Biosurveillance: a review and update

Surveillance of emerging infectious diseases for biosecurity

Emerging infectious diseases, such as COVID-19, continue to pose significant threats to human beings and their surroundings. In addition, biological warfare, bioterrorism, biological accidents, and harmful consequences arising from dual-use biotechnology also pose a challenge for global biosecurity. Improving the early surveillance capabilities is necessary for building a common biosecurity shield for the global community of health for all. Furthermore, surveillance could provide early warning and situational awareness of biosecurity risks. However, current surveillance systems face enormous challenges, including technical shortages, fragmented management, and limited international cooperation. Detecting emerging biological risks caused by unknown or novel pathogens is of particular concern. Surveillance systems must be enhanced to effectively mitigate biosecurity risks. Thus, a global strategy of meaningful cooperation based on efficient integration of surveillance at all levels, including interdisciplinary integration of techniques and interdepartmental integration for effective management, is urgently needed. In this paper, we review the biosecurity risks by analyzing potential factors at all levels globally. In addition to describing biosecurity risks and their impact on global security, we also focus on analyzing the challenges to traditional surveillance and propose suggestions on how to integrate current technologies and resources to conduct effective global surveillance.

Bioaerosol monitoring by integrating DC impedance microfluidic cytometer with wet-cyclone air sampler

The recent outbreak of COVID-19 has highlighted the seriousness of airborne diseases and the need for a proper pathogen detection system. Compared to the ample amount of research on biological detection, work on integrated devices for air monitoring is rare. In this work, we integrated a wet-cyclone air sampler and a DC impedance microfluidic cytometer to build a cyclone-cytometer integrated air monitor (CCAM). The wet-cyclone air sampler sucks the air and concentrates the bioaerosols into 10 mL of aqueous solvent. After 5 min of air sampling, the bioaerosol-containing solution was conveyed to the microfluidic cytometer for detection. The device was tested with aerosolized microbeads, dust, and Escherichia coli (E. coli). CCAM is shown to differentiate particles from 0.96 to 2.95 μm with high accuracy. The wet cyclone air-sampler showed a 28.04% sampling efficiency, and the DC impedance cytometer showed 87.68% detection efficiency, giving a total of 24.59% overall CCAM efficiency. After validation of the device performance, CCAM was used to detect bacterial aerosols and their viability without any separate pretreatment step. Differentiation of dust, live E. coli, and dead E. coli was successfully performed by the addition of BacLight bacterial viability reagent in the sampling solvent. The usage could be further extended to detection of specific species with proper antibody fluorescent label. A promising strategy for aerosol detection is proposed through the constructive integration of a DC impedance microfluidic cytometer and a wet-cyclone air sampler.

Multi-drug resistance of Staphylococcus aureus Strains in Baqiyatallah hospital: a Primary Step Towards Digital Health Biomonitoring Systems

The aim of the study was to evaluate the drug-resistance patterns of Staphylococcus aureus infections in Baqiyatallah hospital within 2010–2019 and to present a novel monitoring and detection system making use of molecular laboratory methods teamed with molecular delimitation analyses. This in turn is a primary step to establishment of a digital health system within Baqiyatallah hospital as a perfect pilot instance for other hospitals to follow upon. Totally, 100 patients of Baqiyatallah hospital suspicious of Staphylococcus aureus infections were sampled. Bacterial identity confirmations were done using routine biochemical test. Antibiograms were made for all the patients in this study. Consequently, bacterial total DNA was extracted and 16S rDNA gene amplified and sequenced for all patients. To uncover any cryptic strain grouping within the samples, a molecular delimitation method, i.e. automated barcode gap discovery (ABGD), was done. Our results showed Ceftaroline to be the most and Erythromycin and Oxacillin the least effective drugs. Delimitation uncovered 19 groups out of which group 19 seemed to have location-specific genetic signals in regards to susceptibility of Erythromycin and Oxacillin. Our results indicate the importance of genetic identification of bacteria with respect to their genetic patterns before antibiotic administration in order to both reduce unnecessary medicine use and to biomonitor the bacterial patterns in respect to their behavior towards general antibiotics.

The Current State of Infectious Disasters Preparedness Around the World: A Qualitative Systematic Review (2007-2019)

Infectious disasters have specific features which require special approaches and facilities. The main challenge is the rate of spread, and their ability to traverse the Earth in a short time. The preparedness of hospitals to face these events is therefore of the utmost importance. This study was designed to assess the preparedness of countries facing biological events worldwide. A qualitative systematic review was done from PubMed (National Library of Medicine, Bethesda, MD), Scopus (Elsevier, Amsterdam, Netherlands), Web of Science (Thomson Reuters, New York, NY), ProQuest (Ann Arbor, MI), and Google Scholar (Google Inc, Mountain View, CA). Two journals were searched as key journals. The search period was from January 1, 2007 to December 30, 2018. Twenty-one (21) documents were selected including 7 (33%) from Asia, 7 (33%) from Europe, 4 (19%) from USA, 2 (10%) from Africa, and 1 (5%) multi-continental. Forty-six (46) common sub-themes were obtained and categorized into 13 themes (infection prevention control, risk perception, planning, essential support services, surveillance, laboratory, vulnerable groups, education and exercise and evaluation, human resource, clinical management of patients, risk communication, budget, and coordination). Not all articles discussed all the identified categories. There is an extended process required to reach complete preparedness for confronting biological events, including adequate and well-managed budget. Medical centers may have trouble dealing with such events, at least in some respects, but most developed countries seem to be more prepared in this regard.

Systematic analysis of the scientific literature on population surveillance

Introduction

Population surveillance provides data on the health status of the population through continuous scrutiny of different indicators. Identifying risk factors is essential for the quickly detecting and controlling of epidemic outbreaks and reducing the incidence of cross-infections and non-communicable diseases. The objective of the present study is to analyze research on population surveillance, identifying the main topics of interest for investigators in the area.

Methodology

We included documents indexed in the Web of Science Core Collection in the period from 2000 to 2019 and assigned with the generic Medical Subject Heading (MeSH) “population surveillance” or its related terms (“public health surveillance,” “sentinel surveillance” or “biosurveillance”). A co-occurrence analysis was undertaken to identify the document clusters comprising the main research topics. Scientific production, collaboration, and citation patterns in each of the clusters were characterized bibliometrically. We also analyzed research on coronaviruses, relating the results obtained to the management of the COVID-19 pandemic.

Results

We included 39,184 documents, which reflected a steady growth in scientific output driven by papers on “Public, Environmental & Occupational Health” (21.62% of the documents) and “Infectious Diseases” (10.49%). Research activity was concentrated in North America (36.41%) and Europe (32.09%). The USA led research in the area (40.14% of documents). Ten topic clusters were identified, including “Disease Outbreaks,” which is closely related to two other clusters (“Genetics” and “Influenza”). Other clusters of note were “Cross Infections” as well as one that brought together general public health concepts and topics related to non-communicable diseases (cardiovascular and coronary diseases, mental diseases, diabetes, wound and injuries, stroke, and asthma). The rest of the clusters addressed “Neoplasms,” “HIV,” “Pregnancy,” “Substance Abuse/Obesity,” and “Tuberculosis.” Although research on coronavirus has focused on population surveillance only occasionally, some papers have analyzed and collated guidelines whose relevance to the dissemination and management of the COVID-19 pandemic has become obvious. Topics include tracing the spread of the virus, limiting mass gatherings that would facilitate its propagation, and the imposition of quarantines. There were important differences in the scientific production and citation of different clusters: the documents on mental illnesses, stroke, substance abuse/obesity, and cross-infections had much higher citations than the clusters on disease outbreaks, tuberculosis, and especially coronavirus, where these values are substantially lower.

Conclusions

The role of population surveillance should be strengthened, promoting research and the development of public health surveillance systems in countries whose contribution to the area is limited.

A re-organizing biosurveillance framework based on fog and mobile edge computing

Biological threats are becoming a serious security issue for many countries across the world. Effective biosurveillance systems can primarily support appropriate responses to biological threats and consequently save human lives. Nevertheless, biosurveillance systems are costly to implement and hard to operate. Furthermore, they rely on static infrastructures that might not cope with the evolving dynamics of the monitored environment. In this paper, we present a reorganizing biosurveillance framework for the detection and localization of biological threats with fog and mobile edge computing support. In the proposed framework, a hierarchy of fog nodes are responsible for aggregating monitoring data within their regions and detecting potential threats. Although fog nodes are deployed on a fixed base station infrastructure, the framework provides an innovative technique for reorganizing the monitored environment structure to adapt to the evolving environmental conditions and to overcome the limitations of the static base station infrastructure. Evaluation results illustrate the ability of the framework to localize biological threats and detect infected areas. Moreover, the results show the effectiveness of the reorganization mechanisms in adjusting the environment structure to cope with the highly dynamic environment.

Factors affecting hospital response in biological disasters: A qualitative study

Background: The fatal pandemics of infectious diseases and the possibility of using microorganisms as biological weapons are both rising worldwide. Hospitals are vital organizations in response to biological disasters and have a crucial role in the treatment of patients. Despite the advances in studies about hospital planning and performance during crises, there are no internationally accepted standards for hospital preparedness and disaster response. Thus, this study was designed to explain the effective factors in hospital performance during biological disasters. Methods: Qualitative content analysis with conventional approach was used in the present study. The setting was Ministry of Health and related hospitals, and other relevant ministries responsible at the time of biologic events in Islamic Republic of Iran (IR of Iran) in 2018. Participants were experts, experienced individuals providing service in the field of biological disaster planning and response, policymakers in the Ministry of Health, and other related organizations and authorities responsible for the accreditation of hospitals in IR of Iran. Data were collected using 12 semi-structured interviews in Persian language. Analysis was performed according to Graneheim method. Results: After analyzing 12 interviews, extraction resulted in 76 common codes, 28 subcategories, and 8 categories, which are as follow: detection; treatment and infection control; coordination, Resources; training and exercises; communication and information system; construction; and planning and assessment. Conclusion: Hospital management in outbreaks of infectious diseases (intentional or unintentional) is complex and requires different actions than during natural disasters. In such disasters, readiness to respond and appropriate action is a multifaceted operation. In IR of Iran, there have been few researches in the field of hospital preparation in biologic events, and the possibility of standardized assessment has be reduced due to lack of key skills in confronting biological events. It is hoped that the aggregated factors in the 8 groups of this study can evaluate hospital performance more coherently.

Implementation System of a Biosurveillance System in the Republic of Korea and Its Legal Ramifications

Laws are fundamental tools that regulate and manage various issues to protect the rights of the people in a society. Legislation on disease surveillance enables agencies to regulate and manage public health, including preventing the spread of infectious diseases. We assessed the Infectious Disease Prevention and Control Act of Korea (IDPCA) through the lens of biosurveillance to understand its effectiveness in protecting public health. In addition, the relevant legislation and regulations of the United States and the World Health Organization were examined. The evaluation concludes that the current IDPCA is limited in terms of providing guidance for early detection of and response to hazards using integrated data and an information-sharing system. Further revision of the laws is needed to enable early detection and warning of potential threats to public health.

The authors assessed the Infectious Disease Prevention and Control Act of Korea (IDPCA) through the lens of biosurveillance to understand its effectiveness in protecting public health. The relevant legislation and regulations of the United States and the World Health Organization also were examined. They concluded that the current IDPCA is limited in terms of providing guidance for early detection of and response to hazards using integrated data and an information-sharing system.

Emerging and Enabling Technologies in Biodefense

The emergence of new biotechnologies provides great promise for biodefense, especially for key objectives of biosurveillance and early warning, microbial forensics, risk and threat assessment, horizon scanning in biotechnology, and medical countermeasure (MCM) development, scale-up, and delivery. Understanding and leveraging the newly developed capabilities afforded by emerging biotechnologies require knowledge about cutting-edge research and its real or proposed application(s), the process through which biotechnologies advance, and the educational and research infrastructure that promotes multi-disciplinary science. Innovation in research and technology development are driven by sector-specific needs and the convergence of the physical, chemical, material, computer, engineering, and/or life sciences. Biotechnologies developed for other sectors could be applied to biodefense, especially if the individuals involved are able to innovate in concept design and development. Of all biodefense objectives, biosurveillance seems to have reaped the most benefit from emerging biotechnologies, specifically the integration and analysis of diverse clinical, biological, demographic, and other relevant data. More recently, scientists have begun applying synthetic biology, genomics, and microfluidics to the development of new products and platforms for MCMs. Unlike these objectives, investments in microbial forensics have been few, limiting its ability to harness biotechnology advances for collecting and analyzing data. Looking to the future, emerging biotechnologies can provide new opportunities for enhancing biodefense by addressing capability gaps.

An Overview of Zoonotic Disease Outbreaks and its Forensic Management Over Time

Most emerging or re-emerging infections are vector-borne or zoonotic and can be disseminated worldwide by infected humans or animals. They are a major public health problem and cause a great impact on economy. Zoonotic outbreaks began to be characterized in the 90s, after the creation of Europol and the FBI. Such investigations are carried by forensic pathologists and other specialists to determine whether an outbreak is natural or deliberate. This review will discuss ten zoonotic outbreaks nonrelated to wars focusing on forensic management. In conclusion, some points should be highlighted in the management of a zoonotic outbreak: (i) its diagnosis and detection by forensic pathologists and the coordination of efforts between other specialists are key factors; (ii) communication guidelines and an efficient healthcare system are crucial for any emergency response; (iii) biosafety of all specialists involved must be guaranteed.

How Prepared Are We for Possible Bioterrorist Attacks: An Approach from Emergency Medicine Perspective

Preparedness for bioterrorist attacks and early recognition of specific agents are essential for public health. Emergency departments may play an important role in this field. The large spectrum of bioterrorism involves not only disastrous terrorism with mass casualties, but also microevents using low technology but producing civil unrest, disruption, disease, disabilities, and death. It aims not only to cause mortality and morbidity, but also to lead to social and political disruption. Preparedness appears to be the most potent defense against possible bioterrorist events. In this article, we aim to create awareness against biological agents and underline the importance of emergency departments in this public health problem.

Primordial and Primary Levels of Biothreat and Bioterrorism Prevention

There is still an abundance of preventive and solving measures against biological attacks that makes confusion and dezorientation among experts and health policy-makers. Our pyramidal model of adversaries, and spherical system of prevention help us to solve this problem. They make clearly to us, which measures should be applied at any of four levels of prevention without robust spending.

Primordial level of prevention should be focused to stop entering perpetrator/source of infection/reservoir of pathogen and biological agent/pathogen on defended territory. This is the first line of biodefense, deeply and multiply linked with the strategies of intelligence and deterrence.

The primary prevention of biological attack is focused on monitoring and surveillance of potential internal sources of biological agents and bioterrorists. We elaborate three types of surveillance: clinical (syndromic), laboratory and environmental.

Both levels of prevention were detailed analyzed, according to the next issues: Perpetrator/source of infection/reservoir of pathogen (Sophistication, Motivation, Intention, Intelligence, Secrecy, Number of perpetrators, Number of sources of infection/reservoirs, Accessibility to sources of agent/pathogen, Accessibility to targets/population at risk), Biological agent/pathogen (A category, B category, C category, Emerging pathogens, Amount of the available agent/pathogen), Means/media of delivery/factors of transmission (Air, Water, Food, Fomites, Vectors, Biological ammunition, Delivery systems, Dispersion systems mechanism of release), Target/susceptible population at risk (Intelligence, Secrecy, Personal control, Control of means/media of delivery/factors of transmission, Physical protection, Protection by chemoprophylaxis, Protection by immunoprophilaxis, Number of people in a target/population at risk, Importance of target/population at risk, Location of target/population, Distribution of people in a target/population at risk), and for each issue a whole spectrum of cheap, simple and effective preventive measures were proposed.

Insights from a Systematic Search for Information on Designs, Costs, and Effectiveness of Poliovirus Environmental Surveillance Systems

Poliovirus surveillance plays a critical role in achieving and certifying eradication and will play a key role in the polio endgame. Environmental surveillance can provide an opportunity to detect circulating polioviruses prior to the observation of any acute flaccid paralysis cases. We completed a systematic review of peer-reviewed publications on environmental surveillance for polio including the search terms "environmental surveillance" or "sewage," and "polio," "poliovirus," or "poliomyelitis," and compared characteristics of the resulting studies. The review included 146 studies representing 101 environmental surveillance activities from 48 countries published between 1975 and 2016. Studies reported taking samples from sewage treatment facilities, surface waters, and various other environmental sources, although they generally did not present sufficient details to thoroughly evaluate the sewage systems and catchment areas. When reported, catchment areas varied from 50 to over 7.3 million people (median of 500,000 for the 25% of activities that reported catchment areas, notably with 60% of the studies not reporting this information and 16% reporting insufficient information to estimate the catchment area population size). While numerous studies reported the ability of environmental surveillance to detect polioviruses in the absence of clinical cases, the review revealed very limited information about the costs and limited information to support quantitative population effectiveness of conducting environmental surveillance. This review motivates future studies to better characterize poliovirus environmental surveillance systems and the potential value of information that they may provide in the polio endgame.

Evaluation of PCR Systems for Field Screening of Bacillus anthracis

There is little published data on the performance of hand-portable polymerase chain reaction (PCR) systems that can be used by first responders to determine if a suspicious powder contains a potential biothreat agent. We evaluated 5 commercially available hand-portable PCR instruments for detection of Bacillus anthracis. We used a cost-effective, statistically based test plan to evaluate systems at performance levels ranging from 0.85-0.95 lower confidence bound (LCB) of the probability of detection (POD) at confidence levels of 80% to 95%. We assessed specificity using purified genomic DNA from 13 B. anthracis strains and 18 Bacillus near neighbors, potential interference with 22 suspicious powders that are commonly encountered in the field by first responders during suspected biothreat incidents, and the potential for PCR inhibition when B. anthracis spores were spiked into these powders. Our results indicate that 3 of the 5 systems achieved 0.95 LCB of the probability of detection with 95% confidence levels at test concentrations of 2,000 genome equivalents/mL (GE/mL), which is comparable to 2,000 spores/mL. This is more than sufficient sensitivity for screening visible suspicious powders. These systems exhibited no false-positive results or PCR inhibition with common suspicious powders and reliably detected B. anthracis spores spiked into these powders, though some issues with assay controls were observed. Our testing approach enables efficient performance testing using a statistically rigorous and cost-effective test plan to generate performance data that allow users to make informed decisions regarding the purchase and use of field biodetection equipment.

The authors evaluated 5 commercially available hand-portable PCR instruments for detecting Bacillus anthracis. These systems exhibited no false-positive results or PCR inhibition with common suspicious powders and reliably detected B. anthracis spores spiked into these powders, though some issues with assay controls were observed.

Measuring Global Disease with Wikipedia: Success, Failure, and a Research Agenda

Effective disease monitoring provides a foundation for effective public health systems. This has historically been accomplished with patient contact and bureaucratic aggregation, which tends to be slow and expensive. Recent internet-based approaches promise to be real-time and cheap, with few parameters. However, the question of when and how these approaches work remains open. We addressed this question using Wikipedia access logs and category links. Our experiments, replicable and extensible using our open source code and data, test the effect of semantic article filtering, amount of training data, forecast horizon, and model staleness by comparing across 6 diseases and 4 countries using thousands of individual models. We found that our minimal-configuration, language-agnostic article selection process based on semantic relatedness is effective for improving predictions, and that our approach is relatively insensitive to the amount and age of training data. We also found, in contrast to prior work, very little forecasting value, and we argue that this is consistent with theoretical considerations about the nature of forecasting. These mixed results lead us to propose that the currently observational field of internet-based disease surveillance must pivot to include theoretical models of information flow as well as controlled experiments based on simulations of disease.

Expanding veterinary biosurveillance in Washington, DC: The creation and utilization of an electronic-based online veterinary surveillance system

OBJECTIVES

To enhance the early detection of emerging infectious diseases and bioterrorism events using companion animal-based surveillance.

METHODS

Washington, DC, small animal veterinary facilities (n=17) were surveyed to determine interest in conducting infectious disease surveillance. Using these results, an electronic-based online reporting system was developed and launched in August 2015 to monitor rates of canine influenza, canine leptospirosis, antibiotic resistant infections, canine parvovirus, and syndromic disease trends.

RESULTS

Nine of the 10 facilities that responded expressed interest conducting surveillance. In September 2015, 17 canine parvovirus cases were reported. In response, a campaign encouraging regular veterinary preventative care was launched and featured on local media platforms. Additionally, during the system's first year of operation it detected 5 canine leptospirosis cases and 2 antibiotic resistant infections. No canine influenza cases were reported and syndromic surveillance compliance varied, peaking during National Special Security Events.

CONCLUSIONS

Small animal veterinarians and the general public are interested in companion animal disease surveillance. The system described can serve as a model for establishing similar systems to monitor disease trends of public health importance in pet populations and enhance biosurveillance capabilities.

Quantitative bias analysis in an asthma study of rescue-recovery workers and volunteers from the 9/11 World Trade Center attacks

PURPOSE

When learning bias analysis, epidemiologists are taught to quantitatively adjust for multiple biases by correcting study results in the reverse order of the error sequence. To understand the error sequence for a particular study, one must carefully examine the health study's epidemiologic data-generating process. In this article, we describe the unique data-generating process of a man-made disaster epidemiologic study.

METHODS

We described the data-generating process and conducted a bias analysis for a study associating September 11, 2001 dust cloud exposure and self-reported newly physician-diagnosed asthma among rescue-recovery workers and volunteers. We adjusted an odds ratio (OR) estimate for the combined effect of missing data, outcome misclassification, and nonparticipation.

RESULTS

Under our assumptions about systematic error, the ORs adjusted for all three biases ranged from 1.33 to 3.84. Most of the adjusted estimates were greater than the observed OR of 1.77 and were outside the 95% confidence limits (1.55, 2.01).

CONCLUSIONS

Man-made disasters present some situations that are not observed in other areas of epidemiology. Future epidemiologic studies of disasters could benefit from a proactive approach that focuses on the technical aspect of data collection and gathers information on bias parameters to provide more meaningful interpretations of results.

Development and Application of Syndromic Surveillance for Severe Weather Events Following Hurricane Sandy

OBJECTIVE

Following Hurricane Superstorm Sandy, the New Jersey Department of Health (NJDOH) developed indicators to enhance syndromic surveillance for extreme weather events in EpiCenter, an online system that collects and analyzes real-time chief complaint emergency department (ED) data and classifies each visit by indicator or syndrome.

METHODS

These severe weather indicators were finalized by using 2 steps: (1) key word inclusion by review of chief complaints from cases where diagnostic codes met selection criteria and (2) key word exclusion by evaluating cases with key words of interest that lacked selected diagnostic codes.

RESULTS

Graphs compared 1-month, 3-month, and 1-year periods of 8 Hurricane Sandy-related severe weather event indicators against the same period in the following year. Spikes in overall ED visits were observed immediately after the hurricane for carbon monoxide (CO) poisoning, the 3 disrupted outpatient medical care indicators, asthma, and methadone-related substance use. Zip code level scan statistics indicated clusters of CO poisoning and increased medicine refill needs during the 2 weeks after Hurricane Sandy. CO poisoning clusters were identified in areas with power outages of 4 days or longer.

CONCLUSIONS

This endeavor gave the NJDOH a clearer picture of the effects of Hurricane Sandy and yielded valuable state preparation information to monitor the effects of future severe weather events. (Disaster Med Public Health Preparedness. 2016;10:463-471).

EPIMIC: A Simple Homemade Computer Program for Real-Time EPIdemiological Surveillance and Alert Based on MICrobiological Data

BACKGROUND AND AIMS

Infectious diseases (IDs) are major causes of morbidity and mortality and their surveillance is critical. In 2002, we implemented a simple and versatile homemade tool, named EPIMIC, for the real-time systematic automated surveillance of IDs at Marseille university hospitals, based on the data from our clinical microbiology laboratory, including clinical samples, tests and diagnoses.

METHODS

This tool was specifically designed to detect abnormal events as IDs are rarely predicted and modeled. EPIMIC operates using Microsoft Excel software and requires no particular computer skills or resources. An abnormal event corresponds to an increase above, or a decrease below threshold values calculated based on the mean of historical data plus or minus 2 standard deviations, respectively.

RESULTS

Between November 2002 and October 2013 (11 years), 293 items were surveyed weekly, including 38 clinical samples, 86 pathogens, 79 diagnosis tests, and 39 antibacterial resistance patterns. The mean duration of surveillance was 7.6 years (range, 1 month-10.9 years). A total of 108,427 Microsoft Excel file cells were filled with counts of clinical samples, and 110,017 cells were filled with counts of diagnoses. A total of 1,390,689 samples were analyzed. Among them, 172,180 were found to be positive for a pathogen. EPIMIC generated a mean number of 0.5 alert/week on abnormal events.

CONCLUSIONS

EPIMIC proved to be efficient for real-time automated laboratory-based surveillance and alerting at our university hospital clinical microbiology laboratory-scale. It is freely downloadable from the following URL: http://www.mediterranee-infection.com/article.php?larub=157&titre=bulletin-epidemiologique (last accessed: 20/11/2015).

Constructing legal authority to facilitate multi-level interagency health data sharing in the United States

Purpose

– The purpose of this paper is to forward specific policy proposals permitting greater sharing of health data across multi-level government agencies with the purpose of improving rapid identification of bioterrorist attack or disease epidemics while protecting patient privacy.

Design/methodology/approach

– A systematic literature review searched the following keyword phrases: knowledge sharing in the public sector, raw data sharing, interagency information systems, federal data sharing technology network and network theory on five primary databases.

Findings

– The volunteer nature of data sharing must evolve through public health policy to permit interagency data access agreements while minimizing privacy infringement. A multi-level information infrastructure network linking agencies tasked to develop medical countermeasures is recommended.

Originality/value

– This study optimizes the health data collection process to create a medical countermeasure network, demonstrates the utility of operationalizing data metrics for a US federal agency and advances meaningful use of electronic medical records.

What Could Be Future Scenarios?-Lessons from the History of Public Health Surveillance for the Future: --A keynote address presented at the 8th World Alliance for Risk Factor Surveillance (WARFS) Global Conference on October 30, 2013, Beijing, China

This article provides insights into the future based on a review of the past and present of public health surveillance-the ongoing systematic collection, analysis, interpretation, and dissemination of health data for the planning, implementation, and evaluation of public health action. Public health surveillance dates back to the first recorded epidemic in 3180 BC in Egypt. A number of lessons and items of interest are summarised from a review of historical perspectives in the past 5,000 years and the current practice of surveillance. Some future scenarios are presented: exploring new frontiers; enhancing computer technology; improving epidemic investigations; improving data collection, analysis, dissemination and use; building on lessons from the past; building capacity; and enhancing global surveillance. It is concluded that learning from the past, reflecting on the present, and planning for the future can further enhance public health surveillance.

Seasonal and Pandemic Influenza Surveillance and Disease Severity

Continuous investments in influenza research, surveillance, and prevention efforts are critical to mitigate the consequences of annual influenza epidemics and pandemics. New influenza viruses emerge due to antigenic drift and antigenic shift evading human immune system and causing annual epidemics and pandemics. Three pandemics with varying disease severity occurred in the last 100 years. The disease burden and determinants of influenza severity depend on circulating viral strains and individual demographic and clinical factors. Surveillance is the most effective strategy for appropriate public health response. Active and passive surveillance methods are utilized to monitor influenza epidemics and emergence of novel viruses. Meaningful use of electronic health records could be a cost-effective approach to improved influenza surveillance

Global disease monitoring and forecasting with Wikipedia

Infectious disease is a leading threat to public health, economic stability, and other key social structures. Efforts to mitigate these impacts depend on accurate and timely monitoring to measure the risk and progress of disease. Traditional, biologically-focused monitoring techniques are accurate but costly and slow; in response, new techniques based on social internet data, such as social media and search queries, are emerging. These efforts are promising, but important challenges in the areas of scientific peer review, breadth of diseases and countries, and forecasting hamper their operational usefulness. We examine a freely available, open data source for this use: access logs from the online encyclopedia Wikipedia. Using linear models, language as a proxy for location, and a systematic yet simple article selection procedure, we tested 14 location-disease combinations and demonstrate that these data feasibly support an approach that overcomes these challenges. Specifically, our proof-of-concept yields models with r2 up to 0.92, forecasting value up to the 28 days tested, and several pairs of models similar enough to suggest that transferring models from one location to another without re-training is feasible. Based on these preliminary results, we close with a research agenda designed to overcome these challenges and produce a disease monitoring and forecasting system that is significantly more effective, robust, and globally comprehensive than the current state of the art.

Using public health scenarios to predict the utility of a national syndromic surveillance programme during the 2012 London Olympic and Paralympic Games

During 2012 real-time syndromic surveillance formed a key part of the daily public health surveillance for the London Olympic and Paralympic Games. It was vital that these systems were evaluated prior to the Games; in particular what types and scales of incidents could and could not be detected. Different public health scenarios were created covering a range of potential incidents that the Health Protection Agency would require syndromic surveillance to rapidly detect and monitor. For the scenarios considered it is now possible to determine what is likely to be detectable and how incidents are likely to present using the different syndromic systems. Small localized incidents involving food poisoning are most likely to be detected the next day via emergency department surveillance, while a new strain of influenza is more likely to be detected via GP or telephone helpline surveillance, several weeks after the first seed case is introduced.

Advancing a framework to enable characterization and evaluation of data streams useful for biosurveillance

In recent years, biosurveillance has become the buzzword under which a diverse set of ideas and activities regarding detecting and mitigating biological threats are incorporated depending on context and perspective. Increasingly, biosurveillance practice has become global and interdisciplinary, requiring information and resources across public health, One Health, and biothreat domains. Even within the scope of infectious disease surveillance, multiple systems, data sources, and tools are used with varying and often unknown effectiveness. Evaluating the impact and utility of state-of-the-art biosurveillance is, in part, confounded by the complexity of the systems and the information derived from them. We present a novel approach conceptualizing biosurveillance from the perspective of the fundamental data streams that have been or could be used for biosurveillance and to systematically structure a framework that can be universally applicable for use in evaluating and understanding a wide range of biosurveillance activities. Moreover, the Biosurveillance Data Stream Framework and associated definitions are proposed as a starting point to facilitate the development of a standardized lexicon for biosurveillance and characterization of currently used and newly emerging data streams. Criteria for building the data stream framework were developed from an examination of the literature, analysis of information on operational infectious disease biosurveillance systems, and consultation with experts in the area of biosurveillance. To demonstrate utility, the framework and definitions were used as the basis for a schema of a relational database for biosurveillance resources and in the development and use of a decision support tool for data stream evaluation.

Biosurveillance enterprise for operational awareness, a genomic-based approach for tracking pathogen virulence

To protect our civilians and warfighters against both known and unknown pathogens, biodefense stakeholders must be able to foresee possible technological trends that could affect their threat risk assessment. However, significant flaws in how we prioritize our countermeasure-needs continue to limit their development. As recombinant biotechnology becomes increasingly simplified and inexpensive, small groups, and even individuals, can now achieve the design, synthesis, and production of pathogenic organisms for offensive purposes. Under these daunting circumstances, a reliable biosurveillance approach that supports a diversity of users could better provide early warnings about the emergence of new pathogens (both natural and manmade), reverse engineer pathogens carrying traits to avoid available countermeasures, and suggest the most appropriate detection, prophylactic, and therapeutic solutions. While impressive in data mining capabilities, real-time content analysis of social media data misses much of the complexity in the factual reality. Quality issues within freeform user-provided hashtags and biased referencing can significantly undermine our confidence in the information obtained to make critical decisions about the natural vs. intentional emergence of a pathogen. At the same time, errors in pathogen genomic records, the narrow scope of most databases, and the lack of standards and interoperability across different detection and diagnostic devices, continue to restrict the multidimensional biothreat assessment. The fragmentation of our biosurveillance efforts into different approaches has stultified attempts to implement any new foundational enterprise that is more reliable, more realistic and that avoids the scenario of the warning that comes too late. This discussion focus on the development of genomic-based decentralized medical intelligence and laboratory system to track emerging and novel microbial health threats in both military and civilian settings and the use of virulence factors for risk assessment. Examples of the use of motif fingerprints for pathogen discrimination are provided.

Accurate and rapid identification of the Burkholderia pseudomallei near-neighbour, Burkholderia ubonensis, using real-time PCR

Burkholderia ubonensis is an environmental bacterium belonging to the Burkholderia cepacia complex (Bcc), a group of genetically related organisms that are associated with opportunistic but generally nonfatal infections in healthy individuals. In contrast, the near-neighbour species Burkholderia pseudomallei causes melioidosis, a disease that can be fatal in up to 95% of cases if left untreated. B. ubonensis is frequently misidentified as B. pseudomallei from soil samples using selective culturing on Ashdown’s medium, reflecting both the shared environmental niche and morphological similarities of these species. Additionally, B. ubonensis shows potential as an important biocontrol agent in B. pseudomallei-endemic regions as certain strains possess antagonistic properties towards B. pseudomallei. Current methods for characterising B. ubonensis are laborious, time-consuming and costly, and as such this bacterium remains poorly studied. The aim of our study was to develop a rapid and inexpensive real-time PCR-based assay specific for B. ubonensis. We demonstrate that a novel B. ubonensis-specific assay, Bu550, accurately differentiates B. ubonensis from B. pseudomallei and other species that grow on selective Ashdown’s agar. We anticipate that Bu550 will catalyse research on B. ubonensis by enabling rapid identification of this organism from Ashdown’s-positive colonies that are not B. pseudomallei.

Evaluation of the FilmArray® system for detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis

Aims

To evaluate the sensitivity and specificity of the BioFire Diagnostics FilmArray® system in combination with their Biothreat Panel for the detection of Bacillus anthracis (Ba), Francisella tularensis (Ft) and Yersinia pestis (Yp) DNA, and demonstrate the detection of Ba spores.

Methods and Results

DNA samples from Ba, Ft and Yp strains and near-neighbours, and live Ba spores were analysed using the FilmArray® Biothreat Panel, a multiplexed PCR-based assay for 17 pathogens and toxins. Sensitivity studies with DNA indicate that the limit of detection is 250 genome equivalents (GEs) per sample or lower. Furthermore, the identification of Ft, Yp or Bacillus species was made in 63 of 72 samples tested at 25 GE or less. With samples containing 25 CFU of Ba Sterne spores, at least one of the two possible Ba markers was identified in all samples tested. We observed no cross-reactivity with near-neighbour DNAs.

Conclusions

Our results indicate that the FilmArray® Biothreat Panel is a sensitive and selective assay for detecting the genetic signatures of Ba, Ft and Yp.

Significance and Impact of the Study

The FilmArray® platform is a complete sample-to-answer system, combining sample preparation, PCR and data analysis. This system is particularly suited for biothreat testing where samples need to be analysed for multiple biothreats by operators with limited training.

Increased knowledge of Francisella genus diversity highlights the benefits of optimised DNA-based assays

Background

Recent advances in sequencing technologies offer promising tools for generating large numbers of genomes, larger typing databases and improved mapping of environmental bacterial diversity. However, DNA-based methods for the detection of Francisella were developed with limited knowledge about genetic diversity. This, together with the high sequence identity between several Francisella species, means there is a high risk of false identification and detection of the highly virulent pathogen Francisella tularensis. Moreover, phylogenetic reconstructions using single or limited numbers of marker sequences often result in incorrect tree topologies and inferred evolutionary distances. The recent growth in publicly accessible whole-genome sequences now allows evaluation of published genetic markers to determine optimal combinations of markers that minimise both time and laboratory costs.

Results

In the present study, we evaluated 38 previously published DNA markers and the corresponding PCR primers against 42 genomes representing the currently known diversity of the genus Francisella. The results highlight that PCR assays for Francisella tularensis are often complicated by low specificity, resulting in a high probability of false positives. A method to select a set of one to seven markers for obtaining optimal phylogenetic resolution or diagnostic accuracy is presented.

Conclusions

Current multiple-locus sequence-typing systems and detection assays of Francisella, could be improved by redesigning some of the primers and reselecting typing markers. The use of only a few optimally selected sequence-typing markers allows construction of phylogenetic topologies with almost the same accuracy as topologies based on whole-genome sequences.

Biodefense Oriented Genomic-Based Pathogen Classification Systems: Challenges and Opportunities

Countermeasures that will effectively prevent or diminish the impact of a biological attack will depend on the rapid and accurate generation and analysis of genomic information. Because of their increasing level of sensitivity, rapidly decreasing cost, and their ability to effectively interrogate the genomes of previously unknown organisms, Next Generation Sequencing (NGS) technologies are revolutionizing the biological sciences. However, the exponential accumulation microbial data is equally outpacing the computational performance of existing analytical tools in their ability to translate DNA information into reliable detection, prophylactic and therapeutic countermeasures. It is now evident that the bottleneck for next-generation sequence data analysis will not be solved simply by scaling up our computational resources, but rather accomplished by implementing novel biodefense-oriented algorithms that overcome exiting vulnerabilities of speed, sensitivity and accuracy. Considering these circumstances, this document highlights the challenges and opportunities that biodefense stakeholders must consider in order to exploit more efficiently genomic information and translate this data into integrated countermeasures. The document overviews different genome analysis methods and explains concepts of DNA fingerprints, motif fingerprints, genomic barcodes and genomic signatures. A series of recommendations to promote genomics and bioinformatics as an effective form of deterrence and a valuable scientific platform for rapid technological insertion of detection, prophylactic, therapeutic countermeasures are discussed.