The recent Ebola and Zika epidemics demonstrate the need for the continuous surveillance, rapid diagnosis and real-time tracking of emerging infectious diseases. Fast, affordable sequencing of ...pathogen genomes - now a staple of the public health microbiology laboratory in well-resourced settings - can affect each of these areas. Coupling genomic diagnostics and epidemiology to innovative digital disease detection platforms raises the possibility of an open, global, digital pathogen surveillance system. When informed by a One Health approach, in which human, animal and environmental health are considered together, such a genomics-based system has profound potential to improve public health in settings lacking robust laboratory capacity.
To examine how stratifying persons born outside Canada according to tuberculosis (TB) incidence in their birth country and other demographic factors refines our understanding of TB epidemiology and ...local TB transmission.
Population-level TB surveillance programs and research studies in low incidence settings often report all persons born outside the country in which the study is conducted as "foreign-born"-a single label for a highly diverse population with variable TB risks. This may mask important TB epidemiologic trends and not accurately reflect local transmission patterns.
We used population-level data from two large cohorts in British Columbia (BC), Canada: an immigration cohort (n = 337,492 permanent residents to BC) and a genotyping cohort (n = 2290 culture-confirmed active TB cases). We stratified active TB case counts, incidence rates, and genotypic clustering (an indicator of TB transmission) in BC by birth country TB incidence, age at immigration, and years since arrival.
Persons from high-incidence countries had a 12-fold higher TB incidence than those emigrating from low-incidence settings. Estimates of local transmission, as captured by genotyping, versus reactivation of latent TB infection acquired outside Canada varied when data were stratified by birthplace TB incidence, as did patient-level characteristics of individuals in each group, such as age and years between immigration and diagnosis.
Categorizing persons beyond simply "foreign-born", particularly in the context of TB epidemiologic and molecular data, is needed for a more accurate understanding of TB rates and patterns of transmission.
Abstract
Motivation
Data visualization is an important tool for exploring and communicating findings from genomic and healthcare datasets. Yet, without a systematic way of organizing and describing ...the design space of data visualizations, researchers may not be aware of the breadth of possible visualization design choices or how to distinguish between good and bad options.
Results
We have developed a method that systematically surveys data visualizations using the analysis of both text and images. Our method supports the construction of a visualization design space that is explorable along two axes: why the visualization was created and how it was constructed. We applied our method to a corpus of scientific research articles from infectious disease genomic epidemiology and derived a Genomic Epidemiology Visualization Typology (GEViT) that describes how visualizations were created from a series of chart types, combinations and enhancements. We have also implemented an online gallery that allows others to explore our resulting design space of visualizations. Our results have important implications for visualization design and for researchers intending to develop or use data visualization tools. Finally, the method that we introduce is extensible to constructing visualizations design spaces across other research areas.
Availability and implementation
Our browsable gallery is available at http://gevit.net and all project code can be found at https://github.com/amcrisan/gevitAnalysisRelease.
Supplementary information
Supplementary data are available at Bioinformatics online.
While seasonal influenza vaccination is recommended for individuals with asthma, uptake in this population is low. We examined how self-rated health impacts reasons for not being immunized against ...influenza in Canadian adults with asthma, focusing on those who have never been immunized.
We pooled four cycles of the Canadian Community Health Survey (cycles 3.1(2005), 2007/08, 2009/10 and 2011/12), grouping individuals by whether their reasons for not having been vaccinated were perceptual or technical. We used a multivariable logistic regression model, adjusted for confounders, to quantify the relationship between self-rated health and their reported reasons for not vaccinating.
Among the 9,836 respondents, 84.4% cited perceptual barriers as a reason for not being vaccinated. After adjusting for socio-demographic characteristics and province of residence, we determined that reporting perceptual barriers was associated with self-rated health status, with the adjusted odds ratios ranging from 1.42 (95%CI: 0.97, 2.09) to 2.64 (95%CI: 1.74, 3.99) for fair and excellent health versus poor health, respectively. Each increase in self-rated health category was associated with greater odds of citing a perceptual rather than technical barrier as a reason for non-vaccination.
Self-reported health influences people's perception of the need for influenza vaccination. Viewing the results through the lens of the precaution adoption process model suggests that personalizing communication around both the risk of influenza and the effectiveness of the vaccine may improve uptake amongst adults with asthma.
Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health ...surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validation. In this Review, we outline the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.
An outbreak of tuberculosis occurred over a 3-year period in a medium-size community in British Columbia, Canada. The results of mycobacterial interspersed repetitive unit–variable-number ...tandem-repeat (MIRU-VNTR) genotyping suggested the outbreak was clonal. Traditional contact tracing did not identify a source. We used whole-genome sequencing and social-network analysis in an effort to describe the outbreak dynamics at a higher resolution.
Mycobacterium tuberculosis
is an important infectious disease even in developed countries with extensive control programs. This is the case in British Columbia, Canada, where the 2007 incidence rate of 6.4 cases per 100,000 population exceeded the national average of 4.7 cases per 100,000 population.
1
In May 2006, a case of smear-negative pleural tuberculosis was diagnosed in an adult in a medium-size community in British Columbia. A second case, manifested as disseminated tuberculosis, was reported in an infant in July 2006. Reverse contact tracing identified nine additional cases between August and October 2006, when the British Columbia Centre for Disease Control . . .
Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission ...routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying transmission inference from genomic data, using illustrative examples from M. tuberculosis and other pathogens routinely sequenced by public health agencies. We describe the laboratory and epidemiological scenarios under which genomics may or may not be used, provide an introduction to sequencing technologies and bioinformatics approaches to identifying transmission‐informative variation and resistance‐associated mutations, and discuss how variation must be considered in the light of available clinical and epidemiological information to infer transmission.
Abstract
Summary
Adjutant is an open-source, interactive and R-based application to support mining PubMed for literature reviews. Given a PubMed-compatible search query, Adjutant downloads the ...relevant articles and allows the user to perform an unsupervised clustering analysis to identify data-driven topic clusters. Following clustering, users can also sample documents using different strategies to obtain a more manageable dataset for further analysis. Adjutant makes explicit trade-offs between speed and accuracy, which are modifiable by the user, such that a complete analysis of several thousand documents can take a few minutes. All analytic datasets generated by Adjutant are saved, allowing users to easily conduct other downstream analyses that Adjutant does not explicitly support.
Availability and implementation
Adjutant is implemented in R, using Shiny, and is available at https://github.com/amcrisan/Adjutant.
Supplementary information
Supplementary data are available at Bioinformatics online.
Myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS) is a syndrome of unknown etiology characterized by profound fatigue exacerbated by physical activity, also known as post-exertional ...malaise (PEM). Previously, we did not detect evidence of immune dysregulation or virus reactivation outside of PEM periods. Here we sought to determine whether cardiopulmonary exercise stress testing of ME/CFS patients could trigger such changes. ME/CFS patients (n = 14) and matched sedentary controls (n = 11) were subjected to cardiopulmonary exercise on 2 consecutive days and followed up to 7 days post-exercise, and longitudinal whole blood samples analyzed by RNA-seq. Although ME/CFS patients showed significant worsening of symptoms following exercise versus controls, with 8 of 14 ME/CFS patients showing reduced oxygen consumption (Formula: see text) on day 2, transcriptome analysis yielded only 6 differentially expressed gene (DEG) candidates when comparing ME/CFS patients to controls across all time points. None of the DEGs were related to immune signaling, and no DEGs were found in ME/CFS patients before and after exercise. Virome composition (P = 0.746 by chi-square test) and number of viral reads (P = 0.098 by paired t-test) were not significantly associated with PEM. These observations do not support transcriptionally-mediated immune cell dysregulation or viral reactivation in ME/CFS patients during symptomatic PEM episodes.
Traditional pathogen detection methods in public health infectious disease surveillance rely upon the identification of agents that are already known to be associated with a particular clinical ...syndrome. The emerging field of metagenomics has the potential to revolutionize pathogen detection in public health laboratories by allowing the simultaneous detection of all microorganisms in a clinical sample, without a priori knowledge of their identities, through the use of next-generation DNA sequencing. A single metagenomics analysis has the potential to detect rare and novel pathogens, and to uncover the role of dysbiotic microbiomes in infectious and chronic human disease. Making use of advances in sequencing platforms and bioinformatics tools, recent studies have shown that metagenomics can even determine the whole-genome sequences of pathogens, allowing inferences about antibiotic resistance, virulence, evolution and transmission to be made. We are entering an era in which more novel infectious diseases will be identified through metagenomics-based methods than through traditional laboratory methods. The impetus is now on public health laboratories to integrate metagenomics techniques into their diagnostic arsenals.
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