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The strive toward sustainability increases the demand for bio-based material production, forcing expansion of the biorefinery feedstock supply from forest wood to non-woody materials such as agricultural residues. As a model organism for legume crops, the aptness of agricultural lupins as a lignocellulose feedstock is investigated. Principle chemical analysis combined with optotracing, in which the fluorescent tracer molecule Carbotrace 680 generates a visual map of the native tissues’ lignocellulose anatomy at sub-cellular resolution, enables informed design of a mild recovery process. A streamlined conversion approach is then designed, yielding lignin-containing microfibrillated cellulose. By monitoring defibrillation and delignification throughout the extraction process, the use of optotracing for non-destructive fiber analytics at unprecedented details across all hierarchical structures of lignocellulosic materials is demonstrated. This crop valorization is a prime illustration of a holistic use of lupin biomass, with seeds serving as plant-based food sources, and other parts as sources for lignocellulose-based materials, thereby expanding both the biorefinery concept and feedstock supply., QC 20240628

The urinary tract is a hydrodynamically challenging microenvironment and uropathogenic Escherichia coli (UPEC) must overcome several physiological challenges in order to adhere and establish a urinary tract infection. Our previous work in vivo revealed a synergy between different UPEC adhesion organelles, which facilitated effective colonization of the renal proximal tubule. To allow highresolution real-time analysis of this colonization behavior, we established a biomimetic proximal-tubule-on-chip (PToC). The PToC allowed for single-cell resolution analysis of the first stages of bacterial interaction with host epithelial cells, under physiological flow. Time-lapse microscopy and single-cell trajectory analysis in the PToC revealed that while the majority of UPEC moved directly through the system, a minority population initiated heterogeneous adhesion, identified as either rolling or bound. Adhesion was predominantly transient andmediated by P pili at the earliest time-points. These bound bacteria initiated a founder populationwhich rapidly divided, leading to 3D microcolonies. Within the first hours, the microcolonies did not express extracellular curli matrix, but rather were dependent on Type 1 fimbriae as the key element in the microcolony structure. Collectively, our results show the application of Organ-on-chip technology to address bacterial adhesion behaviors, demonstrating a well-orchestrated interplay and redundancy between adhesion organelles that enables UPEC to form microcolonies and persist under physiological shear stress., QC 20231201

Effective treatment of bacterial infections requires methods that accurately and quickly identify which antibiotic should be prescribed. This review describes recent research on the development of optotracing methodologies for bacterial and biofilm detection and diagnostics. Optotracers are small, chemically well-defined, anionic fluorescent tracer molecules that detect peptide- and carbohydrate-based biopolymers. This class of organic molecules (luminescent conjugated oligothiophenes) show unique electronic, electrochemical and optical properties originating from the conjugated structure of the compounds. The photophysical properties are further improved as donor-acceptor-donor (D-A-D)-type motifs are incorporated in the conjugated backbone. Optotracers bind their biopolymeric target molecules via electrostatic interactions. Binding alters the optical properties of these tracer molecules, shown as altered absorption and emission spectra, as well as ON-like switch of fluorescence. As the optotracer provides a defined spectral signature for each binding partner, a fingerprint is generated that can be used for identification of the target biopolymer. Alongside their use for in situ experimentation, optotracers have demonstrated excellent use in studies of a number of clinically relevant microbial pathogens. These methods will find widespread use across a variety of communities engaged in reducing the effect of antibiotic resistance. This includes basic researchers studying molecular resistance mechanisms, academia and pharma developing new antimicrobials targeting biofilm infections and tests to diagnose biofilm infections, as well as those developing antibiotic susceptibility tests for biofilm infections (biofilm-AST). By iterating between the microbial world and that of plants, development of the optotracing technology has become a prime example of successful cross-feeding across the boundaries of disciplines. As optotracers offers a capacity to redefine the way we, QC 20230920

Optotracers are conformation-sensitive fluorescent tracer molecules that detect peptide- and carbohydrate-based biopolymers. Their binding to bacterial cell walls allows selective detection and visualisation of Staphylococcus aureus (S. aureus). Here, we investigated the structural properties providing optimal detection of S. aureus. We quantified spectral shifts and fluorescence intensity in mixes of bacteria and optotracers, using automatic peak analysis, cross-correlation, and area-under-curve analysis. We found that the length of the conjugated backbone and the number of charged groups, but not their distribution, are important factors for selective detection of S. aureus. The photophysical properties of optotracers were greatly improved by incorporating a donor-acceptor-donor (D-A-D)-type motif in the conjugated backbone. With significantly reduced background and binding-induced on-switch of fluorescence, these optotracers enabled real-time recordings of S. aureus growth. Collectively, this demonstrates that chemical structure and photophysics are key tunable characteristics in the development of optotracers for selective detection of bacterial species., Funding Agencies|AIMES -Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet [1-249/2019]; KTH Royal Institute of Technology [VF-2019-0110]; Erling-Persson Family Foundation [4-1784/2016]; Swedish Research CouncilSwedish Research CouncilEuropean Commission [00748]; Swedish Foundation for Strategic ResearchSwedish Foundation for Strategic Research [SB12-00347]; Getinge AB [4-1599/2018]

Antimicrobial resistance is a medical threat of global dimensions. Proper antimicrobial susceptibility testing (AST) for drug development, patient diagnosis and treatment is crucial to counteract ineffective drug use and resistance development. Despite the important role of bacterial biofilms in chronic and device-associated in-fections, the efficacy of antibiotics is determined using planktonic cultures. To address the need for antibiotics targeting bacteria in the biofilm lifestyle, we here present an optotracing-based biofilm-AST using Salmonella as model. Our non-disruptive method enables real-time recording of the extracellular matrix (ECM) components, providing specific detection of the biofilm lifestyle. Biofilm formation prior to antibiotic challenge can thus be confirmed and pre-treatment data collected. By introducing Kirby-Bauer discs, we performed a broad screen of the effects of antibiotics representing multiple classes, and identified compounds with ECM inhibitory as well as promoting effects. These compounds were further tested in agar-based dose-response biofilm-AST assays. By quantifying the ECM based on the amount of curli, and by visualizing the biofilm size and morphology, we achieved new information directly reflecting the treated biofilm. This verified the efficacy of several antibiotics that were effective in eradicating pre-formed biofilms, and it uncovered intriguing possible resistance mecha-nisms initiated in response to treatments. By providing deeper insights into the resistances and susceptibilities of microbes, expanded use of the biofilm-AST will contribute to more effective treatments of infections and reduced resistance development., QC 20221115

Candida albicans is the most common fungal pathogen in humans, implicated in hospital-acquired infections, secondary infections in human immunodeficiency virus (HIV) patients, and is a significant contributor to the global antimicrobial resistance (AMR) burden. Early detection of this pathogen is needed to guide preventative strategies and the selection and development of therapeutic treatments. Fungal biofilms are a unique heterogeneous mix of cell types, extracellular carbohydrates and amyloid aggregates. Perhaps due to the dominance of carbohydrates in fungi, to date, few specific methods are available for the detection of fungal biofilms. Here we present a new optotracing-based method for the detection and analysis of yeast and biofilms based on C. albicans SC5314 as a model. Using commercial extracts of cell wall carbohydrates, we showed the capability of the optotracer EbbaBiolight 680 for detecting chitin and beta-glucans. The sensitivity of this tracer to these carbohydrates in their native environment within fungal cells enabled the visualization of both yeast and hyphal forms of the microbe. Analysis of optotracer fluorescence by confocal laser scanning microscopy revealed extensive staining of fungi cell walls as well as the presence of intracellular amyloid aggregates within a subpopulation of cells within the biofilm. Further analysis of the photophysical properties of bound tracers by spectroscopy and spectral imaging revealed polymorphisms between amyloid aggregates within yeast and hyphal cells and enabled their differentiation. With exceptional spatial and temporal resolution, this assay adds a new technique that facilitates future understanding of fungal biofilms and their formation, and enables direct, unbiased diagnostics of these medically relevant biofilms, as well as the development of antifungal strategies., QC 20220930

Biofilms enable bacteria to colonize numerous ecological niches. Bacteria within a biofilm are protected by the extracellular matrix (ECM), of which the fibril-forming amyloid protein curli and polysaccharide cellulose are major components in members of Salmonella, Eschericha and Mycobacterium genus. A shortage of real-time detection methods has limited our understanding of how ECM production contributes to biofilm formation and pathogenicity. Here we present optotracing as a new semi-high throughput method for dynamic monitoring of Salmonella biofilm growth on air-solid interfaces. We show how an optotracer with binding-induced fluorescence acts as a dynamic fluorescent reporter of curli expression during biofilm formation on agar. Using spectrophotometry and microscopic imaging of fluorescence, we analyse in real-time the development of the curli architecture in relation to bacterial cells. With exceptional spatial and temporal precision, this revealed a well-structured, non-uniform distribution of curli organised in distally projecting radial channel patterns. Dynamic monitoring of the biofilm also showed defined regions undergoing different growth phases. ECM structures were found to assemble in regions of late exponential growth phase, suggesting that ECM forms on site after bacteria colonize the surface. As the optotracer biofilm method expedites screening of curli production, providing exceptional spatial-temporal understanding of the surface-associated biofilm lifestyle, this method adds a new technique to further our understanding of bacterial biofilms., QC 20220224

Metal-based high-touch surfaces used for indoor applications such as doorknobs, light switches, handles and desks need to remain their antimicrobial properties even when tarnished or degraded. A novel laboratory methodology of relevance for indoor atmospheric conditions and fingerprint contact has therefore been elaborated for combined studies of both tarnishing/corrosion and antimicrobial properties of such high-touch surfaces. Cu metal was used as a benchmark material. The protocol includes pre-tarnishing/corrosion of the high touch surface for different time periods in a climatic chamber at repeated dry/wet conditions and artificial sweat deposition followed by the introduction of bacteria onto the surfaces via artificial sweat droplets. This methodology provides a more realistic and reproducible approach compared with other reported procedures to determine the antimicrobial efficiency of high-touch surfaces. It provides further a possibility to link the antimicrobial characteristics to physical and chemical properties such as surface composition, chemical reactivity, tarnishing/corrosion, surface roughness and surface wettability. The results elucidate that bacteria interactions as well as differences in extent of tarnishing can alter the physical properties (e.g. surface wettability, surface roughness) as well as the extent of metal release. The results clearly elucidate the importance to consider changes in chemical and physical properties of indoor hygiene surfaces when assessing their antimicrobial properties., QC 20210420

Organic electrochemical transistors (OECTs) are used in research and diagnostic applications due to their facile manufacture, scalability, and biocompatibility. In these devices, the source–drain current upon gate voltage application depends on ion concentration in the electrolyte. This study investigates whether an OECT can be employed to monitor bacterial growth since it is known that the concentration of charged species increases in bacterial cultures during growth. A poly(3,4-ethylenedioxythiophene):polystyrene sulfonate-based single-well OECT, compatible with long-term incubation of bacterial cultures, is fabricated. It is shown that the growth of Salmonella alters the transfer characteristics of the device and demonstrates how it can be applied to monitor growth in real-time by recording the source–drain current at gate voltage +0.5 V. The signal can also be measured in filtrates of bacterial cultures, devoid of bacterial cells. This suggests that the signal originates from charged metabolic products. Bacterial biofilm formation does not alter the device response. This proof-of-principle study presents OECT recordings as an alternative to optical methods, allowing bacterial growth to be monitored in transparent and opaque media alike. By measuring metabolic products rather than bacterial cell multiplication, insight into the stationary phase and other nondividing states may be obtained in the future., QC 20220824