Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission

Background: Carbapenemase-producing Enterobacteriaceae (CPE), including KPC-producing Klebsiella pneumoniae (KPC-Kpn), are an increasing threat to patient safety. Objectives: To use WGS to investigate the extent and complexity of carbapenemase gene dissemination in a controlled KPC outbreak. Materials and methods: Enterobacteriaceae with reduced ertapenem susceptibility recovered from rectal screening swabs/clinical samples, during a 3 month KPC outbreak (2013–14), were investigated for carbapenemase production, antimicrobial susceptibility, variable-number-tandem-repeat profile and WGS [short-read (Illumina), long-read (MinION)]. Short-read sequences were used for MLST and plasmid/Tn4401 fingerprinting, and long-read sequence assemblies for plasmid identification. Phylogenetic analysis used IQTree followed by ClonalFrameML, and outbreak transmission dynamics were inferred using SCOTTI. Results: Twenty patients harboured KPC-positive isolates (6 infected, 14 colonized), and 23 distinct KPC-producing Enterobacteriaceae were identified. Four distinct KPC plasmids were characterized but of 20 KPC-Kpn (from six STs), 17 isolates shared a single pKpQIL-D2 KPC plasmid. All isolates had an identical transposon (Tn4401a), except one KPC-Kpn (ST661) with a single nucleotide variant. A sporadic case of KPC-Kpn (ST491) with Tn4401a-carrying pKpQILD2 plasmid was identified 10 months before the outbreak. This plasmid was later seen in two other species and other KPC-Kpn (ST14,ST661) including clonal spread of KPC-Kpn (ST661) from a symptomatic case to nine ward contacts. Conclusions: WGS of outbreak KPC isolates demonstrated blaKPC dissemination via horizontal transposition (Tn4401a), plasmid spread (pKpQIL-D2) and clonal spread (K. pneumoniae ST661). Despite rapid outbreak control, considerable dissemination of blaKPC still occurred among K. pneumoniae and other Enterobacteriaceae, emphasizing its high transmission potential and the need for enhanced control efforts

Electrical Control of Optical Emitter Relaxation Pathways enabled by Graphene

Controlling the energy flow processes and the associated energy relaxation rates of a light emitter is of high fundamental interest, and has many applications in the fields of quantum optics, photovoltaics, photodetection, biosensing and light emission. While advanced dielectric and metallic systems have been developed to tailor the interaction between an emitter and its environment, active control of the energy flow has remained challenging. Here, we demonstrate in-situ electrical control of the relaxation pathways of excited erbium ions, which emit light at the technologically relevant telecommunication wavelength of 1.5 $\mu$m. By placing the erbium at a few nanometres distance from graphene, we modify the relaxation rate by more than a factor of three, and control whether the emitter decays into either electron-hole pairs, emitted photons or graphene near-infrared plasmons, confined to $<$15 nm to the sheet. These capabilities to dictate optical energy transfer processes through electrical control of the local density of optical states constitute a new paradigm for active (quantum) photonics.Comment: 9 pages, 4 figure

Phonon-mediated mid-infrared photoresponse of graphene

The photoresponse of graphene at mid-infrared frequencies is of high technological interest and is governed by fundamentally different underlying physics than the photoresponse at visible frequencies, as the energy of the photons and substrate phonons involved have comparable energies. Here, we perform a spectrally resolved study of the graphene photoresponse for mid-infrared light by measuring spatially resolved photocurrent over a broad frequency range (1000-1600 cm-1). We unveil the different mechanisms that give rise to photocurrent generation in graphene on a polar substrate. In particular, we find an enhancement of the photoresponse when the light excites bulk or surface phonons of the SiO2 substrate. This work paves the way for the development of graphene-based mid-infrared thermal sensing technology

Review on current scientific literature and overview of commercially available methods for on-site DNA isolation

The development of tools for real-time detection of antimicrobial resistant (AMR) pathogens is a priority topic of the One Health EJP. For real-time analysis to be achievable on-site (away from the laboratory setting), robust culture independent detection methods, employing minimal equipment are required. Metagenomic sequencing using short-read data has provided insight and detailed compositions of a variety of microbial communities, as well as for the detection of potential pathogens and AMR or virulence genes. In addition to the currently bulky nature of short-read technologies and the difficulty to perform this analysis on site, an important limitation is their inability to reliably associate the genetic context of individual genes to bacteria (including pathogens) within a community. The FARMED project aims to address these issues by using the Oxford Nanopore Technologies (ONT) MinION, comparing to the current gold standard short-read technology, to evaluate its capability for diagnostic use on a range of sample matrices, particularly on-site at/near point of sample collection. This is enabled by the portability of the ONT technology, allowing on-site analysis, in contrast to short read sequencing. An additional advantage of using ONT sequencing or long-read metagenomic sequencing, is that the local genetic context of AMR genes can be derived, and as such, the presence of the AMR genes can be attributed to specific species or plasmids, within the bacterial community. This technology will enable the identification of a plethora of bacterial species and linkage of AMR genes to particular species. However, the successful application of on-site microbial detection/monitoring is influenced by various factors such as resource-limited working environment, sample collection and importantly the quality of the input DNA for sequencing. In addition, the availability of on-site sequencing and subsequent data analysis needs to be taken into account. This deliverable will review the scientific literature on existing DNA extraction methods and determine which have the potential/are suitable for rapid on-site metagenomic analysis. For on-site DNA extraction, it is essential that the implemented methods use minimal transportable equipment. Furthermore, the method(s) need to be free of hazardous chemicals for field personnel and the working environment, as well as components that require sub-zero transport conditions. We will also discuss the requirements of DNA for long-read sequencing and suitability of the different methods. We consider methods suitable for on-site DNA extraction from different ‘simple’ and ‘complex’ sample matrices, as each has different considerations. Finally, we will deliver recommendations for the FARMED consortium to be tested using ONT sequencing

Controlling graphene plasmons with resonant metal antennas and spatial conductivity patterns

Graphene plasmons promise unique possibilities for controlling light in nanoscale devices and for merging optics with electronics. Here we introduce a versatile platform technology based on resonant optical antennas and conductivity patterns for launching and controlling of propagating graphene plasmons, constituting an essential step for the development of graphene plasmonic circuits. We demonstrate the launching and focusing of infrared graphene plasmons with geometrically tailored antennas, and how they refract when passing through a 2-dimensional conductivity pattern, here a prism-shaped bilayer. To that end, we directly map the graphene plasmon wavefronts using an imaging method that will also benefit the testing of future design concepts for nanoscale graphene plasmonic circuits and devicesFil: Alonso Gonzalez, P. CIC nanoGUNE. San Sebastian; EspañaFil: Nikitin, A.Y.. CIC nanoGUNE. San Sebastian; España. IKERBASQUE. Bilbao; EspañaFil: Golmar, Federico. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. CIC nanoGUNE. San Sebastian; España. Instituto Nacional de Tecnología Industrial; Argentina. Universidad Nacional de San Martín; ArgentinaFil: Centeno, A. Graphenea SA. San Sebastian; EspañaFil: Pesquera, A. Graphenea SA. San Sebastian; EspañaFil: Velez, S. CIC nanoGUNE. San Sebastian; EspañaFil: Chen, J. CIC nanoGUNE. San Sebastian; EspañaFil: Navickaite, G. Institut de Ciéncies Fotoniques. Barcelona; EspañaFil: Koppens, F.. Institut de Ciéncies Fotoniques. Barcelona; EspañaFil: Zurutuza, A. Graphenea SA. San Sebastian; EspañaFil: Casanova, F.. CIC nanoGUNE. San Sebastian; España. IKERBASQUE. Bilbao; EspañaFil: Hueso, L.. CIC nanoGUNE. San Sebastian; España. IKERBASQUE. Bilbao; EspañaFil: Hillenbrand, R.. IKERBASQUE. Bilbao; España. CIC nanoGUNE. San Sebastian; Españ

Phonon-Mediated Mid-Infrared Photoresponse of Graphene

The photoresponse of graphene at mid-infrared frequencies is of high technological interest and is governed by fundamentally different underlying physics than the photoresponse at visible frequencies, as the energy of the photons and substrate phonons involved have comparable energies. Here, we perform a spectrally resolved study of the graphene photoresponse for mid-infrared light by measuring spatially resolved photocurrent over a broad frequency range (1000–1600 cm^–1). We unveil the different mechanisms that give rise to photocurrent generation in graphene on a polar substrate. In particular, we find an enhancement of the photoresponse when the light excites bulk or surface phonons of the SiO₂ substrate. This work paves the way for the development of graphene-based mid-infrared thermal sensing technology

Nano-imaging of intersubband transitions in van der Waals quantum wells

The science and applications of electronics and optoelectronics have been driven for decades by progress in growth of semiconducting heterostructures. Many applications in the infrared and terahertz frequency range exploit transitions between quantized states in semiconductor quantum wells (intersubband transitions). However, current quantum well devices are limited in functionality and versatility by diffusive interfaces and the requirement of lattice-matched growth conditions. Here, we introduce the concept of intersubband transitions in van der Waals quantum wells and report their first experimental observation. Van der Waals quantum wells are naturally formed by two-dimensional (2D) materials and hold unexplored potential to overcome the aforementioned limitations: They form atomically sharp interfaces and can easily be combined into heterostructures without lattice-matching restrictions. We employ near-field local probing to spectrally resolve and electrostatically control the intersubband absorption with unprecedented nanometer-scale spatial resolution. This work enables exploiting intersubband transitions with unmatched design freedom and individual electronic and optical control suitable for photodetectors, LEDs and lasers