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Background Avian-pathogenic Escherichia coli (APEC) are pathogenic strains of E. coli that are responsible for one of the most predominant bacterial disease affecting poultry worldwide called avian colibacillosis. This study describes the genetic determinants implicated in antimicrobial resistance among APEC isolated from different broiler farms in Egypt. Methods A total of 116 APEC were investigated by serotyping, antimicrobial resistance patterns to 10 antimicrobials, and the genetic mechanisms underlying the antimicrobial-resistant phenotypes. Results Antibiogram results showed that the highest resistance was observed for ampicillin, tetracycline, nalidixic acid, and chloramphenicol. The detected carriage rate of integron was 29.3% (34/116). Further characterization of gene cassettes revealed the presence gene cassettes encoding resistance to trimethoprim ( dfrA1 , dfrA5 , dfrA7 , dfrA12 ), streptomycin/spectinomycin ( aadA1 , aadA2 , aadA5, aadA23 ), and streptothricin ( sat2 ). To our knowledge, this the first description of the presence of aadA23 in APEC isolates. Analysis of other antimicrobial resistance types not associated with integrons revealed the predominance of resistance genes encoding resistance to tetracycline ( tetA and tetB ), ampicillin ( bla TEM ), chloramphenicol ( cat1 ), kanamycin ( aphA1 ), and sulphonamide ( sul1 and sul2 ). Among ciprofloxacin-resistant isolates, the S83L mutation was the most frequently substitution observed in the quinolone resistance-determining region of gyrA (56.3%). The bla TEM and bla CTX−M−1 genes were the most prevalent among APEC isolates producing extended-spectrum beta-lactamase (ESβL). Conclusions These findings provided important clues about the role of integron-mediated resistance genes together with other independent resistance genes and chromosomal mutations in shaping the epidemiology of antimicrobial resistance in E. coli isolates from poultry farms in Egypt.

Background The transmission of Cryptosporidium spp. and Giardia duodenalis into humans varies according to species/genotypes of the pathogens. Although infections with both parasites are recorded in Egypt, few data are available on the distribution of Cryptosporidium species and G. duodenalis genotypes. The present study assessed the occurrence and genetic diversity of Cryptosporidium spp. and G. duodenalis in Egyptian children. Methods In the present study, 585 fecal specimens were collected from children eight years old and younger in three provinces (El-Dakahlia, El-Gharbia and Damietta) during March 2015 to April 2016. PCR-RFLP analysis of the small subunit rRNA gene and sequence analysis of the 60 kDa glycoprotein gene were used to detect and subtype Cryptosporidium spp., respectively, whereas PCR and sequence analyses of the triose phosphate isomerase, glutamate dehydrogenase and β-giardin genes were used to detect and genotype Giardia duodenalis . Results The overall infection rates of Cryptosporidium spp. and G. duodenalis were 1.4% and 11.3%, respectively. The Cryptosporidium species identified included C. hominis and C. parvum , each with three subtype families. The C. hominis subtypes were IbA6G3 ( n = 2), IdA17 ( n = 1), IdA24 ( n = 1) and IfA14G1R5 ( n = 1), while C. parvum subtypes were IIdA20G1 ( n = 1), IIaA15G2R1 ( n = 1), and IIcA5G3a ( n = 1). The G. duodenalis identified included both assemblages A ( n = 31) and B ( n = 34). All G. duodenalis assemblage A belonged to the anthroponotic sub-assemblage AII, while a high genetic heterogeneity was seen within assemblage B. Conclusions Data from this study are useful in our understanding of the genetic diversity of Cryptosporidium spp. and G. duodenalis in Egypt and the potential importance of anthroponotic transmission in the epidemiology of both pathogens.

Blastocystis sp. is a widespread enteric protozoan that frequently infects human and animal groups. Despite its burden and zoonotic potential worldwide, epidemiological investigations remain limited in animal groups that come in contact with humans. Therefore, the largest survey ever conducted in North Africa was performed in Egypt with the aim to investigate the prevalence and subtype (ST) distribution of Blastocystis sp. in animals. For this purpose, a total of 889 fecal specimens were collected from chickens (217), cattle (373), dogs (144) and cats (155) from six governorates of northern Egypt. These specimens were then screened for the presence of Blastocystis sp. using a quantitative real-time PCR, followed by subtyping the isolates. The overall prevalence of Blastocystis sp. reached 9.2% (82/889), with the highest infection rates reported in chickens (17.0%) and domestic cattle (11.0%), highlighting an active circulation of the parasite in both animal groups. In contrast, the low prevalence in cats (2.6%) and the absence of the parasite in dogs suggested that pets are not natural hosts of Blastocystis sp. ST10 and ST14 were largely predominant in cattle, confirming that both STs represented cattle-adapted STs. The report of one ST3 and one ST4 isolate in this animal group could be explained by an accidental zoonosis from humans to animals. All but one of the subtyped isolates in poultry belonged to ST7, which was considered as an avian ST. The presence of a remaining isolate of ST14 likely reflected a transient infection from contact between birds and cattle feces. The same environmental contamination was also likely the source of the ST14 infection in three of the four positive cats, with the remaining animals infected by ST3 as the result of human-to-animal transmission. These occurrences and subtyping data, combined with those previously collected in the Egyptian population, implies that poultry could play a significant role as reservoir for zoonotic transmission, which would not be the case for cattle and pets.

Rabbits are increasingly farmed in Egypt for meat. They are, however, known reservoirs of infectious pathogens. Currently, no information is available on the genetic characteristics of Cryptosporidium spp. in rabbits in Egypt. To understand the prevalence and genetic identity of Cryptosporidium spp. in these animals, 235 fecal samples were collected from rabbits of different ages on nine farms in El-Dakahlia, El-Gharbia, and Damietta Provinces, Egypt during the period from July 2015 to April 2016. PCR-RFLP analysis of the small subunit rRNA gene was used to detect and genotype Cryptosporidium spp. The overall detection rate was 11.9% (28/235). All 28 samples were identified as Cryptosporidium cuniculus. The 16 samples successfully subtyped by the sequence analysis of the partial 60 kDa glycoprotein gene belonged to two subtypes, VbA19 (n = 1) and VbA33 (n = 15). As C. cuniculus is increasingly recognized as a cause of human cryptosporidiosis, Cryptosporidium spp. in rabbits from Egypt have zoonotic potential.

Blastocystis sp. is currently reported as the most frequent single-celled eukaryote inhabiting the intestinal tract of humans and a wide range of animal groups. Its prevalence is especially higher in developing countries linked with fecal peril. Despite a growing interest in this enteric protozoan, certain geographical regions potentially at high risk of infection, such as North Africa, remain under-investigated. Therefore, a large-scale molecular epidemiological survey, including 825 participants presenting digestive disorders or not, was conducted in five governorates located in Northern Egypt. A real-time polymerase chain reaction (qPCR) assay was performed to identify the parasite in stool samples, followed by direct sequencing of the positive PCR products for subtyping and genotyping of the corresponding isolates. The overall prevalence was shown to reach 72.4% in the Egyptian cohort, coupled with a variable frequency depending on the governorate (41.3 to 100%). Among the 597 positive participants, a large proportion of them (39.4%) presented mixed infections, as determined by sequencing. The remaining individuals with single infection were predominantly colonized by subtype 3 (ST3) (48.3%) followed by ST1 (39.5%), ST2 (10.8%), ST14 (1.1%), and ST10 (0.3%). This was the first report of ST10 and ST14 in North Africa. Age, sex, digestive symptoms, and health status of the participants or contact with animals were not identified as significant risk factors for Blastocystis sp. occurrence or affecting the ST distribution. In contrast, substantial variations in the prevalence and ST distribution of the parasite were reported according to the governorate. Genotyping of isolates revealed the lower intra-ST diversity for ST3, followed by ST1 and then ST2. By combining subtyping and genotyping data, a widespread inter-human transmission was strongly suggested for ST3 within the Egyptian cohort. Regarding ST1 and ST2, additional animal or environmental sources of infection by these STs have been proposed, whereas the few cases of colonization by ST10 and ST14 were likely the result of zoonotic transmission from bovid. These investigations clearly emphasized the active circulation of Blastocystis sp. in Northern Egypt and the necessity for health authorities to implement prevention campaigns towards the population and quality control of drinking water, with the aim of reducing the burden of this enteric protozoan in this endemic country.

Given the proven zoonotic potential of the intestinal protozoan Blastocystis sp., a fast-growing number of surveys are being conducted to identify potential animal reservoirs for transmission of the parasite. Nevertheless, few epidemiological studies have been conducted on farmed animals in Egypt. Therefore, a total of 1089 fecal samples were collected from herbivores (sheep, goats, camels, horses, and rabbits) in six Egyptian governorates (Dakahlia, Gharbia, Kafr El Sheikh, Giza, Aswan, and Sharqia). Samples were screened for the presence of Blastocystis sp. by real-time PCR followed by sequencing of positive PCR products and phylogenetic analysis for subtyping of the isolates. Overall, Blastocystis sp. was identified in 37.6% of the samples, with significant differences in frequency between animal groups (sheep, 65.5%; camels, 62.2%; goats, 36.0%; rabbits, 10.1%; horses, 3.3%). Mixed infections were reported in 35.7% of the Blastocystis sp.-positive samples. A wide range of subtypes (STs) with varying frequency were identified from single infections in ruminants including sheep (ST1–ST3, ST5, ST10, ST14, ST21, ST24, ST26, and ST40), goats (ST1, ST3, ST5, ST10, ST26, ST40, ST43, and ST44), and camels (ST3, ST10, ST21, ST24–ST26, ST30, and ST44). Most of them overlapped across these animal groups, highlighting their adaptation to ruminant hosts. In other herbivores, only three and two STs were evidenced in rabbits (ST1–ST3) and horses (ST3 and ST44), respectively. The greater occurrence and wider genetic diversity of parasite isolates among ruminants, in contrast to other herbivores, strongly suggested that dietary habits likely played a significant role in influencing both the colonization rates of Blastocystis sp. and ST preference. Of all the isolates subtyped herein, 66.3% were reported as potentially zoonotic, emphasizing the significant role these animal groups may play in transmitting the parasite to humans. These findings also expand our knowledge on the prevalence, genetic diversity, host specificity, and zoonotic potential of Blastocystis sp. in herbivores.

Aim This study evaluated the effect of co-administration of vitamin C and Arabic gum (AG) supplements on the response of vaccinated (VAC) and challenged laying Japanese quails with avian influenza virus (AIV) H9N2. Materials and methods One hundred and fifty 49-day-old laying Japanese quails were divided into 5 groups (G1-G5): the G1 group was a negative control, G2 group was unvaccinated + H9N2 challenged (Ch), G3 group was unvaccinated + supplements + Ch, G4 group was VAC + Ch, and the G5 group was VAC + supplements + Ch. The supplements ( vitamin C, 1 g/liter of drinking water and AG, 1% ration) were given for 5 weeks post-vaccination (PV). The birds were injected subcutaneously with an inactivated H9N2 vaccine at 49 days of age. The quails were then challenged intranasally with AIV H9N2 at the 3rd week PV. Blood, tracheal swab and tissue samples were collected at the 1st, 2nd, and 3rd weeks PV, and at different time points post-challenge (PC). Results Growth performance, egg production (%), egg and eggshell weights, HI antibody titers, clinical signs, lesions, mortality, virus shedding rates, leukogram, biochemical and immunological parameters and histopathological lesions PC showed significant differences (P  < 0.05) between the vaccinated-unsupplemented (G4) group and the vaccinated-supplemented (G5) group. G5 showed the highest (P  < 0.05) growth performance, egg production, HI antibody titers, and heterophil phagocytic activity and the lowest heterophil/lymphocyte (H/L) ratio, mortality, virus shedding rates, creatinine level and histopathological lesion scores in the lungs. Conclusion The co-administration of vitamin C and AG for 5 weeks can improve growth performance, egg production and the immune response in vaccinated laying quails challenged with AIV H9N2 .

Avian coccidiosis is one of the major parasitic diseases in the poultry industry. The infection is caused by Eimeria species, and its treatment relies mainly on the administration of anticoccidial drugs, which can result in drug resistance and side effects. The recent trends in avian coccidiosis treatment is directed to the development of a new therapy using herbal compounds. S-Methylcysteine (SMC) is considered one of the organosulfur compounds in garlic that showed promising activity in the treatment of different pathological conditions via a wide range of anti-inflammatory and antioxidant mechanisms. In this study, the anticoccidial activity of SMC was investigated in Eimeria tenella -infected chickens compared to diclazuril as a widely used anticoccidial drug. In this regard, 14-day-old broilers were divided into six groups ( n = 18). The first group (G1) was the healthy control group, while the second group (G2) was the non-infected SMC group treated at a dose of 50 mg/kg b.w. (high dose). Moreover, the third group (G3) was the positive control group (infected and non-treated). The fourth group (G4) was the infected group treated with SMC of 25 mg/kg b.w. (low dose), while the fifth group (G5) was the infected group treated with SMC of 50 mg/kg b.w. (high dose). Conversely, the sixth group (G6) was the diclazuril-treated group. The anticoccidial effects of SMC and diclazuril were evaluated by counting oocysts and recording the body weight gain, feed conversion ratio, clinical signs, lesions, and mortality rate. Interestingly, SMC showed potent anticoccidial activity, which was exemplified by reduction of oocyst count. Furthermore, the biochemical, antioxidant, and anti-inflammatory parameters in the cecal tissues were restored toward their control levels in G4, G5, and G6. Histopathological observation of cecal tissues was consistent with the aforementioned results revealing the ameliorative effect of SMC against E. tenella infection. This study concluded novel findings in relation to the anticoccidial role of SMC as a plant-based compound against the E. tenella -induced coccidiosis in broiler chickens combined with its antioxidative and anti-inflammatory properties. Further studies for exploring the mechanistic pathways involved in this activity and the potential benefits from its use in association with conventional anticoccidial drugs are warranted.

This research was conducted to evaluate the impact of dietary or drinking water Ruminococcus sp. supplementation and/or heat stress (HS) on the growth, serum biochemistry, tissue antioxidant, phagocytic assay, histopathology, and bursa gene expression of broilers. Day-old broiler chicks were allotted into six groups according to HS and/or Ruminococcus with or without enzyme supplementation. The first group was the control one, with a formulated diet and normal environmental temperature but without any supplement. The second group fed on Ruminococcus -supplemented diet (1 kg/kg diet). The third group fed on a formulated diet without supplement, and Ruminococcus and digestive enzymes were given in drinking water (0.1 ml/L). The fourth one was the heat stress group, with a normal formulated diet. The fifth and the sixth groups served as second and third groups, respectively, but with heat stress. The results of this experiment indicated that thermal temperature negatively affected the parameters of growth performance, serum biochemical, tissue antioxidants, and phagocytic assay. Moreover, heat stress led to pathological lesions in the internal organs and affected the expression of some genes related to heat stress, including proapoptotic genes such as caspase8 and bax, inflammatory genes such as NF-κβ1, and heat shock protein such as HSP 70 in the bursal tissue. These bad effects and abnormalities were mitigated by Ruminococcus alone or with enzyme supplementation, which improved all the above-mentioned parameters.

A systematic study was undertaken to identify the species, characterize the pathogenicity, and assess the immunization of Eimeria bateri in Japanese quail (Coturnix coturnix japonica). In total, 107 Japanese quail farms were examined. The samples were processed and oocyst shape indices of sporulated oocysts were determined. Out of 107 examined farms, 34 (31.78%) farms were positive. Four Eimeria spp. were morphologically identified. For characterization of the pathogenicity, Japanese quail were orally inoculated with various doses of sporulated oocysts of Eimeria bateri. Weight gain, feed conversion ratio (FCR), mortality, severity of diarrhea, and intestinal lesion scores were examined. The birds inoculated with high doses displayed significantly lower weight gain and poorer FCR, increased mortality, and more intestinal and fecal lesions scores. To quantify the immunization of Japanese quail against coccidiosis, 2-day-old quail were orally inoculated with either 100 or 1,000 sporulated oocysts of E. bateri. At 30 days of age, the immunized and non-immunized challenged birds were orally inoculated with 1 × 105 sporulated oocysts of E. bateri. After challenge, birds immunized with 100 or 1,000 oocysts had better weight gain, FCR, minimal diarrhea, fewer intestinal lesions, and lesser oocyst production compared to non-immunized challenged birds. We concluded that vaccination is a viable method for controlling coccidiosis in Japanese quail.