Shared Mycobacterium avium Genotypes Observed among Unlinked Clinical and Environmental Isolates

Our understanding of the sources of Mycobacterium avium infection is partially based on genotypic matching of pathogen isolates from cases and environmental sources. These approaches assume that genotypic identity is rare in isolates from unlinked cases or sources. To test this assumption, a high-resolution PCR-based genotyping approach, large-sequence polymorphism (LSP)-mycobacterial interspersed repetitive unit–variable-number tandem repeat (MIRU-VNTR), was selected and used to analyze clinical and environmental isolates of M. avium from geographically diverse sources. Among 127 clinical isolates from seven locations in North America, South America, and Europe, 42 genotypes were observed. Among 12 of these genotypes, matches were seen in isolates from apparently unlinked patients in two or more geographic locations. Six of the 12 were also observed in environmental isolates. A subset of these isolates was further analyzed by alternative strain genotyping methods, pulsed-field gel electrophoresis and MIRU-VNTR, which confirmed the existence of geographically dispersed strain genotypes. These results suggest that caution should be exercised in interpreting high-resolution genotypic matches as evidence for an acquisition event

Methods and models to control and predict behavior of two dimensional paper networks for diagnostics

Thesis (Ph.D.)--University of Washington, 2014Medical care is dramatically more efficient when physicians can diagnose their patient's illness to guide appropriate treatment. Currently, there are two classes of diagnostic tests: high-performance gold standard laboratory-based tests that require complex and expensive infrastructure that is not available in clinics, homes, or rural areas; and inexpensive, easy-to-use, rapid lateral flow tests that often have poor sensitivity and specificity. Novel devices that achieve high sensitivity and specificity, while remaining accessible for point-of-care diagnosis in low-resource settings, would dramatically improve heath outcomes around the world. Recent developments toward 2-dimensional paper network (2DPN) diagnostics that combine the sophistication of microfluidics with the simplicity and low cost of lateral flow tests are a promising solution for point-of-care diagnostics. Integration, automation and design of these 2DPN devices would be improved if device engineers could predict how their assays would behave without needing to iterate through dozens of experiments to optimize conditions. These improvements can be realized through the development of techniques to predict and control the behavior of a variety of different components that are used in the assay design process. This project has developed a set of methods and models that are a valuable step toward the goal of fully controlled and "engineerable" assays. First, the process of printing reagents onto nitrocellulose membranes has been characterized--examining and modeling the imbibition of liquids into membranes. Second, techniques were developed to study protein adsorption to nitrocellulose surfaces, and a model was developed to evaluate and compare different rates of this adsorption process. Third, methods were developed to pattern and dry reagents for storage directly within the nitrocellulose membranes, and subsequently rehydrate them in a variety of controlled spatial and temporal distributions in a device. Fourth, a multi-step malaria assay was implemented using solely patterned and dried reagents. Fifth, a computational model of transport and binding of reagents within a single pore was developed to provide insight into the various parameters governing assay signal. Finally, another computational model was built to illustrate the multitude of binding interactions that occur when multivalent analytes and antibodies are used in an assay system

Investigation of Reagent Delivery Formats in a Multivalent Malaria Sandwich Immunoassay and Implications for Assay Performance

Conventional lateral flow tests (LFTs), the current standard bioassay format used in low-resource point-of-care (POC) settings, have limitations that have held back their application in the testing of low concentration analytes requiring high sensitivity and low limits of detection. LFTs use a premix format for a rapid one-step delivery of premixed sample and labeled antibody to the detection region. We have compared the signal characteristics of two types of reagent delivery formats in a model system of a sandwich immunoassay for malarial protein detection. The premix format produced a uniform binding profile within the detection region. In contrast, decoupling the delivery of sample and labeled antibody to the detection region in a sequential format produced a nonuniform binding profile in which the majority of the signal was localized to the upstream edge of the detection region. The assay response was characterized in both the sequential and premix formats. The sequential format had a 4- to 10-fold lower limit of detection than the premix format, depending on assay conjugate concentration. A mathematical model of the assay quantitatively reproduced the experimental binding profiles for a set of rate constants that were consistent with surface plasmon resonance measurements and absorbance measurements of the experimental multivalent malaria system