This study aimed to survey the prevalence, antimicrobial resistance, and virulence-associated genes of Salmonella enterica recovered from broiler chickens and retail shops at El-Sharkia Province in Egypt. Salmonella virulence factors were determined using the polymerase chain reaction assays targeting the invA, csgD, hilC, bcfC, stn, avrA, mgtC, ompF, sopE1 and pefA genes. One hundred tweenty out of 420- samples from broiler chickens’ cloacal swabs, farm environmental samples, and freshly dressed whole chicken carcasses were positive Salmonella species. The isolates were serotyped as S. Enteritidis as the most dominant serotypes. Interestingly, none of the isolates were resistant to imipenem. The multidrug resistance was determined in 76.7% of the isolates with multidrug antibiotic resistance index of 0.2–0.6. Eight virulence genes (invA, csgD, hilC, stn, bcfC, mgtC, avrA, and ompf) were characterized among 120 S. enterica isolates with variable frequencies, while sopE1and pefA genes that were completely absent in all isolates. Based on the combination of presence and absence of virulence genes, the most common genetic profile (P7, 30%) was invA and csgD genes. S. Enteritidis and S. Typhimurium were the most common identified serotypes in the examined sources. Circulation of such strains in broiler farms required introducing special biosecurity and biocontrol measures for control of Salmonella. Such measures might limit the adverse effects of antibiotics and ensure the safety of the environment and animal-derived food.

Pseudomonas aeruginosa is an opportunistic pathogen causing severe infection in animals and humans. This study aimed to determine the ecological distribution and prevalence of multidrug-resistant (MDR) P. aeruginosa isolated from dairy cattle, the environment, and workers’ hand swabs. Samples (n = 440) were collected from farms and households (n = 3, each). Rectal swabs, udder skin swabs, milk, workers’ hand swabs, feed, water, water sources, and beddings were collected. Samples were subjected to the bacterial identification of P. aeruginosa via 16S rRNA. Antimicrobial resistance (AMR) was detected either phenotypically using an antibiotic susceptibility test or genotypically with AMR resistance genes (ARGs) such as drfA, sul1, and ermB. P. aeruginosa was detected on dairy farms and households (10.3–57.5%, respectively), with an average of 23.2%. The resistance of dairy farm strains was observed against sulfamethoxazole, imipenem, cefepime, piperacillin–tazobactam, and gentamycin (100%, 72.7%, 72.7%, 68.8%, and 63.3%, respectively). Meanwhile, the resistance of household strains was observed against sulfamethoxazole, imipenem, amoxicillin, gentamicin, cefepime, and erythromycin by 91.3%, 82.6%, 75.4%, 75.4%, 68.1%, and 63.8%, respectively. The susceptibility of farm strains was detected against norfloxacin, ciprofloxacin, and levofloxacin (90.9%, 84.8%, and 72.7%, respectively). Meanwhile, the susceptibility of household strains was detected against ciprofloxacin, amikacin, and norfloxacin (100%, 84.1%, and 72.5%, respectively). About 81.4% of P. aeruginosa strains were MDR. ARGs (drfA, sul1, and ermB) were detected in farm strains (48.5%, 72.7%, and 24.4%, respectively) and household strains (50.7%, 72.5%, and 47.8%, respectively). Almost all P. aeruginosa had MAR over 0.2, indicating repeated application of antibiotics. P. aeruginosa prevalence was fivefold higher in households than on farms. MDR strains were higher amongst household strains than farm strains.

The aquaculture industry is a fast-growing sector in Egypt; however, the progress of this industry is impeded by many challenges such as poor water quality and associated bacterial infections. Among others, Motile Aeromonas Septicemia (MAS), caused by aeromonads, is among the most important bacterial diseases affecting aquaculture due to its zoonotic potential. In the present work, motile aeromonads were isolated from water samples (n= 8) and Nile tilapia (n= 240) in four fish farms (farms I, II, III, and IV) in Kafr El-Sheikh province during the period March to August 2017. This step was followed by investigation of the prevalence and phenotypic, molecular, and histopathological characterization of aeromonads. In addition, antimicrobial susceptibility and virulence gene detection were analyzed. Interestingly, physicochemical water analysis revealed different ranges in relation to the fish farms and seasons. More importantly, Aeromonas isolates were phenotypically identified in 33.3% and 12.5% from fish and water samples, respectively. The highest prevalence of motile aeromonads (46.7%) was recorded from farm IV, and only 12.5% of water samples were positive for them. Out of 80 isolates, 65 (81.25%) were molecularly identified at the genus level using gyrase B (gyrB). The prevalence of the virulence genes detected in the isolated motile aeromonads was aerolysin (aer), 52.2%; elastase (ahp), 26.25%; hemolysin (hyl), 35%; and lipase (lip), 3.75%. The antibiogram profile revealed that the highest resistance of aeromonads isolates (80%) was recorded to chloramphenicol, kanamycin, and azithromycin. Meanwhile, lower resistance levels of 40%, 30%, and 20% were found for streptomycin, cefotaxime, and amoxicillin, respectively. The multiple antibiotic resistance (MAR) index values ranged between 0.27 and 0.82 of motile aeromonads isolates. Furthermore, the histopathological examinations of naturally diseased tilapia revealed widespread hepatocellular necrosis with diffuse, numerous rod-shaped bacteria in liver with melanomacrophages and lymphocytic depletion with edema and hemosiderosis in the spleen. Our findings provide an updated epidemiological baseline for future reference and highlight the likely role of the adverse impact of water quality in the outbreaks of motile aeromonads with special reference to virulence genes and antibiotic resistant traits.

Avipoxviruses (APVs) are among the most complex viruses that infect a wide range of birds’ species. The infection by APVs is often associated with breathing and swallowing difficulties, reduced growth, decreased egg production, and high mortalities in domestic poultry. In the present study, 200 cutaneous nodular samples were collected from different avian species (chicken, pigeon, turkey, and canary) suspected to be infected with APVs from Dakahlia Governorate, Egypt. Pooled samples (n = 40) were prepared and inoculated in embryonated chicken eggs (ECEs). APVs were then identified by polymerase chain reaction (PCR) and sequence analysis of the APV P4b gene. Furthermore, the forty strains of APVs were screened for the presence of reticuloendotheliosis virus (REV)-5′LTR in their genomes. Interestingly, the phylogenic tree of the APV P4b gene was separated into 2 clades: clade 1, in which our fowlpox virus (FWPV), turkeypox virus (TKPV), and canarypox virus (CNPV) isolates were grouped, along with reference FWPVs and TKPVs retrieved from GenBank, whereas, in clade2, the pigeonpox virus (PGPV) isolate was grouped with PGPVs retrieved from GenBank. Likewise, REV-5′LTR was amplified from 30 strains isolated from chicken, turkey, and canary, while PGPV strains were free from REV-5′LTR integration. To the best of our knowledge, this study involved the detection and characterization of REV-5′LTR insertions in the APVs field isolates in Egypt for the first time. Given the above information, further future research seems recommended to understand the impact of the resulting REV-5′LTR insertions on the pathogenesis, virulence, and inadequate vaccine protection against APVs.

Foodborne infection with Listeria causes potentially life-threatening disease listeriosis. Listeria monocytogenes is widely recognized as the only species of public health concern, and the closely related species Listeria innocua is commonly used by the food industry as an indicator to identify environmental conditions that allow for presence, growth, and persistence of Listeria spp. in general. In our study, we analyze the occurrence of Listeria spp. in a farm-to-fork approach in a poultry production chain in Egypt and identify bacterial entry gates and transmission systems. Prevalence of Listeria innocua at the three production stages (farm, slaughterhouse, food products) ranged from 11% to 28%. The pathogenic species Listeria monocytogenes was not detected, and Listeria innocua strains under study did not show genetic virulence determinants. However, the close genetic relatedness of Listeria innocua isolates (maximum 63 SNP differences) indicated cross-contamination between all stages from farm to final food product. Based on these results, chicken can be seen as a natural source of Listeria. Last but not least, sanitary measures during production should be reassessed to prevent bacterial contamination from entering the food chain and to consequently prevent human listeriosis infections. For this purpose, surveillance must not be restricted to pathogenic species.

Background Multi-resistant Shigella species recovered from raw cow milk and milk products has predominated all over the world especially extended spectrum β-lactamases (ESBLs) and Quaternary ammonium compound E delta 1 (qacE∆1) genes. This study was conducted to investigate the prevalence, antibiotic and disinfectant resistance phenotypes and genotypes as well as plasmid profiles of Shigella species isolated from raw cow milk and milk products in Egypt. The genotypic analysis was determined for the presence of β-lactamase encoding genes (blaTEM, blaCTX-M, blaOXA-1 and blaSHV), tetA(A) and qacE∆. Results Twenty-one (7%) of Shigella isolates (S. dysenteriae, S. flexneri and S. sonnei) were recovered with S. dysenteriae as the most predominant types. Antibiotic sensitivity tests showed 71.4% of multidrug-resistant Shigella isolates. High resistance rates were observed to tetracyclines (100%), ampicillin, amoxicillin-clavulanate (90.5%, each) and cefaclor (66.7%), whilst no resistance was detected against imipenem, sulfamethoxazole/trimethoprim, and azithromycin. Disinfectant susceptibility test of Shigella isolates revealed resistance to phenolic compound (vanillic), while 85.7% of Shigella isolates were benzalkonium chloride resistant. Uniplex PCR analysis exhibit presence of β-lactamase encoding genes (blaTEM in all isolates and blaCTX-M in 28.6% of isolates), tetA(A) in all isolates and 85.7% isolates positive for qacE∆1, while all isolates were negative for blaOXA-1 and blaSHV. All Shigella extended spectrum β-lactamase (ESBL) producers (6, 100%) were positive for blaTEM, blaCTX-M, and qacE∆1 genes. Furthermore, plasmid profiling revealed seven distinct plasmid patterns (P1-P7) ranging from 1.26 to 33.61 kb among all Shigella strains; S. dysenteriae displayed the greatest variance. The co-transfer of β-lactamase genes (blaTEM and blaCTX-M) and qacE∆1 genes was observed by conjugation. Conclusions S. dysenteriae was the most common identified types in the examined sources. Also, the findings imply the emergence of multi-resistant Shigella species either multi-resistant to antibiotics (particularly ESBL producer strains) or disinfectants in Egypt. Thus, the resistance of Shigella species should regularly be monitored and appropriate measures should be taken to manage this problem.