Inference of breed structure in farm animals: Empirical comparison between snp and microsatellite performance

Knowledge of population structure is essential to improve the management and conservation of farm animal genetic resources. Microsatellites, which have long been popular for this type of analysis, are more and more neglected in favor of whole-genome single nucleotide polymorphism (SNP) chips that are now available for the main farmed animal species. In this study, we compared genetic patterns derived from microsatellites to that inferred by SNPs, considering three pairs of datasets of sheep and cattle. Population genetic differentiation analyses (Fixation index, FST ), as well as STRUCTURE analyses showed a very strong consistency between the two types of markers. Microsatellites gave pictures that were largely concordant with SNPs, although less accurate. The best concordance was found in the most complex dataset, which included 17 French sheep breeds (with a Pearson correlation coefficient of 0.95 considering the 136 values of pairwise FST, obtained with both types of markers). The use of microsatellites reduces the cost and the related analyses do not require specific computer equipment (i.e., information technology (IT) infrastructure able to provide adequate computing and storage capacity). Therefore, this tool may still be a very appropriate solution to evaluate, in a first stage, the general state of livestock at national scales. At a time when local breeds are disappearing at an alarming rate, it is urgent to improve our knowledge of them, in particular by promoting tools accessible to the greatest number

West Nile virus in Algeria: a comprehensive overview

West Nile virus (WNV) is a mosquito-borne virus belonging to the genus Flavivirus, related to the Japanese encephalitis antigenic complex of Flaviviridae family. It is transmitted by the bite of infected mosquitoes. The virus is maintained in a mosquito–bird–mosquito transmission cycle. WNV has recently dramatically expanded its geographical range and is now considered the most widespread arbovirus in the world, including the Americas, Europe and countries facing the Mediterranean Basin. In Algeria, West Nile disease (WND) infections with human meningoencephalitis cases have been reported in 1994 in Tinerkouk (southwest Sahara. In autumn 2012, one fatal clinical case of WNV neuroinvasive infection was reported in Jijel (coastal east). During the same year, a retrospective serosurvey performed in Algiers and bordering areas highlighted specific anti-WNV IgG in local population. Between 2013 and 2014 two clinical cases were reported, in Timimoune (south) and Guelma (northeast) respectively. Although no case was reported in equids, serosurveys demonstrated its presence: an animal serosurvey was conducted in Djanet (south) in 1975, and in 2014 a seroprevalence of equids in the northeast part of Algeria highlighted a virus circulation. This review aims to evaluate the global epidemiologic situation of West Nile disease in Algeria, with an updated situation based on human cases, equine reports and entomologic investigations. Our study reinforces the need for building the capacity for surveillance in this region to prevent future emergence of WNV and other arboviruses. Keywords: Algeria, mosquitoes, seroprevalence, West Nile disease, West Nile viru

Seasonal distribution of Rickettsia spp. in ticks in northeast Algeria

This article discusses research conducted on the sampling of two tick species: Ixodes ricinus and Rhipicephalus bursa. Ticks were collected in northern Algeria (El Tarf) in 2014 and studied for differences in abundance and seasonal distribution of population dynamics, as well as tested by PCR for the presence of Rickettsia spp. By molecular tools, four Rickettsia pathogens agents were detected: R. helvetica, R. monacensis, R. raoultii and R. massiliae. Keywords: Algeria, Ixodes, PCR, Rhipicephalus, Rickettsia, tick

Canine leishmaniosis and first report of Leishmania infantum in the blood of equids in Kabylia (Algeria)

International audienc

Canine leishmaniosis and first report of Leishmania infantum in the blood of equids in Kabylia (Algeria)

International audienc

Inventory and update on argasid ticks and associated pathogens in Algeria

International audienc

Bacterial infections in humans and nonhuman primates from Africa : expanding the knowledge

International audienceThe close phylogenetic relationship between humans and other primates creates exceptionally high potential for pathogen exchange. The surveillance of pathogens in primates plays an important role in anticipating possible outbreaks. In this study, we conducted a molecular investigation of pathogenic bacteria in feces from African nonhuman primates (NHPs). We also investigated the pathogens shared by the human population and gorillas living in the same territory in the Republic of Congo. In total, 93% of NHPs (n=176) and 95% (n=38) of humans were found to carry at least one bacterium. Non-pallidum Treponema spp. (including T. succinifaciens, T. berlinense, and several potential new species) were recovered from stools of 70% of great apes, 88% of monkeys, and 79% of humans. Non-tuberculosis Mycobacterium spp. were also common in almost all NHP species as well as in humans. In addition, Acinetobacter spp., members of the primate gut microbiota, were mainly prevalent in human and gorilla. Pathogenic Leptospira spp. were highly present in humans (82%) and gorillas (66%) stool samples in Congo, but were absent in the other NHPs, therefore suggesting a possible gorillas-humans exchange. Particular attention will be necessary for enteropathogenic bacteria detected in humans such as Helicobacter pylori, Salmonella spp. (including S. typhi/paratyphi), Staphyloccocus aureus, and Tropheryma whipplei, some of which were also present in gorillas in the same territory (S. aureus and T. whipplei). This study enhances our knowledge of pathogenic bacteria that threaten African NHPs and humans by using a non-invasive sampling technique. Contact between humans and NHPs results in an exchange of pathogens. Ongoing surveillance, prevention, and treatment strategies alone will limit the spread of these infectious agents

Genetic homogenization of indigenous sheep breeds in Northwest Africa

Northwest-African sheep represent an ideal case-study for assessing the potential impact of genetic homogenization as a threat to the future of traditional breeds that are adapted to local conditions. We studied ten Algerian and Moroccan breeds of sheep, including three transboundary breeds, distributed over a large part of the Maghreb region, which represents a geographically and historically coherent unit. Our analysis of the dataset that involved carrying out Genome-wide SNP genotyping, revealed a high level of homogenization (ADMIXTURE, NetView, fineSTRUCTURE and IBD segments analyses), in such a way that some breeds from different origins appeared genetically undistinguished: by grouping the eight most admixed populations, we obtained a mean global FST value of 0.0024. The sPCA analysis revealed that the major part of Morocco and the Northern part of Algeria were affected by the phenomenon, including most of the breeds considered. Unsupervised cross-breeding with the popular Ouled-Djellal breed was identified as a proximate cause of this homogenization. The issue of transboundary breeds was investigated, and the Hamra breed in particular was examined via ROH fragments analysis. Genetic diversity was considered in the light of historical archives and anthropological works. All of these elements taken together suggest that homogenization as a factor affecting the Maghrebin sheep stock, has been particularly significant over the last few decades, although this process probably started much earlier. In particular, we have identified the policies set by the French administration during the colonial period of the region’s history as a causal factor that probably contributed significantly to this process. The genetic homogenization that we have observed calls into question the integrity of the farm animal genomic resources represented by these local breeds, whose conservation is of critical importance to the future of the livestock sector

MALDI-TOF MS as an innovative tool for detection of Plasmodium parasites ă in Anopheles mosquitoes

International audienceBackground: Malaria is still a major public health issue worldwide, and ă one of the best approaches to fight the disease remains vector control. ă The current methods for mosquito identification include morphological ă methods that are generally time-consuming and require expertise, and ă molecular methods that require laboratory facilities with relatively ă expensive running costs. Matrix-Assisted Laser Desorption Ionization ă Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) technology, routinely ă used for bacterial identification, has recently emerged in the field of ă entomology. The aim of the present study was to assess whether MALDI-TOF ă MS could successfully distinguish Anopheles stephensi mosquitoes ă according to their Plasmodium infection status. ă Methods: C57BL/6 mice experimentally infected with Plasmodium berghei ă were exposed to An. stephensi bites. For the determination of An. ă stephensi infection status, mosquito cephalothoraxes were dissected and ă submitted to mass spectrometry analyses and DNA amplification for ă molecular analysis. Spectra were grouped according to mosquitoes' ă infection status and spectra quality was validated based on intensity ă and reproducibility within each group. The in-lab MALDI-TOF MS arthropod ă reference spectra database, upgraded with representative spectra from ă both groups (infected/non-infected), was subsequently queried blindly ă with cephalothorax spectra from specimens of both groups. ă Results: The MALDI TOF MS profiles generated from protein extracts ă prepared from the cephalothorax of An. stephensi allowed distinction ă between infected and uninfected mosquitoes. Correct classification was ă obtained in blind test analysis for (79/80) 98.75% of all mosquitoes ă tested. Only one of 80 specimens, an infected mosquito, was ă misclassified in the blind test analysis. ă Conclusions: Matrix-Assisted Laser Desorption Ionization Time-Of-Flight ă Mass Spectrometry appears to be a promising, rapid and reliable tool for ă the epidemiological surveillance of Anopheles vectors, including their ă identification and their infection status