Resistance to life-saving antibiotics increases rapidly worldwide, and multiresistant bacteria have become a global threat to human health. Presently, the most serious threat is the increasing spread of Enterobacteriaceae carrying genes coding for extended spectrum β-lactamases (ESBL) and carbapenemases on highly mobile plasmids. We here demonstrate how optical DNA maps of single plasmids can be used as fingerprints to trace plasmids, for example, during resistance outbreaks. We use the assay to demonstrate a potential transmission route of an ESBL-carrying plasmid between bacterial strains/species and between patients, during a polyclonal outbreak at a neonatal ward at Sahlgrenska University Hospital (Gothenburg, Sweden). Our results demonstrate that optical DNA mapping is an easy and rapid method for detecting the spread of plasmids mediating resistance. With the increasing prevalence of multiresistant bacteria, diagnostic tools that can aid in solving ongoing routes of transmission, in particular in hospital settings, will be of paramount importance.

A reduced kinetic mechanism for methanol combustion at spark-ignition (SI) engine conditions is presented. The mechanism consists of 18 species and 55 irreversible reactions, small enough to be suitable for Large Eddy Simulations (LES). The mechanism was reduced and optimized using the comprehensive mechanism (AramcoMech 2.0) as a starting point, to maintain performance at stoichiometric conditions for the pressure (10-50 bar) and temperature ranges relevant for SIengine conditions. The mechanism was validated against experimental data for ignition delay at 1050 -1650 K, flow reactor at 783 K and jet-stirred reactors at 800-1150 K, and simulated validation targets for laminar burning velocity under conditions where no experimental data are available. The mechanism performs well for pollutant formation (CO and CH2O), ignition delay and laminar burning velocity, which are all important properties for LES of engines. Two other reduced mechanisms for methanol combustion, containing around the same number of species and reactions, were tested for comparison. The superior performance of the mechanism developed in the present work is likely a result of that it is specifically produced for the relevant conditions, while the other mechanisms were developed for a limited set of conditions compared to the present work. This highlights the importance of careful selection of reduced mechanisms for implementation in computational fluid dynamics simulations.

The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard “foreign” contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.

Reduced mechanisms for n-heptane combustion have been constructed using the novel ACR method, with the complex mechanism from CRECK, including low-temperature chemistry, as a starting point. Tailored mechanisms for each part of the combustion process, ignition, flame propagation, and extinction, were created to identify differences and common trends in mechanism composition. The simulations were carried out for n-heptane/air mixtures for zero-dimensional homogenous reactors, one-dimensional freely propagating flames, and counter-flow diffusion flames at temperature, pressure, and equivalence ratio conditions relevant to engine combustion. The smallest mechanism, 28 species, only targets laminar burning velocity, while the largest single-property mechanism is for ignition over a wide temperature range, with 48 species. A compound mechanism covering all conditions consists of 65 species, this mechanism includes reaction paths describing important subchemistries like the peroxyl radical chemistry governing low-temperature ignition and the C/H/O chemistry of importance to flame propagation. Compared to the CRECK mechanism, all the reduced mechanisms have fewer than 2% of the number of reactions.

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