Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates

Between 1996 and 2006, the US Centers for Disease Control reported that the only category of food-borne infections increasing in frequency were those caused by members of the genus Vibrio. The Gram-negative bacterium Vibrio vulnificus is a ubiquitous inhabitant of estuarine waters, and is the number one cause of seafood-related deaths in the US. Many V. vulnificus isolates have been studied, and it has been shown that two genetically distinct subtypes, distinguished by 16S rDNA and other gene polymorphisms, are associated predominantly with either environmental or clinical isolation. While local genetic differences between the subtypes have been probed, only the genomes of clinical isolates have so far been completely sequenced. In order to better understand V. vulnificus as an agent of disease and to identify the molecular components of its virulence mechanisms, we have completed whole genome shotgun sequencing of three diverse environmental genotypes using a pyrosequencing approach. V. vulnificus strain JY1305 was sequenced to a depth of 33×, and strains E64MW and JY1701 were sequenced to lesser depth, covering approximately 99.9% of each genome. We have performed a comparative analysis of these sequences against the previously published sequences of three V. vulnificus clinical isolates. We find that the genome of V. vulnificus is dynamic, with 1.27% of genes in the C-genotype genomes not found in the E- genotype genomes. We identified key genes that differentiate between the genomes of the clinical and environmental genotypes. 167 genes were found to be specifically associated with environmental genotypes and 278 genes with clinical genotypes. Genes specific to the clinical strains include components of sialic acid catabolism, mannitol fermentation, and a component of a Type IV secretory pathway VirB4, as well as several other genes with potential significance for human virulence. Genes specific to environmental strains included several that may have implications for the balance between self-preservation under stress and nutritional competence

Commercial Nucleic-Acid Amplification Tests for Diagnosis of Pulmonary Tuberculosis in Respiratory Specimens: Meta-Analysis and Meta-Regression

BACKGROUND: Hundreds of studies have evaluated the diagnostic accuracy of nucleic-acid amplification tests (NAATs) for tuberculosis (TB). Commercial tests have been shown to give more consistent results than in-house assays. Previous meta-analyses have found high specificity but low and highly variable estimates of sensitivity. However, reasons for variability in study results have not been adequately explored. We performed a meta-analysis on the accuracy of commercial NAATs to diagnose pulmonary TB and meta-regression to identify factors that are associated with higher accuracy. METHODOLOGY/PRINCIPAL FINDINGS: We identified 2948 citations from searching the literature. We found 402 articles that met our eligibility criteria. In the final analysis, 125 separate studies from 105 articles that reported NAAT results from respiratory specimens were included. The pooled sensitivity was 0.85 (range 0.36-1.00) and the pooled specificity was 0.97 (range 0.54-1.00). However, both measures were significantly heterogeneous (p<.001). We performed subgroup and meta-regression analyses to identify sources of heterogeneity. Even after stratifying by type of commercial test, we could not account for the variability. In the meta-regression, the threshold effect was significant (p = .01) and the use of other respiratory specimens besides sputum was associated with higher accuracy. CONCLUSIONS/SIGNIFICANCE: The sensitivity and specificity estimates for commercial NAATs in respiratory specimens were highly variable, with sensitivity lower and more inconsistent than specificity. Thus, summary measures of diagnostic accuracy are not clinically meaningful. The use of different cut-off values and the use of specimens other than sputum could explain some of the observed heterogeneity. Based on these observations, commercial NAATs alone cannot be recommended to replace conventional tests for diagnosing pulmonary TB. Improvements in diagnostic accuracy, particularly sensitivity, need to be made in order for this expensive technology to be worthwhile and beneficial in low-resource countries

The Effects of Demographics, Functioning, and Perceptions on the Relationship between Self-Reported and Objective Measures of Driving Exposure and Patterns among Older Adults.

The exploratory study reported here was intended to examine: how strongly subjectively reported driving avoidance behaviors (commonly referred to as self-regulation) and exposure were related to their objectively measured counterparts and whether it depended on the specific behavior; the extent to which gender and age play a role in the association between subjectively reported driving avoidance behaviors and exposure and their objectively measured counterparts; and the extent to which demographics, health and functioning, driving-related perceptions, and cognition influence the association between subjective and objective driving avoidance behaviors overall. The study used data from the Longitudinal Research on Aging Drivers (LongROAD) study, a multisite, prospective cohort study designed to generate empirical data for understanding the role of medical, behavioral, environmental, and technological factors in driving safety during the process of aging. Objective driving measures were derived from GPS/datalogger data from 2131 LongROAD participants’ vehicles. The corresponding subjective measures came from a comprehensive questionnaire administered to participants at baseline that asked them to report on their driving exposure, patterns, and other aspects of driving. Several other variables used in the analyses came from the comprehensive questionnaire and an in-person clinical assessment administered to participants at baseline. A series of simple linear and logistic models were fitted to examine the relationship between the subjective and objective driving measures of interest, and a multivariable analysis was conducted to examine the potential role of selected factors in the relationship between objective and subjective driving avoidance behaviors. Results of the models are presented and overall findings are discussed within the context of the existing research literature.http://deepblue.lib.umich.edu/bitstream/2027.42/193082/2/nihms959301.pdfPublished versio

The Association between Visual Abilities and Objectively-Measured Driving Space, Exposure, and Avoidance among Older Drivers.

http://deepblue.lib.umich.edu/bitstream/2027.42/193078/2/The-Association-Between-Visual-Abilities-and-Objectively-Measured-Driving-Space-Exposure-and-Avoidance-among-Older-Drivers.pdfPublished versio