Nutritive value and energy content of the straw of selected Vicia L. taxa from Tunisia

The chemical composition and energy value of straws of <em>Vicia sativa</em> L. (varieties Languedoc and Mghila, and subspecies <em>amphicarpa</em>) and <em>Vicia villosa</em> Roth. (variety Sejenane and accession 2565) were investigated. The plants were grown in a Mediterranean environment, under identical environmental conditions. Total digestible nutrients (TDN) and energy values (digestible energy, metabolisable energy, and net energy for lactation) were estimated according to the equations developed by the 2001 Dairy National Research Council. Both ether extract (EE) or total fatty acids (FA) amounts, and digestible neutral detergent fibre (dNDF) calculated from chemical analysis or measured using a 48-hour rumen <em>in vitro</em> assay were used for calculations. Significant differences were observed in the chemical composition and energy value of the straws of the considered <em>V. sativa</em> and <em>V. villosa</em> varieties. Within the same variety, the TDN was similar using either EE or FA values for calculation. The energy resulted largely dependent on the dNDF values. Energy was higher when <em>in vitro</em> dNDF was used for calculation in low-NDF straw samples, while the opposite occurred for high-NDF samples

Molecular characterisation of antimicrobial resistance and virulence genes in Escherichia coli strains isolated from diarrhoeic and healthy rabbits in Tunisia

[EN] The purpose of this study was to identify Escherichia coli isolates in diarrhoeic and healthy rabbits in Tunisia and characterise their virulence and antibiotic resistance genes. In the 2014-2015 period, 60 faecal samples from diarrhoeic and healthy rabbits were collected from different breeding farms in Tunisia. Susceptibility to 14 antimicrobial agents was tested by disc diffusion method and the mechanisms of gene resistance were evaluated using polymerase chain reaction and sequencing methods. Forty E. coli isolates were recovered in selective media. High frequency of resistance to tetracycline (95%) was detected, followed by different levels of resistance to sulphonamide (72.5%), streptomycin (62.5%), trimethoprim-sulfamethoxazole (60%), nalidixic acid (32.5%), ampicillin (37.5%) and ticarcillin (35%). E. coli strains were susceptible to cefotaxime, ceftazidime and imipenem. Different variants of blaTEM, tet, sul genes were detected in most of the strains resistant to ampicillin, tetracycline and sulphonamide, respectively. The presence of class 1 integron was studied in 29 sulphonamide-resistant E. coli strains from which 15 harboured class 1 integron with four different arrangements of gene cassettes, dfrA17+aadA5 (n=9), dfrA1 + aadA1 (n=4), dfrA12 + addA2 (n=1), dfrA12+orf+addA2 (n=1). The qnrB gene was detected in six strains out of 13 quinolone-resistant E. coli strains. Seventeen E. coli isolates from diarrhoeic rabbits harboured the enteropathogenic eae genes associated with different virulence genes tested (fimA, cnf1, aer), and affiliated to B2 (n=8) and D (n=9) phylogroups. Isolated E. coli strains from healthy rabbit were harbouring fim A and/or cnf1 genes and affiliated to A and B1 phylogroups. This study showed that E. coli strains from the intestinal tract of rabbits are resistant to the widely prescribed antibiotics in medicine. Therefore, they constitute a reservoir of antimicrobial-resistant genes, which may play a significant role in the spread of antimicrobial resistance. In addition, the eae virulence gene seemed to be implicated in diarrhoea in breeder rabbits in Tunisia.The work was supported by Tunisian Ministry of Higher Education, Scientific Research and Technology (LR16IP03). Many thanks go to the members of the Department of Animal Production, National Institute of Agronomy of Tunisia for their help in collecting the samples.Ben Rhouma, R.; Jouini, A.; Klibi, A.; Hamrouni, S.; Boubaker, A.; Kmiha, S.; Maaroufi, A. (2020). Molecular characterisation of antimicrobial resistance and virulence genes in Escherichia coli strains isolated from diarrhoeic and healthy rabbits in Tunisia. World Rabbit Science. 28(2):81-91. https://doi.org/10.4995/wrs.2020.10879OJS8191282Allen H.K., Donato J., Wang H.H, Cloud-Hansen K.A., Davies J. 2010. Call of the wild: antibiotic resistance genes in natural environments. 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The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Small ruminant value chain in Al-Ruwaished District, Jordan

This study aims to assess the small ruminant value chain in Al-Ruwaished District, Jordan, to identify the potential intervention areas that could improve the production efficiency and guarantee the sustainability of the small ruminant sector in this area. Sheep breeding is the source of livelihood for most of the people in Al-Ruwaished District, which is characterized by the large number of sheep and goats. We surveyed 5.0% of the small ruminant holders in the study area and conducted individual interviews and surveys with the potential actors in the value chain to undertake a small ruminant value chain analysis. From the survey, we found that the small ruminant value chain consists of five core functions, namely, input supply, production management, marketing, processing, and consumption. Despite the large number of holdings that gives an impression of the stability to the small ruminant sector, the surveyed results show a clear fragility in the value chain of small ruminants in this area. The small ruminant production system is negatively impacted by climate change, especially continuous drought. In addition, the high prices of feed that the farmer cannot afford with clear and real absence of the governmental and non-governmental support activities also impact the development of the value chain. The results of strengths, weaknesses, opportunities, and threats (SWOT) analysis reveal that the major constraints faced by this value chain could be divided into external and internal threats. Specifically, the most prominent external threats are the nature of the desert land and continuous drought, while the major internal threats are the absence of appropriate infrastructure, shortage of inputs, and weakness in the production management and marketing. We proposed solutions to these challenges to ensure the sustainability and effectiveness of the sector, such as the formulation of emergency response plans to severe weather, qualifying farmers’ skills, and establishment of agricultural cooperative societies