This paper is a part of a multi-disciplinary research “Application of Decentralized On-Site Water Treatment System in Egypt for Use in Agriculture and Producing Safe Fish and Animal Proteins”.The project aimed to investigate the environmental impact of implementing sewage water before and after treatment using the effluent of the on-site decentralized Japanese' Johkasou system, in agriculture and producing fish protein. The aim is to establish such system in Egypt to strengthen the sanitary conditions of water resources. In the present study, the impact of the sewage pollution in some fish farms at El-Fayyum, Port Said and El-Dakahlia governorates in Egypt was carried out. Water and fish (Oreochromis niloticus and Mugil cephalus) samples were collected from private fish farms of such localities. Bacteriological and chemical examination of water samples revealed the existence of coliforms and many other bacterial species of significant human health hazards. The chemical parameters of water showed a marked deviation from normal levels while examination of fish flesh specimens indicated contamination with Streptococcus Sp., Staphylococcus Sp., and Salmonella in all examined localities. Other bacterial isolates of human health importance (Morganella morganii, Pseudomonas cepacia and Enterococcos durans) were identified. The parasitological examination revealed the presence of encysted metacercariae (EMC); Diplostomatidae, Prohemistomatidae and Heterphyidae. Moreover, two protozoan parasites (Mxyoboulus tilapiae and Ichthyophthirius multifilis) were also recorded. The histopathological examination revealed mild tissue reaction in case of bacterial infection and severe pathological lesions in different organs in case of EMC infection. Lamellar hyperplasia and mononuclear cell infiltration in branchial tissue was common findings. In skeletal muscles, atrophy of muscle fibres, myolysis and myophagia were detected.

In the present study, the daily dose in terms of particle surface area received by citizens living in different low- and middle-income countries, characterized by different lifestyles, habits, and climates, was evaluated. The level of exposure to submicron particles and the dose received by the populations of Accra (Ghana), Cairo (Egypt), Florianopolis (Brazil), and Nur-Sultan (Kazakhstan) were analyzed. A direct exposure assessment approach was adopted to measure the submicron particle concentration levels of volunteers at a personal scale during their daily activities. Non-smoking adult volunteers performing non-industrial jobs were considered. Exposure data were combined with time-activity pattern data (characteristic of each population) and the inhalation rates to estimate the daily dose in terms of particle surface area.The received dose of the populations under investigation varied from 450 mm² (Florianopolis, Brazil) to 1300 mm² (Cairo, Egypt). This work highlights the different contributions of the microenvironments to the daily dose with respect to high-income western populations. It was evident that the contribution of the Cooking & Eating microenvironment to the total exposure (which was previously proven to be one of the main exposure routes for western populations) was only 8%–14% for low- and middle-income populations. In contrast, significant contributions were estimated for Outdoor day and Transport microenvironments (up to 20% for Cairo, Egypt) and the Sleeping & Resting microenvironment (up to 28% for Accra, Ghana), highlighting the effects of different site-specific lifestyles (e.g. time-activity patterns), habits, socioeconomic conditions, climates, and outdoor air quality.

The severe and pervasive effects of multispecies foodborne microbial biofilms highlight the importance of rapid detection and diagnosis of contamination risk in the field using epifluorescence-based techniques (EBT) combined with automatic image-counting software. This study screened the hygiene quality of the environment, the carcass and the slaughtering equipment in the El-Kharga abattoir, New Valley Province, Egypt, to assess possible contamination during slaughter process. In addition, biofilm was assessed, and bacteria was enumerated by epifluorescence microscopy. Using both conventional and EBT, the highest bacterial counts were observed for the slaughtering equipment (6.6 and 5.2 cfu/cm2, respectively), followed by different parts of the carcass (4.1 and 4.4 cfu/cm2, respectively) and environmental samples (3.9 and 4.1 cfu/cm2, respectively). A high prevalence of E. coli O157:H7 was observed on the slaughtering equipment (25%), which also led to carcass (1%) contamination. Moreover, Enterobacteriaceae members were detected during examination, such as Klebsiella pneumoniae, Enterobacter aerogenes, and Raoultella ornithinolytica. Despite the relatively good hygiene quality of the abattoir environment, there is also a high risk associated with biofilm formation by pathogenic microorganisms on the slaughtering equipment. Moreover, EBT showed different structures of the biofilm, including those formed at different maturation stages, such as voids, microbubbles, channels and mushroom shapes. (EBT) microscopy combined with image-counting software could be a candidate substitute to estimate efficiently, precisely and rapidly the microbial aggregation and exposure risk in field than the conventional counting techniques.

Although the poultry production sector plays a key role in sustaining the majority of animal protein demand in Egypt, the deleterious effects of widespread antibiotic resistance on health and environment are currently not well recognized. Litter and dropping samples from broiler and layer poultry farms as well as, tilapia samples from the Nile River and aquaculture farms were collected from Upper Egypt. Samples were extracted and examined for tetracycline residues [tetracycline (TC), chlortetracycline (CTC), oxytetracycline (OTC) and doxycycline (DC)] using HPLC. In addition, tetracycline resistance genes [tet (M), tet (W), tet (Q) and tet (G)] were screened from pooled intestinal contents collected from twelve broiler farms in Upper Egypt. The antibiotic resistance genes results revealed that tet (W) was confirmed to be expressed in all intestinal samples. In contrast, tet (Q) and tet (M) were detected only in 42% and 17% of the samples, respectively. CTC and OTC were the antimicrobial compounds with the highest concentrations in poultry litter and droppings, with concentrations of 6.05 and 2.47 μg g−1 (CTC) and 5.9 and 1.33 μg g−1 (OTC), respectively. However, the concentrations of DC were significantly higher than those of the other compounds in both aquaculture and Nile River tilapia. The tetracycline residue levels in aquaculture tilapia were significantly higher than those in Nile River tilapia. The hazard quotients (HQs) exceeded 1 for OTC, CTC and DC, which highlights the great risk of using broiler litter to fertilize agricultural land. Moreover, the presence of DC and CTC indicates that consumption of aquaculture tilapia poses a considerable health risk. Therefore, poultry litter or droppings containing tetracycline residues and tet resistance determinants used for aquaculture or as farmland fertilizers could be major sources of antibiotic resistance in fish, humans and environment.

The Red Sea is considered one of the youngest oceanic systems, with unique physical, geochemical and biological characteristics. Tourism, industrialization, extensive fishing, oil processing and shipping are extensive sources of pollution in the Red Sea. We analyzed the geochemical characteristics and microbial community of sediments along the Egyptian coast of the Red Sea. Our sites mainly included 1) four ports used for shipping aluminum, ilmenite and phosphate; 2) a site previously reported to have suffered extensive oil spills; and 3) a site impacted by tourism. Two major datasets for the sediment of ten Red Sea coastal sites were generated; i) a chemical dataset included measurements of carbon, hydrogen, nitrogen and sulfur, metals and selected semi-volatile oil; and ii) a 16S rRNA Pyrotags bacterial metagenomic dataset. Based on the taxonomic assignments of the 16S rRNA Pyrotags to major bacterial groups, we report 30 taxa constituting an Egyptian Red Sea Coastal Microbiome. Bacteria that degrade hydrocarbons were predominant in the majority of the sites, particularly in two ports where they reached up to 76% of the total identified genera. In contrast, sulfate-reducing and sulfate-oxidizing bacteria dominated two lakes at the expense of other hydrocarbon metabolizers. Despite the reported “Egyptian Red Sea Coastal Microbiome,” sites with similar anthropogenic pollutants showed unique microbial community abundances. This suggests that the abundance of a specific bacterial community is an evolutionary mechanism induced in response to selected anthropogenic pollutants.

Lake Idku, northern Egypt, receives large quantities of drainage water from four main discharging drains. Ecological and biological status of Lake Idku has been monitored during (autumn 2012 to summer 2013) to examine the lake water quality and eutrophication level in response to the quality as well as the source of the discharging water. Discrete water samples were collected from the lake body and the drains. Chemical analyses revealed an excessive nutrient load goes into the lake. A range of 1.4–10.6 mg nitrites/L was determined for drain waters, however a sudden increase was observed in lake and drain water samples of up to 84 and 74.5 mg/L, respectively. Reactive silicate ranged between 2.9 and 4.8 mg/L; while inorganic phosphate fluctuated between 0.2 and 0.43 mg/L. Transparency varied from 45 cm to 134 cm with better light conditions at drain sites. Biological results indicated a hyper-eutrophic status for the lake with a range of chlorophyll-a varied from a minimum of 39.9 μg/L (at Idku Drains) and a maximum of 104.2 μg/L (at El-Khairy drain). Phytoplankton community structure revealed higher abundance at lake sites compared with the drains. Maximum phytoplankton density was detected during summer with the dominance of Bacilariophyceae (e.g. Cyclotella meneghiniana, Cyclotella comate, Melosira varians) followed by Chlorophycean taxon (e.g. Scenedesmus dimorphus, S. bijuga and Crucigenia tetrapedia). Five indices were applied to evaluate the water quality of the lake. Diversity Index (DI) indicated slight to light pollution along all sites; while Sapropic Index (SI) indicated slight pollution with acceptable oxygen conditions and an availability of sensitive species. Palmer Index (PI) gave a strong evidence of high organic pollution at some sites in the lake, while Generic Diatom Index (GDI) revealed that levels of pollution varied from average to strong. Trophic Index (TI), suggest that there are an obvious signs of eutrophication in the lake.

Egypt is a major agricultural country in Africa with a known past of organochlorine pesticides (OCPs) application, yet data on atmospheric levels of OCPs in Egypt is sparse. Low density polyethylene (LDPE) passive samplers were therefore deployed for 3 weeks each at 11 locations in July, 2010 and January, 2011 in Alexandria to screen for gas-phase OCPs. Performance reference compounds were used to investigate the uptake kinetics. Field-derived sampler-air partitioning coefficients (KPE-As) for OCPs were significantly correlated against the compounds' subcooled liquid vapor pressure (log PL): [log KPE-A = −0.77 ± 0.07*log PL + 6.35 ± 0.13 (R2 = 0.90; n = 17; SE = 0.19; p < 0.001)]. Estimated and measured OCP concentrations in Alexandria agreed well (factor difference ≤ 2) indicating the feasibility of monitoring OCPs using LDPEs. OCP concentrations ranged from <LOD to 168 pg/m3. Calculated isomeric ratios indicated recent usage of chlordanes and endosulfans.

The textile mill industry is one of the major sources of pollution and contributors of metal contaminants to the environment. At the same time, the industry is important for global economy. Pollution caused by the textile industry is characteristic due to a unique set of potentially toxic substances. Darkling beetles (Coleoptera, Tenebrionidae), which live in all biogeographical regions, are especially common in soil quality and soil degradation studies. Our study was designed to assess long-term effects of textile industry (which generates specific pollution) on soil organisms, namely Trachyderma hispida. We especially wanted to find out what changes allow the species to survive and adapt to these specific conditions. Energy-dispersive X-ray spectroscopy of soil and midgut tissues of T. hispida sampled from a polluted site in the Edku textile industrial area in Egypt revealed a high accumulation of chemical elements, compared to a reference site. The concentration of elements in soil was well correlated with their concentration in the midgut of insects. Activity of superoxide dismutase, catalase, ascorbate peroxidase and glutathione S-transferase were negatively correlated with concentration of elements in soil and in the midgut. Meanwhile, malondialdehyde concentration in the midgut revealed an opposite tendency. DNA damage and expression of stress proteins, (HSP70 and metallothionein - MT) were elevated in insects from the polluted site. The activity of textile industry in the area of Edku undoubtedly causes an increase of soil pollution and, in consequence, causes a number of changes in the bodies of organisms living in these areas, including T. hispidus. Therefore, it is necessary to find a solution which limits the emission of waste from the textile industry, as well as to design modern strategies of processing, storing and utilizing it.

The aim of this study was to assess the soil contamination caused by potentially toxic elements (Al, As, Co, Cr, Cu, Fe, Mn, Mo, Ni, Se, V, and Zn) using various indices and the associated risk of human health for adults and children in selected soils from Germany (Calcic Luvisols, Tidalic Fluvisols, Haplic Gleysols, and Eutric Fluvisols) and Egypt (Haplic Calcisols, Sodic Fluvisols, and Eutric Fluvisols). Soil contamination degree has been assessed using indices such as contamination factor (CF), pollution load index (PLI), geo-accumulation index (Igₑₒ), and enrichment factor. We also assessed the health risk for children and for male and female adults. Chromium, Cu, As, Mo, Ni, Se, and Zn in the German Fluvisols had high CF of >6, while in the Egyptian Fluvisols Se, Mo, As, and Al revealed a high CF. The PLI (1.1–5.2) was higher than unity in most soils (except for Tidalic Fluvisols), while the most important contributor was Se, followed by Mo and As in the Egyptian Fluvisols, and by Cr, Cu, and Zn in the German Fluvisols. The median value of hazard index (HI) for children in the studied soils indicated an elevated health risk (higher than one), especially in the German Fluvisols (HI = 4.0–29.0) and in the Egyptian Fluvisols (HI = 2.2–5.2). For adults, median HIs in all soils were lower than unity for both males and females. The key contributor to HI was As in the whole soil profiles, accounting for about 59% of the total HIs in all three person groupings. Our findings show that in the studied multi-element contaminated soils the risk for children’s health is higher than for adults; while mainly As (and Al, Cr, Cu, and Fe) contributed significantly to soil-derived health risk.

Environmental reservoirs of antibiotic resistance (AR) are a growing concern that are gathering more attention as potential sources for human infection. Carbapenem-resistant Enterobacteriaceae (CRE) are extremely dangerous, as carbapenems are often drugs of last resort that are used to treat multi-drug resistant infections. Among the genes capable of conferring carbapenem resistance to bacteria, the most transferrable are those that produce carbapenemase, an enzyme that hydrolyzes carbapenems and other β-lactam antibiotics. The goal of this review was to comprehensively identify global environmental reservoirs of carbapenemase-producing genes, as well as identify potential routes of transmission to humans. The genes of interest were Klebsiella pneumoniae carbapenemase (KPC), New Delhi Metallo-β-lactamase (NDM), Oxacillinase-48-type carbapenemases (OXA-48), and Verona Integron-Mediated Metallo-β-lactamase (VIM). Carbapenemase genes have been reported in the environment on almost every continent. Hospital and municipal wastewater, drinking water, natural waterways, sediments, recreational waters, companion animals, wildlife, agricultural environments, food animals, and retail food products were identified as current reservoirs of carbapenemase-producing bacteria and genes. Humans have been recorded as carrying CRE, without recent admittance to a hospital or long-term care facility in France, Egypt, and China. CRE infections from the environment have been reported in patients in Montpellier, France and Cairo, Egypt. This review demonstrates the need for 1) comprehensive monitoring of AR not only in waterways, but also other types of environmental matrices, such as aerosol, dusts, periphyton, and surfaces in indoor environments; and 2) action to reduce the prevalence and mitigate the effects of these potentially deadly resistance genes. In order to develop an accurate quantitative model for environmental dimensions of AR, longitudinal sampling and quantification of AR genes and bacteria are needed, using a One Health approach.