We present evidence for the coexistence and coevolution of antibiotic resistance and biosynthesis genes in soil bacteria. The distribution of the streptomycin (strA) and viomycin (vph) resistance genes was examined in Streptomyces isolates. strA and vph were found either within a biosynthetic gene cluster or independently. Streptomyces griseus strains possessing the streptomycin cluster formed part of a clonal complex. All S. griseus strains possessing solely strA belonged to two clades; both were closely related to the streptomycin producers. Other more distantly related S. griseus strains did not contain strA. S. griseus strains with only vph also formed two clades, but they were more distantly related to the producers and to one another. The expression of the strA gene was constitutive in a resistance-only strain whereas streptomycin producers showed peak strA expression in late log phase that correlates with the switch on of streptomycin biosynthesis. While there is evidence that antibiotics have diverse roles in nature, our data clearly support the coevolution of resistance in the presence of antibiotic biosynthetic capability within closely related soil dwelling bacteria. This reinforces the view that, for some antibiotics at least, the primary role is one of antibiosis during competition in soil for resources.

Streptomycin resistant streptomycetes were isolated from four diverse sites. Two sites in Germany were sampled and included an agricultural experimental plot of apple trees which had a history of streptomycin application (AR) and a control site without antibiotic application (CR). Two sites in the UK were sampled; a pastureland site which had sewage injection (DW) and an agricultural site (CW). The actinomycete counts indicated a high proportion of streptomycin resistant isolates in the CW soil. Streptomycetes were identified by partial sequencing of the 16S rDNA. PCR product of the hypervariable gamma region of 16S rDNA allowed analysis by denaturing gradient gel electrophoresis to assess the diversity within the isolates. The streptomycin and sewage sludge treated sites showed decreased diversity within streptomycete populations. Isolates were screened for the streptomycin resistance gene, strA, and flanking biosynthesis gene, strB1. Distribution of these genes indicated the prevalence of str genes in the streptomycin treated soil. Evidence of horizontal gene transfer was recorded in isolates identified as Streptomyces platensis recovered from CR and AR sites which had acquired a streptomycin resistance gene homologous to that found in Streptomyces griseus. Members of the latter species were the most abundant streptomycin resistant streptomycetes isolated from all soils.

Background: Actinobacteria is as a group of advanced filamentous bacteria. Rare Actinobacteria are of special interest as they are rarely isolated from the environments. They are a major source of important bioactive compounds. Determining the proper strategy for the identification of Actinobacteria harboring biosynthetic gene clusters and producing bioactive molecules is a challenging platform. Methodology: In this review, we discuss a consequence of microbiological and molecular methods for the identification of rare Actinobacteria. In addition to that, we shed light on rare Actinobacteria's significance in antibiotic production. We also clarified molecular approaches for the manipulation of novel biosynthetic gene clusters via PCR screening, fosmid libraries, and Illumina whole-genome sequencing in combination with bioinformatics analysis. Conclusion: Perceptions of the conventional and molecular identification of Actinobacteria were conducted. This will open the door for the genetic manipulation of novel antibiotic gene clusters in heterologous hosts. Also, these conclusions will lead to constructing new bioactive molecules via genetically engineering biosynthetic pathways.

A distinct strain named Micromonospora sp. Rc5 was isolated from Sinai desert of Egypt and recorded high antagonistic activities against some food and bloodborne pathogens. Morphological and chemotaxonomy characterization confirmed that this isolate belongs to genus Micromonospora. Sequencing of partial 16S rDNA and BLASTN showed that isolate Rc5 is identical to Micromonospora haikouensis (99%) but with low bootstrap value in NJ phylogenetic tree. Comprehensive optimization of several growth factors was performed including initial pH, incubation periods, and different sources of carbon and nitrogen. The highest yield of antimicrobial agent production was obtained after 8 days of incubation at 30°C, pH 6.0, 3 x 10 5 CFU/ml in soya bean meal broth media with agitation of 150 rpm. A dramatic proportional decrease occurred with Original Research Article

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C ARBAPENEM resistant Acinetobacter baumannii (CRAB) now leads the WHO's critical priority list of nosocomial pathogens worldwide. Carbapenem Hydrolysing Class D β-lactamases (CHDL) -"OXA-type β-lactamases"-is of great concern. In this study, bacterial isolates recovered from different clinical samples collected from three different hospitals in Cairo from October 2014 to May 2015. The isolates were identified using Vitek 2 and partial 16S rRNA gene sequencing. Acinetobacter baumannii isolates represented 16.1% of the total Gram negative isolates. Susptibility test revealed that 88.9% were CRAB, 65% of imipenem resistant isolates and 57.5% of meropenem resistant isolates had chromosomal mediated resistance. Forty CRAB isolates were identified and screened for bla OXA-23-like , bla OXA-24-like , bla OXA-51-like and bla OXA-58-like genes.The most prevalent gene was bla OXA-51-like which was detected in 95% of the isolates followed by bla OXA-23-like and bla OXA-24-like in 90% of the isolates. However, bla OXA-58-like was not detected in any of the isolates. The absence of bla OXA-51-like in 5% of CRAB isolates proving the inconvenience of using bla OXA-51-like as a species specific region for identification of CRAB by PCR. In addition, all isolates harbored more than one OXA gene, 75% were bla OXA-23/OXA-24/OXA-51 carriers while 25% harbored two OXA genes. This study revealed the emergence of bla OXA-24-like gene in CRAB for the first time in Egyptian hospitals.

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Background: Antibiotic resistance occurs rapidly and naturally. However, the misuse of antibiotics is accelerating the process. And therefore, exploring new antibiotics has been a great demand in order to save people's life. Actinobacteria have been the major source of antibiotics. In this study, we focused on rare types of actinobacteria which are hard to isolate from the environment by traditional methods. Fifty rare actinobacteria were isolated from Egyptian soils, and they were screened against some bacterial pathogens (Staphylococcus aureus ATCC 6538, Pseudomonas aeruginosa ATCC 10145, Klebsiella pneumonia CCM 4415, Streptococcus mutans ATCC 25175, Escherichia coli O157:H7 ATCC 51659, and Salmonella enterica ATCC 25566). Illumina whole genome sequencing was performed for potent isolates. The whole genomes of selected rare actinobacteria were investigated via bioinformatics analysis using neighbor-joining phylogenetic analysis and Antibiotics and Secondary Metabolite Analysis SHell. Results: Isolates Rc5 and Ru87 showed the highest inhibition activity against selected Gram-positive and Gramnegative pathogens. Neighbor-joining phylogenetic analysis confirmed that isolate Rc5 belonged to Micromonospora oryzae and Micromonospora harpali with 73% bootstrap value while isolate Ru87 was grouped with Streptomyces gingianensis and Streptomyces morales with 89% bootstrap value. Bioinformatics analysis using antiSMASH 3.0 predicted 33 and 19 secondary metabolite gene clusters in Micromonospora sp. Rc5 and Streptomyces sp. Ru87, respectively. Gene annotation predicted the presence of valuable biosynthetic gene clusters in both strains such as polyketides, non-ribosomal peptides, terpenes, siderophores, bacteriocin, lasso peptide, ectoine, and lantipeptide. Conclusion: We concluded that exploring cryptic and novel biosynthetic gene clusters via Illumina whole genome sequencing and bioinformatics analysis is a useful method. We confirmed that Egyptian soil is very rich in high potential biosynthetic of rare actinobacteria. Further genetic engineering manipulation of biosynthetic pathways would eventually lead to producing novel bioactive molecules.