Digital Repository for Department of Microbiology & Parasitology

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global health threat. This virus is the causative agent for coronavirus disease 2019 (COVID-19). Pandemic prevention is best addressed through an integrated One Health (OH) approach. Understanding zoonotic pathogen fatality and spillover from wildlife to humans are effective for controlling and preventing zoonotic outbreaks. The OH concept depends on the interface of humans, animals, and their environment. Collaboration among veterinary medicine, public health workers and clinicians, and veterinary public health is necessary for rapid response to emerging zoonotic pathogens. SARS-CoV-2 affects aquatic environments, primarily through untreated sewage. Patients with COVID-19 discharge the virus in urine and feces into residential wastewater. Thus, marine organisms may be infected with SARS-CoV-2 by the subsequent discharge of partially treated or untreated wastewater to marine waters. Viral loads can be monitored in sewage and surface waters. Furthermore, shellfish are vulnerable to SARS-CoV-2 infection. Filter-feeding organisms might be monitored to protect consumers. Finally, the stability of SARS-CoV-2 to various environmental factors aids in viral studies. This article highlights the presence and survival of SARS-CoV-2 in the marine environment and its potential to enter marine ecosystems through wastewater. Furthermore, the OH approach is discussed for improving readiness for successive outbreaks. This review analyzes information from public health and epidemiological monitoring tools to control COVID-19 transmission.
Ibrahim Eldaghayes(6-2022)

There were only 75 confirmed cases of coronavirus disease 2019 (COVID-19) reported in Libya by the National Center for Disease Control during the first two months following the first confirmed case on 24 March 2020. However, there was dramatic increase in positive cases from June to now; as of 19 November 2020, approximately 357940 samples have been tested by reverse transcription polymerase chain reaction, and the results have revealed a total number of 76808 confirmed cases, 47587 recovered cases and 1068 deaths. The case fatality ratio was estimated to be 1.40%, and the mortality rate was estimated to be 15.90 in 100000 people. The epidemiological situation markedly changed from mid-July to the beginning of August, and the country proceeded to the cluster phase. COVID-19 has spread in almost all Libyan cities, and this reflects the high transmission rate of the virus at the regional level with the highest positivity rates, at an average of 14.54%. Apparently, there is an underestimation of the actual number of COVID-19 cases due to the low testing capacity. Consequently, the Libyan health authority needs to initiate a large-scale case-screening process and enforce testing capacities and contact testing within the time frame, which is not an easy task. Advisably, the Libyan health authority should improve the public health capacities and conduct strict hygienic measures among the societies and vaccinate as many people against COVID-19 to minimize both the case fatality ratio and socio-economic impacts of the pandemic in Libya.
Ibrahim Eldaghayes(7-2021)

Foot-and-mouth disease (FMD) affects the livestock industry and socioeconomic sustainability of many African countries. The success of FMD control programs in Africa depends largely on understanding the dynamics of FMD virus (FMDV) spread. In light of the recent outbreaks of FMD that affected the North-Western African countries in 2018 and 2019, we investigated the evolutionary phylodynamics of the causative serotype O viral strains all belonging to the East-Africa 3 topotype (O/EA-3). We analyzed a total of 489 sequences encoding the FMDV VP1 genome region generated from samples collected from 25 African and Western Asian countries between 1974 and 2019. Using Bayesian evolutionary models on genomic and epidemiological data, we inferred the routes of introduction and migration of the FMDV O/EA-3 topotype at the inter-regional scale. We inferred a mean substitution rate of 6.64 × 10−3 nt/site/year and we predicted that the most recent common ancestor for our panel of samples circulated between February 1967 and November 1973 in Yemen, likely reflecting the epidemiological situation in under sampled cattle-exporting East African countries. Our study also reinforces the role previously described of Sudan and South Sudan as a frequent source of FMDVs spread. In particular, we identified two transboundary routes of O/EA-3 diffusion: the first from Sudan to North-East Africa, and from the latter into Israel and Palestine AT; a second from Sudan to Nigeria, Cameroon, and from there to further into West and North-West Africa. This study highlights the necessity to reinforce surveillance at an inter-regional scale in Africa and Western Asia, in particular along the identified migration routes for the implementation of efficient control measures in the fight against FMD.
Ibrahim Eldaghayes(4-2022)

Background and Aim: Foodborne illnesses are a serious challenge to human health and the economic sector. For example, salmonellosis remains a burden in developed and developing nations. Rapid and reliable molecular methods to identify Salmonella strains are essential for minimizing human infection. This study aimed to identify Salmonella spp. in raw milk and dairy products using conventional and molecular techniques and to test the antibiotic susceptibility of the isolated strains. Materials and Methods: One hundred and thirty-one milk and dairy product samples were randomly collected from different localities in Libya. Samples were examined for the presence of Salmonella by conventional culture techniques, including cultivation in Rappaport-Vassiliadis broth and streaking on xylose lysine deoxycholate agar. Identification also used polymerase chain reaction and partial sequencing of 16S rDNA. Twenty-four antibiotics were used for the examination of antimicrobial resistance of Salmonella spp. isolates with the agar disk diffusion method (Kirby–Bauer technique). Multi-antibiotic resistance index and antibiotic resistance index (ARI)for Salmonella enterica isolates were calculated. Results: Twenty-one of 131 samples (16%) were positive for Salmonella spp. recovered from 9 (16%), 2 (11%), 4 (22.2%), and 6 (46%) samples of raw cow milk, fermented raw milk, and fresh locally made soft cheeses, Maasora and Ricotta), respectively. Samples of ice cream, milk powder, and infant formula showed no Salmonella spp. contamination. Only 9 of 21 (42.8%) isolates were confirmed as S. enterica by partial sequence 16S rDNA analysis. All isolates were resistant to amoxycillin, bacitracin, penicillin G, lincomycin, vancomycin, clindamycin, and cloxacillin with an ARI of 0.042. In contrast, all tested strains were sensitive to levofloxacin, doxycycline, and ciprofloxacin. In addition, all of the tested isolates (100%) were resistant to more than one antibiotic. Conclusion: This study demonstrated the applicability of molecular techniques, compared with conventional methods, as preferable for the identification of Salmonella in milk and dairy products and thus reduction of milk-borne transmission to the consumers. From the view of public health, isolation and identification of Salmonella multidrug-resistant strains from raw cow's milk and locally prepared dairy products sold in the Libyan markets indicate the need to improve the handling and processing of milk and dairy products to minimize the prevalence of Salmonella, one of the most important foodborne microorganisms that cause food poisoning.
Ibrahim Eldaghayes(5-2022)

Live vaccines against fowlpox virus, which causes moderate pathology in poultry and is the type species of the Avipoxvirus genus, were developed in the 1920s. Development of recombinant fowlpox virus vector vaccines began in the 1980s, for use not only in poultry, but also in mammals including humans. In common with other avipoxviruses, such as canarypox virus, fowlpox virus enters mammalian cells and expresses proteins, but replicates abortively. The use of fowlpox virus as a safe vehicle for expression of foreign antigens and host immunomodulators, is being evaluated in numerous clinical trials of vaccines against cancer, malaria, tuberculosis and AIDS, notably in heterologous prime–boost regimens. In this article, technical approaches to, and issues surrounding, the use of fowlpox virus as a recombinant vaccine vector in poultry and mammals are reviewed.
Ibrahim Eldaghayes(1-2014)

Paratuberculosis (Johne's disease) was suspected in a herd of approximately 033 sheep after weight loss and scouring had increased in adult animals despite repeated treatment with anthelmintics, antibiotics, multivitamins and minerals. The herd is located near Tarhouna city. Herd history revealed that a total of 60 ewes showed clinical symptoms and deaths during the last two years. The last case that we attended was submitted to the National Center of Animal Health (NCAH) for a detailed laboratory examination. Gross pathological and histological examination of tissue samples revealed results that were highly comparable with Johne's disease. A definitive diagnosis was made only by histopathological identification of Mycobacterium paratuberculosis in the intestines using Ziehl-Neelsen stain. This is the first documented case of M. paratuberculosis in sheep in Libya.
Ibrahim Eldaghayes(11-2013)

Foot-and-mouth disease viruses are often restricted to specific geographical regions and spread to new areas may lead to significant epidemics. Phylogenetic analysis of sequences of the VP1 genome region of recent outbreak viruses from Libya and Saudi Arabia has revealed a lineage, O-Ind-2001, normally found in the Indian subcontinent. This paper describes the characterization of field viruses collected from these cases and provides information about a new real-time RT-PCR assay that can be used to detect viruses from this lineage and discriminate them from other endemic FMD viruses that are co-circulating in North Africa and western Eurasia.
Ibrahim Eldaghayes(12-2014)

This report describes an avian mycobacteriosis in pigeon. An adult female pigeon (two years old) was brought for post-mortem examination on the same day of expiry. Granulomatous nodular lesions of various sizes with yellow to grey colours were found in the internal organs. Tuberculous lesions were observed in the spleen and intestine. Mycobacterial infection was confirmed by post-mortem examination and by detection of acid-fast bacilli in these granulomatous nodular lesions. This is the first report of avian tuberculosis in pigeons in Libya.
Ibrahim Eldaghayes(12-2012)