Treatment of community urinary tract infections (UTIs) caused by extended-spectrum β lactamase (ESBL)- producing Escherichia coli (E. coli) is more expensive than treating ESBL-negative opposites. Evaluation of the prevalence of ESBL-production among urinary E. coli isolates is crucial due to its great impact on the choice of proper antimicrobials. Accordingly, the aim of this work was to detect and characterize ESBL-producing E. coli isolated from outpatients with signs of UTIs in Upper Egypt. Urinary E. coli isolates were identified by 16S rRNA and their ESBL-production was confirmed by Modified Double Disc Synergy Test (MDDST) and ESBL- CHROMagar media. Isolates were then subjected to Polymerase Chain Reaction (PCR) for new Clermont phylogrouping, ESBL genes detection and CTX-M typing. The study enrolled 583 patients with clinically diagnosed UTIs. Uropathogens were found in 400 urine samples (68.6%) out of which 134 E. coli isolates were identified. Among the examined uropathogenic E. coli (UPEC), 80 (59.7%) were recognized as ESBL-producers. Greater than half of the ESBL-producers were multi-drug resistant (MDR) (62%). All of them were susceptible to meropenem. Most of the E. coli isolates were distributed in 4 phylogenetic groups: B2 = 42 (52.5%), F = 17 (21.25%) and Clade I or II = 10 (12.5%). The predominant gene types were TEM 60 (75%) and CTX-M gene 45 (56.25%). The CTX-M-1 group was the most prevalent (62.2%), including the CTX-M-15 enzyme, followed by the CTX-M-2 group, CTX-M-8 group and CTX-M-9 group. In conclusion, the results present alarming evidence of a serious spread of ESBL genes in Egypt, especially the epidemiological CTX-M 15, with the potential for the dissemination of MDR UPEC strains in the community.

Ten bacteriophages specific for Bacillus megaterium were isolated from a clay loam soil sample collected from the Experimental Farm of Faculty of Agriculture, Minia University, Minia, Egypt. Four out of ten isolates were inactivated after exposure to 80°C for 10 min and three isolates were inactivated at 78°C for 10 min. Whereas, the other three phage isolates were inactivated at 82°C for 10 min. The isolated phages were found to be tolerant to wide range of pH 5-9. The longevity in vitro varied between the phage isolates. The highest longevity in vitro was recorded for four phage isolates (192 h). Electron micrographs of the isolated phages indicated that all phage isolates were of the head and tail types. Two different host specificities were observed for the ten phage isolates (two different populations). Six phage isolates (population 1) were found to be infectious to B. megaterium among the four species tested (i.e., B. megaterium, B. circulans, B. polymexa and B. subtilis). Whereas, the rest of the phage isolates (population 2) were found to be infectious to B. megaterium and B. subtilis. The dendrogram separated the 10 phage isolates into two main clusters (two populations) and then each cluster was separated into two sub clusters. Isolates that belonged to the same host range were grouped together. The percentage of variation was 9% among populations and 91% within populations. The five most remarkable isolates were submitted to the bacillus database and named BMC1, BMC2, BMC3, BMC4 and BMC5.

The efficiency of free and alginate-encapsulated Azotobacter chroococcum in fixing nitrogen and their susceptibility to bacteriophages were studied in pure liquid cultures (in vitro) and under cultivated soil conditions (in vivo). Bacteriophages of A. chroococcum were isolated and were found to be common in soil of the Experimental Farm of Fac. Agric., Minia Univ., Egypt.In pure liquid cultures, the immobilized cells exhibited much higher nitrogenase activity (about 57 fold) than the free ones. The encapsulation system offered high protection to A. chroococcum against their phages. No nitrogenase activity was detected for the free cells in presence of phages.Uner cultivated soil conditions, inoculation of maize plants (Zea mays, cv. GIZA 2) with immobilized A. chroococcum, markedly increased rhizosphere and rhizoplane Azotobacter population, significantly increased plant N% as well as dry weight/plant, compared to those inoculated with free cells. In free cells inoculated-plants, bacteriophages had a marked depressive effect on rhizosphere and rhizoplane Azotobacter population, significantly reduced plant N% and dry weight/plant, as compared to plants inoculated with free cells in absence of phages. In plants inoculated with immobilized cells, no significant effect for presence of phages was detected in plant N% and dry weight/plant, whereas, a slight reduction in rhizosphere and rhizoplane Azotobacter population was observed.

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Next-Generation Sequencing (NGS) technologies provide unique possibilities for the comprehensive assessment of the environmental diversity of bacteriophages. Several Bacillus bacteriophages have been isolated, but very few Bacillus megaterium bacteriophages have been characterized. In this study, we describe the biological characteristics, whole genome sequences, and annotations for two new isolates of the B. megaterium bacteriophages (BM5 and BM10), which were isolated from Egyptian soil samples. Growth analyses indicated that the phages BM5 and BM10 have a shorter latent period (25 and 30 min, respectively) and a smaller burst size (103 and 117 PFU, respectively), in comparison to what is typical for Bacillus phages. The genome sizes of the phages BM5 and BM10 were 165,031 bp and 165,213 bp, respectively, with modular organization. Bioinformatic analyses of these genomes enabled the assignment of putative functions to 97 and 65 putative ORFs, respectively. Comparative analysis of the BM5 and BM10 genome structures, in conjunction with other B. megaterium bacteriophages, revealed relatively high levels of sequence and organizational identity. Both genomic comparisons and phylogenetic analyses support the conclusion that the sequenced phages (BM5 and BM10) belong to different sub-clusters (L5 and L7, respectively), within the L-cluster, and display different lifestyles (lysogenic and lytic, respectively). Moreover, sequenced phages encode proteins associated with Bacillus pathogenesis. In addition, BM5 does not contain any tRNA sequences, whereas BM10 genome codes for 17 tRNAs.