Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), is a serious re-emerging disease in both animals and humans. The evolution of the Multi- and Extensively drug-resistant M. bovis strains (MDR-TB and XDR-TB) represents a global threat to public health. Worldwide, the disease is responsible for great economic losses in the veterinary field, serious threat to the ecosystem, and about 3.1% of human TB cases, up to 16% in Tanzania. Only thorough investigation to understand the pathogen's epidemiology can help in controlling the disease and minimizing its threat. For this purpose, various tools have been developed for use in advanced molecular epidemiological studies of bTB, either alone or in combination with standard conventional epidemiological approaches. These techniques enable the analysis of the intra- and inter-species transmission dynamics of bTB. The delivered data can reveal detailed insights into the source of infection, correlations among human and bovine isolates, strain diversity and evolution, spread, geographical localization, host preference, tracing of certain virulence factors such as antibiotic resistance genes, and finally the risk factors for the maintenance and spread of M. bovis. They also allow for the determination of epidemic and endemic strains. This, in turn, has a significant diagnostic impact and helps in vaccine development for bTB eradication programs. The present review discusses many topics including the aetiology, epidemiology and importance of M. bovis, the prevalence of bTB in humans and animals in various countries, the molecular epidemiology of M. bovis, and finally applied molecular epidemiological techniques.

Background and Aim: Raoultella ornithinolytica is one of the emerging gram-negative bacteria, which associated with foodborne illness. Researches affirmed that distinguish between R. ornithinolytica and Klebsiella oxytoca are difficult, as they are phylogenetic related. The evolution of multidrug resistance of Raoultella strains gained more concern for recognition of the pathogen which supports in controlling the disease and minify its threat. This study sought to find a reliable tool for the identification of Raoultella ornithinolytica, isolated from chicken product samples, and assessed the resistance profile of R. ornithinolytica using antibiogram sensitivity tests. Materials and Methods: Forty samples of chicken products were collected between January and September 2019 from different markets in Alexandria Governorate, Egypt. The products included nuggets, strips, burgers, luncheon meats, pane, frankfurters, and minced chicken meat. The samples were transferred to the Reference Laboratory. The samples were subjected to isolation, biochemical reaction testing, phenotypic system analytical profile index (API) E20, and a detection of antimicrobial susceptibility test. Phenotypic identification was confirmed through matrix-assisted laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Results: Thirty-three bacterial isolates (82.50%) out of 40 samples were isolated into pure cultures from the chicken samples. Three isolates (9.09%) were positive for R. ornithinolytica, while 30 isolates (90.91%) exhibited growth characters for different pathogens (Escherichia coli, Enterobacter aerogenes, Proteus vulgaris, R. ornithinolytica, and Klebsiella pneumoniae). The isolates of R. ornithinolytica were resistant to five types of antibiotics and sensitive to two types of antibiotics. Conclusion: This study reported the first case of R. ornithinolytica found in chicken products in Egypt. Phenotypic system API 20E and MALDI-TOF MS were found to be reliable tools for confirming the diagnosis of R. ornithinolytica. As it provides rapid identification with high sensitivity and specificity for R. ornithinolytica, which often do not require a molecular procedure for confirmation.

Aim: This study aimed to characterize the genetic diversity, evolutionary level, and prevalence of genotypes of common isolates of Salmonella (Salmonella Enteritidis and Salmonella Typhimurium). Using one of the most advanced molecular recognition techniques, multilocus variable number of tandem repeat analysis (MLVA), we characterized the genotype and prevalence of S. Enteritidis and S. Typhimurium. Materials and Methods: One hundred and twenty-five internal organ samples were collected from the major chicken slaughterhouses in Egypt, and Salmonella species were isolated. PCR was utilized to amplify the IE-1 and Flic-C genes to identify S. Enteritidis and S. Typhimurium DNA, respectively, from Salmonella isolates. MLVA was applied on nine samples of S. Enteritidis DNA and three samples of S. Typhimurium DNA. Six variable number tandem repeat (VNTR) loci (Sal02, Sal04, Sal06, Sal10, Sal20, and Sal23) were amplified. Results: Of the examined samples (n=125), a total of 12 isolates (9.6%) were either identified as Enteritidis or Typhimurium. PCR-mediated amplification of IE-1 and Flic-C revealed that 75% (n=9) of the 12 Salmonella isolates were S. Enteritidis and 25% (n=3) were S. Typhimurium. The six loci amplified through MLVA had allelic diversity. The most discriminatory heterogenic locus for S. Enteritidis was Sal20. Sal04 and Sal23 were the most discriminatory heterogenic loci for S. Typhimurium. VNTR allelic profile analysis revealed nine unique genotypes for S. Enteritidis and three for S. Typhimurium. Conclusion: This study was the first to use MLVA analysis to identify S. Enteritidis and S. Typhimurium strains isolated from chickens in Egypt. The molecular typing data reported herein allowed us to characterize the genotypes of S. Enteritidis and S. Typhimurium that are most prevalent in Egyptian chickens. Moreover, this epidemiological information provides valuable insight on how to prevent disease transmission. Moreover, our methods provide an alternative to traditional serotyping techniques that may produce inaccurate strain identifications for organisms with rough lipopolysaccharide structures.

Key words ABSTRACT: Mycobacterium tuberculosis; Polymerase Chain Reaction (PCR); IS6110Tuberculosis remains a global epidemic, especially in developing countries; early diagnosis plays a critical role in controlling the disease. Traditional method is not reliable because isolation and identification of mycobacteria may take up to several weeks or more in achieving results. The aim of this study is to compare the efficacy of different protocols of mycobacterial DNA extraction in order to standardize a trustable DNA extraction protocol providing high quality DNA for molecular diagnosis. DNA was extracted using six different protocols. PCR was performed using primer of IS6110 that specific for all the members of M. tuberculosis complex. The highest DNA extraction efficiency (68.75%) was observed using the protocol number 3, and DNA extraction was proved to give a higher accuracy to IS6110 PCR in comparison with the other protocols. It could be concluded that most of DNA extraction kit dependent protocols are costly but of high quality DNA extraction, otherwise some of the classical methods are easy, low cost and simple but the purity of the DNA are of low quality.