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.

Nosocomial outbreaks: A review of governmental reporting systems

OBJECTIVE

Identifying and describing components of existent governmental reporting systems of NO aiming at informing the design of the implementation of NO reporting systems in countries where they were not fully established.

DESIGN

A systematic search was carried out on PubMed, Embase, and the Latin American and Caribbean Health Sciences Literature database. We included studies published from January 2007 to June 2019 describing NO governmental reporting systems. Additionally, we included studies from the list of references in the identified papers, to gather more information about NO reporting systems. We also reviewed documents published in the governmental health department's Web sites, such as outbreak management guidelines and surveillance protocols, provided they were cited in the papers.

RESULTS

NO reporting systems were reported in France (Alsace Region), Germany, Norway, United Kingdom, United States (New York State; New York City), Australia (Victoria State), Sweden (Skane Region), Ireland, Scotland (Lothian Region), and Canada (Winnipeg; Ontario). These systems vary according to the type of targeted NO event, such as gastroenteritis, influenza-like illness, invasive group A streptococcal disease or all-health care-acquired infection NO. Germany, Norway, New York City, New York State, Ireland, Winnipeg, and Ontario have established a mandatory reporting for NO.

CONCLUSIONS

There is high variability among countries regarding governmental NO reporting systems. This may hinder opportune inter- and intracountries communication concerning NO of potential international public health relevance.

Using MALDI-TOF spectra in epidemiological surveillance for the detection of bacterial subgroups with a possible epidemic potential

Background

For the purpose of epidemiological surveillance, the Hospital University Institute Méditerranée infection has implemented since 2013 a system named MIDaS, based on the systematic collection of routine activity materials, including MALDI-TOF spectra, and results. The objective of this paper is to present the pipeline we use for processing MALDI-TOF spectra during epidemiological surveillance in order to disclose proteinic cues that may suggest the existence of epidemic processes in complement of incidence surveillance. It is illustrated by the analysis of an alarm observed for Streptococcus pneumoniae.

Methods

The MALDI-TOF spectra analysis process looks for the existence of clusters of spectra characterized by a double time and proteinic close proximity. This process relies on several specific methods aiming at contrasting and clustering the spectra, presenting graphically the results for an easy epidemiological interpretation, and for determining the discriminating spectra peaks with their possible identification using reference databases.

Results

The use of this pipeline in the case of an alarm issued for Streptococcus pneumoniae has made it possible to reveal a cluster of spectra with close proteinic and temporal distances, characterized by the presence of three discriminant peaks (5228.8, 5917.8, and 8974.3 m/z) and the absence of peak 4996.9 m/z. A further investigation on UniProt KB showed that peak 5228.8 is possibly an OxaA protein and that the absent peak may be a transposase.

Conclusion

This example shows this pipeline may support a quasi-real time identification and characterization of clusters that provide essential information on a potentially epidemic situation. It brings valuable information for epidemiological sensemaking and for deciding on the continuation of the epidemiological investigation, in particular the involving of additional costly resources to confirm or invalidate the alarm.

Clinical trials registration

NCT03626987.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06803-3.

Rapid COVID-19 Molecular Diagnostic System Using Virus Enrichment Platform

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, is rapidly spreading and severely straining the capacities of public health communities and systems around the world. Therefore, accurate, rapid, and robust diagnostic tests for COVID-19 are crucial to prevent further spread of the infection, alleviate the burden on healthcare and diagnostic facilities, and ensure timely therapeutic intervention. To date, several detection methods based on nucleic acid amplification have been developed for the rapid and accurate detection of SARS-CoV-2. Despite the myriad of advancements in the detection methods for SARS-CoV-2, rapid sample preparation methods for RNA extraction from viruses have rarely been explored. Here, we report a rapid COVID-19 molecular diagnostic system that combines a self-powered sample preparation assay and loop-mediated isothermal amplification (LAMP) based naked-eye detection method for the rapid and sensitive detection of SARS-CoV-2. The self-powered sample preparation assay with a hydrophilic polyvinylidene fluoride filter and dimethyl pimelimidate can be operated by hand, without the use of any sophisticated instrumentation, similar to the reverse transcription (RT)-LAMP-based lateral flow assay for the naked-eye detection of SARS-CoV-2. The COVID-19 molecular diagnostic system enriches the virus population, extracts and amplifies the target RNA, and detects SARS-CoV-2 within 60 min. We validated the accuracy of the system by using 23 clinical nasopharyngeal specimens. We envision that this proposed system will enable simple, facile, efficient, and inexpensive diagnosis of COVID-19 at home and the clinic as a pre-screening platform to reduce the burden on the medical staff in this pandemic era.

Towards a Framework for High-Performance Simulation of Livestock Disease Outbreak: A Case Study of Spread of African Swine Fever in Vietnam

Simple Summary

Disease transmission simulation programs in veterinary epidemiology in general and in simulation of African swine fever in particular are often very diverse and require great computing power. However, such programs often share similar workflows from processing input/output data, performing simulations, or storing data. Our paper proposes a common architectural framework for livestock disease transmission simulation programs in order to both improve simulation performance and reduce the effort of developing new simulation programs. Our framework was evaluated with a simulation program of African swine fever transmission currently raging in Vietnam and some other countries around the world. The results from the evaluation experiments not only demonstrate the effectiveness of the framework in terms of performance but also have practical consulting value for decision makers in Vietnam and for international colleagues.

Abstract

The spread of disease in livestock is an important research topic of veterinary epidemiology because it provides warnings or advice to organizations responsible for the protection of animal health in particular and public health in general. Disease transmission simulation programs are often deployed with different species, disease types, or epidemiological models, and each research team manages its own set of parameters relevant to their target diseases and concerns, resulting in limited cooperation and reuse of research results. Furthermore, these simulation and decision support tools often require a large amount of computational power, especially for models involving tens of thousands of herds with millions of individuals spread over a large geographical area such as a region or a country. It is a matter of fact that epidemic simulation programs are often heterogeneous, but they often share some common workflows including processing of input data and execution of simulation, as well as storage, analysis, and visualization of results. In this article, we propose a novel architectural framework for simultaneously deploying any epidemic simulation program both on premises and on the cloud to improve performance and scalability. We also conduct some experiments to evaluate the proposed architectural framework on some aspects when applying it to simulate the spread of African swine fever in Vietnam.

Sensitive fluorescence detection of SARS-CoV-2 RNA in clinical samples via one-pot isothermal ligation and transcription

The control of viral outbreaks requires nucleic acid diagnostic tests that are sensitive, simple and fast. Here, we report a highly sensitive and specific one-pot assay for the fluorescence-based detection of RNA from pathogens. The assay, which can be performed within 30-50 min of incubation time and can reach a limit of detection of 0.1-attomolar RNA concentration, relies on a sustained isothermal reaction cascade producing an RNA aptamer that binds to a fluorogenic dye. The RNA aptamer is transcribed by the T7 RNA polymerase from the ligation product of a promoter DNA probe and a reporter DNA probe that hybridize with the target single-stranded RNA sequence via the SplintR ligase (a Chlorella virus DNA ligase). In 40 nasopharyngeal SARS-CoV-2 samples, the assay reached positive and negative predictive values of 95 and 100%, respectively. We also show that the assay can rapidly detect a range of viral and bacterial RNAs.

The critical role of laboratory medicine during coronavirus disease 2019 (COVID-19) and other viral outbreaks

Coronavirus disease 2019, abbreviated to COVID-19 and sustained by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the latest biological hazard to assume the relevance of insidious worldwide threat. One obvious question that is now engaging the minds of many scientists and healthcare professionals is whether and eventually how laboratory medicine could efficiently contribute to counteract this and other (future) viral outbreaks. Despite there being evidence that laboratory tests are vital throughout many clinical pathways, there are at least three major areas where in vitro diagnostics can also provide essential contributions to diagnostic reasoning and managed care of patients with suspected or confirmed SARS-CoV-2 infection. These include etiological diagnosis, patient monitoring, as well as epidemiologic surveillance. Nonetheless, some structural and practical aspects may generate substantial hurdles in providing timely and efficient response to this infectious emergency, which basically include inadequate (insufficient) environment and shortage of technical and human resources for facing enhanced volume of tests on many infected patients, some of whom are with severe disease. Some proactive and reactive strategies may hence be identified to confront this serious healthcare challenge, which entail major investments on conventional laboratory resources, reinforcement of regional networks of clinical laboratories, installation of mobile laboratories, as well as being proactive in establishing laboratory emergency plans.

Scientific Advances in the Diagnosis of Emerging and Reemerging Viral Human Pathogens

Despite scientific advances, the diagnosis of infectious diseases is primarily possible through vaccination and later by antibiotics. Emerging and reemerging pathologies are still considered to be dangerous to humanity because of the unique nature of these diseases: it is the encounter between two living organisms that have coexisted for millions of years within the people on the same planet without being previously recognized. These infectious agents, such as bacteria, viruses, fungi, or parasites, pose no threat to humans. In fact, only a few hundred are able to inflict damage to the human host. In addition, the spectrum of human disease caused by a particular pathogen varies considerably depending on the factors related to the ecological agent, the host, and the infectious agents.

Several emerging or reemerging infectious agents are organisms that could be used in biological control. The differentiation of a natural epidemic from a bioterrorian event is based on several epidemiological indices as well as on the molecular characterization of the pathogen(s) involved.

The role of pathologists is indeed very important. It is in this context that this chapter aims to discuss the various scientific advances, particularly molecular, in terms of diagnosis of these diseases; the new discoveries in the role of nanotechnologies and nanobiosensors; and also the implication of biomarkers, especially microRNAs (miRNAs), since it was reported that a single miRNA has the ultimate capacity to target multiple genes simultaneously. In a viral infection context, miRNAs have been connected with the interplay between host and pathogen and occupy a major role in the host–parasite interaction and pathogenesis. It is in this context that various molecular and nanomethods for the detection of emerging viruses and experimental validation of miRNAs during quelling viruses target transcripts will be discussed in this chapter.

Acquired immunity and asymptomatic reservoir impact on frontline and airport ebola outbreak syndromic surveillance and response

The number of surveillance networks for infectious disease diagnosis and response has been growing. In 2000, the World Health Organization (WHO) established the Global Outbreak Alert and Response Network, which has been endorsed by each of the 46 WHO African members since then. Yet, taming the dynamics and plague of the vicious Ebola virus disease (EVD) in African countries has been patchy and erratic due to inadequate surveillance and contact tracing, community defiance and resistance, a lack of detection and response systems, meager/weak knowledge and information on the disease, inadequacies in protective materials protocols, contact tracing nightmare and differing priorities at various levels of the public health system. Despite the widespread acceptance of syndromic surveillance (SS) systems, their ability to provide early warning alerts and notifications of outbreaks is still unverified. Information is often too limited for any outbreak, or emerging or otherwise unexpected disease, to be recognized at either the community or the national level. Indeed, little is known about the role and the interactions between the Ebola infection and exposure to other syndemics and the development of acquired immunity, asymptomatic reservoir, and Ebola seroconversion. Can lessons be learnt from smallpox, polio, and influenza immunity, and can immunization against these serve as a guide? In most endemic countries, community health centers and disease control and prevention at airports solely relies on passive routine immunization control and reactive syndromic response. The frontline and airport Ebola SS systems in West Africa have shown deficiencies in terms of responding with an alarming number of case fatalities, and suggest that more detailed insights into Ebola, and proactive actions, are needed. The quest for effective early indicators (EEE) in shifting the public and global health paradigm requires the development and implementation of a comprehensive and effective community or regional integrated pandemic preparedness and surveillance response systems tailored to local contexts. These systems must have mechanisms for early identification, rapid contact tracing and tracking, confirmation, and communication with the local population and the global community, and must endeavor to respond in a timely manner.

Clinical microbiology informatics

The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing. This review discusses the diverse informatics aspects that are relevant to the clinical microbiology laboratory, including the following: the microbiology laboratory information system, decision support tools, expert systems, instrument interfaces, total laboratory automation, telemicrobiology, automated image analysis, nucleic acid sequence databases, electronic reporting of infectious agents to public health agencies, and disease outbreak surveillance. The breadth and utility of informatics tools used in clinical microbiology have made them indispensable to contemporary clinical and laboratory practice. Continued advances in technology and development of these informatics tools will further improve patient and public health care in the future.

Reverse transcription-PCR-electrospray ionization mass spectrometry for rapid detection of biothreat and common respiratory pathogens

Electrospray ionization mass spectrometry (ESI-MS) analysis of reverse transcription (RT)-PCR amplicons from human respiratory samples allows for broad pathogen identification approximately 8 h after collection. We investigated the performance characteristics of a high-throughput RT-PCR-coupled ESI-MS assay for distinguishing biothreat (BT) agents from common bacterial, fungal, and viral respiratory pathogens in bronchoalveolar lavage (BAL) fluid specimens from subjects with suspected respiratory infections. In a retrospective case series, 202 BAL fluid specimens were collected at the Johns Hopkins Hospital between August 2010 and February 2011 from patients with suspected acute respiratory infections. Samples were processed using standard bacterial, viral, and fungal testing in the clinical microbiology laboratory as part of routine care and then were blindly spiked with either water or nucleic acids from BT organisms (Bacillus anthracis, Yersinia pestis, Francisella tularensis, Brucella spp., Burkholderia spp., and Rickettsia prowazekii) and tested by RT-PCR-ESI-MS. The sensitivities and specificities of RT-PCR-ESI-MS versus standard clinical methods were as follows: for mock BT DNA, 98.5% sensitivity (95% confidence interval [CI], 94.2 to 99.7%) and 100% specificity (95% CI, 93.1 to 100.0%); for bacterial pathogens, 81.8% sensitivity (95% CI, 74.3 to 87.6%) and 73.6% specificity (95% CI, 64.2 to 81.4%); for viral pathogens, 93.3% sensitivity (95% CI, 66.0 to 99.7%) and 97.3% specificity (95% CI, 89.7 to 99.5%); for fungal pathogens, 42.6% sensitivity (95% CI, 29.5 to 56.7%) and 97.8% specificity (95% CI, 91.8 to 99.6%). Our data suggest that RT-PCR-ESI-MS is a useful adjunct to standard culture protocols for rapid detection of both BT and common respiratory pathogens; further study is required for assay validation, especially for fungal detection, and potential implementation.

Development of ClickClinica: a novel smartphone application to generate real-time global disease surveillance and clinical practice data

Background

Identification and tracking of important communicable diseases is pivotal to our understanding of the geographical distribution of disease, the emergence and spread of novel and resistant infections, and are of particular importance for public health policy planning. Moreover, understanding of current clinical practice norms is essential to audit clinical care, identify areas of concern, and develop interventions to improve care quality.

However, there are several barriers to obtaining these research data. For example current disease surveillance mechanisms make it difficult for the busy doctor to know which diseases to notify, to whom and how, and are also time consuming. Consequently, many cases go un-notified. In addition assessments of current clinical practice are typically limited to small retrospective audits in individual hospitals.

Therefore, we developed a free smartphone application to try to increase the identification of major infectious diseases and other acute medical presentations and improve our understanding of clinical practice.

Description

Within the first month there were over 1000 downloads and over 600 specific disease notifications, coming from a broad range of specialities, grades and from all across the globe, including some resource poor settings.

Notifications have already provided important information, such as new cases of TB meningitis, resistant HIV and rabies, and important clinical information, such as where patient with myocardial infarctions are and are not receiving potentially life-saving therapy.

The database generated can also answer new, dynamic and targeted questions. When a new guideline is released, for example for a new pandemic infection, we can track, in real-time, the global usage of the guideline and whether the recommendations are being followed. In addition this allows identification of where cases with key markers of severe disease are occurring. This is a potential resource for guideline-producing bodies, clinical governance and public health institutions and also for patient recruitment into ongoing studies.

Conclusions

Further parallel studies are needed to assess the clinical and epidemiological utility of novel disease surveillance applications, such as this, with direct comparisons made to data collected through routine surveillance routes.

Nevertheless, current disease surveillance mechanisms do not always comprehensively and accurately reflect disease distribution for many conditions. Smartphone applications, such as ClickClinica, are a novel approach with the potential to generate real-time disease surveillance data that may augment current methods.

Improving resolution of public health surveillance for human Salmonella enterica serovar Typhimurium infection: 3 years of prospective multiple-locus variable-number tandem-repeat analysis (MLVA)

Background

Prospective typing of Salmonella enterica serovar Typhimurium (STM) by multiple-locus variable-number tandem-repeat analysis (MLVA) can assist in identifying clusters of STM cases that might otherwise have gone unrecognised, as well as sources of sporadic and outbreak cases. This paper describes the dynamics of human STM infection in a prospective study of STM MLVA typing for public health surveillance.

Methods

During a three-year period between August 2007 and September 2010 all confirmed STM isolates were fingerprinted using MLVA as part of the New South Wales (NSW) state public health surveillance program.

Results

A total of 4,920 STM isolates were typed and a subset of 4,377 human isolates was included in the analysis. The STM spectrum was dominated by a small number of phage types, including DT170 (44.6% of all isolates), DT135 (13.9%), DT9 (10.8%), DT44 (4.5%) and DT126 (4.5%). There was a difference in the discriminatory power of MLVA types within endemic phage types: Simpson's index of diversity ranged from 0.109 and 0.113 for DTs 9 and 135 to 0.172 and 0.269 for DTs 170 and 44, respectively. 66 distinct STM clusters were observed ranging in size from 5 to 180 cases and in duration from 4 weeks to 25 weeks. 43 clusters had novel MLVA types and 23 represented recurrences of previously recorded MLVA types. The diversity of the STM population remained relatively constant over time. The gradual increase in the number of STM cases during the study was not related to significant changes in the number of clusters or their size. 667 different MLVA types or patterns were observed.

Conclusions

Prospective MLVA typing of STM allows the detection of community outbreaks and demonstrates the sustained level of STM diversity that accompanies the increasing incidence of human STM infections. The monitoring of novel and persistent MLVA types offers a new benchmark for STM surveillance.

A part of this study was presented at the MEEGID × (Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases) Conference, 3-5 November 2010, Amsterdam, The Netherlands

Health information exchange usage in emergency departments and clinics: the who, what, and why

OBJECTIVE

Health information exchange (HIE) systems are being developed across the nation. Understanding approaches taken by existing successful exchanges can help new exchange efforts determine goals and plan implementations. The goal of this study was to explore characteristics of use and users of a successful regional HIE.

DESIGN

We used a mixed-method analysis, consisting of cross-sectional audit log data, semi-structured interviews, and direct observation in a sample of emergency departments and ambulatory safety net clinics actively using HIE. For each site, we measured overall usage trends, user logon statistics, and data types accessed by users. We also assessed reasons for use and outcomes of use.

RESULTS

Overall, users accessed HIE for 6.8% of all encounters, with higher rates of access for repeat visits, for patients with comorbidities, for patients known to have data in the exchange, and at sites providing HIE access to both nurses and physicians. Discharge summaries and test reports were the most frequently accessed data in the exchange. Providers consistently noted retrieving additional history, preventing repeat tests, comparing new results to retrieved results, and avoiding hospitalizations as a consequence of HIE access.

CONCLUSION

HIE use in emergency departments and ambulatory clinics was focused on patients where missing information was believed to be present in the exchange and was related to factors including the roles of people with access, the setting, and other site-specific issues that impacted the overall breadth of routine system use. These data should form an important foundation as other sites embark upon HIE implementation.

Biosurveillance: a review and update

Since the terrorist attacks and anthrax release in 2001, almost $32 billion has been allocated to biodefense and biosurveillance in the USA alone. Surveillance in health care refers to the continual systematic collection, analysis, interpretation, and dissemination of data. When attempting to detect agents of bioterrorism, surveillance can occur in several ways. Syndromic surveillance occurs by monitoring clinical manifestations of certain illnesses. Laboratory surveillance occurs by looking for certain markers or laboratory data, and environmental surveillance is the process by which the ambient air or environment is continually sampled for the presence of biological agents. This paper focuses on the ways by which we detect bioterrorism agents and the effectiveness of these systems.

Redefining syndromic surveillance

With growing concerns about international spread of disease and expanding use of early disease detection surveillance methods, the field of syndromic surveillance has received increased attention over the last decade. The purpose of this article is to clarify the various meanings that have been assigned to the term syndromic surveillance and to propose a refined categorization of the characteristics of these systems. Existing literature and conference proceedings were examined on syndromic surveillance from 1998 to 2010, focusing on low- and middle-income settings. Based on the 36 unique definitions of syndromic surveillance found in the literature, five commonly accepted principles of syndromic surveillance systems were identified, as well as two fundamental categories: specific and non-specific disease detection. Ultimately, the proposed categorization of syndromic surveillance distinguishes between systems that focus on detecting defined syndromes or outcomes of interest and those that aim to uncover non-specific trends that suggest an outbreak may be occurring. By providing an accurate and comprehensive picture of this field's capabilities, and differentiating among system types, a unified understanding of the syndromic surveillance field can be developed, encouraging the adoption, investment in, and implementation of these systems in settings that need bolstered surveillance capacity, particularly low- and middle-income countries.

Veterinary syndromic surveillance: Current initiatives and potential for development

This paper reviews recent progress in the development of syndromic surveillance systems for veterinary medicine. Peer-reviewed and grey literature were searched in order to identify surveillance systems that explicitly address outbreak detection based on systematic monitoring of animal population data, in any phase of implementation. The review found that developments in veterinary syndromic surveillance are focused not only on animal health, but also on the use of animals as sentinels for public health, representing a further step towards One Medicine. The main sources of information are clinical data from practitioners and laboratory data, but a number of other sources are being explored. Due to limitations inherent in the way data on animal health is collected, the development of veterinary syndromic surveillance initially focused on animal health data collection strategies, analyzing historical data for their potential to support systematic monitoring, or solving problems of data classification and integration. Systems based on passive notification or data transfers are now dealing with sustainability issues. Given the ongoing barriers in availability of data, diagnostic laboratories appear to provide the most readily available data sources for syndromic surveillance in animal health. As the bottlenecks around data source availability are overcome, the next challenge is consolidating data standards for data classification, promoting the integration of different animal health surveillance systems, and also the integration to public health surveillance. Moreover, the outputs of systems for systematic monitoring of animal health data must be directly connected to real-time decision support systems which are increasingly being used for disease management and control.

Requirements and design of the PROSPER protocol for implementation of information infrastructures supporting pandemic response: a Nominal Group study

BACKGROUND

Advanced technical systems and analytic methods promise to provide policy makers with information to help them recognize the consequences of alternative courses of action during pandemics. Evaluations still show that response programs are insufficiently supported by information systems. This paper sets out to derive a protocol for implementation of integrated information infrastructures supporting regional and local pandemic response programs at the stage(s) when the outbreak no longer can be contained at its source.

METHODS

Nominal group methods for reaching consensus on complex problems were used to transform requirements data obtained from international experts into an implementation protocol. The analysis was performed in a cyclical process in which the experts first individually provided input to working documents and then discussed them in conferences calls. Argument-based representation in design patterns was used to define the protocol at technical, system, and pandemic evidence levels.

RESULTS

The Protocol for a Standardized information infrastructure for Pandemic and Emerging infectious disease Response (PROSPER) outlines the implementation of information infrastructure aligned with pandemic response programs. The protocol covers analyses of the community at risk, the response processes, and response impacts. For each of these, the protocol outlines the implementation of a supporting information infrastructure in hierarchical patterns ranging from technical components and system functions to pandemic evidence production.

CONCLUSIONS

The PROSPER protocol provides guidelines for implementation of an information infrastructure for pandemic response programs both in settings where sophisticated health information systems already are used and in developing communities where there is limited access to financial and technical resources. The protocol is based on a generic health service model and its functions are adjusted for community-level analyses of outbreak detection and progress, and response program effectiveness. Scientifically grounded reporting principles need to be established for interpretation of information derived from outbreak detection algorithms and predictive modeling.

Diagnosing emerging and reemerging infectious diseases: the pivotal role of the pathologist

CONTEXT

Molecular diagnostics continues to evolve very rapidly, and its impact in the diagnosis of infectious diseases is undeniable. Molecular tools have played a pivotal role in discovering and characterizing several emerging infectious agents and have now become the gold standard for the diagnosis of infectious diseases caused by fastidious or uncultivable agents. Multiple challenges still remain for the widespread use of cost-effective, validated, and commercially available molecular tools. Automated instruments capable of sample processing and multiplex nucleic acid amplification and postamplification analysis have already been approved by the US Food and Drug Administration (FDA) for use in the clinical setting. Nanobiotechnology is beginning to impact laboratory diagnostics in the clinical setting.

OBJECTIVE

To address current nucleic acid techniques used in the clinical laboratory for diagnosis of infectious diseases. FDA-approved tests are listed, as well as molecular techniques (amplification and postamplification analysis). A comprehensive list of emerging pathogens during the last 4 decades is also presented. Biosurveillance systems are discussed in the context of molecular tools. The rapidly evolving field of nanobiotechnology is briefly addressed.

DATA SOURCES

Original publications, major reviews, and book chapters were used to present a comprehensive, yet short, review of molecular diagnostics in infectious diseases.

CONCLUSIONS

We will continue to witness an exponential growth of molecular techniques used for the initial diagnosis of infectious diseases. Molecular tools will also continue to have an impact on disease prognosis and response to therapeutic interventions. Automation, multiplexing, and miniaturization will continue to be driving forces in the development of new instruments.

[How the new generations of microbiologists view the specialty]

Despite their pivotal role in the Spanish healthcare system, clinical microbiology laboratories are experiencing difficult times and tough challenges. The following changes are required to adapt to the new situation: a) the use of molecular diagnostics to provide rapid diagnosis; b) the development of diagnostic capabilities to identify emerging or imported infectious diseases; c) the ability to advise on the interpretation of microbiological results; d) encouragement of the implantation of point-of-care testing and assessment of its performance and development; e) the implantation of quality control systems in the laboratory; f) the implementation of laboratory information systems to support real-time communication between hospital and community clinicians, public health laboratories and managers; g) the design of networking systems with professionals from other disciplines, and h) the promotion of training and teaching programs. Only if they are well prepared will clinical microbiology laboratories be able to implant the new technologies, be recognized as a cornerstone of the healthcare system, and achieve better recognition by society at large, hospital administrators and healthcare authorities.

Informatics for Infectious Disease Research and Control

The goal of infectious disease informatics is to optimize the clinical and public health management of infectious diseases through improvements in the development and use of antimicrobials, the design of more effective vaccines, the identification of biomarkers for life-threatening infections, a better understanding of host-pathogen interactions, and biosurveillance and clinical decision support. Infectious disease informatics can lead to more targeted and effective approaches for the prevention, diagnosis and treatment of infections through a comprehensive review of the genetic repertoire and metabolic profiles of a pathogen. The developments in informatics have been critical in boosting the translational science and in supporting both reductionist and integrative research paradigms.