Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens.

Phage therapy is gaining increasing interest in the fight against critically antibiotic-resistant nosocomial pathogens. However, the narrow host range of bacteriophages hampers the development of broadly effective phage therapeutics and demands precision approaches. Here, we combine large-scale phylogeographic analysis with high-throughput phage typing to guide the development of precision phage cocktails targeting carbapenem-resistant Acinetobacter baumannii, a top-priority pathogen. Our analysis reveals that a few strain types dominate infections in each world region, with their geographical distribution remaining stable within 6 years. As we demonstrate in Eastern Europe, this spatiotemporal distribution enables preemptive preparation of region-specific phage collections that target most local infections. Finally, we showcase the efficacy of phage cocktails against prevalent strain types using in vitro and animal infection models. Ultimately, genomic surveillance identifies patients benefiting from the same phages across geographical scales, thus providing a scalable framework for precision phage therapy.

A novel method to determine the elastic modulus of extremely soft materials.

Determination of the elastic moduli of extremely soft materials that may deform under their own weight is a rather difficult experimental task. A new method has been elaborated by means of which the elastic modulus of such materials can be determined. This method is generally applicable to all soft materials with purely neo-Hookean elastic deformation behaviour with elastic moduli lower than 1 kPa. Our novel method utilises the self-deformation of pendent gel cylinders under gravity. When suspended, the material at the very top bears the weight of the entire gel cylinder, but that at the bottom carries no load at all. Due to the non-uniform stress distribution along the gel sample both the stress and the resulting strain show position dependence. The cross-sectional area of the material is lowest at the top of the sample and gradually increases towards its bottom. The equilibrium geometry of the pendant gel is used to evaluate the elastic modulus. Experimental data obtained by the proposed new method were compared to the results obtained from underwater measurements. The parameters affecting the measurement uncertainty were studied by a Pareto analysis of a series of adaptive Monte Carlo simulations. It has been shown that our method provides an easily achievable method to provide an accurate determination of the elastic modulus of extremely soft matter typically applicable for moduli below 1 kPa.

Ecotoxicity attenuation by acid-resistant nanofiltration in scandium recovery from TiO2 production waste.

The lack of high-grade scandium (Sc) ores and recovery strategies has stimulated research on the exploitation of non-ore-related secondary sources that have great potential to safeguard the critical raw materials supply of the EU's economy. Waste materials may satisfy the growing global Sc demand, specifically residues from titanium dioxide (TiO2) production. New technologies are being developed for the recovery of Sc from such residues; however, the possible environmental impacts of intermediary products and residues are usually not considered. In order to provide a comprehensive ecotoxicity characterisation of the wastes and intermediate residues resulting from one promising new technology, acid-resistant nanofiltration (arNF), a waste-specific ecotoxicity toolkit was established. Three ecotoxicity assays were selected with specific test parameters providing the most diverse outcome for toxicity characterisation at different trophic levels: Aliivibrio fischeri (bacteria) bioluminescence inhibition (30 min exposure), Daphnia magna (crustacean) lethality and immobilisation (24 h exposure) and Lemna minor (plant) growth inhibition with determination of the frond number (7 d exposure). According to our results, the environmental impact of the generated intermediate and final residues on the aquatic ecosystem was mitigated by the consecutive steps of the filtration methods applied. High and statistically significant toxicity attenuation was achieved according to each test organism: toxicity was lowered based on EC20 values, according to the A. fischeri bioluminescence inhibition assay (by 97%), D. magna lethality (by 99%) and L. minor frond number (by 100%), respectively, after the final filtration step, nanofiltration, in comparison to the original waste. Our results underline the importance of assessing chemical technologies' ecotoxicological and environmental impacts with easy-to-apply and cost-effective test methods to showcase the best available technologies.

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.