to an outbreak of bluetongue disease in Brazil, and this episode emphasizes the need for continuing serological and entomological surveillance programs. Additionally, this report describes the isolation of Bluetongue virus serotype 4 in sheep in the Americas.
Blood smears from a 24-year-old male rhesus macaque (Macaca mulatta) used for cognitive function studies were evaluated. The macaque had an 8-month history of gradual weight loss and increasing lymphocytosis. Most of the lymphocytes present were small to medium and had a mature morphology. Based on the degree and duration of the lymphocytosis, and the appearance of the lymphocytes, a diagnosis of chronic lymphocytic leukemia was made. The animal tested negative for 4 viral diseases that are commonly associated with lymphoproliferative disorders in Old World monkeys. Over the course of 12 months, the lymphocytosis progressed from 18.4 to 384 x 103 lymphocytes/µl (reference range: 0.8–17 x 103 cells/µl), and euthanasia was elected. On histologic examination, cluster of differentiation (CD)3- and CD8-positive, CD79-negative neoplastic cells comprised 40–60% of the bone marrow, diffusely obscured the normal splenic architecture, and were present in the vascular channels in other organs. Findings were characteristic of T-cell lymphocytic leukemia. Naturally occurring T-cell lymphocytic leukemia has been rarely reported in rhesus macaques and, to the authors’ knowledge, never in males. A persistent lymphocytosis characterized by a monomorphic population of CD3- and CD8-positive cytotoxic T-lymphocytes and the presence of neoplastic cells in the bone marrow led to a diagnosis in the current case.
Cutaneous meningiomas are rare tumors in human beings and animals. Two canine cases of cutaneous meningiomas affecting the eyelid are described in the current study: the first from a 5-week-old female Springer Spaniel dog with an 8 cm in diameter congenital mass expanding the left upper eyelid and medial canthus; the second from a 10-year-old female spayed Maltese–Poodle mix dog with 3 firm subcutaneous nodules affecting the right upper eyelid. All masses were removed surgically. Histologically, tumors were composed of spindle-to-epithelioid cells arranged in small lobules forming solid concentric whorls. Neoplastic cells were positive for vimentin and S100 and negative for pancytokeratin, glial fibrillar acid protein, and neurofilament. Transmission electron microscopy revealed meningothelial cells with convoluted interdigitating processes, desmosomes, and hemidesmosomes, and moderate numbers of cytoplasmic microfilaments. None of the cases presented a primary neuroaxial meningioma. The first case presents clinicopathological features consistent with human type I (congenital) cutaneous meningioma. The second case is consistent with a type II (acquired ectopic) tumor, and both are hypothesized to arise from ectopic arachnoid cells displaced during development.
An unusual case of osteomyelitis caused by Nocardia cyriacigeorgica infection and resulting in mandibular osteomyelitis and cellulitis (lumpy jaw) is described in a young cat. A 1-cm hard nodular mass was an incidental finding in the right mandible of a 14-month-old cat during routine physical examination. The lesion was fast growing, reaching up to 6 cm in its largest dimension over a 5-week period. A core biopsy of the affected mandible revealed foci of osteolysis, woven bone formation, and a few large clusters of filamentous bacteria surrounded by fine eosinophilic amorphous material bordered by neutrophils, plasma cells, macrophages, and occasional multinucleated giant cells. Pure cultures of acid-fast variable, Gram-positive filamentous bacteria were recovered on blood and chocolate agar plates at 48-hr postinoculation. On amplification and sequencing of the 16S ribosomal RNA and 65-kDa heat shock protein genes, the microorganisms were identified as N. cyriacigeorgica, within the actinomycetes.
Moraxella bovoculi was isolated and identified in ocular fluid samples collected from 9 racehorses with infectious keratoconjunctivitis in China in 2013. All 9 M. bovoculi isolates were hemolytic, Gram-negative diplococci that were phenylalanine deaminase positive. The sequence of the 16S ribosomal DNA (rDNA) gene of the isolates matched the 16S rDNA sequence of M. bovoculi. Amplification of the 16S–23S intergenic spacer region followed by AfaI digestion produced a 600–base pair product, a result characteristic of M. bovoculi isolates. The phylogenetic analysis based on the 16S rDNA sequence confirmed the strain isolated in the current study had genetic homology with M. bovoculi.
D’ici la fin du siècle, la sécurité alimentaire sera affectée par plusieurs facteurs : croissance démographique, changements climatiques, iniquité économique, épuisement des ressources naturelles, etc. Aussi, cette question constitue un défi majeur pour la recherche. C’est la raison pour laquelle, le Cirad et l’Inra unissent leurs forces au travers d’une programmation conjointe sur la durée dans le cadre d’un métaprogramme. Les deux organismes exploreront des questions novatrices, situées à la croisée des voies de recherche plus classiques dans ce domaine. Dénommé GloFoodS pour Transitions pour la sécurité alimentaire mondiale, le métaprogramme a été lancé à Montpellier en juin 2014.
How do human societies influence crop evolution processes? Researchers from CIRAD and their partners recently demonstrated that sorghum genetic diversity distribution in eastern Kenya was linked to the ethnolinguistic origin of farmers. Taking this into account would make genetic resource collection and characterization programmes more efficienct. This is a major issue for resource conservation.
Comment les sociétés humaines influent-elles sur les processus d’évolution des plantes cultivées ? Les chercheurs du Cirad et leurs partenaires viennent de démontrer que la distribution de la diversité génétique du sorgho dans l’est du Kenya est liée à l’appartenance ethnique des agriculteurs. En intégrant cette dimension, les programmes de collecte et de caractérisation des ressources génétiques gagneraient en efficacité. Un enjeu majeur pour la conservation de ces ressources.
Fruit flies are one of the main types of pests found on fruit crops in Réunion. However, the control methods used up to now have two drawbacks: impregnation of the fruit if insecticides are applied directly, and the development of resistance in the flies. In response to these constraints, researchers from CIRAD and their partners tested and proved the efficacy of a new system: mass trapping. It makes it possible to use very small quantities of insecticide, without any direct application on the fruits. The traps contain a sachet of food attractant and a small quantity of insecticide. The researchers concentrated on two fly species for which promising attractants already exist for the females of the species. Their trials served to compare various components of the trap and the possible combinations, using different attractant formulas and traps. The results pinpointed the most effective traps and attractants for use in trapping systems.
On les accuse de bien des maux et même de transmettre des maladies mortelles. Les chauves-souris seraient en effet le réservoir de virus tels qu’Ebola, Marburg, Nipah, rage etc.
Pire, elles sont soupçonnées de contaminer aussi bien les hommes que les animaux.
