Phage Therapy of Mycobacterium Infections: Compassionate Use of Phages in 20 Patients With Drug-Resistant Mycobacterial Disease

Background: Nontuberculous Mycobacterium infections, particularly Mycobacterium abscessus, are increasingly common among patients with cystic fibrosis and chronic bronchiectatic lung diseases. Treatment is challenging due to intrinsic antibiotic resistance. Bacteriophage therapy represents a potentially novel approach. Relatively few active lytic phages are available and there is great variation in phage susceptibilities among M. abscessus isolates, requiring personalized phage identification. Methods: Mycobacterium isolates from 200 culture-positive patients with symptomatic disease were screened for phage susceptibilities. One or more lytic phages were identified for 55 isolates. Phages were administered intravenously, by aerosolization, or both to 20 patients on a compassionate use basis and patients were monitored for adverse reactions, clinical and microbiologic responses, the emergence of phage resistance, and phage neutralization in serum, sputum, or bronchoalveolar lavage fluid. Results: No adverse reactions attributed to therapy were seen in any patient regardless of the pathogen, phages administered, or the route of delivery. Favorable clinical or microbiological responses were observed in 11 patients. Neutralizing antibodies were identified in serum after initiation of phage delivery intravenously in 8 patients, potentially contributing to lack of treatment response in 4 cases, but were not consistently associated with unfavorable responses in others. Eleven patients were treated with only a single phage, and no phage resistance was observed in any of these. Conclusions: Phage treatment of Mycobacterium infections is challenging due to the limited repertoire of therapeutically useful phages, but favorable clinical outcomes in patients lacking any other treatment options support continued development of adjunctive phage therapy for some mycobacterial infections

Long-range surface plasmon resonance imaging for bioaffinity sensing

A novel bioaffinity sensor based on surface plasmon resonance (SPR) imaging measurements of a multiple-layered structure that supports the generation of long-range surface plasmons (LRSPs) at the water−metal interface is reported. LRSPs possess longer surface propagation lengths, higher electric field strengths, and sharper angular resonance curves than conventional surface plasmons. LRSPR imaging is a version of SPR imaging that requires a symmetric dielectric arrangement around the gold thin film. This arrangement is created using an SF10 prism/Cytop/gold/water multilayer film structure where Cytop is an amorphous fluoropolymer with a refractive index very close to that of water. LRSPR imaging experiments are performed at a fixed incident angle and lead to an enhanced response for the detection of surface binding interactions. As an example, the hybridization adsorption of a 16-mer single-stranded DNA (ssDNA) onto a two-component ssDNA array was monitored with LRSPR imaging. The ssDNA array was created using a new fabrication technology appropriate for the LRSPR multilayers

Creating advanced multifunctional biosensors with surface enzymatic transformations

This paper summarizes our recent work on the coupling of surface enzyme chemistry and bioaffinity interactions on biopolymer microarrays for the creation of multiplexed biosensors with enhanced selectivity and sensitivity. The surface sensitive techniques of surface plasmon resonance imaging (SPRI) and surface plasmon fluorescence spectroscopy (SPFS) are used to detect the surface enzymatic transformations in real time. Three specific examples of novel coupled surface bioaffinity/surface enzymatic processes are demonstrated: (i) a surface enzymatic amplification method utilizing the enzyme ribonuclease H (RNase H) in conjunction with RNA microarrays that permits the ultrasensitive direct detection of genomic DNA at a concentration of 1 fM without labeling or PCR amplification, (ii) the use of RNADNA ligation chemistry to create renewable RNA microarrays from single stranded DNA microarrays, and (iii) the application of T7RNApolymerase for the on-chip replication ofRNAfrom double strandedDNAmicroarray elements. In addition, a simple yet powerful theoretical framework that includes the contributions of both enzyme adsorption and surface enzyme kinetics is used to quantitate surface enzyme reactivity. This model is successfully applied to SPRI and SPFS measurements of surface hydrolysis reactions of RNase H and Exonuclease III (Exo III) on oligonucleotide microarray

Enhanced bioaffinity sensing using surface plasmons, surface enzyme reactions, nanoparticles and diffraction gratings

This paper introduces a novel approach to surface bioaffinity sensing based on the adsorption of nanoparticles onto a gold diffraction grating that supports the excitation of planar surface plasmons. A surface enzymatic amplification reaction is also incorporated into the detection scheme to enhance the sensitivity and utility of the nanoparticle-enhanced diffraction grating (NEDG) sensors. As a demonstration, the detection of microRNA is described where a combination of a surface polymerase reaction and DNA-modified nanoparticles is used to detect the bioaffinity adsorption of the target onto the probe-functionalized gold grating surface. The enzymatically-amplified NEDG sensors possess a great potential for a wide range of applications including the detection of biosecurity agents, DNA and RNA viruses, biomarkers, and proteins

Attomole detection of microRNAs by nanoparticle-amplified SPR imaging measurements of surface polyadenylation reactions

Multiple microRNAs (miRNAs) are detected in a microarray format using a novel approach that combines a surface enzyme reaction with nanoparticle-amplified SPR imaging (SPRI). The surface reaction of poly(A) polymerase creates poly(A) tails on miRNAs hybridized onto locked nucleic acid (LNA) microarrays. DNA-modified nanoparticles are then adsorbed onto the poly(A) tails and detected with SPRI. This ultrasensitive nanoparticle-amplified SPRI methodology can be used for miRNA profiling at attomole levels

Fabricating RNA microarrays with RNA-DNA surface ligation chemistry

A novel surface attachment strategy that utilizes RNA−DNA surface ligation chemistry to create renewable RNA microarrays from single-stranded DNA (ssDNA) microarrays on gold surfaces is demonstrated. The enzyme T4 DNA ligase was used to catalyze the formation of a phosphodiester bond between 5‘-phosphate-modified ssDNA attached to the surface and the 3‘-hydroxyl group of unlabeled RNA molecules from solution in the presence of a complementary template DNA strand. Surface plasmon resonance imaging (SPRI) measurements were performed to characterize the ligation process as well as to verify the bioactivity of the ssRNA microarray in terms of (i) the hybridization adsorption of complementary DNA onto the RNA array to form a surface RNA−DNA heteroduplex and (ii) the hydrolysis of the RNA microarrays with either ribonuclease S or ribonuclease H (RNase H). The hydrolysis of the surface-bound RNA with RNase H required the presence of a surface heteroduplex and, upon completion, regenerated the original 5‘-phosphate-terminated ssDNA array elements. These ssDNA array elements could be ligated again to create a new RNA microarray. These RNA microarrays can be used in the study of RNA−protein/RNA/aptamer bioaffinity interactions and for the enzymatically amplified SPRI detection of DNA in the presence of RNase H

Nanoparticle-enhanced diffraction gratings for ultrasensitive surface plasmon biosensing

Ultrasensitive surface bioaffinity sensors are created by the adsorption of gold nanoparticles onto gold diffraction gratings. An enhanced diffraction obtained in a surface plasmon resonance geometry is observed due to the optical coupling of the planar surface plasmons in the grating to the localized surface plasmons in the gold nanoparticles. As a first example, these nanoparticle grating biosensors are employed to detect unmodified DNA at a concentration of 10 fM

Surface enzyme kinetics for biopolymer microarrays : a combination of Langmuir and Michaelis-Menten concepts

Real-time surface plasmon resonance (SPR) imaging measurements of surface enzymatic reactions on DNA microarrays are analyzed using a kinetics model that couples the contributions of both enzyme adsorption and surface enzyme reaction kinetics. For the case of a 1:1 binding of an enzyme molecule (E) to a surface-immobilized substrate (S), the overall enzymatic reaction can be described in terms of classical Langmuir adsorption and Michaelis−Menten concepts and three rate constants:  enzyme adsorption (ka), enzyme desorption (kd) and enzyme catalysis (kcat). In contrast to solution enzyme kinetics, the amount of enzyme in solution is in excess as compared to the amount of substrate on the surface. Moreover, the surface concentration of the intermediary enzyme−substrate complex (ES) is not constant with time, but goes to zero as the reaction is completed. However, kinetic simulations show that the fractional surface coverage of ES on the remaining unreacted sites does reach a steady-state value throughout the course of the surface reaction. This steady-state value approaches the Langmuir equilibrium value for cases where ka[E] kcat. Experiments using the 3‘ → 5‘ exodeoxyribonuclease activity of Exonuclease III on double-stranded DNA microarrays as a function of temperature and enzyme concentration are used to demonstrate how this model can be applied to quantitatively analyze the SPR imaging data

Enhancement of the second harmonic signal from Hg1−xCdxTe (MCT) in the presence of an anodic oxide film

Second harmonic generation (SHG) is now widely regarded as a valuable tool for investigating electrode surfaces. Typically, most studies have been limited to substrates which lack bulk symmetry and monitoring events such as sub-monolayer formation and surface reconstruction. Here, the development of a model that can be used to quantitatively describe the enhanced SH signal observed in the presence of an anodic oxide film on a non-centrosymmetric substrate, Hg1xCdxTe (MCT), is described. The aim is to further expand the utility of SHG for probing different electrode systems. The growth of the high quality oxide films was first followed by in-situ ellipsometry. For thin films (<100 nm) grown at a constant current density of 150 A cm2, an effectively uniform oxide layer is found with a refractive index n of ~2.15 0.05 and exhibiting no absorption of the incident radiation at 632.8 nm (1.96 eV). In the presence of such an oxide film of 58 nm thickness, the second harmonic (SH) signal intensity measured in reflection is found to be significantly enhanced in both the PIN-POUT and PIN-SOUT polarization configurations. To quantify the changes observed, each layer in the model is assigned its own symmetry and optical constants (at the fundamental, and harmonic (= 2) frequencies and a defined thickness. Modeling of the SH rotational anisotropy experiments carried out at different angles of incidence indicated that most of this increase could be accounted for by multiple reflections of the fundamental wave = 1064 nm (1.17 eV) in the composite ambient/oxide/MCT layer, with little contribution from charge accumulation at the buried MCT/oxide interface for this oxide thickness

Diagnostics of spectrally resolved transient absorption : surface plasmon resonance of metal nanoparticles

Time and frequency resolved transient absorption measurements yield two-dimensional images that map the dynamical correlation between the center and width of the scattering function. Global analysis of such data allows unique diagnostics of the mechanics underlying the time evolution. We specialize in the case of surface plasmon resonances of optically driven nanoparticles. We present a catalog of 2D maps that can be used to fingerprint physically meaningful cases, and we provide two experimental examples to illustrate the diagnostic value of the maps and their utility in extracting the various time constants at play. In silver nanorods, the experiment shows a π/2 phase shift between the oscillations of the center and the width of the plasmon resonance. Inspection of the maps allows the assignment that the center of the plasmon resonance tracks the strain in shape-oscillations, while the width tracks the strain rate. This finding is the basis of the novel mechanism of plasmon damping due to electron scattering from the electrophoretic potential generated by the motion of the interfacial double layer in colloidal nanoparticles. Measurements in gold nanoparticles show over-damped oscillations, which obscure the phase correlation between the center and width of the plasmon. The damping is dominated by inhomogeneous dephasing, and the time dependence of the width, which follows the temperature of the nanoparticles, and is diagnostic of the interband transition contribution to the plasmon resonance