A Novel Stool PCR Test for Helicobacter pylori May Predict Clarithromycin Resistance and Eradication of Infection at a High Rate.

Clarithromycin-based regimens are commonly used as a first-line therapy for Helicobacter pylori-positive patients; however, resistance to clarithromycin has led to treatment failures. The aim of this study was to evaluate the feasibility of using stool samples to detect the presence of H. pylori DNA while concurrently detecting mutations associated with resistance to clarithromycin. For this purpose, total DNA was extracted from 294 raw stool specimens from H. pylori-positive and -negative patients. TaqMan real-time PCR amplification was used to detect the presence of H. pylori as well as to predict the phenotype of the organism and the related outcome for patients treated with clarithromycin. Clarithromycin resistance was determined upon analysis of the PCR result. Patients were also tested by a urea breath test and were subjected to esophagogastroduodenoscopy, followed by histology, culture, and a rapid urease test, in order to obtain a consensus patient infection status. Of 294 total stool samples, 227 were deemed true positive. The sensitivity of H. pylori detection by PCR was 93.8%. Of 213 true-positive samples that were sequenced, 36.2% showed point mutations associated with clarithromycin resistance (A2142C, A2142G, A2143G). The final correlation of the mutant genotypes as determined by sequencing with the eradication of infection was 86%. We found that Helicobacter pylori DNA can be detected in human stool specimens with high sensitivity and can therefore be used to determine the presence of the bacterium without obtaining a biopsy sample. Moreover, genotypic resistance to clarithromycin can be predicted without obtaining a biopsy sample, facilitating the choice of the right therapeutic approach.

The role of T cells in the regulation of acrolein-induced pulmonary inflammation and epithelial-cell pathology.

Exposure to acrolein in the ambient air in urban environments represents a considerable hazard to human health. Acrolein exposure causes airway inflammation, accumulation of monocytes, macrophages, and lymphocytes in the interstitium, mucous-cell metaplasia, and airspace enlargement. Currently, the mechanisms that control these events are unclear, and the relative contribution of T-cell subpopulations to pulmonary pathology after exposure to air toxics is unknown. In this study, we used a mouse model of pulmonary pathology induced by repeated acrolein exposure to examine whether pulmonary lymphocyte subpopulations differentially regulate inflammatory-cell accumulation and epithelial-cell pathology. To examine the role of the lymphocyte subpopulations, we used transgenic mice genetically deficient in either alphabeta T cells or gammadelta T cells and measured changes in several cellular, molecular, and pathologic outcomes associated with repeated inhalation exposure to 2.0 ppm or 0.5 ppm acrolein. To examine the potential functions of the lymphocyte subpopulations, we purified these cells from lung tissue of mice repeatedly exposed to 2.0 ppm acrolein, isolated and amplified the messenger RNA (mRNA*) transcripts, and performed oligonucleotide microarray analysis. Our data demonstrate that alphabeta T cells are primarily responsible for the accumulation of macrophages after acrolein exposure, whereas gammadelta T cells are the primary regulators of epithelial-cell homeostasis after repeated acrolein exposure. These findings are supported by the results of microarray analyses indicating that the two T-cell subpopulations have distinct gene-expression profiles after acrolein exposure. These data provide strong evidence that the T-cell subpopulations in the lung are major determinants of the response to pulmonary toxicant exposure and suggest that it is advantageous to elucidate the effector functions of these cells in the modulation of lung pathophysiology.

Development of a high throughput human stool specimen processing method for a molecular Helicobacter pylori clarithromycin resistance assay.

It has become critical to detect Helicobacter pylori (H. pylori) infection due to the link to gastric cancer with some strains. These strains are also increasing in resistance to antibiotics with clarithromycin leading the way as the first line treatment. Resistance to clarithromycin has been shown to correlate with the A2142G, A2142C, and A2143G mutations on the rrl gene. In the last few decades, non-invasive specimens, such as stool, have been a reliable alternate to gastric biopsy for immunoassay tests. More recently, it has been proven feasible for stool to be used in molecular based tests. Many of the core laboratories in the United States need a high throughput sample preparation to run this test. Here, a high throughput assay is compared to a previously published manual sample prep H. pylori molecular based assay. Using the Magna Pure 96 (Roche), at least 96 stool species and 96 biopsy specimens can be tested in an 8-hour shift of a clinical lab. The high throughput sample prep had a positive percent agreement (PPA) of 87% compared to the manual sample prep using the same testing configuration. The genotype predictions from the high throughput assay matched genotype predictions from the manual sample prep with the same stool sample 92% of the time. A concordance rate of 89% was observed with genotype predictions from the high throughput assay of the same patient stool and biopsy. In stool samples from the high throughput assay, there was 100% concordance between the quantitative polymerase chain reaction (qPCR)-derived genomic prediction and DNA sequencing data. The high throughput workflow can get more patients tested faster in addition to detection of mutations associated with clarithromycin resistance.

Development of a microplate-based fluorescence immunoassay using quantum dot streptavidin conjugates for enumeration of putative marine bacteria, Alteromonas sp., associated with a benthic harpacticoid copepod.

Attached bacteria inhabit the surfaces of many marine animals--a process that may play important roles in the survival and transport through aquatic systems. However, efficient detection of these bacteria has been problematic, especially small aquatic animals such as benthic harpacticoid copepod. Quantum dots (QD) have recently emerged as a significant tool in immunofluorescence detection because of their unique properties compared to other fluorescent probes. In the present study, a polyclonal antibody was raised against the Gram-negative marine bacterium, Alteromonas sp. A microplate-based immunofluorescence bioassay using QD strepavidin conjugates was developed for quantifying putative Alteromonas sp. cells located on the surfaces of a marine harpacticoid copepod, Microarthridion littorale. The number of attached Alteromonas sp. was estimated to be 10(2)+/-8 CFU using this method. The QD approach, coupled to a microplate assay can potentially provide an efficient and accurate method for rapidly detecting multiple bacteria species attached to small invertebrate animals because of their unique excitation and emission characteristics.

The Applicability of TaqMan-Based Quantitative Real-Time PCR Assays for Detecting and Enumerating Cryptosporidium spp. Oocysts in the Environment.

Quantitative real-time polymerase chain reaction (qPCR) assays to detect Cryptosporidium oocysts in clinical samples are increasingly being used to diagnose human cryptosporidiosis, but a parallel approach for detecting and identifying Cryptosporidium oocyst contamination in surface water sources has yet to be established for current drinking water quality monitoring practices. It has been proposed that Cryptosporidium qPCR-based assays could be used as viable alternatives to current microscopic-based detection methods to quantify levels of oocysts in drinking water sources; however, data on specificity, analytical sensitivity, and the ability to accurately quantify low levels of oocysts are limited. The purpose of this study was to provide a comprehensive evaluation of TaqMan-based qPCR assays, which were developed for either clinical or environmental investigations, for detecting Cryptosporidium oocyst contamination in water. Ten different qPCR assays, six previously published and four developed in this study were analyzed for specificity and analytical sensitivity. Specificity varied between all ten assays, and in one particular assay, which targeted the Cryptosporidium 18S rRNA gene, successfully detected all Cryptosporidium spp. tested, but also cross-amplified T. gondii, fungi, algae, and dinoflagellates. When evaluating the analytical sensitivity of these qPCR assays, results showed that eight of the assays could reliably detect ten flow-sorted oocysts in reagent water or environmental matrix. This study revealed that while a qPCR-based detection assay can be useful for detecting and differentiating different Cryptosporidium species in environmental samples, it cannot accurately measure low levels of oocysts that are typically found in drinking water sources.

Application of photostable quantum dots for indirect immunofluorescent detection of specific bacterial serotypes on small marine animals.

An indirect immunofluorescence approach was developed using semiconductor quantum dot nanocrystals to label and detect a specific bacterial serotype of the bacterial human pathogen Vibrio parahaemolyticus, attached to small marine animals (i.e. benthic harpacticoid copepods), which are suspected pathogen carriers. This photostable labeling method using nanotechnology will potentially allow specific serotypes of other bacterial pathogens to be detected with high sensitivity in a range of systems, and can be easily applied for sensitive detection to other Vibrio species such as Vibrio cholerae.

CD8+ T cells contribute to macrophage accumulation and airspace enlargement following repeated irritant exposure.

BACKGROUND: Persistent macrophage accumulation and alveolar enlargement are hallmark features of chronic obstructive pulmonary disease (COPD). A role for CD8(+) lymphocytes in the development of COPD is suggested based on observations that this T cell subset is increased in the airways and parenchyma of smokers that develop COPD with airflow limitation. In this study, we utilize a mouse model of COPD to examine the contributions of CD8(+) T cells in the persistent macrophage accumulation and airspace enlargement resulting from chronic irritant exposure. METHODS: We analyzed pulmonary inflammation and alveolar destruction in wild-type and Cd8-deficient mice chronically exposed to acrolein, a potent respiratory tract irritant. We further examined cytokine mRNA expression levels by RNase protection assay, matrix metalloproteinase (MMP) activity by gelatin zymography, and epithelial cell apoptosis by active caspase3 immunohistochemistry in wild-type and Cd8-deficient mice exposed chronically to acrolein. RESULTS: These studies demonstrate that CD8(+) T cells are important mediators of macrophage accumulation in the lung and the progressive airspace enlargement in response to chronic acrolein exposures. The expression of several inflammatory cytokines (IP-10, IFN-gamma, IL-12, RANTES, and MCP-1), MMP2 and MMP9 gelatinase activity, and caspase3 immunoreactivity in pulmonary epithelial cells were attenuated in the Cd8-deficient mice compared to wild-type. CONCLUSIONS: These results indicate that CD8(+) T cells actively contribute to macrophage accumulation and the development of irritant-induced airspace enlargement.