Digital Repository for Department of Microbiology & Parasitology

Foot-and-mouth disease (FMD) is a highly contagious disease of livestock affecting animal production and trade throughout Asia and Africa. Understanding FMD virus (FMDV) global movements and evolution can help to reconstruct the disease spread between endemic regions and predict the risks of incursion into FMD-free countries. Global expansion of a single FMDV lineage is rare but can result in severe economic consequences. Using extensive sequence data we have reconstructed the global space-time transmission history of the O/ME-SA/Ind-2001 lineage (which normally circulates in the Indian sub-continent) providing evidence of at least 15 independent escapes during 2013–2017 that have led to outbreaks in North Africa, the Middle East, Southeast Asia, the Far East and the FMD-free islands of Mauritius. We demonstrated that sequence heterogeneity of this emerging FMDV lineage is accommodated within two co-evolving divergent sublineages and that recombination by exchange of capsid-coding sequences can impact upon the reconstructed evolutionary histories. Thus, we recommend that only sequences encoding the outer capsid proteins should be used for broad-scale phylogeographical reconstruction. These data emphasise the importance of the Indian subcontinent as a source of FMDV that can spread across large distances and illustrates the impact of FMDV genome recombination on FMDV molecular epidemiology.
Ibrahim Eldaghayes(10-2018)

The epidemiological patterns of Bluetongue (BT) in North Africa and Mediterranean Basin (MB) dramatically changed by emergence of subsequent episodes of novel bluetongue virus (BTV) serotypes with highly pathogenic indexes and socio-economic impacts. The objective of the study was to investigate the sero-prevalence and serotype distribution of BTV in Libya. During 2015-2016, a total of 826 serum samples were collected from domestic ruminants in Libya. All sera were assayed by competitive enzyme-linked immunosorbent assays (c-ELISA). C-Elisa-positive samples (43.3%; 173/400) were further analyzed by virus neutralization assay to identify BTV serotypes and determine the antibody titre of positive samples. An overall BTV sero-prevalence was 48.4% (95% CI: 45.0%-51.8%). Neutralizing antibodies were detected against the following BTV serotypes namely: BTV-1, BTV-2, BTV-3, BTV-4, BTV-9 and BTV-26. While BTV-1, BTV-2, BTV-4 and BTV-9 circulation was unsurprising as they have been responsible of the last year outbreaks in Northern African Countries, the detection of BTV-3 and BTV-26 was definitely new and concerning for the animal health of the countries facing the Mediterranean Basin. It is crucial that European and Northern African authorities collaborate in organizing common surveillance programmes to early detect novel strains or emerging serotypes in order to set up proper preventive measures, and, in case, develop specific vaccines and plan coordinated vaccination campaigns.
Ibrahim Eldaghayes(11-2018)

Aim: The aim of the current investigation was to screen the presence of Staphylococci spp., especially S. aureus in meat, meat products of different animal species, and some seafood sold in some retail markets in Libya using cultural and molecular techniques, and to study their antibiotics resistance profiles. Materials and Methods: A total of 139 samples from red meat, meat products, and seafood were collected from many areas in Libya. Enumeration and isolation of Staphylococci spp. and S. aureus by normal cultural methods followed by molecular identification using molecular techniques by bacterial DNA extraction and partial sequencing of 16S rDNA. Results: Out of 139 samples, 112 (80.6%) were contaminated with different species of Staphylococci based on cultural characteristics of Staphylococci on Baird-Parker medium, for which S. aureus was detected in only 32 samples (23%). However, only six out of 18 (33.3%) isolates sent for sequencing were confirmed to be S. aureus using the molecular technique. The six identified isolates of S. aureus were tested for antimicrobial resistance against 24 most commonly used antibiotics. All isolates were resistant to only two antibiotics (cefotaxime and clindamycin). Among these six isolates, only one confirmed to be methicillin-resistant Staphylococcus aureus. Conclusion: Results of this study suggest that food of animal origin could be a source of S. aureus with antimicrobial resistance characteristics that can be spread through the food chain, and raise the importance of these results for public health.
Ibrahim Eldaghayes(6-2019)

North Africa has a great diversity of indigenous sheep breeds whose origin is linked to its environmental characteristics and to certain historical events that took place in the region. To date, few genome-wide studies have been conducted to investigate the population structure of North African indigenous sheep. The objective of the present study was to provide a detailed assessment of the genetic structure and admixture patterns of six Maghreb sheep populations using the Illumina 50K Ovine BeadChip and comparisons with 22 global populations of sheep and mouflon. Regardless of the method of analysis used, patterns of multiple hybridization events were observed within all North African populations, leading to a heterogeneous genetic architecture that varies according to the breed. The Barbarine population showed the lowest genetic heterogeneity and major southwest Asian ancestry, providing additional support to the Asian origin of the North African fat-tailed sheep. All other breeds presented substantial Merino introgression ranging from 15% for D'man to 31% for Black Thibar. We highlighted several signals of ancestral introgression between North African and southern European sheep. In addition, we identified two opposite gradients of ancestry, southwest Asian and central European, occurring between North Africa and central Europe. Our results provide further evidence of the weak global population structure of sheep resulting from high levels of gene flow among breeds occurring worldwide. At the regional level, signs of recent admixture among North African populations, resulting in a change of the original genomic architecture of minority breeds, were also detected.
Ibrahim Eldaghayes(8-2019)

This study was focused mainly on the third of these components to measure the level of NSP antibodies as indicator of past or current FMDV infection, irrespective of the vaccination status. Foot-and-mouth disease (FMD) outbreaks have been sporadic in Libya for nearly fifty years. A countrywide serosurvey was conducted in the spring of 2013 to assess the extent of FMD virus circulation and identify FMD virus serotypes in the country. A total of 4221 sera were collected, comprising samples from large ruminants (LR; n=1428 samples from 357 farms) and small ruminants (SR; n=2793 samples from 141 farms). FMD sero-prevalence of NSP antibodies determined by ELISA were 19.0% (271/1428) with 95% CI (16.9 - 21.0) and 13.5% (378/2793) with 95% CI (12.3 - 14.8) for LR and SR samples, respectively. The sero-prevalence of NSP antibodies in LR was 12.3% and 19.8% for age group < year and 1 year, respectively (X2=4.95,P=0.026), while in SR was 3.7%, 13.6% and 21.3% for age group 2 year, respectively (X2=118.1,P=0.000). These observed NSP serologic profiles support the hypothesis of an endemic level of FMD circulation in Libya. All positive sera were tested for SP antibodies for O, A and SAT-2 FMD virus serotypes. Serotype O was the dominant circulating serotype followed by serotype A, while evidence of SAT-2 was not found. These data provide an insight into the wider epidemiology of FMD in Libya, and contribute to field and laboratory investigations that during 2013 serotype 0 (O/ME-SA/Ind-2001 lineage) was isolated from clinical samples collected from the country. To have a better understanding of livestock production, data collecting on the management system, and risk factor analysis, more study should be done. As a result of the findings, scientists can better understand the epidemiology of FMD and design scientifically sound disease control techniques to reduce the impact of FMD on Libyan livestock.
Ibrahim Eldaghayes(4-2022)

Background: Whole muscle meat, meat products, and seafood contain different nutrients in adequate quantity providing a better environment for presence and replication of different microorganisms. There are underreported and inaccurate estimations of foodborne diseases due to the lack of effective surveillance systems in Libya. Aim: To determine the extent of microbiological contamination of whole muscle meat, meat products, and seafood. Methods: A total number of 731 samples of retail meat were collected from different stores in four cities in Libya. Samples were analyzed for aerobic plate count and subjected to microbiological enumeration and isolation techniques, followed by molecular identification by PCR and partial sequencing of 16S rDNA. Results: The results showed contamination of samples with enteric and spoilage bacteria. Fifteen genera of spoilage bacteria yielded 149 isolates which were detected and identified by PCR and partial sequencing of 16S rDNA as: Proteus spp., Provedencia spp., Raouttella ornithinolytical, Citrobacter spp., Enterobacter spp., Morganella morgi, Shewanella algea, Rhodobacter capsulatus, Listonella pelagia, Kluyvera spp., Pectobacterium spp., Brenneria spp., Klebsiella spp., Acintobacter radioresistens, and Pantoea spp. While for pathogenic bacteria, 143 isolates distributed among nine genera were identified by PCR and partial sequencing of 16S rDNA as: Bacillus spp., Escherichia spp., Shigella spp., Enterococci spp., Cronobacter spp., Staphylococci spp., Salmonella spp., Aeromonas spp., and Vibrio spp.. Many isolated bacteria are zoonotic bacteria with high importance for public health. Conclusion: Excessive handling and processing of meat and meat products seems to be one of the poorest microbiological qualities. These findings ought to be helpful in risk assessments and quality assurance of meat in order to improve food safety.
Ibrahim Eldagahyes(9-2020)

Coronavirus disease 2019 (COVID-19) is a pandemic that affected almost all countries worldwide with more than 29,439,120 confirmed cases and 932,486 deaths recorded till on September 14, 2020. However, on May 25, 2020, after 2 months from the first reported case of COVID-19 in Libya, the country was among very few countries in the world that had very few cases of COVID-19 with a total of 75 confirmed cases and three deaths during the first 2 months since the detection of the first case on March 24, 2020. Based on the global epidemiological pattern of the disease, the magnitude of COVID-19 in Libya could have been much worse. However, the reality is eccentrically different and the epidemiology exhibited different scenario with very few cases being recorded during the first 2 months of pandemic in Libya. In this article, a review of COVID-19 situation in Libya is presented with thoughts about the potential reasons that could explain the very few cases of COVID-19 in the country in context with the global figures of the pandemic.
Ibrahim Eldaghayes(11-2020)

Abstract Background: Although bone tumors are common pathologies in companion animals, limited reports describe nasal osteosarcoma (OSA) in cats. Case description: A case of nasal OSA in a local Libyan cat was admitted to the Veterinary Teaching Hospital at the Faculty of Veterinary Medicine, University of Tripoli–Libya, with nasal swelling and discharges and facial deformity. The radiological findings revealed nasal osteolysis with the absence of evidence of lung metastasis. In addition, fungal growth was not identified in microbiological culture. Furthermore, the pathological examination has grossly revealed a destructed nasal bone due to the presence of a tumor mass, with a mucohemorrhagic nasal discharge and absence of metastasis. OSA was confirmed histopathologically. Conclusion: This report presents the clinical, radiological, and pathological findings of a primary nasal OSA in a Libyan cat with no tumor metastasis to other body organs. Keywords: Cat, Nasal cavity, Primary osteosarcoma.
Mohamed Hamrouni S. Abushhiwa, Seham AL-Abed Hassan AL-Azreg, ٍٍSamer Khalifa Khalil Tmumen, Abdulrhman Mohamed Salah Alrtib, Abdulkareem Khalifa Ali Elbaz, Mahir A. Kubba, Al-Asayed R. Al-Attar, Emad M R Bennour(1-2019)