Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains.

Functional metagenomics is a powerful experimental tool to identify antibiotic resistance genes (ARGs) in the environment, but the range of suitable host bacterial species is limited. This limitation affects both the scope of the identified ARGs and the interpretation of their clinical relevance. Here we present a functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). This approach combines and improves the use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. These modified phage particles were used to introduce large metagenomic plasmid libraries into clinically relevant bacterial pathogens. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, we demonstrate that this approach substantially expands the list of identified ARGs. Many ARGs have species-specific effects on resistance; they provide a high level of resistance in one bacterial species but yield very limited resistance in a related species. Finally, we identified mobile ARGs against antibiotics that are currently under clinical development or have recently been approved. Overall, DEEPMINE expands the functional metagenomics toolbox for studying microbial communities.

Barrier behaviour of partially N-acetylated chitosan layers in aqueous media.

Chitosan coatings of 353 ± 12 nm thickness were prepared on glass and zinc substrates by dip-coating method to study their barrier-behaviour. The coatings were chemically modified to increase their degree of acetylation (DA) from ca. 44 % up to ca. 98 % resulting a quasi-chitin coating. The effect of the acetylation reaction was studied by infrared spectroscopy, and the structural changes of the native and acetylated coatings were investigated by UV-Vis spectrophotometry and X-ray diffraction. The surface properties of the coated samples were characterized by wettability measurements - advancing water contact angle decreased from ca. 80° (native) to ca. 43° (fully acetylated) - and microscopic (SEM, AFM) studies. The barrier behaviour of the chitosan layer depending on the DA was evaluated by electrochemical impedance spectroscopy studies and with a special mesoporous silica - chitosan bilayer system by measuring the amount of dye (Rhodamine 6G) accumulated in the silica through the chitosan coating during an impregnation step. These methods showed significant decrease in the barrier-effect of the coatings with increasing DA (accumulation of approximately six times more dye and a reduction of charge transfer resistance by an order of magnitude), due to the structural and ionization changes in the coatings.