Using genomics for surveillance of veterinary infectious agents.

PubMed

Mathijs, E; Vandenbussche, F; Van Borm, S

2016-04-01

Factors such as globalisation, climate change and agricultural intensification can increase the risk of microbial emergence. As a result, there is a growing need for flexible laboratory-based surveillance tools to rapidly identify, characterise and monitor global (re-)emerging diseases. Although many tools are available, novel sequencing technologies have launched a new era in pathogen surveillance. Here, the authors review the potential applications of high-throughput genomic technologies for the surveillance of veterinary pathogens. They focus on the two types of surveillance that will benefit most from these new tools: hazard-specific surveillance (pathogen identification and typing) and early-warning surveillance (pathogen discovery). The paper reviews how the resulting sequencing data can be used to improve diagnosis and concludes by highlighting the major challenges that hinder the routine use of this technology in the veterinary field.

Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database.

PubMed

Allard, Marc W; Strain, Errol; Melka, David; Bunning, Kelly; Musser, Steven M; Brown, Eric W; Timme, Ruth

2016-08-01

The FDA has created a United States-based open-source whole-genome sequencing network of state, federal, international, and commercial partners. The GenomeTrakr network represents a first-of-its-kind distributed genomic food shield for characterizing and tracing foodborne outbreak pathogens back to their sources. The GenomeTrakr network is leading investigations of outbreaks of foodborne illnesses and compliance actions with more accurate and rapid recalls of contaminated foods as well as more effective monitoring of preventive controls for food manufacturing environments. An expanded network would serve to provide an international rapid surveillance system for pathogen traceback, which is critical to support an effective public health response to bacterial outbreaks. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Description and validation of a new automated surveillance system for Clostridium difficile in Denmark.

PubMed

Chaine, M; Gubbels, S; Voldstedlund, M; Kristensen, B; Nielsen, J; Andersen, L P; Ellermann-Eriksen, S; Engberg, J; Holm, A; Olesen, B; Schønheyder, H C; Østergaard, C; Ethelberg, S; Mølbak, K

2017-09-01

The surveillance of Clostridium difficile (CD) in Denmark consists of laboratory based data from Departments of Clinical Microbiology (DCMs) sent to the National Registry of Enteric Pathogens (NREP). We validated a new surveillance system for CD based on the Danish Microbiology Database (MiBa). MiBa automatically collects microbiological test results from all Danish DCMs. We built an algorithm to identify positive test results for CD recorded in MiBa. A CD case was defined as a person with a positive culture for CD or PCR detection of toxin A and/or B and/or binary toxin. We compared CD cases identified through the MiBa-based surveillance with those reported to NREP and locally in five DCMs representing different Danish regions. During 2010-2014, NREP reported 13 896 CD cases, and the MiBa-based surveillance 21 252 CD cases. There was a 99·9% concordance between the local datasets and the MiBa-based surveillance. Surveillance based on MiBa was superior to the current surveillance system, and the findings show that the number of CD cases in Denmark hitherto has been under-reported. There were only minor differences between local data and the MiBa-based surveillance, showing the completeness and validity of CD data in MiBa. This nationwide electronic system can greatly strengthen surveillance and research in various applications.

Capacity building efforts and perceptions for wildlife surveillance to detect zoonotic pathogens: comparing stakeholder perspectives.

PubMed

Schwind, Jessica S; Goldstein, Tracey; Thomas, Kate; Mazet, Jonna A K; Smith, Woutrina A

2014-07-04

The capacity to conduct zoonotic pathogen surveillance in wildlife is critical for the recognition and identification of emerging health threats. The PREDICT project, a component of United States Agency for International Development's Emerging Pandemic Threats program, has introduced capacity building efforts to increase zoonotic pathogen surveillance in wildlife in global 'hot spot' regions where zoonotic disease emergence is likely to occur. Understanding priorities, challenges, and opportunities from the perspectives of the stakeholders is a key component of any successful capacity building program. A survey was administered to wildlife officials and to PREDICT-implementing in-country project scientists in 16 participating countries in order to identify similarities and differences in perspectives between the groups regarding capacity needs for zoonotic pathogen surveillance in wildlife. Both stakeholder groups identified some human-animal interfaces (i.e. areas of high contact between wildlife and humans with the potential risk for disease transmission), such as hunting and markets, as important for ongoing targeting of wildlife surveillance. Similarly, findings regarding challenges across stakeholder groups showed some agreement in that a lack of sustainable funding across regions was the greatest challenge for conducting wildlife surveillance for zoonotic pathogens (wildlife officials: 96% and project scientists: 81%). However, the opportunity for improving zoonotic pathogen surveillance capacity identified most frequently by wildlife officials as important was increasing communication or coordination among agencies, sectors, or regions (100% of wildlife officials), whereas the most frequent opportunities identified as important by project scientists were increasing human capacity, increasing laboratory capacity, and the growing interest or awareness regarding wildlife disease or surveillance programs (all identified by 69% of project scientists). A One Health approach to capacity building applied at local and global scales will have the greatest impact on improving zoonotic pathogen surveillance in wildlife. This approach will involve increasing communication and cooperation across ministries and sectors so that experts and stakeholders work together to identify and mitigate surveillance gaps. Over time, this transdisciplinary approach to capacity building will help overcome existing challenges and promote efficient targeting of high risk interfaces for zoonotic pathogen transmission.

Medical Surveillance Monthly Report (MSMR). Volume 4, Number 6, September 1998

DTIC Science & Technology

1998-09-01

bacterial pathogens (from both cases and noncases) were Salmonella enteritidis , entero-adherent E. coli (EAEC), entero- toxigenic E. coli (ETEC), and...Isolation rate (% of cultures + for pathogen) No. of cultures + for pathogen Isolation rate (% of cultures + for pathogen) Salmonella enteritidis 32...infections ............. 8 ARD surveillance update .................................................. 13 Foodborne outbreak, Salmonella

PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance

PubMed Central

Nadon, Celine; Van Walle, Ivo; Gerner-Smidt, Peter; Campos, Josefina; Chinen, Isabel; Concepcion-Acevedo, Jeniffer; Gilpin, Brent; Smith, Anthony M.; Kam, Kai Man; Perez, Enrique; Trees, Eija; Kubota, Kristy; Takkinen, Johanna; Nielsen, Eva Møller; Carleton, Heather

2017-01-01

PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives. To meet the needs of real-time surveillance, the PulseNet International network will standardise subtyping via WGS using whole genome multilocus sequence typing (wgMLST), which delivers sufficiently high resolution and epidemiological concordance, plus unambiguous nomenclature for the purposes of surveillance. Standardised protocols, validation studies, quality control programmes, database and nomenclature development, and training should support the implementation and decentralisation of WGS. Ideally, WGS data collected for surveillance purposes should be publicly available, in real time where possible, respecting data protection policies. WGS data are suitable for surveillance and outbreak purposes and for answering scientific questions pertaining to source attribution, antimicrobial resistance, transmission patterns, and virulence, which will further enable the protection and improvement of public health with respect to food-borne disease. PMID:28662764

9 CFR 145.15 - Diagnostic surveillance program for low pathogenic avian influenza.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false Diagnostic surveillance program for low pathogenic avian influenza. 145.15 Section 145.15 Animals and Animal Products ANIMAL AND PLANT... PLAN FOR BREEDING POULTRY General Provisions § 145.15 Diagnostic surveillance program for low...

9 CFR 145.15 - Diagnostic surveillance program for low pathogenic avian influenza.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Diagnostic surveillance program for low pathogenic avian influenza. 145.15 Section 145.15 Animals and Animal Products ANIMAL AND PLANT... PLAN FOR BREEDING POULTRY General Provisions § 145.15 Diagnostic surveillance program for low...

Incidence and Trends of Infections with Pathogens Transmitted Commonly Through Food and the Effect of Increasing Use of Culture-Independent Diagnostic Tests on Surveillance - Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2013-2016.

PubMed

Marder, Ellyn P; Cieslak, Paul R; Cronquist, Alicia B; Dunn, John; Lathrop, Sarah; Rabatsky-Ehr, Therese; Ryan, Patricia; Smith, Kirk; Tobin-D'Angelo, Melissa; Vugia, Duc J; Zansky, Shelley; Holt, Kristin G; Wolpert, Beverly J; Lynch, Michael; Tauxe, Robert; Geissler, Aimee L

2017-04-21

Foodborne diseases represent a substantial public health concern in the United States. CDC's Foodborne Diseases Active Surveillance Network (FoodNet) monitors cases reported from 10 U.S. sites* of laboratory-diagnosed infections caused by nine enteric pathogens commonly transmitted through food. This report describes preliminary surveillance data for 2016 on the nine pathogens and changes in incidences compared with 2013-2015. In 2016, FoodNet identified 24,029 infections, 5,512 hospitalizations, and 98 deaths caused by these pathogens. The use of culture-independent diagnostic tests (CIDTs) by clinical laboratories to detect enteric pathogens has been steadily increasing since FoodNet began surveying clinical laboratories in 2010 (1). CIDTs complicate the interpretation of FoodNet surveillance data because pathogen detection could be affected by changes in health care provider behaviors or laboratory testing practices (2). Health care providers might be more likely to order CIDTs because these tests are quicker and easier to use than traditional culture methods, a circumstance that could increase pathogen detection (3). Similarly, pathogen detection could also be increasing as clinical laboratories adopt DNA-based syndromic panels, which include pathogens not often included in routine stool culture (4,5). In addition, CIDTs do not yield isolates, which public health officials rely on to distinguish pathogen subtypes, determine antimicrobial resistance, monitor trends, and detect outbreaks. To obtain isolates for infections identified by CIDTs, laboratories must perform reflex culture † ; if clinical laboratories do not, the burden of culturing falls to state public health laboratories, which might not be able to absorb that burden as the adoption of these tests increases (2). Strategies are needed to preserve access to bacterial isolates for further characterization and to determine the effect of changing trends in testing practices on surveillance.

Cost Analysis of Various Low Pathogenic Avian Influenza Surveillance Systems in the Dutch Egg Layer Sector

PubMed Central

Rutten, Niels; Gonzales, José L.; Elbers, Armin R. W.; Velthuis, Annet G. J.

2012-01-01

Background As low pathogenic avian influenza viruses can mutate into high pathogenic viruses the Dutch poultry sector implemented a surveillance system for low pathogenic avian influenza (LPAI) based on blood samples. It has been suggested that egg yolk samples could be sampled instead of blood samples to survey egg layer farms. To support future decision making about AI surveillance economic criteria are important. Therefore a cost analysis is performed on systems that use either blood or eggs as sampled material. Methodology/Principal Findings The effectiveness of surveillance using egg or blood samples was evaluated using scenario tree models. Then an economic model was developed that calculates the total costs for eight surveillance systems that have equal effectiveness. The model considers costs for sampling, sample preparation, sample transport, testing, communication of test results and for the confirmation test on false positive results. The surveillance systems varied in sampled material (eggs or blood), sampling location (farm or packing station) and location of sample preparation (laboratory or packing station). It is shown that a hypothetical system in which eggs are sampled at the packing station and samples prepared in a laboratory had the lowest total costs (i.e. € 273,393) a year. Compared to this a hypothetical system in which eggs are sampled at the farm and samples prepared at a laboratory, and the currently implemented system in which blood is sampled at the farm and samples prepared at a laboratory have 6% and 39% higher costs respectively. Conclusions/Significance This study shows that surveillance for avian influenza on egg yolk samples can be done at lower costs than surveillance based on blood samples. The model can be used in future comparison of surveillance systems for different pathogens and hazards. PMID:22523543

Pathogen profiling for disease management and surveillance.

PubMed

Sintchenko, Vitali; Iredell, Jonathan R; Gilbert, Gwendolyn L

2007-06-01

The usefulness of rapid pathogen genotyping is widely recognized, but its effective interpretation and application requires integration into clinical and public health decision-making. How can pathogen genotyping data best be translated to inform disease management and surveillance? Pathogen profiling integrates microbial genomics data into communicable disease control by consolidating phenotypic identity-based methods with DNA microarrays, proteomics, metabolomics and sequence-based typing. Sharing data on pathogen profiles should facilitate our understanding of transmission patterns and the dynamics of epidemics.

Food safety trends in the U.S. and update on pathogenic E. coli

USDA-ARS?s Scientific Manuscript database

Foodborne Diseases Active Surveillance Network (FoodNet): FoodNet is a main part of the Centers for Disease Control and Prevention’s (CDC) Emerging Pathogens Program and was established in 1995 as a population-based sentinel surveillance system to monitor changes in the incidence of nine pathogens ...

Exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens.

PubMed

Bokhari, Habib

2018-03-07

Emerging infectious diseases remain among the leading causes of global mortality. Traditional laboratory diagnostic approaches designed to detect and track infectious disease agents provide a framework for surveillance of bio threats. However, surveillance and outbreak investigations using such time-consuming approaches for early detection of pathogens remain the major pitfall. Hence, reasonable real-time surveillance systems to anticipate threats to public health and environment are critical for identifying specific aetiologies and preventing the global spread of infectious disease. The current review discusses the growing need for monitoring and surveillance of pathogens with the same zeal and approach as adopted by microbial forensics laboratories, and further strengthening it by integrating with the innovative nanotechnology for rapid detection of microbial pathogens. Such innovative diagnostics platforms will help to track pathogens from high risk areas and environment by pre-emptive approach that will minimize damages. The various scenarios with the examples are discussed where the high risk associated human pathogens in particular were successfully detected using various nanotechnology approaches with potential future prospects in the field of microbial forensics.

International surveillance of wheat rust pathogens: progress and challenges

USDA-ARS?s Scientific Manuscript database

Surveillance of wheat rust pathogens, including assessments of rust incidence and virulence characterization via either trap plots or race (pathotype) surveys, has provided information fundamental in formulating and adopting appropriate national and international policies, investments and strategies...

Surveillance of vector-borne pathogens under imperfect detection: lessons from Chagas disease risk (mis)measurement.

PubMed

Minuzzi-Souza, Thaís Tâmara Castro; Nitz, Nadjar; Cuba, César Augusto Cuba; Hagström, Luciana; Hecht, Mariana Machado; Santana, Camila; Ribeiro, Marcelle; Vital, Tamires Emanuele; Santalucia, Marcelo; Knox, Monique; Obara, Marcos Takashi; Abad-Franch, Fernando; Gurgel-Gonçalves, Rodrigo

2018-01-09

Vector-borne pathogens threaten human health worldwide. Despite their critical role in disease prevention, routine surveillance systems often rely on low-complexity pathogen detection tests of uncertain accuracy. In Chagas disease surveillance, optical microscopy (OM) is routinely used for detecting Trypanosoma cruzi in its vectors. Here, we use replicate T. cruzi detection data and hierarchical site-occupancy models to assess the reliability of OM-based T. cruzi surveillance while explicitly accounting for false-negative and false-positive results. We investigated 841 triatomines with OM slides (1194 fresh, 1192 Giemsa-stained) plus conventional (cPCR, 841 assays) and quantitative PCR (qPCR, 1682 assays). Detections were considered unambiguous only when parasitologists unmistakably identified T. cruzi in Giemsa-stained slides. qPCR was >99% sensitive and specific, whereas cPCR was ~100% specific but only ~55% sensitive. In routine surveillance, examination of a single OM slide per vector missed ~50-75% of infections and wrongly scored as infected ~7% of the bugs. qPCR-based and model-based infection frequency estimates were nearly three times higher, on average, than OM-based indices. We conclude that the risk of vector-borne Chagas disease may be substantially higher than routine surveillance data suggest. The hierarchical modelling approach we illustrate can help enhance vector-borne disease surveillance systems when pathogen detection is imperfect.

Using Informatics-, Bioinformatics- and Genomics-Based Approaches for the Molecular Surveillance and Detection of Biothreat Agents

NASA Astrophysics Data System (ADS)

Seto, Donald

The convergence and wealth of informatics, bioinformatics and genomics methods and associated resources allow a comprehensive and rapid approach for the surveillance and detection of bacterial and viral organisms. Coupled with the continuing race for the fastest, most cost-efficient and highest-quality DNA sequencing technology, that is, "next generation sequencing", the detection of biological threat agents by `cheaper and faster' means is possible. With the application of improved bioinformatic tools for the understanding of these genomes and for parsing unique pathogen genome signatures, along with `state-of-the-art' informatics which include faster computational methods, equipment and databases, it is feasible to apply new algorithms to biothreat agent detection. Two such methods are high-throughput DNA sequencing-based and resequencing microarray-based identification. These are illustrated and validated by two examples involving human adenoviruses, both from real-world test beds.

Selection tool for foodborne norovirus outbreaks.

PubMed

Verhoef, Linda P B; Kroneman, Annelies; van Duynhoven, Yvonne; Boshuizen, Hendriek; van Pelt, Wilfrid; Koopmans, Marion

2009-01-01

Detection of pathogens in the food chain is limited mainly to bacteria, and the globalization of the food industry enables international viral foodborne outbreaks to occur. Outbreaks from 2002 through 2006 recorded in a European norovirus surveillance database were investigated for virologic and epidemiologic indicators of food relatedness. The resulting validated multivariate logistic regression model comparing foodborne (n = 224) and person-to-person (n = 654) outbreaks was used to create a practical web-based tool that can be limited to epidemiologic parameters for nongenotyping countries. Non-genogroup-II.4 outbreaks, higher numbers of cases, and outbreaks in restaurants or households characterized (sensitivity = 0.80, specificity = 0.86) foodborne outbreaks and reduced the percentage of outbreaks requiring source-tracing to 31%. The selection tool enabled prospectively focused follow-up. Use of this tool is likely to improve data quality and strain typing in current surveillance systems, which is necessary for identification of potential international foodborne outbreaks.

A conceptual framework for the evaluation of HLB surveillance activities.

USDA-ARS?s Scientific Manuscript database

Surveillance activities play an integral part in disease prevention and control, and underpin the three main stages of disease mitigation: the prevention of entry and establishment of exotic pathogens; the detailed investigation of more established pathogens; and the monitoring of disease control me...

National animal health surveillance: Return on investment.

PubMed

Scott, Aaron E; Forsythe, Kenneth W; Johnson, Cynthia L

2012-08-01

A weighted benefit-cost analysis (BCA) supports prioritization of animal health surveillance activities to safeguard animal agriculture industries and reduce the impact of disease on the national economy. We propose to determine the value of investment in surveillance by assessing benefits from: avoiding disease incursion and expansion modified by the probability of occurrence of the disease event, the sensitivity of systems to detect it, and the degree to which we can mitigate disease impact when detected. The weighted benefit-cost ratio is the modified value of surveillance as laid out above divided by the cost of surveillance. We propose flexible, stream-based surveillance that capitalizes on combining multiple streams of information from both specific pathogen based and non-pathogen based surveillance. This stream-based type of system provides high value with lower costs and will provide a high return for the funds invested in animal health surveillance. Published by Elsevier B.V.

Optimal strategies for the surveillance and control of forest pathogens: A case study with oak wilt

Treesearch

Tetsuya Horie; Robert G. Haight; Frances R. Homans; Robert C. Venette

2013-01-01

Cost-effective strategies are needed to find and remove diseased trees in forests damaged by pathogens. We develop a model of cost-minimizing surveillance and control of forest pathogens across multiple sites where there is uncertainty about the extent of the infestation in each site and when the goal is to minimize the expected number of new infections. We allow for a...

Invasion of two tick-borne diseases across New England: harnessing human surveillance data to capture underlying ecological invasion processes

PubMed Central

Walter, Katharine S.; Pepin, Kim M.; Webb, Colleen T.; Gaff, Holly D.; Krause, Peter J.; Pitzer, Virginia E.; Diuk-Wasser, Maria A.

2016-01-01

Modelling the spatial spread of vector-borne zoonotic pathogens maintained in enzootic transmission cycles remains a major challenge. The best available spatio-temporal data on pathogen spread often take the form of human disease surveillance data. By applying a classic ecological approach—occupancy modelling—to an epidemiological question of disease spread, we used surveillance data to examine the latent ecological invasion of tick-borne pathogens. Over the last half-century, previously undescribed tick-borne pathogens including the agents of Lyme disease and human babesiosis have rapidly spread across the northeast United States. Despite their epidemiological importance, the mechanisms of tick-borne pathogen invasion and drivers underlying the distinct invasion trajectories of the co-vectored pathogens remain unresolved. Our approach allowed us to estimate the unobserved ecological processes underlying pathogen spread while accounting for imperfect detection of human cases. Our model predicts that tick-borne diseases spread in a diffusion-like manner with occasional long-distance dispersal and that babesiosis spread exhibits strong dependence on Lyme disease. PMID:27252022

Sieve analysis using the number of infecting pathogens.

PubMed

Follmann, Dean; Huang, Chiung-Yu

2017-12-14

Assessment of vaccine efficacy as a function of the similarity of the infecting pathogen to the vaccine is an important scientific goal. Characterization of pathogen strains for which vaccine efficacy is low can increase understanding of the vaccine's mechanism of action and offer targets for vaccine improvement. Traditional sieve analysis estimates differential vaccine efficacy using a single identifiable pathogen for each subject. The similarity between this single entity and the vaccine immunogen is quantified, for example, by exact match or number of mismatched amino acids. With new technology, we can now obtain the actual count of genetically distinct pathogens that infect an individual. Let F be the number of distinct features of a species of pathogen. We assume a log-linear model for the expected number of infecting pathogens with feature "f," f=1,…,F. The model can be used directly in studies with passive surveillance of infections where the count of each type of pathogen is recorded at the end of some interval, or active surveillance where the time of infection is known. For active surveillance, we additionally assume that a proportional intensity model applies to the time of potentially infectious exposures and derive product and weighted estimating equation (WEE) estimators for the regression parameters in the log-linear model. The WEE estimator explicitly allows for waning vaccine efficacy and time-varying distributions of pathogens. We give conditions where sieve parameters have a per-exposure interpretation under passive surveillance. We evaluate the methods by simulation and analyze a phase III trial of a malaria vaccine. © 2017, The International Biometric Society.

Directing Environmental Science towards Disease Surveillance Objectives: Waterborne Pathogens in the Developed World

NASA Astrophysics Data System (ADS)

Bridge, J. W.; Oliver, D.; Heathwaite, A.; Banwart, S.; Going Underground: Human Pathogens in The Soil-Water Environment Working Group

2010-12-01

We present the findings and recommendations of a recent UK working group convened to identify research priorities in environmental science and epidemiology of waterborne pathogens. Robust waterborne disease surveillance in the developed world remains a critical need, despite broad success of regulation and water treatment. Recent estimates suggest waterborne pathogens result in between 12 million and 19.5 million cases of illness per year in the US alone. Across the developed world, the value of preventing acute waterborne disease in 150 million people using small community or single-user supplies is estimated at above US$ 4,671 million. The lack of a high quality, reliable environmental knowledge base for waterborne pathogens is a key obstacle. Substantial improvements in understanding of pathogen survival and transport in soils, sediments and water are required both to aid identification of environmental aetiologies for organisms isolated in disease cases and to support novel mitigation responses directed towards specific exposure risks. However, the focus in monitoring and regulation on non-pathogenic faecal indicator organisms (easier and cheaper to detect in water samples) creates a lack of motivation to conduct detailed environmental studies of the actual pathogens likely to be encountered in disease surveillance. Robust disease surveillance may be regarded as an essential objective in epidemiology; but it constitutes a significant shift in perspective for the water industry. The health sector can play a vital role in changing attitudes by explicitly placing value on environmental water research which looks beyond compliance with water quality standards towards informing disease surveillance and influencing health outcomes. The summary of critical research priorities we outline provides a focus for developing and strengthening dialogue between health and water sectors to achieve a common goal - sophisticated management of waterborne diseases through sophisticated understanding of their environmental sources and dynamics.

Surveillance plan for the early detection of H5N1 highly pathogenic avian influenza virus in migratory birds in the United States: surveillance year 2009

USGS Publications Warehouse

Brand, Christopher J.

2009-01-01

Executive Summary: This Surveillance Plan (Plan) describes plans for conducting surveillance of wild birds in the United States and its Territories and Freely-Associated States to provide for early detection of the introduction of the H5N1 Highly Pathogenic Avian Influenza (HPAI) subtype of the influenza A virus by migratory birds during the 2009 surveillance year, spanning the period of April 1, 2009 - March 31, 2010. The Plan represents a continuation of surveillance efforts begun in 2006 under the Interagency Strategic Plan for the Early Detection of H5N1 Highly Pathogenic Avian Influenza in Wild Migratory Birds (U.S. Department of Agriculture and U.S. Department of the Interior, 2006). The Plan sets forth sampling plans by: region, target species or species groups to be sampled, locations of sampling, sample sizes, and sampling approaches and methods. This Plan will be reviewed annually and modified as appropriate for subsequent surveillance years based on evaluation of information from previous years of surveillance, changing patterns and threats of H5N1 HPAI, and changes in funding availability for avian influenza surveillance. Specific sampling strategies will be developed accordingly within each of six regions, defined here as Alaska, Hawaiian/Pacific Islands, Lower Pacific Flyway (Washington, Oregon, California, Idaho, Nevada, Arizona), Central Flyway, Mississippi Flyway, and Atlantic Flyway.

West Nile Virus State of the Art Report of MALWEST Project

PubMed Central

Marka, Andriani; Diamantidis, Alexandros; Papa, Anna; Valiakos, George; Chaintoutis, Serafeim C.; Doukas, Dimitrios; Tserkezou, Persefoni; Giannakopoulos, Alexios; Papaspyropoulos, Konstantinos; Patsoula, Eleni; Badieritakis, Evangelos; Baka, Agoritsa; Tseroni, Maria; Pervanidou, Danai; Papadopoulos, Nikos T.; Koliopoulos, George; Tontis, Dimitrios; Dovas, Chrysostomos I.; Billinis, Charalambos; Tsakris, Athanassios; Kremastinou, Jenny; Hadjichristodoulou, Christos

2013-01-01

During the last three years Greece is experiencing the emergence of West Nile virus (WNV) epidemics. Within this framework, an integrated surveillance and control programme (MALWEST project) with thirteen associate partners was launched aiming to investigate the disease and suggest appropriate interventions. One out of seven work packages of the project is dedicated to the State of the Art report for WNV. Three expert working groups on humans, animals and mosquitoes were established. Medical databases (PubMed, Scopus) were searched together with websites: e.g., WHO, CDC, ECDC. In total, 1,092 relevant articles were initially identified and 258 of them were finally included as references regarding the current knowledge about WNV, along with 36 additional sources (conference papers, reports, book chapters). The review is divided in three sections according to the fields of interest: (1) WNV in humans (epidemiology, molecular characteristics, transmission, diagnosis, treatment, prevention, surveillance); (2) WNV in animals (epidemiological and transmission characteristics concerning birds, horses, reptiles and other animal species) and (3) WNV in mosquitoes (control, surveillance). Finally, some examples of integrated surveillance programmes are presented. The introduction and establishment of the disease in Greece and other European countries further emphasizes the need for thorough research and broadening of our knowledge on this viral pathogen. PMID:24317379

A method of determining where to target surveillance efforts in heterogeneous epidemiological systems

PubMed Central

van den Bosch, Frank; Gottwald, Timothy R.; Alonso Chavez, Vasthi

2017-01-01

The spread of pathogens into new environments poses a considerable threat to human, animal, and plant health, and by extension, human and animal wellbeing, ecosystem function, and agricultural productivity, worldwide. Early detection through effective surveillance is a key strategy to reduce the risk of their establishment. Whilst it is well established that statistical and economic considerations are of vital importance when planning surveillance efforts, it is also important to consider epidemiological characteristics of the pathogen in question—including heterogeneities within the epidemiological system itself. One of the most pronounced realisations of this heterogeneity is seen in the case of vector-borne pathogens, which spread between ‘hosts’ and ‘vectors’—with each group possessing distinct epidemiological characteristics. As a result, an important question when planning surveillance for emerging vector-borne pathogens is where to place sampling resources in order to detect the pathogen as early as possible. We answer this question by developing a statistical function which describes the probability distributions of the prevalences of infection at first detection in both hosts and vectors. We also show how this method can be adapted in order to maximise the probability of early detection of an emerging pathogen within imposed sample size and/or cost constraints, and demonstrate its application using two simple models of vector-borne citrus pathogens. Under the assumption of a linear cost function, we find that sampling costs are generally minimised when either hosts or vectors, but not both, are sampled. PMID:28846676

9 CFR 145.15 - Diagnostic surveillance program for low pathogenic avian influenza.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 1 2013-01-01 2013-01-01 false Diagnostic surveillance program for low pathogenic avian influenza. 145.15 Section 145.15 Animals and Animal Products ANIMAL AND PLANT... antigen detection test. Memoranda of understanding or other means must be used to establish testing and...

9 CFR 145.15 - Diagnostic surveillance program for low pathogenic avian influenza.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 1 2012-01-01 2012-01-01 false Diagnostic surveillance program for low pathogenic avian influenza. 145.15 Section 145.15 Animals and Animal Products ANIMAL AND PLANT... antigen detection test. Memoranda of understanding or other means must be used to establish testing and...

9 CFR 145.15 - Diagnostic surveillance program for low pathogenic avian influenza.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 1 2014-01-01 2014-01-01 false Diagnostic surveillance program for low pathogenic avian influenza. 145.15 Section 145.15 Animals and Animal Products ANIMAL AND PLANT... antigen detection test. Memoranda of understanding or other means must be used to establish testing and...

Surveillance programs for detection and characterization of emergent pathogens and antimicrobial resistance: results from the Division of Infectious Diseases, UNIFESP.

PubMed

Colombo, Arnaldo L; Janini, Mario; Salomão, Reinaldo; Medeiros, Eduardo A S; Wey, Sergio B; Pignatari, Antonio C C

2009-09-01

Several epidemiological changes have occurred in the pattern of nosocomial and community acquired infectious diseases during the past 25 years. Social and demographic changes possibly related to this phenomenon include a rapid population growth, the increase in urban migration and movement across international borders by tourists and immigrants, alterations in the habitats of animals and arthropods that transmit disease, as well as the raise of patients with impaired host defense abilities. Continuous surveillance programs of emergent pathogens and antimicrobial resistance are warranted for detecting in real time new pathogens, as well as to characterize molecular mechanisms of resistance. In order to become more effective, surveillance programs of emergent pathogens should be organized as a multicenter laboratory network connected to the main public and private infection control centers. Microbiological data should be integrated to guide therapy, adapting therapy to local ecology and resistance patterns. This paper presents an overview of data generated by the Division of Infectious Diseases, Federal University of São Paulo, along with its participation in different surveillance programs of nosocomial and community acquired infectious diseases.

Integrated cluster- and case-based surveillance for detecting stage III zoonotic pathogens: an example of Nipah virus surveillance in Bangladesh.

PubMed

Naser, A M; Hossain, M J; Sazzad, H M S; Homaira, N; Gurley, E S; Podder, G; Afroj, S; Banu, S; Rollin, P E; Daszak, P; Ahmed, B-N; Rahman, M; Luby, S P

2015-07-01

This paper explores the utility of cluster- and case-based surveillance established in government hospitals in Bangladesh to detect Nipah virus, a stage III zoonotic pathogen. Physicians listed meningo-encephalitis cases in the 10 surveillance hospitals and identified a cluster when ⩾2 cases who lived within 30 min walking distance of one another developed symptoms within 3 weeks of each other. Physicians collected blood samples from the clustered cases. As part of case-based surveillance, blood was collected from all listed meningo-encephalitis cases in three hospitals during the Nipah season (January-March). An investigation team visited clustered cases' communities to collect epidemiological information and blood from the living cases. We tested serum using Nipah-specific IgM ELISA. Up to September 2011, in 5887 listed cases, we identified 62 clusters comprising 176 encephalitis cases. We collected blood from 127 of these cases. In 10 clusters, we identified a total of 62 Nipah cases: 18 laboratory-confirmed and 34 probable. We identified person-to-person transmission of Nipah virus in four clusters. From case-based surveillance, we identified 23 (4%) Nipah cases. Faced with thousands of encephalitis cases, integrated cluster surveillance allows targeted deployment of investigative resources to detect outbreaks by stage III zoonotic pathogens in resource-limited settings.

Etiological epidemiology of viral diarrhea on the basis of sentinel surveillance in children younger than 5 years in Gansu, northwest China, 2009-2013.

PubMed

Liu, Xiaoning; Meng, Lei; Li, Juansheng; Liu, Xinfeng; Bai, Yana; Yu, Deshan; Ren, Xiaowei; Liu, Haixia; Shen, Xiping; Wang, Peng; Hu, Xiaobin; Wei, Kongfu; Pei, Hongbo; Kang, Qian

2015-12-01

To explore the etiological spectrum of diarrhea and its epidemiological characteristics in diarrhea symptoms surveillance cases younger than 5 years from 2009 to 2013 in Gansu province, northwest China. Systematic diarrhea symptoms surveillance were conducted in 27 sentinel sites in Gansu province and outpatients with three or more loose, watery, or sticky pus stools per day were defined as surveillance cases. All stool specimens were tested for Rotavirus, Human calicivirus, Adenovirus, and Astrovirus. Totally, 1,119 cases (51.54%) were identified as any enteric virus. The average isolation rate of Rotavirus was 51.13%, Astrovirus was 10.84%, Adenovirus was 6.94%, and Human calicivirus was 6.60% (P < 0.01). Rotavirus was identified with the highest frequency among these enteric pathogens except in 2011, with a notable downward trend over time (P < 0.01). Rotavirus A was the most proportion in rotavirus, G3P[8] and G9P[8] were the most common combination. Rotavirus mixed Human calicivirus infections was the most common mixed infected patterns. Viral-positive rate was higher among children aged group of 0-12 and 13-24 months (P < 0.01, respectively). The isolation rates of four enteric viral pathogens showed a similar distinct seasonal variation with a higher rate in spring, autumn, and winter months. Rotavirus was the major epidemiological viral pathogen in diarrhea symptom surveillance cases in Gansu province, northwest China, during period 2009-2013. Seasonal and age-related variations were observed in enteric viral pathogen isolation rate. The comprehensive and continuous surveillance is needed to identify the prevalence of different enteric viral pathogens. © 2015 Wiley Periodicals, Inc.

How can a climate change perspective be integrated into public health surveillance?

PubMed

Pascal, M; Viso, A C; Medina, S; Delmas, M C; Beaudeau, P

2012-08-01

Climate change may be considered as a key factor for environmental change, exposure to health risks and pathogens, consequently impairing the state of health among populations. Efficient health surveillance systems are required to support adaptation to climate change. However, despite a growing awareness, the public health surveillance sector has had very little involvement in the drafting of adaptation plans. This paper proposes a method to raise awareness about climate change in the public health community, to identify possible health risks and to assess the needs for reinforced health surveillance systems. A working group was set up comprising surveillance experts in the following fields: environmental health; chronic diseases and; infectious diseases. Their goal was to define common objectives, to propose a framework for risk analysis, and to apply it to relevant health risks in France. The framework created helped to organize available information on climate-sensitive health risks, making a distinction between three main determinants as follows: (1) environment; (2) individual and social behaviours; and (3) demography and health status. The process is illustrated using two examples: heatwaves and airborne allergens. Health surveillance systems can be used to trigger early warning systems, to create databases which improve scientific knowledge about the health impacts of climate change, to identify and prioritize needs for intervention and adaptation measures, and to evaluate these measures. Adaptation requires public health professionals to consider climate change as a concrete input parameter in their studies and to create partnerships with professionals from other disciplines. Copyright © 2012 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Live Bird Markets of Bangladesh: H9N2 Viruses and the Near Absence of Highly Pathogenic H5N1 Influenza

PubMed Central

Negovetich, Nicholas J.; Feeroz, Mohammed M.; Jones-Engel, Lisa; Walker, David; Alam, S. M. Rabiul; Hasan, Kamrul; Seiler, Patrick; Ferguson, Angie; Friedman, Kim; Barman, Subrata; Franks, John; Turner, Jasmine; Krauss, Scott; Webby, Richard J.; Webster, Robert G.

2011-01-01

Avian influenza surveillance in Bangladesh has been passive, relying on poultry farmers to report suspected outbreaks of highly pathogenic H5N1 influenza. Here, the results of an active surveillance effort focusing on the live-bird markets are presented. Prevalence of influenza infection in the birds of the live bird markets is 23.0%, which is similar to that in poultry markets in other countries. Nearly all of the isolates (94%) were of the non-pathogenic H9N2 subtype, but viruses of the H1N2, H1N3, H3N6, H4N2, H5N1, and H10N7 subtypes were also observed. The highly pathogenic H5N1-subtype virus was observed at extremely low prevalence in the surveillance samples (0.08%), and we suggest that the current risk of infection for humans in the retail poultry markets in Bangladesh is negligible. However, the high prevalence of the H9 subtype and its potential for interaction with the highly pathogenic H5N1-subtype, i.e., reassortment and attenuation of host morbidity, highlight the importance of active surveillance of the poultry markets. PMID:21541296

Improving vector-borne pathogen surveillance: A laboratory-based study exploring the potential to detect dengue virus and malaria parasites in mosquito saliva.

PubMed

Melanson, Vanessa R; Jochim, Ryan; Yarnell, Michael; Ferlez, Karen Bingham; Shashikumar, Soumya; Richardson, Jason H

2017-01-01

Vector-borne pathogen surveillance programmes typically rely on the collection of large numbers of potential vectors followed by screening protocols focused on detecting pathogens in the arthropods. These processes are laborious, time consuming, expensive, and require screening of large numbers of samples. To streamline the surveillance process, increase sample throughput, and improve cost-effectiveness, a method to detect dengue virus and malaria parasites (Plasmodium falciparum) by leveraging the sugar-feeding behaviour of mosquitoes and their habit of expectorating infectious agents in their saliva during feeding was investigated in this study. Dengue virus 2 (DENV-2) infected female Aedes aegypti mosquitoes and P. falciparum infected female Anopheles stephensi mosquitoes were allowed to feed on honey coated Flinders Technical Associates -FTA® cards dyed with blue food colouring. The feeding resulted in deposition of saliva containing either DENV-2 particles or P. falciparum sporozoites onto the FTA card. Nucleic acid was extracted from each card and the appropriate real-time PCR (qPCR) assay was run to detect the pathogen of interest. As little as one plaque forming unit (PFU) of DENV-2 and as few as 60 P. falciparum parasites deposited on FTA cards from infected mosquitoes were detected via qPCR. Hence, their use to collect mosquito saliva for pathogen detection is a relevant technique for vector surveillance. This study provides laboratory confirmation that FTA cards can be used to capture and stabilize expectorated DENV-2 particles and P. falciparum sporozoites from infectious, sugar-feeding mosquitoes in very low numbers. Thus, the FTA card-based mosquito saliva capture method offers promise to overcome current limitations and revolutionize traditional mosquito-based pathogen surveillance programmes. Field testing and further method development are required to optimize this strategy.

Lessons learned from research and surveillance directed at highly pathogenic influenza A viruses in wild birds inhabiting North America

USDA-ARS?s Scientific Manuscript database

Following detections of highly pathogenic (HP) influenza A viruses (IAVs) in wild birds inhabiting East Asia after the turn of the millennium, the intensity of sampling of wild birds for IAVs increased throughout much of North America and the objectives for many research and surveillance efforts wer...

[Antimicrobial resistance in gram negative bacteria isolated from intensive care units of Colombian hospitals, WHONET 2003, 2004 and 2005].

PubMed

Miranda, María Consuelo; Pérez, Federico; Zuluaga, Tania; Olivera, María del Rosario; Correa, Adriana; Reyes, Sandra Lorena; Villegas, Maria Virginia

2006-09-01

Surveillance systems play a key role in the detection and control of bacterial resistance. It is necessary to constantly collect information from all institutions because the mechanisms of bacterial resistance can operate in different ways between countries, cities and even in hospitals in the same area. Therefore local information is important in order to learn about bacterial behaviour and design appropriate interventions for each institution. Between January 2003 and December 2004, the Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM) developed a surveillance project in 10 tertiary hospitals in 6 cities of Colombia. Describe the trends of antibiotic resistance among the isolates of Escherichia coli, Klebsiella pneumoniae, Pseudomona aeruginosa, Acinetobacter baumannii and Enterobacter cloacae, five of the most prevalent nosocomial Gram negative pathogens. The susceptibility tests were performed by automated methods in 9 hospitals and by Kirby Bauer in 1 hospital. Antibiotics with known activity against Gram negatives, according to the Clinical Laboratory Standards Institute guidelines, were selected. The laboratories performed internal and external quality controls. During the study period, the information was downloaded monthly from the databases of each microbiology laboratory and sent to CIDEIM where it was centralized in a database using the system WHONET 5.3. The high resistance rates reported especially for A. baumannii, evidenced the presence of multidrug resistant bacteria in both ICUs and wards at every studied institution. The creation of a national surveillance network to improve our capabilities to detect, follow up, and control the antibiotic resistance in Colombia is urgently needed.

Value of lower respiratory tract surveillance cultures to predict bacterial pathogens in ventilator-associated pneumonia: systematic review and diagnostic test accuracy meta-analysis.

PubMed

Brusselaers, Nele; Labeau, Sonia; Vogelaers, Dirk; Blot, Stijn

2013-03-01

In ventilator-associated pneumonia (VAP), early appropriate antimicrobial therapy may be hampered by involvement of multidrug-resistant (MDR) pathogens. A systematic review and diagnostic test accuracy meta-analysis were performed to analyse whether lower respiratory tract surveillance cultures accurately predict the causative pathogens of subsequent VAP in adult patients. Selection and assessment of eligibility were performed by three investigators by mutual consideration. Of the 525 studies retrieved, 14 were eligible for inclusion (all in English; published since 1994), accounting for 791 VAP episodes. The following data were collected: study and population characteristics; in- and exclusion criteria; diagnostic criteria for VAP; microbiological workup of surveillance and diagnostic VAP cultures. Sub-analyses were conducted for VAP caused by Staphylococcus aureus, Pseudomonas spp., and Acinetobacter spp., MDR microorganisms, frequency of sampling, and consideration of all versus the most recent surveillance cultures. The meta-analysis showed a high accuracy of surveillance cultures, with pooled sensitivities up to 0.75 and specificities up to 0.92 in culture-positive VAP. The area under the curve (AUC) of the hierarchical summary receiver-operating characteristic curve demonstrates moderate accuracy (AUC: 0.90) in predicting multidrug resistance. A sampling frequency of >2/week (sensitivity 0.79; specificity 0.96) and consideration of only the most recent surveillance culture (sensitivity 0.78; specificity 0.96) are associated with a higher accuracy of prediction. This study provides evidence for the benefit of surveillance cultures in predicting MDR bacterial pathogens in VAP. However, clinical and statistical heterogeneity, limited samples sizes, and bias remain important limitations of this meta-analysis.

Surveillance theory applied to virus detection: a case for targeted discovery

USGS Publications Warehouse

Bogich, Tiffany L.; Anthony, Simon J.; Nichols, James D.

2013-01-01

Virus detection and mathematical modeling have gone through rapid developments in the past decade. Both offer new insights into the epidemiology of infectious disease and characterization of future risk; however, modeling has not yet been applied to designing the best surveillance strategies for viral and pathogen discovery. We review recent developments and propose methods to integrate viral and pathogen discovery and mathematical modeling through optimal surveillance theory, arguing for a more targeted approach to novel virus detection guided by the principles of adaptive management and structured decision-making.

Avian influenza surveillance of wild birds

USGS Publications Warehouse

Slota, Paul

2007-01-01

The President's National Strategy for Pandemic Influenza directs federal agencies to expand the surveillance of United States domestic livestock and wildlife to ensure early warning of hightly pathogenic avian influenza (HPAI) in the U.S. The immediate concern is a potential introduction of HPAI H5N1 virus into the U.S. The presidential directive resulted in the U.S. Interagency Strategic Plan for Early Detection of H5N1 Highly Pathogenic Avian Influenza in Wild Migratory Birds (referred to as the Wild Bird Surveillance Plan or the Plan).

9 CFR 146.14 - Diagnostic surveillance program for H5/H7 low pathogenic avian influenza.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 1 2013-01-01 2013-01-01 false Diagnostic surveillance program for H5/H7 low pathogenic avian influenza. 146.14 Section 146.14 Animals and Animal Products ANIMAL AND PLANT... antigen detection test. Memoranda of understanding or other means must be used to establish testing and...

9 CFR 146.14 - Diagnostic surveillance program for H5/H7 low pathogenic avian influenza.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Diagnostic surveillance program for H5/H7 low pathogenic avian influenza. 146.14 Section 146.14 Animals and Animal Products ANIMAL AND PLANT... antigen detection test. Memoranda of understanding or other means must be used to establish testing and...

9 CFR 146.14 - Diagnostic surveillance program for H5/H7 low pathogenic avian influenza.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false Diagnostic surveillance program for H5/H7 low pathogenic avian influenza. 146.14 Section 146.14 Animals and Animal Products ANIMAL AND PLANT... antigen detection test. Memoranda of understanding or other means must be used to establish testing and...

9 CFR 146.14 - Diagnostic surveillance program for H5/H7 low pathogenic avian influenza.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 1 2012-01-01 2012-01-01 false Diagnostic surveillance program for H5/H7 low pathogenic avian influenza. 146.14 Section 146.14 Animals and Animal Products ANIMAL AND PLANT... antigen detection test. Memoranda of understanding or other means must be used to establish testing and...

9 CFR 146.14 - Diagnostic surveillance program for H5/H7 low pathogenic avian influenza.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 1 2014-01-01 2014-01-01 false Diagnostic surveillance program for H5/H7 low pathogenic avian influenza. 146.14 Section 146.14 Animals and Animal Products ANIMAL AND PLANT... antigen detection test. Memoranda of understanding or other means must be used to establish testing and...

Dynamic intervention: pathogen disarmament of mitochondrial-based immune surveillance.

PubMed

Holland, Robin L; Blanke, Steven R

2014-11-12

In this issue of Cell Host & Microbe, Suzuki et al. (2014) describe a Vibrio cholerae Type-III-secreted effector that targets mitochondrial dynamics to dampen host innate immune signaling. This suggests that mammalian hosts possess surveillance mechanisms to monitor pathogen-mediated alterations in the integrity of normal cellular processes and organelles. Copyright © 2014 Elsevier Inc. All rights reserved.

Rate of introduction of a low pathogenic avian influenza virus infection in different poultry production sectors in the Netherlands

PubMed Central

Gonzales, Jose L.; Stegeman, Jan A.; Koch, Guus; de Wit, Sjaak J.; Elbers, Armin R. W.

2012-01-01

Please cite this paper as: Gonzales et al. (2012) Rate of introduction of a low pathogenic avian influenza virus infection in different poultry production sectors in the Netherlands. Influenza and Other Respiratory Viruses DOI: 10.1111/j.1750‐2659.2012.00348.x. Background  Targeted risk‐based surveillance of poultry types (PT) with different risks of introduction of low pathogenic avian influenza virus (LPAIv) infection may improve the sensitivity of surveillance. Objective  To quantify the rate of introduction of LPAIv infections in different PT. Methods  Data from the Dutch LPAIv surveillance programme (2007–2010) were analysed using a generalised linear mixed and spatial model. Results  Outdoor‐layer, turkey, duck‐breeder and meat‐duck, farms had a 11, 8, 24 and 13 times higher rate of introduction of LPAIv than indoor‐layer farms, respectively. Conclusion  Differences in the rate of introduction of LPAIv could be used to (re)design a targeted risk‐based surveillance programme. PMID:22376126

IDD Info: a software to manage surveillance data of Iodine Deficiency Disorders.

PubMed

Liu, Peng; Teng, Bai-Jun; Zhang, Shu-Bin; Su, Xiao-Hui; Yu, Jun; Liu, Shou-Jun

2011-08-01

IDD info, a new software for managing survey data of Iodine Deficiency Disorders (IDD), is presented in this paper. IDD Info aims to create IDD project databases, process, analyze various national or regional surveillance data and form final report. It has series measures of choosing database from existing ones, revising it, choosing indicators from pool to establish database and adding indicators to pool. It also provides simple tools to scan one database and compare two databases, to set IDD standard parameters, to analyze data by single indicator and multi-indicators, and finally to form typeset report with content customized. IDD Info was developed using Chinese national IDD surveillance data of 2005. Its validity was evaluated by comparing with survey report given by China CDC. The IDD Info is a professional analysis tool, which succeeds in speeding IDD data analysis up to about 14.28% with respect to standard reference routines. It consequently enhances analysis performance and user compliance. IDD Info is a practical and accurate means of managing the multifarious IDD surveillance data that can be widely used by non-statisticians in national and regional IDD surveillance. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Circuits of Surveillance

PubMed Central

Williams, Robin; Johnson, Paul

2005-01-01

This paper examines the increasing police use of DNA profiling and databasing as a developing instrumentality of modern state surveillance. It briefly notes previously published work on a variety of surveillance technologies and their role in the governance of social action and social order. It then argues that there are important differences amongst the ways in which several such technologies construct and use identificatory artefacts, their orientations to human subjectivity, and their role in the governmentality of citizens and others. The paper then describes the novel and powerful form of bio-surveillance offered by DNA profiling and illustrates this by reference to an ongoing empirical study of the police uses of the UK National DNA Database for the investigation of crime. It is argued that DNA profiling and databasing enable the construction of a ‘closed circuit’ of surveillance of a defined population. PMID:16467920

Veterinary Research Manpower Development for Defense

DTIC Science & Technology

2007-09-01

Participatory Disease Surveillance Method for Detection of Highly Pathogenic Avian Influenza in Java, Indonesia Rebecca Steers Dr. Lindenmeyer Detection of...Transmission of Nipah Virus in Bangladesh Summary: My project aims to investigate the risk of zoonotic transmission of Nipah virus as a food-borne...Participatory Disease Surveillance Method for Detection of Highly Pathogenic Avian Influenza in Java, Indonesia Summary: Two epidemics of H5N1 Highly

Community incidence of pathogen-specific gastroenteritis: reconstructing the surveillance pyramid for seven pathogens in seven European Union member states.

PubMed

Haagsma, J A; Geenen, P L; Ethelberg, S; Fetsch, A; Hansdotter, F; Jansen, A; Korsgaard, H; O'Brien, S J; Scavia, G; Spitznagel, H; Stefanoff, P; Tam, C C; Havelaar, A H

2013-08-01

By building reconstruction models for a case of gastroenteritis in the general population moving through different steps of the surveillance pyramid we estimated that millions of illnesses occur annually in the European population, leading to thousands of hospitalizations. We used data on the healthcare system in seven European Union member states in relation to pathogen characteristics that influence healthcare seeking. Data on healthcare usage were obtained by harmonized cross-sectional surveys. The degree of under-diagnosis and underreporting varied by pathogen and country. Overall, underreporting and under-diagnosis were estimated to be lowest for Germany and Sweden, followed by Denmark, The Netherlands, UK, Italy and Poland. Across all countries, the incidence rate was highest for Campylobacter spp. and Salmonella spp. Incidence estimates resulting from the pyramid reconstruction approach are adjusted for biases due to different surveillance systems and are therefore a better basis for international comparisons than reported data.

High Throughput Sequencing for Detection of Foodborne Pathogens

PubMed Central

Sekse, Camilla; Holst-Jensen, Arne; Dobrindt, Ulrich; Johannessen, Gro S.; Li, Weihua; Spilsberg, Bjørn; Shi, Jianxin

2017-01-01

High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic “natural” strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade. PMID:29104564

Eradication of tephritid fruit fly pest populations: outcomes and prospects.

PubMed

Suckling, David Maxwell; Kean, John M; Stringer, Lloyd D; Cáceres-Barrios, Carlos; Hendrichs, Jorge; Reyes-Flores, Jesus; Dominiak, Bernard C

2016-03-01

The number of insect eradication programmes is rising in response to globalisation. A database of arthropod and plant pathogen eradications covers 1050 incursion responses, with 928 eradication programmes on 299 pest and disease taxa in 104 countries (global eradication database b3.net.nz/gerda). A subset of the database was assembled with 211 eradication or response programmes against 17 species of fruit flies (Tephritidae) in 31 countries, in order to investigate factors affecting the outcome. The failure rate for fruit fly eradication programmes was about 7%, with 0% for Ceratitis capitata (n = 85 programmes) and 0% for two Anastrepha species (n = 12 programmes), but 12% for 13 Bactrocera species (n = 108 programmes). A number of intended eradication programmes against long-established populations were not initiated because of cost and other considerations, or evolved during the planning phase into suppression programmes. Cost was dependent on area, ranged from $US 0.1 million to $US 240 million and averaged about $US 12 million (normalised to $US in 2012). In addition to the routine use of surveillance networks, quarantine and fruit destruction, the key tactics used in eradication programmes were male annihilation, protein bait sprays (which can attract both sexes), fruit destruction and the sterile insect technique. Eradication success generally required the combination of several tactics applied on an area-wide basis. Because the likelihood of eradication declines with an increase in the area infested, it pays to invest in effective surveillance networks that allow early detection and delimitation while invading populations are small, thereby greatly favouring eradication success. © 2014 Society of Chemical Industry.

Evaluation of a statewide foodborne illness complaint surveillance system in Minnesota, 2000 through 2006.

PubMed

Li, John; Smith, Kirk; Kaehler, Dawn; Everstine, Karen; Rounds, Josh; Hedberg, Craig

2010-11-01

Foodborne outbreaks are detected by recognition of similar illnesses among persons with a common exposure or by identification of case clusters through pathogen-specific surveillance. PulseNet USA has created a national framework for pathogen-specific surveillance, but no comparable effort has been made to improve surveillance of consumer complaints of suspected foodborne illness. The purpose of this study was to characterize the complaint surveillance system in Minnesota and to evaluate its use for detecting outbreaks. Minnesota Department of Health foodborne illness surveillance data from 2000 through 2006 were analyzed for this study. During this period, consumer complaint surveillance led to detection of 79% of confirmed foodborne outbreaks. Most norovirus infection outbreaks were detected through complaints. Complaint surveillance also directly led or contributed to detection of 25% of salmonellosis outbreaks. Eighty-one percent of complainants did not seek medical attention. The number of ill persons in a complainant's party was significantly associated with a complaint ultimately resulting in identification of a foodborne outbreak. Outbreak confirmation was related to a complainant's ability to identify a common exposure and was likely related to the process by which the Minnesota Department of Health chooses complaints to investigate. A significant difference (P < 0.001) was found in incubation periods between complaints that were outbreak associated (median, 27 h) and those that were not outbreak associated (median, 6 h). Complaint systems can be used to detect outbreaks caused by a variety of pathogens. Case detection for foodborne disease surveillance in Minnesota happens through a multitude of mechanisms. The ability to integrate these mechanisms and carry out rapid investigations leads to improved outbreak detection.

Achievable Rate Estimation of IEEE 802.11ad Visual Big-Data Uplink Access in Cloud-Enabled Surveillance Applications.

PubMed

Kim, Joongheon; Kim, Jong-Kook

2016-01-01

This paper addresses the computation procedures for estimating the impact of interference in 60 GHz IEEE 802.11ad uplink access in order to construct visual big-data database from randomly deployed surveillance camera sensing devices. The acquired large-scale massive visual information from surveillance camera devices will be used for organizing big-data database, i.e., this estimation is essential for constructing centralized cloud-enabled surveillance database. This performance estimation study captures interference impacts on the target cloud access points from multiple interference components generated by the 60 GHz wireless transmissions from nearby surveillance camera devices to their associated cloud access points. With this uplink interference scenario, the interference impacts on the main wireless transmission from a target surveillance camera device to its associated target cloud access point with a number of settings are measured and estimated under the consideration of 60 GHz radiation characteristics and antenna radiation pattern models.

Genomic paradigms for food-borne enteric pathogen analysis at the USFDA: case studies highlighting method utility, integration and resolution.

PubMed

Elkins, C A; Kotewicz, M L; Jackson, S A; Lacher, D W; Abu-Ali, G S; Patel, I R

2013-01-01

Modern risk control and food safety practices involving food-borne bacterial pathogens are benefiting from new genomic technologies for rapid, yet highly specific, strain characterisations. Within the United States Food and Drug Administration (USFDA) Center for Food Safety and Applied Nutrition (CFSAN), optical genome mapping and DNA microarray genotyping have been used for several years to quickly assess genomic architecture and gene content, respectively, for outbreak strain subtyping and to enhance retrospective trace-back analyses. The application and relative utility of each method varies with outbreak scenario and the suspect pathogen, with comparative analytical power enhanced by database scale and depth. Integration of these two technologies allows high-resolution scrutiny of the genomic landscapes of enteric food-borne pathogens with notable examples including Shiga toxin-producing Escherichia coli (STEC) and Salmonella enterica serovars from a variety of food commodities. Moreover, the recent application of whole genome sequencing technologies to food-borne pathogen outbreaks and surveillance has enhanced resolution to the single nucleotide scale. This new wealth of sequence data will support more refined next-generation custom microarray designs, targeted re-sequencing and "genomic signature recognition" approaches involving a combination of genes and single nucleotide polymorphism detection to distil strain-specific fingerprinting to a minimised scale. This paper examines the utility of microarrays and optical mapping in analysing outbreaks, reviews best practices and the limits of these technologies for pathogen differentiation, and it considers future integration with whole genome sequencing efforts.

A true real-time, on-line security system for waterborne pathogen surveillance

NASA Astrophysics Data System (ADS)

Adams, John A.; McCarty, David L.

2008-04-01

Over the past several years many advances have been made to monitor potable water systems for toxic threats. However, the need for real-time, on-line systems to detect the malicious introduction of deadly pathogens still exists. Municipal water distribution systems, government facilities and buildings, and high profile public events remain vulnerable to terrorist-related biological contamination. After years of research and development, an instrument using multi-angle light scattering (MALS) technology has been introduced to achieve on-line, real-time detection and classification of a waterborne pathogen event. The MALS system utilizes a continuous slip stream of water passing through a flow cell in the instrument. A laser beam, focused perpendicular to the water flow, strikes particles as they pass through the beam generating unique light scattering patterns that are captured by photodetectors. Microorganisms produce patterns termed 'bio-optical signatures' which are comparable to fingerprints. By comparing these bio-optical signatures to an on-board database of microorganism patterns, detection and classification occurs within minutes. If a pattern is not recognized, it is classified as an 'unknown' and the unidentified contaminant is registered as a potential threat. In either case, if the contaminant exceeds a customer's threshold, the system will immediately alert personnel to the contamination event while extracting a sample for confirmation. The system, BioSentry TM, developed by JMAR Technologies is now field-tested and commercially available. BioSentry is cost effective, uses no reagents, operates remotely, and can be used for continuous microbial surveillance in many water treatment environments. Examples of HLS installations will be presented along with data from the US EPA NHSRC Testing and Evaluation Facility.

NATIONAL NOSOCOMIAL INFECTIONS SURVEILLANCE SYSTEM (NNIS)

EPA Science Inventory

The National Nosocomial Infections Surveillance (NNIS) System is a cooperative effort that began in 1970 between the Centers for Disease Control and Prevention (CDC) and participating hospitals to create a national nosocomial infections database. The database is used to describe ...

Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach.

PubMed

Kohl, Thomas A; Diel, Roland; Harmsen, Dag; Rothgänger, Jörg; Walter, Karen Meywald; Merker, Matthias; Weniger, Thomas; Niemann, Stefan

2014-07-01

Whole-genome sequencing (WGS) allows for effective tracing of Mycobacterium tuberculosis complex (MTBC) (tuberculosis pathogens) transmission. However, it is difficult to standardize and, therefore, is not yet employed for interlaboratory prospective surveillance. To allow its widespread application, solutions for data standardization and storage in an easily expandable database are urgently needed. To address this question, we developed a core genome multilocus sequence typing (cgMLST) scheme for clinical MTBC isolates using the Ridom SeqSphere(+) software, which transfers the genome-wide single nucleotide polymorphism (SNP) diversity into an allele numbering system that is standardized, portable, and not computationally intensive. To test its performance, we performed WGS analysis of 26 isolates with identical IS6110 DNA fingerprints and spoligotyping patterns from a longitudinal outbreak in the federal state of Hamburg, Germany (notified between 2001 and 2010). The cgMLST approach (3,041 genes) discriminated the 26 strains with a resolution comparable to that of SNP-based WGS typing (one major cluster of 22 identical or closely related and four outlier isolates with at least 97 distinct SNPs or 63 allelic variants). Resulting tree topologies are highly congruent and grouped the isolates in both cases analogously. Our data show that SNP- and cgMLST-based WGS analyses facilitate high-resolution discrimination of longitudinal MTBC outbreaks. cgMLST allows for a meaningful epidemiological interpretation of the WGS genotyping data. It enables standardized WGS genotyping for epidemiological investigations, e.g., on the regional public health office level, and the creation of web-accessible databases for global TB surveillance with an integrated early warning system. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Communicable Diseases Prioritized for Surveillance and Epidemiological Research: Results of a Standardized Prioritization Procedure in Germany, 2011

PubMed Central

Balabanova, Yanina; Gilsdorf, Andreas; Buda, Silke; Burger, Reinhard; Eckmanns, Tim; Gärtner, Barbara; Groß, Uwe; Haas, Walter; Hamouda, Osamah; Hübner, Johannes; Jänisch, Thomas; Kist, Manfred; Kramer, Michael H.; Ledig, Thomas; Mielke, Martin; Pulz, Matthias; Stark, Klaus; Suttorp, Norbert; Ulbrich, Uta; Wichmann, Ole; Krause, Gérard

2011-01-01

Introduction To establish strategic priorities for the German national public health institute (RKI) and guide the institute's mid-term strategic decisions, we prioritized infectious pathogens in accordance with their importance for national surveillance and epidemiological research. Methods We used the Delphi process with internal (RKI) and external experts and a metric-consensus approach to score pathogens according to ten three-tiered criteria. Additional experts were invited to weight each criterion, leading to the calculation of a median weight by which each score was multiplied. We ranked the pathogens according to the total weighted score and divided them into four priority groups. Results 127 pathogens were scored. Eighty-six experts participated in the weighting; “Case fatality rate” was rated as the most important criterion. Twenty-six pathogens were ranked in the highest priority group; among those were pathogens with internationally recognised importance (e.g., Human Immunodeficiency Virus, Mycobacterium tuberculosis, Influenza virus, Hepatitis C virus, Neisseria meningitides), pathogens frequently causing large outbreaks (e.g., Campylobacter spp.), and nosocomial pathogens associated with antimicrobial resistance. Other pathogens in the highest priority group included Helicobacter pylori, Respiratory Syncytial Virus, Varicella zoster virus and Hantavirus. Discussion While several pathogens from the highest priority group already have a high profile in national and international health policy documents, high scores for other pathogens (e.g., Helicobacter pylori, Respiratory syncytial virus or Hantavirus) indicate a possible under-recognised importance within the current German public health framework. A process to strengthen respective surveillance systems and research has been started. The prioritization methodology has worked well; its modular structure makes it potentially useful for other settings. PMID:21991334

Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences.

PubMed

Padliya, Neerav D; Garrett, Wesley M; Campbell, Kimberly B; Tabb, David L; Cooper, Bret

2007-11-01

LC-MS/MS has demonstrated potential for detecting plant pathogens. Unlike PCR or ELISA, LC-MS/MS does not require pathogen-specific reagents for the detection of pathogen-specific proteins and peptides. However, the MS/MS approach we and others have explored does require a protein sequence reference database and database-search software to interpret tandem mass spectra. To evaluate the limitations of database composition on pathogen identification, we analyzed proteins from cultured Ustilago maydis, Phytophthora sojae, Fusarium graminearum, and Rhizoctonia solani by LC-MS/MS. When the search database did not contain sequences for a target pathogen, or contained sequences to related pathogens, target pathogen spectra were reliably matched to protein sequences from nontarget organisms, giving an illusion that proteins from nontarget organisms were identified. Our analysis demonstrates that when database-search software is used as part of the identification process, a paradox exists whereby additional sequences needed to detect a wide variety of possible organisms may lead to more cross-species protein matches and misidentification of pathogens.

Description of the MHS Health Level 7 Chemistry Laboratory for Public Health Surveillance

DTIC Science & Technology

2012-09-01

document provides a history of the HL7 chemistry database and its contents, explains the creation of chemistry/serology records, describes the pathway...in health surveillance activities. This technical document discusses the chemistry database by providing a history of the dataset and its contents...source for its usefulness in public health surveillance. While HL7 data also includes radiology, anatomic pathology reports and pharmacy transactions

Highly pathogenic avian influenza A(H7N9) virus, Tennessee, USA, March 2017

USDA-ARS?s Scientific Manuscript database

In March 2017, highly pathogenic avian influenza A(H7N9) was detected at 2 poultry farms in Tennessee, USA. Surveillance data and genetic analyses indicated multiple introductions of low pathogenicity avian influenza virus before mutation to high pathogenicity and interfarm transmission. Poultry sur...

Host-pathogen interactions: A cholera surveillance system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wright, Aaron T.

2016-02-22

Bacterial pathogen-secreted proteases may play a key role in inhibiting a potentially widespread host-pathogen interaction. Activity-based protein profiling enabled the identification of a major Vibrio cholerae serine protease that limits the ability of a host-derived intestinal lectin to bind to the bacterial pathogen in vivo.

Zoonotic viruses associated with illegally imported wildlife products

USGS Publications Warehouse

Smith, Kristine M.; Anthony, Simon J.; Switzer, William M.; Epstein, Jonathan H.; Seimon, Tracie; Jia, Hongwei; Sanchez, Maria D.; Huynh, Thanh Thao; Galland, G. Gale; Shapiro, Sheryl E.; Sleeman, Jonathan M.; McAloose, Denise; Stuchin, Margot; Amato, George; Kolokotronis, Sergios-Orestis; Lipkin, W. Ian; Karesh, William B.; Daszak, Peter; Marano, Nina

2012-01-01

The global trade in wildlife has historically contributed to the emergence and spread of infectious diseases. The United States is the world's largest importer of wildlife and wildlife products, yet minimal pathogen surveillance has precluded assessment of the health risks posed by this practice. This report details the findings of a pilot project to establish surveillance methodology for zoonotic agents in confiscated wildlife products. Initial findings from samples collected at several international airports identified parts originating from nonhuman primate (NHP) and rodent species, including baboon, chimpanzee, mangabey, guenon, green monkey, cane rat and rat. Pathogen screening identified retroviruses (simian foamy virus) and/or herpesviruses (cytomegalovirus and lymphocryptovirus) in the NHP samples. These results are the first demonstration that illegal bushmeat importation into the United States could act as a conduit for pathogen spread, and suggest that implementation of disease surveillance of the wildlife trade will help facilitate prevention of disease emergence.

Zoonotic Viruses Associated with Illegally Imported Wildlife Products

PubMed Central

Switzer, William M.; Epstein, Jonathan H.; Seimon, Tracie; Jia, Hongwei; Sanchez, Maria D.; Huynh, Thanh Thao; Galland, G. Gale; Shapiro, Sheryl E.; Sleeman, Jonathan M.; McAloose, Denise; Stuchin, Margot; Amato, George; Kolokotronis, Sergios-Orestis; Lipkin, W. Ian; Karesh, William B.; Daszak, Peter; Marano, Nina

2012-01-01

The global trade in wildlife has historically contributed to the emergence and spread of infectious diseases. The United States is the world's largest importer of wildlife and wildlife products, yet minimal pathogen surveillance has precluded assessment of the health risks posed by this practice. This report details the findings of a pilot project to establish surveillance methodology for zoonotic agents in confiscated wildlife products. Initial findings from samples collected at several international airports identified parts originating from nonhuman primate (NHP) and rodent species, including baboon, chimpanzee, mangabey, guenon, green monkey, cane rat and rat. Pathogen screening identified retroviruses (simian foamy virus) and/or herpesviruses (cytomegalovirus and lymphocryptovirus) in the NHP samples. These results are the first demonstration that illegal bushmeat importation into the United States could act as a conduit for pathogen spread, and suggest that implementation of disease surveillance of the wildlife trade will help facilitate prevention of disease emergence. PMID:22253731

Constructing Rigorous and Broad Biosurveillance Networks for Detecting Emerging Zoonotic Outbreaks

PubMed Central

Brown, Mac; Moore, Leslie; McMahon, Benjamin; Powell, Dennis; LaBute, Montiago; Hyman, James M.; Rivas, Ariel; Jankowski, Mark; Berendzen, Joel; Loeppky, Jason; Manore, Carrie; Fair, Jeanne

2015-01-01

Determining optimal surveillance networks for an emerging pathogen is difficult since it is not known beforehand what the characteristics of a pathogen will be or where it will emerge. The resources for surveillance of infectious diseases in animals and wildlife are often limited and mathematical modeling can play a supporting role in examining a wide range of scenarios of pathogen spread. We demonstrate how a hierarchy of mathematical and statistical tools can be used in surveillance planning help guide successful surveillance and mitigation policies for a wide range of zoonotic pathogens. The model forecasts can help clarify the complexities of potential scenarios, and optimize biosurveillance programs for rapidly detecting infectious diseases. Using the highly pathogenic zoonotic H5N1 avian influenza 2006-2007 epidemic in Nigeria as an example, we determined the risk for infection for localized areas in an outbreak and designed biosurveillance stations that are effective for different pathogen strains and a range of possible outbreak locations. We created a general multi-scale, multi-host stochastic SEIR epidemiological network model, with both short and long-range movement, to simulate the spread of an infectious disease through Nigerian human, poultry, backyard duck, and wild bird populations. We chose parameter ranges specific to avian influenza (but not to a particular strain) and used a Latin hypercube sample experimental design to investigate epidemic predictions in a thousand simulations. We ranked the risk of local regions by the number of times they became infected in the ensemble of simulations. These spatial statistics were then complied into a potential risk map of infection. Finally, we validated the results with a known outbreak, using spatial analysis of all the simulation runs to show the progression matched closely with the observed location of the farms infected in the 2006-2007 epidemic. PMID:25946164

Exotic mosquito threats require strategic surveillance and response planning.

PubMed

Webb, Cameron E; Doggett, Stephen L

2016-12-14

Mosquito-borne diseases caused by endemic pathogens such as Ross River, Barmah Forest and Murray Valley encephalitis viruses are an annual concern in New South Wales (NSW), Australia. More than a dozen mosquito species have been implicated in the transmission of these pathogens, with each mosquito occupying a specialised ecological niche that influences their habitat associations, host feeding preferences and the environmental drivers of their abundance. The NSW Arbovirus Surveillance and Mosquito Monitoring Program provides an early warning system for potential outbreaks of mosquito-borne disease by tracking annual activity of these mosquitoes and their associated pathogens. Although the program will effectively track changes in local mosquito populations that may increase with a changing climate, urbanisation and wetland rehabilitation, it will be less effective with current surveillance methodologies at detecting or monitoring changes in exotic mosquito threats, where different surveillance strategies need to be used. Exotic container-inhabiting mosquitoes such as Aedes aegypti and Ae. albopictus pose a threat to NSW because they are nuisance-biting pests and vectors of pathogens such as dengue, chikungunya and Zika viruses. International movement of humans and their belongings have spread these mosquitoes to many regions of the world. In recent years, these two mosquitoes have been detected by the Australian Government Department of Agriculture and Water Resources at local airports and seaports. To target the detection of these exotic mosquitoes, new trapping technologies and networks of surveillance locations are required. Additionally, incursions of these mosquitoes into urban areas of the state will require strategic responses to minimise substantial public health and economic burdens to local communities.

A new data management system for the French National Registry of human alveolar echinococcosis cases.

PubMed

Charbonnier, Amandine; Knapp, Jenny; Demonmerot, Florent; Bresson-Hadni, Solange; Raoul, Francis; Grenouillet, Frédéric; Millon, Laurence; Vuitton, Dominique Angèle; Damy, Sylvie

2014-01-01

Alveolar echinococcosis (AE) is an endemic zoonosis in France due to the cestode Echinococcus multilocularis. The French National Reference Centre for Alveolar Echinococcosis (CNR-EA), connected to the FrancEchino network, is responsible for recording all AE cases diagnosed in France. Administrative, epidemiological and medical information on the French AE cases may currently be considered exhaustive only on the diagnosis time. To constitute a reference data set, an information system (IS) was developed thanks to a relational database management system (MySQL language). The current data set will evolve towards a dynamic surveillance system, including follow-up data (e.g. imaging, serology) and will be connected to environmental and parasitological data relative to E. multilocularis to better understand the pathogen transmission pathway. A particularly important goal is the possible interoperability of the IS with similar European and other databases abroad; this new IS could play a supporting role in the creation of new AE registries. © A. Charbonnier et al., published by EDP Sciences, 2014.

A new data management system for the French National Registry of human alveolar echinococcosis cases

PubMed Central

Charbonnier, Amandine; Knapp, Jenny; Demonmerot, Florent; Bresson-Hadni, Solange; Raoul, Francis; Grenouillet, Frédéric; Millon, Laurence; Vuitton, Dominique Angèle; Damy, Sylvie

2014-01-01

Alveolar echinococcosis (AE) is an endemic zoonosis in France due to the cestode Echinococcus multilocularis. The French National Reference Centre for Alveolar Echinococcosis (CNR-EA), connected to the FrancEchino network, is responsible for recording all AE cases diagnosed in France. Administrative, epidemiological and medical information on the French AE cases may currently be considered exhaustive only on the diagnosis time. To constitute a reference data set, an information system (IS) was developed thanks to a relational database management system (MySQL language). The current data set will evolve towards a dynamic surveillance system, including follow-up data (e.g. imaging, serology) and will be connected to environmental and parasitological data relative to E. multilocularis to better understand the pathogen transmission pathway. A particularly important goal is the possible interoperability of the IS with similar European and other databases abroad; this new IS could play a supporting role in the creation of new AE registries. PMID:25526544

A Study of 279 General Outbreaks of Gastrointestinal Infection in the North-East Region of England

PubMed Central

Tebbutt, Grahame M.; Wilson, Deborah; Holtby, Ian

2009-01-01

All outbreaks of infectious intestinal disease reported to the authorities were entered on a computer database with outbreak control teams being established to investigate larger or more significant incidents. The outbreak database and, when set up, the notes of outbreak team meetings were examined for the 279 outbreaks reported in a three-year period (2003–2005). Faeces specimens submitted as part of an outbreak were examined for microbial pathogens and the results cross-matched to the outbreak number. Almost half of the general outbreaks reported (137) occurred in long-term care facilities for the elderly, 51 outbreaks were recorded in hospitals and 31 occurred in the wider community. In 76 outbreaks no specimen was logged. A microbial cause was confirmed in about one-third of outbreaks, with noroviruses being the most common (19%). Salmonellas accounted for 12 of the 21 community outbreaks linked to social events and all were foodborne. Suggestions for improving notification and surveillance are discussed. PMID:19440398

Advancements in web-database applications for rabies surveillance.

PubMed

Rees, Erin E; Gendron, Bruno; Lelièvre, Frédérick; Coté, Nathalie; Bélanger, Denise

2011-08-02

Protection of public health from rabies is informed by the analysis of surveillance data from human and animal populations. In Canada, public health, agricultural and wildlife agencies at the provincial and federal level are responsible for rabies disease control, and this has led to multiple agency-specific data repositories. Aggregation of agency-specific data into one database application would enable more comprehensive data analyses and effective communication among participating agencies. In Québec, RageDB was developed to house surveillance data for the raccoon rabies variant, representing the next generation in web-based database applications that provide a key resource for the protection of public health. RageDB incorporates data from, and grants access to, all agencies responsible for the surveillance of raccoon rabies in Québec. Technological advancements of RageDB to rabies surveillance databases include (1) automatic integration of multi-agency data and diagnostic results on a daily basis; (2) a web-based data editing interface that enables authorized users to add, edit and extract data; and (3) an interactive dashboard to help visualize data simply and efficiently, in table, chart, and cartographic formats. Furthermore, RageDB stores data from citizens who voluntarily report sightings of rabies suspect animals. We also discuss how sightings data can indicate public perception to the risk of racoon rabies and thus aid in directing the allocation of disease control resources for protecting public health. RageDB provides an example in the evolution of spatio-temporal database applications for the storage, analysis and communication of disease surveillance data. The database was fast and inexpensive to develop by using open-source technologies, simple and efficient design strategies, and shared web hosting. The database increases communication among agencies collaborating to protect human health from raccoon rabies. Furthermore, health agencies have real-time access to a wide assortment of data documenting new developments in the raccoon rabies epidemic and this enables a more timely and appropriate response.

Advancements in web-database applications for rabies surveillance

PubMed Central

2011-01-01

Background Protection of public health from rabies is informed by the analysis of surveillance data from human and animal populations. In Canada, public health, agricultural and wildlife agencies at the provincial and federal level are responsible for rabies disease control, and this has led to multiple agency-specific data repositories. Aggregation of agency-specific data into one database application would enable more comprehensive data analyses and effective communication among participating agencies. In Québec, RageDB was developed to house surveillance data for the raccoon rabies variant, representing the next generation in web-based database applications that provide a key resource for the protection of public health. Results RageDB incorporates data from, and grants access to, all agencies responsible for the surveillance of raccoon rabies in Québec. Technological advancements of RageDB to rabies surveillance databases include 1) automatic integration of multi-agency data and diagnostic results on a daily basis; 2) a web-based data editing interface that enables authorized users to add, edit and extract data; and 3) an interactive dashboard to help visualize data simply and efficiently, in table, chart, and cartographic formats. Furthermore, RageDB stores data from citizens who voluntarily report sightings of rabies suspect animals. We also discuss how sightings data can indicate public perception to the risk of racoon rabies and thus aid in directing the allocation of disease control resources for protecting public health. Conclusions RageDB provides an example in the evolution of spatio-temporal database applications for the storage, analysis and communication of disease surveillance data. The database was fast and inexpensive to develop by using open-source technologies, simple and efficient design strategies, and shared web hosting. The database increases communication among agencies collaborating to protect human health from raccoon rabies. Furthermore, health agencies have real-time access to a wide assortment of data documenting new developments in the raccoon rabies epidemic and this enables a more timely and appropriate response. PMID:21810215

Results of Four-Year Rectal Vancomycin-Resistant Enterococci Surveillance in a Pediatric Hematology-Oncology Ward: From Colonization to Infection.

PubMed

Aktürk, Hacer; Sütçü, Murat; Somer, Ayper; Karaman, Serap; Acar, Manolya; Ünüvar, Ayşegül; Anak, Sema; Karakaş, Zeynep; Özdemir, Aslı; Sarsar, Kutay; Aydın, Derya; Salman, Nuran

2016-09-05

To investigate the clinical impact of vancomycin-resistant enterococci (VRE) colonization in patients with hematologic malignancies and associated risk factors. Patients colonized and infected with VRE were identified from an institutional surveillance database between January 2010 and December 2013. A retrospective case-control study was performed to identify the risk factors associated with development of VRE infection in VRE-colonized patients. Fecal VRE colonization was documented in 72 of 229 children (31.4%). Seven VRE-colonized patients developed subsequent systemic VRE infection (9.7%). Types of VRE infections included bacteremia (n=5), urinary tract infection (n=1), and meningitis (n=1). Enterococcus faecium was isolated in all VRE infections. Multivariate analysis revealed severe neutropenia and previous bacteremia with another pathogen as independent risk factors for VRE infection development in colonized patients [odds ratio (OR): 35.4, confidence interval (CI): 1.7-72.3, p=0.02 and OR: 20.6, CI: 1.3-48.6, p=0.03, respectively]. No deaths attributable to VRE occurred. VRE colonization has important consequences in pediatric cancer patients.

Climate Change, Foodborne Pathogens and Illness in Higher-Income Countries.

PubMed

Lake, I R; Barker, G C

2018-03-01

We present a review of the likely consequences of climate change for foodborne pathogens and associated human illness in higher-income countries. The relationships between climate and food are complex and hence the impacts of climate change uncertain. This makes it difficult to know which foodborne pathogens will be most affected, what the specific effects will be, and on what timescales changes might occur. Hence, a focus upon current capacity and adaptation potential against foodborne pathogens is essential. We highlight a number of developments that may enhance preparedness for climate change. These include the following: Adoption of novel surveillance methods, such as syndromic methods, to speed up detection and increase the fidelity of intervention in foodborne outbreaks Genotype-based approaches to surveillance of food pathogens to enhance spatiotemporal resolution in tracing and tracking of illness Ever increasing integration of plant, animal and human surveillance systems, One Health, to maximise potential for identifying threats Increased commitment to cross-border (global) information initiatives (including big data) Improved clarity regarding the governance of complex societal issues such as the conflict between food safety and food waste Strong user-centric (social) communications strategies to engage diverse stakeholder groups The impact of climate change upon foodborne pathogens and associated illness is uncertain. This emphasises the need to enhance current capacity and adaptation potential against foodborne illness. A range of developments are explored in this paper to enhance preparedness.

PulseNet China, a model for future laboratory-based bacterial infectious disease surveillance in China.

PubMed

Li, Wei; Lu, Shan; Cui, Zhigang; Cui, Jinghua; Zhou, Haijian; Wang, Yiqing; Shao, Zhujun; Ye, Changyun; Kan, Biao; Xu, Jianguo

2012-12-01

Surveillance is critical for the prevention and control of infectious disease. China's real-time web-based infectious disease reporting system is a distinguished achievement. However, many aspects of the current China Infectious Disease Surveillance System do not yet meet the demand for timely outbreak detection and identification of emerging infectious disease. PulseNet, the national molecular typing network for foodborne disease surveillance was first established by the Centers for Disease Control and Prevention of the United States in 1995 and has proven valuable in the early detection of outbreaks and tracing the pathogen source. Since 2001, the China CDC laboratory for bacterial pathogen analysis has been a member of the PulseNet International family; and has been adapting the idea and methodology of PulseNet to develop a model for a future national laboratory-based surveillance system for all bacterial infectious disease.We summarized the development progress for the PulseNet China system and discussed it as a model for the future of China's national laboratory-based surveillance system.

Deep sequencing of H7N8 avian influenza viruses from surveillance zone supports H7N8 high pathogenicity avian influenza was limited to a single outbreak farm in Indiana during 2016

USDA-ARS?s Scientific Manuscript database

In mid-January 2016, an outbreak of H7N8 high pathogenicity avian influenza (HPAI) virus in commercial turkeys occurred in Indiana. The outbreak was first detected by an increase in mortality followed by laboratory confirmation of H7N8 HPAI virus. Surveillance within the 10 km Control Zone detected...

Point prevalence survey for tick-borne pathogens in military working dogs, shelter animals, and pet populations in northern Colombia.

PubMed

McCown, M E; Alleman, A; Sayler, K A; Chandrashekar, R; Thatcher, B; Tyrrell, P; Stillman, B; Beall, M; Barbet, A F

2014-01-01

Based on the high tick-borne pathogen results from a 2011 surveillance study in three Colombian cities, an in-depth point prevalence survey was conducted to determine the seroprevalence of tick-borne pathogens at a specific point in time in 70 working dogs, 101 shelter dogs, and 47 client-owned dogs in Barranquilla, Colombia. Of the 218 serum samples, 163 (74%) were positive for Ehrlichia canis and 116 (53%) for Anaplasma platys. Exposure to tick-borne pathogens was highest in shelter and working dogs where more than 90% of the samples were seropositive or positive on polymerase chain reaction for one or more organisms as compared to 51% in client-owned animals. Surveillance for exposure to tick-borne pathogens provides vital information necessary to protect and conserve the health of local humans and animals, deployed military service members, and working dogs in various parts of the world. This study and resultant data demonstrate the value of following a broad-based surveillance study with a more specific, focused analysis in an area of concern. This area?s high levels of exposure warrant emphasis by medical planners and advisors on precautionary measures for military dogs, Special Operations Forces personnel, and the local public. 2014.

Infection with Pathogens Transmitted Commonly Through Food and the Effect of Increasing Use of Culture-Independent Diagnostic Tests on Surveillance--Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2012-2015.

PubMed

Huang, Jennifer Y; Henao, Olga L; Griffin, Patricia M; Vugia, Duc J; Cronquist, Alicia B; Hurd, Sharon; Tobin-D'Angelo, Melissa; Ryan, Patricia; Smith, Kirk; Lathrop, Sarah; Zansky, Shelley; Cieslak, Paul R; Dunn, John; Holt, Kristin G; Wolpert, Beverly J; Patrick, Mary E

2016-04-15

To evaluate progress toward prevention of enteric and foodborne illnesses in the United States, the Foodborne Diseases Active Surveillance Network (FoodNet) monitors the incidence of laboratory-confirmed infections caused by nine pathogens transmitted commonly through food in 10 U.S. sites. This report summarizes preliminary 2015 data and describes trends since 2012. In 2015, FoodNet reported 20,107 confirmed cases (defined as culture-confirmed bacterial infections and laboratory-confirmed parasitic infections), 4,531 hospitalizations, and 77 deaths. FoodNet also received reports of 3,112 positive culture-independent diagnostic tests (CIDTs) without culture-confirmation, a number that has markedly increased since 2012. Diagnostic testing practices for enteric pathogens are rapidly moving away from culture-based methods. The continued shift from culture-based methods to CIDTs that do not produce the isolates needed to distinguish between strains and subtypes affects the interpretation of public health surveillance data and ability to monitor progress toward prevention efforts. Expanded case definitions and strategies for obtaining bacterial isolates are crucial during this transition period.

Bioaerosol Sampling in Modern Agriculture: A Novel Approach for Emerging Pathogen Surveillance?

PubMed Central

Anderson, Benjamin D.; Ma, Mengmeng; Xia, Yao; Wang, Tao; Shu, Bo; Lednicky, John A.; Ma, Mai-Juan; Lu, Jiahai; Gray, Gregory C.

2016-01-01

Background. Modern agricultural practices create environmental conditions conducive to the emergence of novel pathogens. Current surveillance efforts to assess the burden of emerging pathogens in animal production facilities in China are sparse. In Guangdong Province pig farms, we compared bioaerosol surveillance for influenza A virus to surveillance in oral pig secretions and environmental swab specimens. Methods. During the 2014 summer and fall/winter seasons, we used 3 sampling techniques to study 5 swine farms weekly for influenza A virus. Samples were molecularly tested for influenza A virus, and positive specimens were further characterized with culture. Risk factors for influenza A virus positivity for each sample type were assessed. Results. Seventy-one of 354 samples (20.1%) were positive for influenza A virus RNA by real-time reverse-transcription polymerase chain reaction analysis. Influenza A virus positivity in bioaerosol samples was a statistically significant predictor for influenza A virus positivity in pig oral secretion and environmental swab samples. Temperature of <20°C was a significant predictor of influenza A virus positivity in bioaerosol samples. Discussions. Climatic factors and routine animal husbandry practices may increase the risk of human exposure to aerosolized influenza A viruses in swine farms. Data suggest that bioaerosol sampling in pig barns may be a noninvasive and efficient means to conduct surveillance for novel influenza viruses. PMID:27190187

Electronic surveillance and using administrative data to identify healthcare associated infections.

PubMed

Gastmeier, Petra; Behnke, Michael

2016-08-01

Traditional surveillance of healthcare associated infections (HCAI) is time consuming and error-prone. We have analysed literature of the past year to look at new developments in this field. It is divided into three parts: new algorithms for electronic surveillance, the use of administrative data for surveillance of HCAI, and the definition of new endpoints of surveillance, in accordance with an automatic surveillance approach. Most studies investigating electronic surveillance of HCAI have concentrated on bloodstream infection or surgical site infection. However, the lack of important parameters in hospital databases can lead to misleading results. The accuracy of administrative coding data was poor at identifying HCAI. New endpoints should be defined for automatic detection, with the most crucial step being to win clinicians' acceptance. Electronic surveillance with conventional endpoints is a successful method when hospital information systems implemented key changes and enhancements. One requirement is the access to systems for hospital administration and clinical databases.Although the primary source of data for HCAI surveillance is not administrative coding data, these are important components of a hospital-wide programme of automated surveillance. The implementation of new endpoints for surveillance is an approach which needs to be discussed further.

Antimicrobial Drug Use and Resistance in Europe

PubMed Central

van de Sande-Bruinsma, Nienke; Verloo, Didier; Tiemersma, Edine; Monen, Jos; Goossens, Herman; Ferech, Matus

2008-01-01

Our study confronts the use of antimicrobial agents in ambulatory care with the resistance trends of 2 major pathogens, Streptococcus pneumoniae and Escherichia coli, in 21 European countries in 2000–2005 and explores whether the notion that antimicrobial drug use determines resistance can be supported by surveillance data at national aggregation levels. The data obtained from the European Surveillance of Antimicrobial Consumption and the European Antimicrobial Resistance Surveillance System suggest that variation of consumption coincides with the occurrence of resistance at the country level. Linear regression analysis showed that the association between antimicrobial drug use and resistance was specific and robust for 2 of 3 compound pathogen combinations, stable over time, but not sensitive enough to explain all of the observed variations. Ecologic studies based on routine surveillance data indicate a relation between use and resistance and support interventions designed to reduce antimicrobial drug consumption at a national level in Europe. PMID:18976555

Prisoners' expectations of the national forensic DNA database: surveillance and reconfiguration of individual rights.

PubMed

Machado, Helena; Santos, Filipe; Silva, Susana

2011-07-15

In this paper we aim to discuss how Portuguese prisoners know and what they feel about surveillance mechanisms related to the inclusion and deletion of the DNA profiles of convicted criminals in the national forensic database. Through a set of interviews with individuals currently imprisoned we focus on the ways this group perceives forensic DNA technologies. While the institutional and political discourses maintain that the restricted use and application of DNA profiles within the national forensic database protects individuals' rights, the prisoners claim that police misuse of such technologies potentially makes it difficult to escape from surveillance and acts as a mean of reinforcing the stigma of delinquency. The prisoners also argue that additional intensive and extensive use of surveillance devices might be more protective of their own individual rights and might possibly increase potential for exoneration. Crown Copyright © 2011. Published by Elsevier Ireland Ltd. All rights reserved.

Cost-effectiveness of ceftolozane/tazobactam plus metronidazole compared with piperacillin/tazobactam as empiric therapy for the treatment of complicated intra-abdominal infections based on the in-vitro surveillance of bacterial isolates in the UK.

PubMed

Prabhu, Vimalanand; Foo, Jason; Ahir, Harblas; Sarpong, Eric; Merchant, Sanjay

2017-08-01

An increase in the prevalence of antimicrobial resistance among gram-negative pathogens has been noted recently. A challenge in empiric treatment of complicated intra-abdominal infection (cIAI) is identifying initial appropriate antibiotic therapy, which is associated with reduced length of stay and mortality compared with inappropriate therapy. The objective of this study was to assess the cost-effectiveness of ceftolozane/tazobactam + metronidazole compared with piperacillin/tazobactam (commonly used in this indication) in the treatment of patients with cIAI in UK hospitals. A decision-analytic Monte Carlo simulation model was used to compare costs (antibiotic and hospitalization costs) and quality-adjusted life years (QALYs) of patients infected with gram-negative cIAI and treated empirically with either ceftolozane/tazobactam + metronidazole or piperacillin/tazobactam. Bacterial isolates were randomly drawn from the Program to Assess Ceftolozane/Tazobactam Susceptibility (PACTS) database, a surveillance database of non-duplicate bacterial isolates collected from patients in the UK infected with gram-negative pathogens. Susceptibility to initial empiric therapy was based on the measured susceptibilities reported in the PACTS database. Ceftolozane/tazobactam + metronidazole was cost-effective when compared with piperacillin/tazobactam, with an incremental cost-effectiveness ratio (ICER) of £4,350/QALY and 0.36 hospitalization days/patient saved. Costs in the ceftolozane/tazobactam + metronidazole arm were £2,576/patient, compared with £2,168/patient in the piperacillin/tazobactam arm. The ceftolozane/tazobactam + metronidazole arm experienced a greater number of QALYs than the piperacillin/tazobactam arm (14.31/patient vs 14.21/patient, respectively). Ceftolozane/tazobactam + metronidazole remained cost-effective in one-way sensitivity and probabilistic sensitivity analyses. Economic models can help to identify the appropriate choice of empiric therapy for the treatment of cIAI. Results indicated that empiric use of ceftolozane/tazobactam + metronidazole is cost-effective vs piperacillin/tazobactam in UK patients with cIAI at risk of resistant infection. This will be valuable to commissioners and clinicians to aid decision-making on the targeting of resources for appropriate antibiotic therapy under the premise of antimicrobial stewardship.

Surveillance of infectious diseases in the Arctic.

PubMed

Bruce, M; Zulz, T; Koch, A

2016-08-01

This study reviews how social and environmental issues affect health in Arctic populations and describes infectious disease surveillance in Arctic Nations with a special focus on the activities of the International Circumpolar Surveillance (ICS) project. We reviewed the literature over the past 2 decades looking at Arctic living conditions and their effects on health and Arctic surveillance for infectious diseases. In regards to other regions worldwide, the Arctic climate and environment are extreme. Arctic and sub-Arctic populations live in markedly different social and physical environments compared to those of their more southern dwelling counterparts. A cold northern climate means people spending more time indoors, amplifying the effects of household crowding, smoking and inadequate ventilation on the person-to-person spread of infectious diseases. The spread of zoonotic infections north as the climate warms, emergence of antibiotic resistance among bacterial pathogens, the re-emergence of tuberculosis, the entrance of HIV into Arctic communities, the specter of pandemic influenza or the sudden emergence and introduction of new viral pathogens pose new challenges to residents, governments and public health authorities of all Arctic countries. ICS is a network of hospitals, public health agencies, and reference laboratories throughout the Arctic working together for the purposes of collecting, comparing and sharing of uniform laboratory and epidemiological data on infectious diseases of concern and assisting in the formulation of prevention and control strategies (Fig. 1). In addition, circumpolar infectious disease research workgroups and sentinel surveillance systems for bacterial and viral pathogens exist. The ICS system is a successful example of collaborative surveillance and research in an extreme environment. Published by Elsevier Ltd.

Occupational injury among migrant workers in China: a systematic review.

PubMed

Fitzgerald, Simon; Chen, Xin; Qu, Hui; Sheff, Mira Grice

2013-10-01

This review considers the state of occupational injury surveillance and prevention among migrant workers in China and suggests areas of focus for future research on the topic. Bibliographic databases were searched for qualitative and quantitative studies on surveillance of and interventions to prevent occupational injury among migrant workers in mainland China. Additional abstracts were identified from the citations of relevant articles from the database search. Studies fitting the inclusion criteria were evaluated, and findings were extracted and summarised. The search uncovered 726 studies in the English-language databases searched, and 3109 in the Chinese database. This article analyses a total of 19 research articles that fit the inclusion criteria with qualitative or quantitative data on occupational injury surveillance and prevention of migrant workers in China. Despite evidence of the vulnerability of migrant workers in the workplace, there is little systematic surveillance of occupational injury and few evaluated interventions. Migrant workers account for a disproportionate burden of occupational injury morbidity and mortality in China. However, data are inconsistent and inadequate to detail injury incidence or to evaluate interventions. The following are suggestions to decrease injury incidence among migrants: strengthen the national system of occupational injury surveillance; focus surveillance and interventions on high-risk occupations employing migrants such as construction, manufacturing and small mining operations; improve occupational safety training and access to appropriate safety equipment; evaluate recent changes in occupational health and safety and evaluate outcome of multi-party interventions to reduce occupational injury among migrant workers.

Occupational injury among migrant workers in China: a systematic review

PubMed Central

Fitzgerald, Simon; Chen, Xin; Qu, Hui; Sheff, Mira Grice

2017-01-01

Objectives This review considers the state of occupational injury surveillance and prevention among migrant workers in China and suggests areas of focus for future research on the topic. Methods Bibliographic databases were searched for qualitative and quantitative studies on surveillance of and interventions to prevent occupational injury among migrant workers in mainland China. Additional abstracts were identified from the citations of relevant articles from the database search. Studies fitting the inclusion criteria were evaluated, and findings were extracted and summarised. Results The search uncovered 726 studies in the English-language databases searched, and 3109 in the Chinese database. This article analyses a total of 19 research articles that fit the inclusion criteria with qualitative or quantitative data on occupational injury surveillance and prevention of migrant workers in China. Despite evidence of the vulnerability of migrant workers in the workplace, there is little systematic surveillance of occupational injury and few evaluated interventions. Conclusions Migrant workers account for a disproportionate burden of occupational injury morbidity and mortality in China. However, data are inconsistent and inadequate to detail injury incidence or to evaluate interventions. The following are suggestions to decrease injury incidence among migrants: strengthen the national system of occupational injury surveillance; focus surveillance and interventions on high-risk occupations employing migrants such as construction, manufacturing and small mining operations; improve occupational safety training and access to appropriate safety equipment; evaluate recent changes in occupational health and safety and evaluate outcome of multi-party interventions to reduce occupational injury among migrant workers. PMID:23710065

Measuring changes in transmission of neglected tropical diseases, malaria, and enteric pathogens from quantitative antibody levels.

PubMed

Arnold, Benjamin F; van der Laan, Mark J; Hubbard, Alan E; Steel, Cathy; Kubofcik, Joseph; Hamlin, Katy L; Moss, Delynn M; Nutman, Thomas B; Priest, Jeffrey W; Lammie, Patrick J

2017-05-01

Serological antibody levels are a sensitive marker of pathogen exposure, and advances in multiplex assays have created enormous potential for large-scale, integrated infectious disease surveillance. Most methods to analyze antibody measurements reduce quantitative antibody levels to seropositive and seronegative groups, but this can be difficult for many pathogens and may provide lower resolution information than quantitative levels. Analysis methods have predominantly maintained a single disease focus, yet integrated surveillance platforms would benefit from methodologies that work across diverse pathogens included in multiplex assays. We developed an approach to measure changes in transmission from quantitative antibody levels that can be applied to diverse pathogens of global importance. We compared age-dependent immunoglobulin G curves in repeated cross-sectional surveys between populations with differences in transmission for multiple pathogens, including: lymphatic filariasis (Wuchereria bancrofti) measured before and after mass drug administration on Mauke, Cook Islands, malaria (Plasmodium falciparum) before and after a combined insecticide and mass drug administration intervention in the Garki project, Nigeria, and enteric protozoans (Cryptosporidium parvum, Giardia intestinalis, Entamoeba histolytica), bacteria (enterotoxigenic Escherichia coli, Salmonella spp.), and viruses (norovirus groups I and II) in children living in Haiti and the USA. Age-dependent antibody curves fit with ensemble machine learning followed a characteristic shape across pathogens that aligned with predictions from basic mechanisms of humoral immunity. Differences in pathogen transmission led to shifts in fitted antibody curves that were remarkably consistent across pathogens, assays, and populations. Mean antibody levels correlated strongly with traditional measures of transmission intensity, such as the entomological inoculation rate for P. falciparum (Spearman's rho = 0.75). In both high- and low transmission settings, mean antibody curves revealed changes in population mean antibody levels that were masked by seroprevalence measures because changes took place above or below the seropositivity cutoff. Age-dependent antibody curves and summary means provided a robust and sensitive measure of changes in transmission, with greatest sensitivity among young children. The method generalizes to pathogens that can be measured in high-throughput, multiplex serological assays, and scales to surveillance activities that require high spatiotemporal resolution. Our results suggest quantitative antibody levels will be particularly useful to measure differences in exposure for pathogens that elicit a transient antibody response or for monitoring populations with very high- or very low transmission, when seroprevalence is less informative. The approach represents a new opportunity to conduct integrated serological surveillance for neglected tropical diseases, malaria, and other infectious diseases with well-defined antigen targets.

Measuring changes in transmission of neglected tropical diseases, malaria, and enteric pathogens from quantitative antibody levels

PubMed Central

van der Laan, Mark J.; Hubbard, Alan E.; Steel, Cathy; Kubofcik, Joseph; Hamlin, Katy L.; Moss, Delynn M.; Nutman, Thomas B.; Priest, Jeffrey W.; Lammie, Patrick J.

2017-01-01

Background Serological antibody levels are a sensitive marker of pathogen exposure, and advances in multiplex assays have created enormous potential for large-scale, integrated infectious disease surveillance. Most methods to analyze antibody measurements reduce quantitative antibody levels to seropositive and seronegative groups, but this can be difficult for many pathogens and may provide lower resolution information than quantitative levels. Analysis methods have predominantly maintained a single disease focus, yet integrated surveillance platforms would benefit from methodologies that work across diverse pathogens included in multiplex assays. Methods/Principal findings We developed an approach to measure changes in transmission from quantitative antibody levels that can be applied to diverse pathogens of global importance. We compared age-dependent immunoglobulin G curves in repeated cross-sectional surveys between populations with differences in transmission for multiple pathogens, including: lymphatic filariasis (Wuchereria bancrofti) measured before and after mass drug administration on Mauke, Cook Islands, malaria (Plasmodium falciparum) before and after a combined insecticide and mass drug administration intervention in the Garki project, Nigeria, and enteric protozoans (Cryptosporidium parvum, Giardia intestinalis, Entamoeba histolytica), bacteria (enterotoxigenic Escherichia coli, Salmonella spp.), and viruses (norovirus groups I and II) in children living in Haiti and the USA. Age-dependent antibody curves fit with ensemble machine learning followed a characteristic shape across pathogens that aligned with predictions from basic mechanisms of humoral immunity. Differences in pathogen transmission led to shifts in fitted antibody curves that were remarkably consistent across pathogens, assays, and populations. Mean antibody levels correlated strongly with traditional measures of transmission intensity, such as the entomological inoculation rate for P. falciparum (Spearman’s rho = 0.75). In both high- and low transmission settings, mean antibody curves revealed changes in population mean antibody levels that were masked by seroprevalence measures because changes took place above or below the seropositivity cutoff. Conclusions/Significance Age-dependent antibody curves and summary means provided a robust and sensitive measure of changes in transmission, with greatest sensitivity among young children. The method generalizes to pathogens that can be measured in high-throughput, multiplex serological assays, and scales to surveillance activities that require high spatiotemporal resolution. Our results suggest quantitative antibody levels will be particularly useful to measure differences in exposure for pathogens that elicit a transient antibody response or for monitoring populations with very high- or very low transmission, when seroprevalence is less informative. The approach represents a new opportunity to conduct integrated serological surveillance for neglected tropical diseases, malaria, and other infectious diseases with well-defined antigen targets. PMID:28542223

Constructing rigorous and broad biosurveillance networks for detecting emerging zoonotic outbreaks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Mac; Moore, Leslie; McMahon, Benjamin

Determining optimal surveillance networks for an emerging pathogen is difficult since it is not known beforehand what the characteristics of a pathogen will be or where it will emerge. The resources for surveillance of infectious diseases in animals and wildlife are often limited and mathematical modeling can play a supporting role in examining a wide range of scenarios of pathogen spread. We demonstrate how a hierarchy of mathematical and statistical tools can be used in surveillance planning help guide successful surveillance and mitigation policies for a wide range of zoonotic pathogens. The model forecasts can help clarify the complexities ofmore » potential scenarios, and optimize biosurveillance programs for rapidly detecting infectious diseases. Using the highly pathogenic zoonotic H5N1 avian influenza 2006-2007 epidemic in Nigeria as an example, we determined the risk for infection for localized areas in an outbreak and designed biosurveillance stations that are effective for different pathogen strains and a range of possible outbreak locations. We created a general multi-scale, multi-host stochastic SEIR epidemiological network model, with both short and long-range movement, to simulate the spread of an infectious disease through Nigerian human, poultry, backyard duck, and wild bird populations. We chose parameter ranges specific to avian influenza (but not to a particular strain) and used a Latin hypercube sample experimental design to investigate epidemic predictions in a thousand simulations. We ranked the risk of local regions by the number of times they became infected in the ensemble of simulations. These spatial statistics were then complied into a potential risk map of infection. Finally, we validated the results with a known outbreak, using spatial analysis of all the simulation runs to show the progression matched closely with the observed location of the farms infected in the 2006-2007 epidemic.« less

Constructing rigorous and broad biosurveillance networks for detecting emerging zoonotic outbreaks

DOE PAGES

Brown, Mac; Moore, Leslie; McMahon, Benjamin; ...

2015-05-06

Determining optimal surveillance networks for an emerging pathogen is difficult since it is not known beforehand what the characteristics of a pathogen will be or where it will emerge. The resources for surveillance of infectious diseases in animals and wildlife are often limited and mathematical modeling can play a supporting role in examining a wide range of scenarios of pathogen spread. We demonstrate how a hierarchy of mathematical and statistical tools can be used in surveillance planning help guide successful surveillance and mitigation policies for a wide range of zoonotic pathogens. The model forecasts can help clarify the complexities ofmore » potential scenarios, and optimize biosurveillance programs for rapidly detecting infectious diseases. Using the highly pathogenic zoonotic H5N1 avian influenza 2006-2007 epidemic in Nigeria as an example, we determined the risk for infection for localized areas in an outbreak and designed biosurveillance stations that are effective for different pathogen strains and a range of possible outbreak locations. We created a general multi-scale, multi-host stochastic SEIR epidemiological network model, with both short and long-range movement, to simulate the spread of an infectious disease through Nigerian human, poultry, backyard duck, and wild bird populations. We chose parameter ranges specific to avian influenza (but not to a particular strain) and used a Latin hypercube sample experimental design to investigate epidemic predictions in a thousand simulations. We ranked the risk of local regions by the number of times they became infected in the ensemble of simulations. These spatial statistics were then complied into a potential risk map of infection. Finally, we validated the results with a known outbreak, using spatial analysis of all the simulation runs to show the progression matched closely with the observed location of the farms infected in the 2006-2007 epidemic.« less

Applied learning-based color tone mapping for face recognition in video surveillance system

NASA Astrophysics Data System (ADS)

Yew, Chuu Tian; Suandi, Shahrel Azmin

2012-04-01

In this paper, we present an applied learning-based color tone mapping technique for video surveillance system. This technique can be applied onto both color and grayscale surveillance images. The basic idea is to learn the color or intensity statistics from a training dataset of photorealistic images of the candidates appeared in the surveillance images, and remap the color or intensity of the input image so that the color or intensity statistics match those in the training dataset. It is well known that the difference in commercial surveillance cameras models, and signal processing chipsets used by different manufacturers will cause the color and intensity of the images to differ from one another, thus creating additional challenges for face recognition in video surveillance system. Using Multi-Class Support Vector Machines as the classifier on a publicly available video surveillance camera database, namely SCface database, this approach is validated and compared to the results of using holistic approach on grayscale images. The results show that this technique is suitable to improve the color or intensity quality of video surveillance system for face recognition.

Pathogens and antimicrobial susceptibility profiles in critically ill patients with bloodstream infections: a descriptive study.

PubMed

Savage, Rachel D; Fowler, Robert A; Rishu, Asgar H; Bagshaw, Sean M; Cook, Deborah; Dodek, Peter; Hall, Richard; Kumar, Anand; Lamontagne, François; Lauzier, François; Marshall, John; Martin, Claudio M; McIntyre, Lauralyn; Muscedere, John; Reynolds, Steven; Stelfox, Henry T; Daneman, Nick

2016-01-01

Surveillance of antimicrobial resistance is vital to guiding empirical treatment of infections. Collating and reporting routine data on clinical isolate testing may offer more timely information about resistance patterns than traditional surveillance network methods. Using routine microbiology testing data collected from the Bacteremia Antibiotic Length Actually Needed for Clinical Effectiveness retrospective cohort study, we conducted a descriptive secondary analysis among critically ill patients in whom bloodstream infections had been diagnosed in 14 intensive care units (ICUs) in Canada. The participating sites were located within tertiary care teaching hospitals and represented 6 provinces and 10 cities. More than 80% of the study population was accrued from 2011-2013. We assessed the epidemiologic features of the infections and corresponding antimicrobial susceptibility profiles. Susceptibility testing was done according to Clinical Laboratory Standards Institute guidelines at accredited laboratories. A total of 1416 pathogens were isolated from 1202 patients. The most common organisms were Escherichia coli (217 isolates [15.3%]), Staphylococcus aureus (175 [12.4%]), coagulase-negative staphylococci (117 [8.3%]), Klebsiella pneumoniae (86 [6.1%]) and Streptococcus pneumoniae (85 [6.0%]). The contribution of individual pathogens varied by site. For 13 ICUs, gram-negative susceptibility rates were high for carbapenems (95.4%), tobramycin (91.2%) and piperacillin - tazobactam (90.0%); however, the proportion of specimens susceptible to these agents ranged from 75.0%-100%, 66.7%-100% and 75.0%-100%, respectively, across sites. Fewer gram-negative bacteria were susceptible to fluoroquinolones (84.5% [range 64.1%-97.2%]). A total of 145 patients (12.1%) had infections caused by highly resistant microorganisms, with significant intersite variation (range 2.6%-24.0%, χ2 = 57.50, p < 0.001). We assessed the epidemiologic features of bloodstream infections in a geographically diverse cohort of critically ill Canadian patients using routine pathogen and susceptibility data extracted from readily available microbiology testing databases. Expanding data sharing across more ICUs, with serial measurement and prompt reporting, could provide much-needed guidance for empiric treatment for patients as well as system-wide prevention methods to limit antimicrobial resistance.

Pathogens and antimicrobial susceptibility profiles in critically ill patients with bloodstream infections: a descriptive study

PubMed Central

Savage, Rachel D.; Fowler, Robert A.; Rishu, Asgar H.; Bagshaw, Sean M.; Cook, Deborah; Dodek, Peter; Hall, Richard; Kumar, Anand; Lamontagne, François; Lauzier, François; Marshall, John; Martin, Claudio M.; McIntyre, Lauralyn; Muscedere, John; Reynolds, Steven; Stelfox, Henry T.; Daneman, Nick

2016-01-01

Background: Surveillance of antimicrobial resistance is vital to guiding empirical treatment of infections. Collating and reporting routine data on clinical isolate testing may offer more timely information about resistance patterns than traditional surveillance network methods. Methods: Using routine microbiology testing data collected from the Bacteremia Antibiotic Length Actually Needed for Clinical Effectiveness retrospective cohort study, we conducted a descriptive secondary analysis among critically ill patients in whom bloodstream infections had been diagnosed in 14 intensive care units (ICUs) in Canada. The participating sites were located within tertiary care teaching hospitals and represented 6 provinces and 10 cities. More than 80% of the study population was accrued from 2011-2013. We assessed the epidemiologic features of the infections and corresponding antimicrobial susceptibility profiles. Susceptibility testing was done according to Clinical Laboratory Standards Institute guidelines at accredited laboratories. Results: A total of 1416 pathogens were isolated from 1202 patients. The most common organisms were Escherichia coli (217 isolates [15.3%]), Staphylococcus aureus (175 [12.4%]), coagulase-negative staphylococci (117 [8.3%]), Klebsiella pneumoniae (86 [6.1%]) and Streptococcus pneumoniae (85 [6.0%]). The contribution of individual pathogens varied by site. For 13 ICUs, gram-negative susceptibility rates were high for carbapenems (95.4%), tobramycin (91.2%) and piperacillin-tazobactam (90.0%); however, the proportion of specimens susceptible to these agents ranged from 75.0%-100%, 66.7%-100% and 75.0%-100%, respectively, across sites. Fewer gram-negative bacteria were susceptible to fluoroquinolones (84.5% [range 64.1%-97.2%]). A total of 145 patients (12.1%) had infections caused by highly resistant microorganisms, with significant intersite variation (range 2.6%-24.0%, χ2 = 57.50, p < 0.001). Interpretation: We assessed the epidemiologic features of bloodstream infections in a geographically diverse cohort of critically ill Canadian patients using routine pathogen and susceptibility data extracted from readily available microbiology testing databases. Expanding data sharing across more ICUs, with serial measurement and prompt reporting, could provide much-needed guidance for empiric treatment for patients as well as system-wide prevention methods to limit antimicrobial resistance. PMID:28018869

Transcriptome amplification coupled with nanopore sequencing as a surveillance tool for plant pathogens in plant and insect tissues

USDA-ARS?s Scientific Manuscript database

There are many plant pathogen-specific diagnostic assays, based on PCR and immune-detection. However, the ability to test for large numbers of pathogens simultaneously is lacking. Next generation sequencing (NGS) allows one to detect all organisms within a given sample, but has computational limitat...

Ticks and Tick-Borne Pathogens of the Caribbean: Current Understanding and Future Directions for More Comprehensive Surveillance.

PubMed

Gondard, Mathilde; Cabezas-Cruz, Alejandro; Charles, Roxanne A; Vayssier-Taussat, Muriel; Albina, Emmanuel; Moutailler, Sara

2017-01-01

Ticks are obligate hematophagous arthropods of significant importance to human and veterinary medicine. They transmit a vast array of pathogens, including bacteria, viruses, protozoa, and helminths. Most epidemiological data on ticks and tick-borne pathogens (TBPs) in the West Indies are limited to common livestock pathogens such as Ehrlichia ruminantium, Babesia spp. (i.e., B. bovis and B. bigemina ), and Anaplasma marginale , and less information is available on companion animal pathogens. Of note, human tick-borne diseases (TBDs) remain almost completely uncharacterized in the West Indies. Information on TBP presence in wildlife is also missing. Herein, we provide a comprehensive review of the ticks and TBPs affecting human and animal health in the Caribbean, and introduce the challenges associated with understanding TBD epidemiology and implementing successful TBD management in this region. In particular, we stress the need for innovative and versatile surveillance tools using high-throughput pathogen detection (e.g., high-throughput real-time microfluidic PCR). The use of such tools in large epidemiological surveys will likely improve TBD prevention and control programs in the Caribbean.

Viral etiology, seasonality and severity of hospitalized patients with severe acute respiratory infections in the Eastern Mediterranean Region, 2007-2014.

PubMed

Horton, Katherine C; Dueger, Erica L; Kandeel, Amr; Abdallat, Mohamed; El-Kholy, Amani; Al-Awaidy, Salah; Kohlani, Abdul Hakim; Amer, Hanaa; El-Khal, Abel Latif; Said, Mayar; House, Brent; Pimentel, Guillermo; Talaat, Maha

2017-01-01

Little is known about the role of viral respiratory pathogens in the etiology, seasonality or severity of severe acute respiratory infections (SARI) in the Eastern Mediterranean Region. Sentinel surveillance for SARI was conducted from December 2007 through February 2014 at 20 hospitals in Egypt, Jordan, Oman, Qatar and Yemen. Nasopharyngeal and oropharyngeal swabs were collected from hospitalized patients meeting SARI case definitions and were analyzed for infection with influenza, respiratory syncytial virus (RSV), adenovirus (AdV), human metapneumovirus (hMPV) and human parainfluenza virus types 1-3 (hPIV1-3). We analyzed surveillance data to calculate positivity rates for viral respiratory pathogens, describe the seasonality of those pathogens and determine which pathogens were responsible for more severe outcomes requiring ventilation and/or intensive care and/or resulting in death. At least one viral respiratory pathogen was detected in 8,753/28,508 (30.7%) samples tested for at least one pathogen and 3,497/9,315 (37.5%) of samples tested for all pathogens-influenza in 3,345/28,438 (11.8%), RSV in 3,942/24,503 (16.1%), AdV in 923/9,402 (9.8%), hMPV in 617/9,384 (6.6%), hPIV1 in 159/9,402 (1.7%), hPIV2 in 85/9,402 (0.9%) and hPIV3 in 365/9,402 (3.9%). Multiple pathogens were identified in 501/9,316 (5.4%) participants tested for all pathogens. Monthly variation, indicating seasonal differences in levels of infection, was observed for all pathogens. Participants with hMPV infections and participants less than five years of age were significantly less likely than participants not infected with hMPV and those older than five years of age, respectively, to experience a severe outcome, while participants with a pre-existing chronic disease were at increased risk of a severe outcome, compared to those with no reported pre-existing chronic disease. Viral respiratory pathogens are common among SARI patients in the Eastern Mediterranean Region. Ongoing surveillance is important to monitor changes in the etiology, seasonality and severity of pathogens of interest.

Surveillance of antimicrobial resistance in clinical isolates of Pasteurella multocida and Streptococcus suis from Ontario swine.

PubMed

Glass-Kaastra, Shiona K; Pearl, David L; Reid-Smith, Richard J; McEwen, Beverly; Slavic, Durda; Fairles, Jim; McEwen, Scott A

2014-10-01

Susceptibility results for Pasteurella multocida and Streptococcus suis isolated from swine clinical samples were obtained from January 1998 to October 2010 from the Animal Health Laboratory at the University of Guelph, Guelph, Ontario, and used to describe variation in antimicrobial resistance (AMR) to 4 drugs of importance in the Ontario swine industry: ampicillin, tetracycline, tiamulin, and trimethoprim-sulfamethoxazole. Four temporal data-analysis options were used: visualization of trends in 12-month rolling averages, logistic-regression modeling, temporal-scan statistics, and a scan with the "What's strange about recent events?" (WSARE) algorithm. The AMR trends varied among the antimicrobial drugs for a single pathogen and between pathogens for a single antimicrobial, suggesting that pathogen-specific AMR surveillance may be preferable to indicator data. The 4 methods provided complementary and, at times, redundant results. The most appropriate combination of analysis methods for surveillance using these data included temporal-scan statistics with a visualization method (rolling-average or predicted-probability plots following logistic-regression models). The WSARE algorithm provided interesting results for quality control and has the potential to detect new resistance patterns; however, missing data created problems for displaying the results in a way that would be meaningful to all surveillance stakeholders.

Surveillance of antimicrobial resistance in clinical isolates of Pasteurella multocida and Streptococcus suis from Ontario swine

PubMed Central

Glass-Kaastra, Shiona K.; Pearl, David L.; Reid-Smith, Richard J.; McEwen, Beverly; Slavic, Durda; Fairles, Jim; McEwen, Scott A.

2014-01-01

Susceptibility results for Pasteurella multocida and Streptococcus suis isolated from swine clinical samples were obtained from January 1998 to October 2010 from the Animal Health Laboratory at the University of Guelph, Guelph, Ontario, and used to describe variation in antimicrobial resistance (AMR) to 4 drugs of importance in the Ontario swine industry: ampicillin, tetracycline, tiamulin, and trimethoprim–sulfamethoxazole. Four temporal data-analysis options were used: visualization of trends in 12-month rolling averages, logistic-regression modeling, temporal-scan statistics, and a scan with the “What’s strange about recent events?” (WSARE) algorithm. The AMR trends varied among the antimicrobial drugs for a single pathogen and between pathogens for a single antimicrobial, suggesting that pathogen-specific AMR surveillance may be preferable to indicator data. The 4 methods provided complementary and, at times, redundant results. The most appropriate combination of analysis methods for surveillance using these data included temporal-scan statistics with a visualization method (rolling-average or predicted-probability plots following logistic-regression models). The WSARE algorithm provided interesting results for quality control and has the potential to detect new resistance patterns; however, missing data created problems for displaying the results in a way that would be meaningful to all surveillance stakeholders. PMID:25355992

Insights into host-finding by Culex mosquitoes: New tools for surveillance?

USDA-ARS?s Scientific Manuscript database

Culex mosquitoes are important vectors of pathogens and parasites causing diseases such as West Nile virus, St. Louis encephalitis, Japanese encephalitis, Venezuelan equine encephalitis and bancroftian filariasis. Surveillance of these species is based on traps using conventional mosquito attractan...

Validation of a common data model for active safety surveillance research

PubMed Central

Ryan, Patrick B; Reich, Christian G; Hartzema, Abraham G; Stang, Paul E

2011-01-01

Objective Systematic analysis of observational medical databases for active safety surveillance is hindered by the variation in data models and coding systems. Data analysts often find robust clinical data models difficult to understand and ill suited to support their analytic approaches. Further, some models do not facilitate the computations required for systematic analysis across many interventions and outcomes for large datasets. Translating the data from these idiosyncratic data models to a common data model (CDM) could facilitate both the analysts' understanding and the suitability for large-scale systematic analysis. In addition to facilitating analysis, a suitable CDM has to faithfully represent the source observational database. Before beginning to use the Observational Medical Outcomes Partnership (OMOP) CDM and a related dictionary of standardized terminologies for a study of large-scale systematic active safety surveillance, the authors validated the model's suitability for this use by example. Validation by example To validate the OMOP CDM, the model was instantiated into a relational database, data from 10 different observational healthcare databases were loaded into separate instances, a comprehensive array of analytic methods that operate on the data model was created, and these methods were executed against the databases to measure performance. Conclusion There was acceptable representation of the data from 10 observational databases in the OMOP CDM using the standardized terminologies selected, and a range of analytic methods was developed and executed with sufficient performance to be useful for active safety surveillance. PMID:22037893

Microbiological pathogens: Live poultry considerations

USDA-ARS?s Scientific Manuscript database

Food-borne illness is a significant worldwide public health problem. Salmonella is the predominate food-borne pathogen worldwide, and poultry and poultry products are, reportedly, a prevailing vehicle for salmonellosis. More recently, population-based active surveillance by investigators of the Fo...

Foodborne and waterborne pathogenic bacteria in selected Organisation for Economic Cooperation and Development (OECD) countries.

PubMed

Curtis, Dennis; Hill, Arthur; Wilcock, Anne; Charlebois, Sylvain

2014-10-01

The World Ranking Food Safety Performance reports by Charlebois in 2008 and 2010 importantly stimulated international discussion and encouraged efforts to establish realistic international benchmarks for food safety performance among Organisation for Economic Cooperation and Development (OECD) countries. This paper presents the international incidence of 5 common foodborne pathogens and describes the challenges of comparing international data. Data were compiled from surveillance authorities in the countries, such as the Natl. Notifiable Diseases Surveillance System of Australia; the Canadian Notifiable Diseases Surveillance System; the European Food Safety Authority, EFSA; the Ministry of Health, Labour and Welfare of Japan; New Zealand Food Safety Authority; and the U.S. Center for Disease Control and Prevention. The highest average rates in cases per 100000 people over the 12-y period from 2000 to 2011 for Campylobacter spp. (237.47), Salmonella spp. (67.08), Yersinia spp. (12.09), Verotoxigenic/Shiga toxin producing Escherichia coli (3.38), and Listeria monocytogenes (1.06) corresponded, in order, to New Zealand, Belgium, Finland, Canada, and Denmark. Comparatively, annual average rates for these 5 pathogens showed an increase over the 12-y period in 28%, 17%, 14%, 50%, and 6% of the countries for which data were available. Salmonella spp. showed a decrease in 56% of the countries, while incidence of L. monocytogenes was constant in most countries (94%). Variable protocols for monitoring incidence of pathogens among OECD countries remain. Nevertheless, there is evidence of sufficient standardization of monitoring protocols such as the European Surveillance System, which has contributed to reduce this gap. © 2014 Institute of Food Technologists®

Nationwide surveillance of bacterial respiratory pathogens conducted by the surveillance committee of Japanese Society of Chemotherapy, the Japanese Association for Infectious Diseases, and the Japanese Society for Clinical Microbiology in 2012: General view of the pathogens' antibacterial susceptibility.

PubMed

Yanagihara, Katsunori; Watanabe, Akira; Aoki, Nobuki; Matsumoto, Tetsuya; Yoshida, Masaki; Sato, Junko; Wakamura, Tomotaro; Sunakawa, Keisuke; Kadota, Junichi; Kiyota, Hiroshi; Iwata, Satoshi; Kaku, Mitsuo; Hanaki, Hideaki; Ohsaki, Yoshinobu; Fujiuchi, Satoru; Takahashi, Manabu; Takeuchi, Kenichi; Takeda, Hiroaki; Ikeda, Hideki; Miki, Makoto; Nakanowatari, Susumu; Takahashi, Hiroshi; Utagawa, Mutsuko; Nishiya, Hajime; Kawakami, Sayoko; Morino, Eriko; Takasaki, Jin; Mezaki, Kazuhisa; Chonabayashi, Naohiko; Tanaka, Chie; Sugiura, Hideko; Goto, Hajime; Saraya, Takeshi; Kurai, Daisuke; Katono, Yasuhiro; Inose, Rika; Niki, Yoshihito; Takuma, Takahiro; Kudo, Makoto; Ehara, Shigeru; Sato, Yoshimi; Tsukada, Hiroki; Watabe, Nobuei; Honma, Yasuo; Mikamo, Hiroshige; Yamagishi, Yuka; Nakamura, Atsushi; Ohashi, Minoru; Seki, Masafumi; Hamaguchi, Shigeto; Toyokawa, Masahiro; Fujikawa, Yasunori; Mitsuno, Noriko; Ukimura, Akira; Miyara, Takayuki; Nakamura, Takahito; Mikasa, Keiichi; Kasahara, Kei; Ui, Koji; Fukuda, Saori; Nakamura, Akihiro; Morimura, Mika; Yamashita, Mikio; Takesue, Yoshio; Wada, Yasunao; Sugimoto, Keisuke; Kusano, Nobuchika; Nose, Motoko; Mihara, Eiichirou; Kuwabara, Masao; Doi, Masao; Watanabe, Yaeko; Tokuyasu, Hirokazu; Hino, Satoshi; Negayama, Kiyoshi; Mukae, Hiroshi; Kawanami, Toshinori; Ota, Toshiyuki; Fujita, Masaki; Honda, Junichi; Hiramatsu, Kazufumi; Aoki, Yosuke; Fukuoka, Mami; Magarifuchi, Hiroki; Nagasawa, Zenzo; Kaku, Norihito; Fujita, Jiro; Higa, Futoshi; Tateyama, Masao

2017-09-01

The nationwide surveillance on antimicrobial susceptibility of bacterial respiratory pathogens from the patients in Japan was conducted by Japanese Society of Chemotherapy, Japanese association for infectious diseases and Japanese society for Clinical Microbiology in 2012. The isolates were collected from clinical specimens obtained from well-diagnosed adult patients with respiratory tract infections during the period between January and December in 2012 by three societies. Antimicrobial susceptibility testing was conducted at the central reference laboratory according to the method recommended by Clinical Laboratory Standard Institutes. Susceptibility testing was evaluated in 1236 strains (232 Staphylococcus aureus, 225 Streptococcus pneumoniae, 16 Streptococcus pyogenes, 231 Haemophilus influenzae, 147 Moraxella catarrhalis, 167 Klebsiella pneumoniae and 218 Pseudomonas aeruginosa). Ratio of methicillin-resistant S. aureus was 51.3%, and those of penicillin-intermediate S. pneumoniae was 0.4%. Among H. influenzae, 5.6% of them were found to be β-lactamase-producing ampicillin-resistant strains, and 37.2% to be β-lactamase-non-producing ampicillin-resistant strains. Extended spectrum β-lactamase-producing K. pneumoniae and multi-drug resistant P. aeruginosa with metallo β-lactamase were 4.2% and 3.2%, respectively. Continuous national surveillance is important to determine the actual situation of the resistance shown by bacterial respiratory pathogens to antimicrobial agents. Copyright © 2017 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Detection of Pathogen Exposure in African Buffalo Using Non-Specific Markers of Inflammation

PubMed Central

Glidden, Caroline K.; Beechler, Brianna; Buss, Peter Erik; Charleston, Bryan; de Klerk-Lorist, Lin-Mari; Maree, Francois Frederick; Muller, Timothy; Pérez-Martin, Eva; Scott, Katherine Anne; van Schalkwyk, Ockert Louis; Jolles, Anna

2018-01-01

Detecting exposure to new or emerging pathogens is a critical challenge to protecting human, domestic animal, and wildlife health. Yet, current techniques to detect infections typically target known pathogens of humans or economically important animals. In the face of the current surge in infectious disease emergence, non-specific disease surveillance tools are urgently needed. Tracking common host immune responses indicative of recent infection may have potential as a non-specific diagnostic approach for disease surveillance. The challenge to immunologists is to identify the most promising markers, which ideally should be highly conserved across pathogens and host species, become upregulated rapidly and consistently in response to pathogen invasion, and remain elevated beyond clearance of infection. This study combined an infection experiment and a longitudinal observational study to evaluate the utility of non-specific markers of inflammation [NSMI; two acute phase proteins (haptoglobin and serum amyloid A), two pro-inflammatory cytokines (IFNγ and TNF-α)] as indicators of pathogen exposure in a wild mammalian species, African buffalo (Syncerus caffer). Specifically, in the experimental study, we asked (1) How quickly do buffalo mount NSMI responses upon challenge with an endemic pathogen, foot-and-mouth disease virus; (2) for how long do NSMI remain elevated after viral clearance and; (3) how pronounced is the difference between peak NSMI concentration and baseline NSMI concentration? In the longitudinal study, we asked (4) Are elevated NSMI associated with recent exposure to a suite of bacterial and viral respiratory pathogens in a wild population? Among the four NSMI that we tested, haptoglobin showed the strongest potential as a surveillance marker in African buffalo: concentrations quickly and consistently reached high levels in response to experimental infection, remaining elevated for almost a month. Moreover, elevated haptoglobin was indicative of recent exposure to two respiratory pathogens assessed in the longitudinal study. We hope this work motivates studies investigating suites of NSMI as indicators for pathogen exposure in a broader range of both pathogen and host species, potentially transforming how we track disease burden in natural populations. PMID:29375568

Forecasting ESKAPE infections through a time-varying auto-adaptive algorithm using laboratory-based surveillance data.

PubMed

Ballarin, Antonio; Posteraro, Brunella; Demartis, Giuseppe; Gervasi, Simona; Panzarella, Fabrizio; Torelli, Riccardo; Paroni Sterbini, Francesco; Morandotti, Grazia; Posteraro, Patrizia; Ricciardi, Walter; Gervasi Vidal, Kristian A; Sanguinetti, Maurizio

2014-12-06

Mathematical or statistical tools are capable to provide a valid help to improve surveillance systems for healthcare and non-healthcare-associated bacterial infections. The aim of this work is to evaluate the time-varying auto-adaptive (TVA) algorithm-based use of clinical microbiology laboratory database to forecast medically important drug-resistant bacterial infections. Using TVA algorithm, six distinct time series were modelled, each one representing the number of episodes per single 'ESKAPE' (E nterococcus faecium, S taphylococcus aureus, K lebsiella pneumoniae, A cinetobacter baumannii, P seudomonas aeruginosa and E nterobacter species) infecting pathogen, that had occurred monthly between 2002 and 2011 calendar years at the Università Cattolica del Sacro Cuore general hospital. Monthly moving averaged numbers of observed and forecasted ESKAPE infectious episodes were found to show a complete overlapping of their respective smoothed time series curves. Overall good forecast accuracy was observed, with percentages ranging from 82.14% for E. faecium infections to 90.36% for S. aureus infections. Our approach may regularly provide physicians with forecasted bacterial infection rates to alert them about the spread of antibiotic-resistant bacterial species, especially when clinical microbiological results of patients' specimens are delayed.

Expanding severe acute respiratory infection (SARI) surveillance beyond influenza: The process and data from 1 year of implementation in Vietnam.

PubMed

Alroy, Karen A; Do, Trang Thuy; Tran, Phu Dac; Dang, Tan Quang; Vu, Long Ngoc; Le, Nga Thi Hang; Dang, Anh Duc; Ngu, Nghia Duy; Ngo, Tu Huy; Hoang, Phuong Vu Mai; Phan, Lan Trong; Nguyen, Thuong Vu; Nguyen, Long Thanh; Nguyen, Thinh Viet; Vien, Mai Quang; Le, Huy Xuan; Dao, Anh The; Nguyen, Trieu Bao; Pham, Duoc Tho; Nguyen, Van Thi Tuyet; Pham, Thanh Ngoc; Phan, Binh Hai; Whitaker, Brett; Do, Thuy Thi Thu; Dao, Phuong Anh; Balajee, S Arunmozhi; Mounts, Anthony W

2018-05-13

In 2016, as a component of the Global Health Security Agenda, the Vietnam Ministry of Health expanded its existing influenza sentinel surveillance for severe acute respiratory infections (SARI) to include testing for 7 additional viral respiratory pathogens. This article describes the steps taken to implement expanded SARI surveillance in Vietnam and reports data from 1 year of expanded surveillance. The process of expanding the suite of pathogens for routine testing by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) included laboratory trainings, procurement/distribution of reagents, and strengthening and aligning SARI surveillance epidemiology practices at sentinel sites and regional institutes (RI). Surveillance data showed that of 4003 specimens tested by the RI laboratories, 20.2% (n = 810) were positive for influenza virus. Of the 3193 influenza-negative specimens, 41.8% (n = 1337) were positive for at least 1 non-influenza respiratory virus, of which 16.2% (n = 518), 13.4% (n = 428), and 9.6% (n = 308) tested positive for respiratory syncytial virus, rhinovirus, and adenovirus, respectively. The Government of Vietnam has demonstrated that expanding respiratory viral surveillance by strengthening and building upon an influenza platform is feasible, efficient, and practical. © 2018 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

Highly Pathogenic Avian Influenza Virus among Wild Birds in Mongolia

PubMed Central

Gilbert, Martin; Jambal, Losolmaa; Karesh, William B.; Fine, Amanda; Shiilegdamba, Enkhtuvshin; Dulam, Purevtseren; Sodnomdarjaa, Ruuragchaa; Ganzorig, Khuukhenbaatar; Batchuluun, Damdinjav; Tseveenmyadag, Natsagdorj; Bolortuya, Purevsuren; Cardona, Carol J.; Leung, Connie Y. H.; Peiris, J. S. Malik; Spackman, Erica; Swayne, David E.; Joly, Damien O.

2012-01-01

Mongolia combines a near absence of domestic poultry, with an abundance of migratory waterbirds, to create an ideal location to study the epidemiology of highly pathogenic avian influenza virus (HPAIV) in a purely wild bird system. Here we present the findings of active and passive surveillance for HPAIV subtype H5N1 in Mongolia from 2005–2011, together with the results of five outbreak investigations. In total eight HPAIV outbreaks were confirmed in Mongolia during this period. Of these, one was detected during active surveillance employed by this project, three by active surveillance performed by Mongolian government agencies, and four through passive surveillance. A further three outbreaks were recorded in the neighbouring Tyva Republic of Russia on a lake that bisects the international border. No HPAIV was isolated (cultured) from 7,855 environmental fecal samples (primarily from ducks), or from 2,765 live, clinically healthy birds captured during active surveillance (primarily shelducks, geese and swans), while four HPAIVs were isolated from 141 clinically ill or dead birds located through active surveillance. Two low pathogenic avian influenza viruses (LPAIV) were cultured from ill or dead birds during active surveillance, while environmental feces and live healthy birds yielded 56 and 1 LPAIV respectively. All Mongolian outbreaks occurred in 2005 and 2006 (clade 2.2), or 2009 and 2010 (clade 2.3.2.1); all years in which spring HPAIV outbreaks were reported in Tibet and/or Qinghai provinces in China. The occurrence of outbreaks in areas deficient in domestic poultry is strong evidence that wild birds can carry HPAIV over at least moderate distances. However, failure to detect further outbreaks of clade 2.2 after June 2006, and clade 2.3.2.1 after June 2010 suggests that wild birds migrating to and from Mongolia may not be competent as indefinite reservoirs of HPAIV, or that HPAIV did not reach susceptible populations during our study. PMID:22984464

Use of media and public-domain Internet sources for detection and assessment of plant health threats

PubMed Central

Thomas, Carla S.; Nelson, Noele P.; Jahn, Gary C.; Niu, Tianchan; Hartley, David M.

2011-01-01

Event-based biosurveillance is a recognized approach to early warning and situational awareness of emerging health threats. In this study, we build upon previous human and animal health work to develop a new approach to plant pest and pathogen surveillance. We show that monitoring public domain electronic media for indications and warning of epidemics and associated social disruption can provide information about the emergence and progression of plant pest infestation or disease outbreak. The approach is illustrated using a case study, which describes a plant pest and pathogen epidemic in China and Vietnam from February 2006 to December 2007, and the role of ducks in contributing to zoonotic virus spread in birds and humans. This approach could be used as a complementary method to traditional plant pest and pathogen surveillance to aid global and national plant protection officials and political leaders in early detection and timely response to significant biological threats to plant health, economic vitality, and social stability. This study documents the inter-relatedness of health in human, animal, and plant populations and emphasizes the importance of plant health surveillance. PMID:24149031

Migratory and adhesive cues controlling innate-like lymphocyte surveillance of the pathogen-exposed surface of the lymph node.

PubMed

Zhang, Yang; Roth, Theodore L; Gray, Elizabeth E; Chen, Hsin; Rodda, Lauren B; Liang, Yin; Ventura, Patrick; Villeda, Saul; Crocker, Paul R; Cyster, Jason G

2016-08-03

Lymph nodes (LNs) contain innate-like lymphocytes that survey the subcapsular sinus (SCS) and associated macrophages for pathogen entry. The factors promoting this surveillance behavior have not been defined. Here, we report that IL7R(hi)Ccr6(+) lymphocytes in mouse LNs rapidly produce IL17 upon bacterial and fungal challenge. We show that these innate-like lymphocytes are mostly LN resident. Ccr6 is required for their accumulation near the SCS and for efficient IL17 induction. Migration into the SCS intrinsically requires S1pr1, whereas movement from the sinus into the parenchyma involves the integrin LFA1 and its ligand ICAM1. CD169, a sialic acid-binding lectin, helps retain the cells within the sinus, preventing their loss in lymph flow. These findings establish a role for Ccr6 in augmenting innate-like lymphocyte responses to lymph-borne pathogens, and they define requirements for cell movement between parenchyma and SCS in what we speculate is a program of immune surveillance that helps achieve LN barrier immunity.

Use of media and public-domain Internet sources for detection and assessment of plant health threats.

PubMed

Thomas, Carla S; Nelson, Noele P; Jahn, Gary C; Niu, Tianchan; Hartley, David M

2011-09-05

Event-based biosurveillance is a recognized approach to early warning and situational awareness of emerging health threats. In this study, we build upon previous human and animal health work to develop a new approach to plant pest and pathogen surveillance. We show that monitoring public domain electronic media for indications and warning of epidemics and associated social disruption can provide information about the emergence and progression of plant pest infestation or disease outbreak. The approach is illustrated using a case study, which describes a plant pest and pathogen epidemic in China and Vietnam from February 2006 to December 2007, and the role of ducks in contributing to zoonotic virus spread in birds and humans. This approach could be used as a complementary method to traditional plant pest and pathogen surveillance to aid global and national plant protection officials and political leaders in early detection and timely response to significant biological threats to plant health, economic vitality, and social stability. This study documents the inter-relatedness of health in human, animal, and plant populations and emphasizes the importance of plant health surveillance.

Molecular-based surveillance of campylobacteriosis in New Zealand--from source attribution to genomic epidemiology.

PubMed

Muellner, P; Pleydell, E; Pirie, R; Baker, M G; Campbell, D; Carter, P E; French, N P

2013-01-17

Molecular-based surveillance of campylobacteriosis in New Zealand contributed to the implementation of interventions that led to a 50% reduction in notified and hospitalised cases of the country's most important zoonosis. From a pre-intervention high of 384 per 100,000 population in 2006, incidence dropped by 50% in 2008; a reduction that has been sustained since. This article illustrates many aspects of the successful use of molecular-based surveillance, including the distinction between control-focused and strategy-focused surveillance and advances in source attribution. We discuss how microbial genetic data can enhance the understanding of epidemiological explanatory and response variables and thereby enrich the epidemiological analysis. Sequence data can be fitted to evolutionary and epidemiological models to gain new insights into pathogen evolution, the nature of associations between strains of pathogens and host species, and aspects of between-host transmission. With the advent of newer sequencing technologies and the availability of rapid, high-coverage genome sequence data, such techniques may be extended and refined within the emerging discipline of genomic epidemiology. The aim of this article is to summarise the experience gained in New Zealand with molecular-based surveillance of campylobacteriosis and to discuss how this experience could be used to further advance the use of molecular tools in surveillance.

The Enemy within: Innate Surveillance-Mediated Cell Death, the Common Mechanism of Neurodegenerative Disease

PubMed Central

Richards, Robert I.; Robertson, Sarah A.; O'Keefe, Louise V.; Fornarino, Dani; Scott, Andrew; Lardelli, Michael; Baune, Bernhard T.

2016-01-01

Neurodegenerative diseases comprise an array of progressive neurological disorders all characterized by the selective death of neurons in the central nervous system. Although, rare (familial) and common (sporadic) forms can occur for the same disease, it is unclear whether this reflects several distinct pathogenic pathways or the convergence of different causes into a common form of nerve cell death. Remarkably, neurodegenerative diseases are increasingly found to be accompanied by activation of the innate immune surveillance system normally associated with pathogen recognition and response. Innate surveillance is the cell's quality control system for the purpose of detecting such danger signals and responding in an appropriate manner. Innate surveillance is an “intelligent system,” in that the manner of response is relevant to the magnitude and duration of the threat. If possible, the threat is dealt with within the cell in which it is detected, by degrading the danger signal(s) and restoring homeostasis. If this is not successful then an inflammatory response is instigated that is aimed at restricting the spread of the threat by elevating degradative pathways, sensitizing neighboring cells, and recruiting specialized cell types to the site. If the danger signal persists, then the ultimate response can include not only the programmed cell death of the original cell, but the contents of this dead cell can also bring about the death of adjacent sensitized cells. These responses are clearly aimed at destroying the ability of the detected pathogen to propagate and spread. Innate surveillance comprises intracellular, extracellular, non-cell autonomous and systemic processes. Recent studies have revealed how multiple steps in these processes involve proteins that, through their mutation, have been linked to many familial forms of neurodegenerative disease. This suggests that individuals harboring these mutations may have an amplified response to innate-mediated damage in neural tissues, and renders innate surveillance mediated cell death a plausible common pathogenic pathway responsible for neurodegenerative diseases, in both familial and sporadic forms. Here we have assembled evidence in favor of the hypothesis that neurodegenerative disease is the cumulative result of chronic activation of the innate surveillance pathway, triggered by endogenous or environmental danger or damage associated molecular patterns in a progressively expanding cascade of inflammation, tissue damage and cell death. PMID:27242399

Comparison of outpatient medically attended and community-level influenza-like illness-New York City, 2013-2015.

PubMed

Russell, Kate E; Fowlkes, Ashley; Stockwell, Melissa S; Vargas, Celibell Y; Saiman, Lisa; Larson, Elaine L; LaRussa, Philip; Di Lonardo, Steve; Popowich, Michael; St George, Kirsten; Steffens, Andrea; Reed, Carrie

2018-05-01

Surveillance of influenza-like illness (ILI) in the United States is primarily conducted through medical settings despite a significant burden of non-medically attended ILI. To assess consistency between surveillance for respiratory viruses in outpatient and community settings using ILI surveillance from the Centers for Disease Control and Prevention Influenza Incidence Surveillance Project (IISP) and the Mobile Surveillance for Acute Respiratory Infections (ARI) and Influenza-Like Illness in the Community (MoSAIC) Study. The Influenza Incidence Surveillance Project conducts ILI surveillance in 3 primary care clinics in New York City, and MoSAIC conducts community-based ILI/ARI surveillance through text messaging among a cohort of New York City residents. Both systems obtain respiratory specimens from participants with ILI/ARI and test for multiple pathogens. We conducted a retrospective review of ILI cases in IISP and MoSAIC from January 2013 to May 2015 with descriptive analyses of clinical and laboratory data. Five-hundred twelve MoSAIC and 669 IISP participants met an ILI criteria (fever with cough or sore throat) and were included. Forty percent of MoSAIC participants sought care; the majority primary care. Pathogens were detected in 63% of MoSAIC and 70% of IISP cases. The relative distribution of influenza and other respiratory viruses detected was similar; however, there were statistically significant differences in the frequency that were not explained by care seeking. Outpatient and community-based surveillance in the one found similar timing and relative distribution of respiratory viruses, but community surveillance in a single neighborhood may not fully capture the variations in ILI etiology that occur more broadly. Published 2018. This article is a U.S. Government work and is in the public domain in the USA. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.

Differences in the Reporting of Racial and Socioeconomic Disparities among Three Large National Databases for Breast Reconstruction.

PubMed

Kamali, Parisa; Zettervall, Sara L; Wu, Winona; Ibrahim, Ahmed M S; Medin, Caroline; Rakhorst, Hinne A; Schermerhorn, Marc L; Lee, Bernard T; Lin, Samuel J

2017-04-01

Research derived from large-volume databases plays an increasing role in the development of clinical guidelines and health policy. In breast cancer research, the Surveillance, Epidemiology and End Results, National Surgical Quality Improvement Program, and Nationwide Inpatient Sample databases are widely used. This study aims to compare the trends in immediate breast reconstruction and identify the drawbacks and benefits of each database. Patients with invasive breast cancer and ductal carcinoma in situ were identified from each database (2005-2012). Trends of immediate breast reconstruction over time were evaluated. Patient demographics and comorbidities were compared. Subgroup analysis of immediate breast reconstruction use per race was conducted. Within the three databases, 1.2 million patients were studied. Immediate breast reconstruction in invasive breast cancer patients increased significantly over time in all databases. A similar significant upward trend was seen in ductal carcinoma in situ patients. Significant differences in immediate breast reconstruction rates were seen among races; and the disparity differed among the three databases. Rates of comorbidities were similar among the three databases. There has been a significant increase in immediate breast reconstruction; however, the extent of the reporting of overall immediate breast reconstruction rates and of racial disparities differs significantly among databases. The Nationwide Inpatient Sample and the National Surgical Quality Improvement Program report similar findings, with the Surveillance, Epidemiology and End Results database reporting results significantly lower in several categories. These findings suggest that use of the Surveillance, Epidemiology and End Results database may not be universally generalizable to the entire U.S.

67 FR 64386 - Enhancement of Surveillance for Trimethoprim-Sulfamethoxazole Resistant Invasive Respiratory and...

Federal Register 2010, 2011, 2012, 2013, 2014

2002-10-18

... cerebrospinal fluid infections caused by key Pathogens-Streptococcus Pneumoniae, Haemophilus Influenzae, and non... pathogens causing meningitis (pneumococcus, Haemophilus Influenzae, and Meningococcus). The infrastructure... testing, for meningitis agents including pneumococcus and Haemophilus Influenzae. Laboratory staff have...

High Resolution Melting as a rapid, reliable, accurate and cost-effective emerging tool for genotyping pathogenic bacteria and enhancing molecular epidemiological surveillance: a comprehensive review of the literature.

PubMed

Tamburro, M; Ripabelli, G

2017-01-01

Rapid, reliable and accurate molecular typing methods are essential for outbreaks detection and infectious diseases control, for monitoring the evolution and dynamics of microbial populations, and for effective epidemiological surveillance. The introduction of a novel method based on the analysis of melting temperature of amplified products, known as High Resolution Melting (HRM) since 2002, has found applications in epidemiological studies, either for identification of bacterial species or molecular typing, as well as an extensive and increasing use in many research fields. HRM method is based on the use of saturating third generation dyes, advanced real-time PCR platforms, and bioinformatics tools. To describe, by a comphrehensive review of the literature, the use, application and usefulness of HRM for the genotyping of bacterial pathogens in the context of epidemiological surveillance and public health. A literature search was carried out during July-August 2016, by consulting the biomedical databases PubMed/Medline, Scopus, EMBASE, and ISI Web of Science without limits. The search strategy was performed according to the following keywords: high resolution melting analysis and bacteria and genotyping or molecular typing. All the articles evaluating the application of HRM for bacterial pathogen genotyping were selected and reviewed, taking into account the objective of each study, the rationale explaining the use of this technology, and the main results obtained in comparison with gold standards and/or alternative methods, when available. HRM method was extensively used for molecular typing of both Gram-positive and Gram-negative bacterial pathogens, representing a versatile genetic tool: a) to evaluate genetic diversity and subtype at species/subspecies level, based also on allele discrimination/identification and mutation screening; b) to recognize phylogenetic groupings (lineage, sublineage, subgroups); c) to identify antimicrobial resistance; d) to detect and screen for mutations related to drug-resistance; e) to discriminate gene isoforms. HRM method showed, in almost all instances, excellent typeability and discriminatory power, with high concordance of typing results obtained with gold standards or comparable methods. Conversely, for the evaluation of genetic determinants associated to antibiotic-resistance or for screening of associated mutations in key gene fragments, the sensitivity and specificity was not optimal, because the targeted amplicons did not encompass all the crucial mutations. Despite the recent introduction of sequencing-based methods, the HRM method deserves consideration in research fields of infectious diseases, being characterized by low cost, rapidity, flexibility and versatility. However, there are some limitations to HRM assays development, which should be carefully considered. The most common application of HRM for bacterial typing is related to Single Nucleotide Polymorphism (SNP)-based genotyping with the analysis of gene fragments within the multilocus sequence typing (MLST) loci, following an approach termed mini-MLST or Minim typing. Although the resolving power is not totally correspondent to MLST, the Simpson's Index of Diversity provided by HRM method typically >0.95. Furthermore, the cost of this approach is less than MLST, enabling low cost surveillance and rapid response for outbreak control. Hence, the potential of HRM technology can strongly facilitate routine research and diagnostics in the epidemiological studies, as well as advance and streamline the genetic characterization of bacterial pathogens.

Wild bird surveillance for highly pathogenic avian influenza H5 in North America

USGS Publications Warehouse

Flint, Paul L.; Pearce, John M.; Franson, J. Christian; Derksen, Dirk V.

2015-01-01

It is unknown how the current Asian origin highly pathogenic avian influenza H5 viruses arrived, but these viruses are now poised to become endemic in North America. Wild birds harbor these viruses and have dispersed them at regional scales. What is unclear is how the viruses may be moving from the wild bird reservoir into poultry holdings. Active surveillance of live wild birds is likely the best way to determine the true distribution of these viruses. We also suggest that sampling be focused on regions with the greatest risk for poultry losses and attempt to define the mechanisms of transfer to enhance biosecurity. Responding to the recent outbreaks of highly pathogenic avian influenza in North America requires an efficient plan with clear objectives and potential management outcomes.

Detecting the emergence of novel, zoonotic viruses pathogenic to humans.

PubMed

Rosenberg, Ronald

2015-03-01

RNA viruses, with their high potential for mutation and epidemic spread, are the most common class of pathogens found as new causes of human illness. Despite great advances made in diagnostic technology since the 1950s, the annual rate at which novel virulent viruses have been found has remained at 2-3. Most emerging viruses are zoonoses; they have jumped from mammal or bird hosts to humans. An analysis of virus discovery indicates that the small number of novel viruses discovered annually is an artifact of inadequate surveillance in tropical and subtropical countries, where even established endemic pathogens are often misdiagnosed. Many of the emerging viruses of the future are already infecting humans but remain to be uncovered by a strategy of disease surveillance in selected populations.

A Quantitative Prioritisation of Human and Domestic Animal Pathogens in Europe

PubMed Central

McIntyre, K. Marie; Setzkorn, Christian; Hepworth, Philip J.; Morand, Serge; Morse, Andrew P.; Baylis, Matthew

2014-01-01

Disease or pathogen risk prioritisations aid understanding of infectious agent impact within surveillance or mitigation and biosecurity work, but take significant development. Previous work has shown the H-(Hirsch-)index as an alternative proxy. We present a weighted risk analysis describing infectious pathogen impact for human health (human pathogens) and well-being (domestic animal pathogens) using an objective, evidence-based, repeatable approach; the H-index. This study established the highest H-index European pathogens. Commonalities amongst pathogens not included in previous surveillance or risk analyses were examined. Differences between host types (humans/animals/zoonotic) in pathogen H-indices were explored as a One Health impact indicator. Finally, the acceptability of the H-index proxy for animal pathogen impact was examined by comparison with other measures. 57 pathogens appeared solely in the top 100 highest H-indices (1) human or (2) animal pathogens list, and 43 occurred in both. Of human pathogens, 66 were zoonotic and 67 were emerging, compared to 67 and 57 for animals. There were statistically significant differences between H-indices for host types (humans, animal, zoonotic), and there was limited evidence that H-indices are a reasonable proxy for animal pathogen impact. This work addresses measures outlined by the European Commission to strengthen climate change resilience and biosecurity for infectious diseases. The results include a quantitative evaluation of infectious pathogen impact, and suggest greater impacts of human-only compared to zoonotic pathogens or scientific under-representation of zoonoses. The outputs separate high and low impact pathogens, and should be combined with other risk assessment methods relying on expert opinion or qualitative data for priority setting, or could be used to prioritise diseases for which formal risk assessments are not possible because of data gaps. PMID:25136810

Estimation of the sensitivity of the surveillance system for avian influenza in the western region of Cuba.

PubMed

Ferrer, Edyniesky; Calistri, Paolo; Fonseca, Osvaldo; Ippoliti, Carla; Alfonso, Pastor; Iannetti, Simona; Abeledo, María A; Fernández, Octavio; Percedo, María I; Pérez, Antonio

2013-01-01

Although avian influenza (AI) virus of H5 and H7 subtypes has the potential to mutate to a highly pathogenic form and cause very high mortalities in some poultry species, most AI infections in poultry are due to low pathogenic AI (LPAI). Hence serological surveys, coupled with passive surveillance activities, are essential to detect sub-clinical infections by LPAI viruses, H5 and H7 subtypes. However the proper planning of an active surveillance system should be based on a careful estimation of its performance. Therefore, the sensitivity of the active surveillance system for AI in the western region of Cuba was assessed by a stochastic model quantifying the probability of revealing at least one animal infected by H5 or H7 subtype. The diagnostic sensitivity of the haemagglutination inhibition assay and different levels of within-flock prevalence (5%, 12% and 30%) were considered. The sensitivity of the surveillance system was then assessed under five different samples size scenarios: testing 20, 30, 40, 50 or 60 animals in each flock. Poultry flock sites in the western region of Cuba with a size ranging from 10,000 to 335,000 birds were included in the study.

Evaluation of Electronic Healthcare Databases for Post-Marketing Drug Safety Surveillance and Pharmacoepidemiology in China.

PubMed

Yang, Yu; Zhou, Xiaofeng; Gao, Shuangqing; Lin, Hongbo; Xie, Yanming; Feng, Yuji; Huang, Kui; Zhan, Siyan

2018-01-01

Electronic healthcare databases (EHDs) are used increasingly for post-marketing drug safety surveillance and pharmacoepidemiology in Europe and North America. However, few studies have examined the potential of these data sources in China. Three major types of EHDs in China (i.e., a regional community-based database, a national claims database, and an electronic medical records [EMR] database) were selected for evaluation. Forty core variables were derived based on the US Mini-Sentinel (MS) Common Data Model (CDM) as well as the data features in China that would be desirable to support drug safety surveillance. An email survey of these core variables and eight general questions as well as follow-up inquiries on additional variables was conducted. These 40 core variables across the three EHDs and all variables in each EHD along with those in the US MS CDM and Observational Medical Outcomes Partnership (OMOP) CDM were compared for availability and labeled based on specific standards. All of the EHDs' custodians confirmed their willingness to share their databases with academic institutions after appropriate approval was obtained. The regional community-based database contained 1.19 million people in 2015 with 85% of core variables. Resampled annually nationwide, the national claims database included 5.4 million people in 2014 with 55% of core variables, and the EMR database included 3 million inpatients from 60 hospitals in 2015 with 80% of core variables. Compared with MS CDM or OMOP CDM, the proportion of variables across the three EHDs available or able to be transformed/derived from the original sources are 24-83% or 45-73%, respectively. These EHDs provide potential value to post-marketing drug safety surveillance and pharmacoepidemiology in China. Future research is warranted to assess the quality and completeness of these EHDs or additional data sources in China.

A Method of Determining Where to Target Surveillance Efforts in Heterogeneous Epidemiological Systems

USDA-ARS?s Scientific Manuscript database

The spread of pathogens into new environments poses a considerable threat to health, ecosystems, and agricultural productivity worldwide. Early detection through effective surveillance is a key strategy to reduce the risk of their establishment. Whilst it is well established that statistical and eco...

Estimating the burden of foodborne diseases in Japan

PubMed Central

Kumagai, Yuko; Gilmour, Stuart; Ota, Erika; Momose, Yoshika; Onishi, Toshiro; Bilano, Ver Luanni Feliciano; Kasuga, Fumiko; Sekizaki, Tsutomu

2015-01-01

Abstract Objective To assess the burden posed by foodborne diseases in Japan using methods developed by the World Health Organization’s Foodborne Disease Burden Epidemiology Reference Group (FERG). Methods Expert consultation and statistics on food poisoning during 2011 were used to identify three common causes of foodborne disease in Japan: Campylobacter and Salmonella species and enterohaemorrhagic Escherichia coli (EHEC). We conducted systematic reviews of English and Japanese literature on the complications caused by these pathogens, by searching Embase, the Japan medical society abstract database and Medline. We estimated the annual incidence of acute gastroenteritis from reported surveillance data, based on estimated probabilities that an affected person would visit a physician and have gastroenteritis confirmed. We then calculated disability-adjusted life-years (DALYs) lost in 2011, using the incidence estimates along with disability weights derived from published studies. Findings In 2011, foodborne disease caused by Campylobacter species, Salmonella species and EHEC led to an estimated loss of 6099, 3145 and 463 DALYs in Japan, respectively. These estimated burdens are based on the pyramid reconstruction method; are largely due to morbidity rather than mortality; and are much higher than those indicated by routine surveillance data. Conclusion Routine surveillance data may indicate foodborne disease burdens that are much lower than the true values. Most of the burden posed by foodborne disease in Japan comes from secondary complications. The tools developed by FERG appear useful in estimating disease burdens and setting priorities in the field of food safety. PMID:26478611

Rapidly expanding range of highly pathogenic avian influenza viruses

USGS Publications Warehouse

Hall, Jeffrey S.; Dusek, Robert J.; Spackman, Erica

2015-01-01

The movement of highly pathogenic avian influenza (H5N8) virus across Eurasia and into North America and the virus’ propensity to reassort with co-circulating low pathogenicity viruses raise concerns among poultry producers, wildlife biologists, aviculturists, and public health personnel worldwide. Surveillance, modeling, and experimental research will provide the knowledge required for intelligent policy and management decisions.

Rapidly Expanding Range of Highly Pathogenic Avian Influenza Viruses.

PubMed

Hall, Jeffrey S; Dusek, Robert J; Spackman, Erica

2015-07-01

The movement of highly pathogenic avian influenza (H5N8) virus across Eurasia and into North America and the virus' propensity to reassort with co-circulating low pathogenicity viruses raise concerns among poultry producers, wildlife biologists, aviculturists, and public health personnel worldwide. Surveillance, modeling, and experimental research will provide the knowledge required for intelligent policy and management decisions.

Uses of tuberculosis mortality surveillance to identify programme errors and improve database reporting.

PubMed

Selig, L; Guedes, R; Kritski, A; Spector, N; Lapa E Silva, J R; Braga, J U; Trajman, A

2009-08-01

In 2006, 848 persons died from tuberculosis (TB) in Rio de Janeiro, Brazil, corresponding to a mortality rate of 5.4 per 100 000 population. No specific TB death surveillance actions are currently in place in Brazil. Two public general hospitals with large open emergency rooms in Rio de Janeiro City. To evaluate the contribution of TB death surveillance in detecting gaps in TB control. We conducted a survey of TB deaths from September 2005 to August 2006. Records of TB-related deaths and deaths due to undefined causes were investigated. Complementary data were gathered from the mortality and TB notification databases. Seventy-three TB-related deaths were investigated. Transmission hazards were identified among firefighters, health care workers and in-patients. Management errors included failure to isolate suspected cases, to confirm TB, to correct drug doses in underweight patients and to trace contacts. Following the survey, 36 cases that had not previously been notified were included in the national TB notification database and the outcome of 29 notified cases was corrected. TB mortality surveillance can contribute to TB monitoring and evaluation by detecting correctable and specific programme- and hospital-based care errors, and by improving the accuracy of TB database reporting. Specific local and programmatic interventions can be proposed as a result.

The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes.

PubMed

Hamilton, John P; Neeno-Eckwall, Eric C; Adhikari, Bishwo N; Perna, Nicole T; Tisserat, Ned; Leach, Jan E; Lévesque, C André; Buell, C Robin

2011-01-01

The Comprehensive Phytopathogen Genomics Resource (CPGR) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. Tools are available to search and analyze annotated genome sequences of 74 bacterial, fungal and oomycete pathogens. Oomycete and fungal genomes are obtained directly from GenBank, whereas bacterial genome sequences are downloaded from the A Systematic Annotation Package (ASAP) database that provides curation of genomes using comparative approaches. Curated lists of bacterial genes relevant to pathogenicity and avirulence are also provided. The Plant Pathogen Transcript Assemblies Database provides annotated assemblies of the transcribed regions of 82 eukaryotic genomes from publicly available single pass Expressed Sequence Tags. Data-mining tools are provided along with tools to create candidate diagnostic markers, an emerging use for genomic sequence data in plant pathology. The Plant Pathogen Ribosomal DNA (rDNA) database is a resource for pathogens that lack genome or transcriptome data sets and contains 131 755 rDNA sequences from GenBank for 17 613 species identified as plant pathogens and related genera. Database URL: http://cpgr.plantbiology.msu.edu.

Application of Broad-Spectrum Resequencing Microarray for Genotyping Rhabdoviruses▿

PubMed Central

Dacheux, Laurent; Berthet, Nicolas; Dissard, Gabriel; Holmes, Edward C.; Delmas, Olivier; Larrous, Florence; Guigon, Ghislaine; Dickinson, Philip; Faye, Ousmane; Sall, Amadou A.; Old, Iain G.; Kong, Katherine; Kennedy, Giulia C.; Manuguerra, Jean-Claude; Cole, Stewart T.; Caro, Valérie; Gessain, Antoine; Bourhy, Hervé

2010-01-01

The rapid and accurate identification of pathogens is critical in the control of infectious disease. To this end, we analyzed the capacity for viral detection and identification of a newly described high-density resequencing microarray (RMA), termed PathogenID, which was designed for multiple pathogen detection using database similarity searching. We focused on one of the largest and most diverse viral families described to date, the family Rhabdoviridae. We demonstrate that this approach has the potential to identify both known and related viruses for which precise sequence information is unavailable. In particular, we demonstrate that a strategy based on consensus sequence determination for analysis of RMA output data enabled successful detection of viruses exhibiting up to 26% nucleotide divergence with the closest sequence tiled on the array. Using clinical specimens obtained from rabid patients and animals, this method also shows a high species level concordance with standard reference assays, indicating that it is amenable for the development of diagnostic assays. Finally, 12 animal rhabdoviruses which were currently unclassified, unassigned, or assigned as tentative species within the family Rhabdoviridae were successfully detected. These new data allowed an unprecedented phylogenetic analysis of 106 rhabdoviruses and further suggest that the principles and methodology developed here may be used for the broad-spectrum surveillance and the broader-scale investigation of biodiversity in the viral world. PMID:20610710

Antimicrobial therapy of selected diseases in turkeys, laying hens, and minor poultry species in Canada

PubMed Central

Agunos, Agnes; Carson, Carolee; Léger, Dave

2013-01-01

This paper identifies common poultry diseases requiring antimicrobial therapy, antimicrobials deemed efficacious to treat these diseases, and antimicrobial resistance (AMR) in these commodity-pathogen combinations, and describes current residue issues and minor use minor species (MUMS) guidelines. Veterinarians with turkey/layer expertise and diagnosticians were surveyed to determine the bacterial and protozoal diseases diagnosed in the last 5 years. Avian pathogenic Escherichia coli, Staphylococcus aureus, and Ornithobacterium rhinotracheale were the 3 most frequently diagnosed pathogens of turkeys. In layers, E. coli-peritonitis, and Clostridium perfringens/Eimeria spp. infections were the most common diagnoses. A literature review identified 32 antimicrobials as efficacious and/or recommended for treating these diseases. Surveillance and monitoring indicate the presence of enteric resistant organisms from some of these avian species (including resistance to antimicrobials of very high importance to human medicine). This paper highlights the need for surveillance of pathogen frequency, antimicrobial use (AMU), and AMR particularly in turkeys. PMID:24179239

Informatics infrastructure for syndrome surveillance, decision support, reporting, and modeling of critical illness.

PubMed

Herasevich, Vitaly; Pickering, Brian W; Dong, Yue; Peters, Steve G; Gajic, Ognjen

2010-03-01

To develop and validate an informatics infrastructure for syndrome surveillance, decision support, reporting, and modeling of critical illness. Using open-schema data feeds imported from electronic medical records (EMRs), we developed a near-real-time relational database (Multidisciplinary Epidemiology and Translational Research in Intensive Care Data Mart). Imported data domains included physiologic monitoring, medication orders, laboratory and radiologic investigations, and physician and nursing notes. Open database connectivity supported the use of Boolean combinations of data that allowed authorized users to develop syndrome surveillance, decision support, and reporting (data "sniffers") routines. Random samples of database entries in each category were validated against corresponding independent manual reviews. The Multidisciplinary Epidemiology and Translational Research in Intensive Care Data Mart accommodates, on average, 15,000 admissions to the intensive care unit (ICU) per year and 200,000 vital records per day. Agreement between database entries and manual EMR audits was high for sex, mortality, and use of mechanical ventilation (kappa, 1.0 for all) and for age and laboratory and monitored data (Bland-Altman mean difference +/- SD, 1(0) for all). Agreement was lower for interpreted or calculated variables, such as specific syndrome diagnoses (kappa, 0.5 for acute lung injury), duration of ICU stay (mean difference +/- SD, 0.43+/-0.2), or duration of mechanical ventilation (mean difference +/- SD, 0.2+/-0.9). Extraction of essential ICU data from a hospital EMR into an open, integrative database facilitates process control, reporting, syndrome surveillance, decision support, and outcome research in the ICU.

Vector-borne disease intelligence: strategies to deal with disease burden and threats.

PubMed

Braks, Marieta; Medlock, Jolyon M; Hubalek, Zdenek; Hjertqvist, Marika; Perrin, Yvon; Lancelot, Renaud; Duchyene, Els; Hendrickx, Guy; Stroo, Arjan; Heyman, Paul; Sprong, Hein

2014-01-01

Owing to the complex nature of vector-borne diseases (VBDs), whereby monitoring of human case patients does not suffice, public health authorities experience challenges in surveillance and control of VBDs. Knowledge on the presence and distribution of vectors and the pathogens that they transmit is vital to the risk assessment process to permit effective early warning, surveillance, and control of VBDs. Upon accepting this reality, public health authorities face an ever-increasing range of possible surveillance targets and an associated prioritization process. Here, we propose a comprehensive approach that integrates three surveillance strategies: population-based surveillance, disease-based surveillance, and context-based surveillance for EU member states to tailor the best surveillance strategy for control of VBDs in their geographic region. By classifying the surveillance structure into five different contexts, we hope to provide guidance in optimizing surveillance efforts. Contextual surveillance strategies for VBDs entail combining organization and data collection approaches that result in disease intelligence rather than a preset static structure.

Vector-Borne Disease Intelligence: Strategies to Deal with Disease Burden and Threats

PubMed Central

Braks, Marieta; Medlock, Jolyon M.; Hubalek, Zdenek; Hjertqvist, Marika; Perrin, Yvon; Lancelot, Renaud; Duchyene, Els; Hendrickx, Guy; Stroo, Arjan; Heyman, Paul; Sprong, Hein

2014-01-01

Owing to the complex nature of vector-borne diseases (VBDs), whereby monitoring of human case patients does not suffice, public health authorities experience challenges in surveillance and control of VBDs. Knowledge on the presence and distribution of vectors and the pathogens that they transmit is vital to the risk assessment process to permit effective early warning, surveillance, and control of VBDs. Upon accepting this reality, public health authorities face an ever-increasing range of possible surveillance targets and an associated prioritization process. Here, we propose a comprehensive approach that integrates three surveillance strategies: population-based surveillance, disease-based surveillance, and context-based surveillance for EU member states to tailor the best surveillance strategy for control of VBDs in their geographic region. By classifying the surveillance structure into five different contexts, we hope to provide guidance in optimizing surveillance efforts. Contextual surveillance strategies for VBDs entail combining organization and data collection approaches that result in disease intelligence rather than a preset static structure. PMID:25566522

Early detection surveillance for an emerging plant pathogen: a rule of thumb to predict prevalence at first discovery.

PubMed

Parnell, S; Gottwald, T R; Cunniffe, N J; Alonso Chavez, V; van den Bosch, F

2015-09-07

Emerging plant pathogens are a significant problem for conservation and food security. Surveillance is often instigated in an attempt to detect an invading epidemic before it gets out of control. Yet in practice many epidemics are not discovered until already at a high prevalence, partly due to a lack of quantitative understanding of how surveillance effort and the dynamics of an invading epidemic relate. We test a simple rule of thumb to determine, for a surveillance programme taking a fixed number of samples at regular intervals, the distribution of the prevalence an epidemic will have reached on first discovery (discovery-prevalence) and its expectation E(q*). We show that E(q*) = r/(N/Δ), i.e. simply the rate of epidemic growth divided by the rate of sampling; where r is the epidemic growth rate, N is the sample size and Δ is the time between sampling rounds. We demonstrate the robustness of this rule of thumb using spatio-temporal epidemic models as well as data from real epidemics. Our work supports the view that, for the purposes of early detection surveillance, simple models can provide useful insights in apparently complex systems. The insight can inform decisions on surveillance resource allocation in plant health and has potential applicability to invasive species generally. © 2015 The Author(s).

Early detection surveillance for an emerging plant pathogen: a rule of thumb to predict prevalence at first discovery

PubMed Central

Parnell, S.; Gottwald, T. R.; Cunniffe, N. J.; Alonso Chavez, V.; van den Bosch, F.

2015-01-01

Emerging plant pathogens are a significant problem for conservation and food security. Surveillance is often instigated in an attempt to detect an invading epidemic before it gets out of control. Yet in practice many epidemics are not discovered until already at a high prevalence, partly due to a lack of quantitative understanding of how surveillance effort and the dynamics of an invading epidemic relate. We test a simple rule of thumb to determine, for a surveillance programme taking a fixed number of samples at regular intervals, the distribution of the prevalence an epidemic will have reached on first discovery (discovery-prevalence) and its expectation E(q*). We show that E(q*) = r/(N/Δ), i.e. simply the rate of epidemic growth divided by the rate of sampling; where r is the epidemic growth rate, N is the sample size and Δ is the time between sampling rounds. We demonstrate the robustness of this rule of thumb using spatio-temporal epidemic models as well as data from real epidemics. Our work supports the view that, for the purposes of early detection surveillance, simple models can provide useful insights in apparently complex systems. The insight can inform decisions on surveillance resource allocation in plant health and has potential applicability to invasive species generally. PMID:26336177

Whole genome sequencing may not be adequate to determine genome relatedness for surveillance and outbreak investigation of foodborne pathogens

USDA-ARS?s Scientific Manuscript database

Introduction: Advances in genomic technologies have improve the speed and precision of foodborne disease outbreak detection and response. For the past two decades, pulsed field gel electrophoresis (PFGE) has been the method of choice for surveillance and outbreak investigation with foodborne pathoge...

Toward Decentralized Agrigenomic Surveillance? A Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Approach for Adaptable and Rapid Detection of User-Defined Fungal Pathogens in Potato Crops.

PubMed

Kambouris, Manousos E; Manoussopoulos, Yiannis; Kritikou, Stavroula; Milioni, Aphroditi; Mantzoukas, Spyridon; Velegraki, Aristea

2018-04-01

Agrigenomics is one of the emerging focus areas for omics sciences. Yet, agrigenomics differs from medical omics applications such as pharmacogenomics and precision medicine, by virtue of vastly distributed geography of applications at the intersection of agriculture, nutrition, and genomics research streams. Crucially, agrigenomics can address diagnostics and safety surveillance needs in remote and rural farming communities or decentralized food, crop, and environmental monitoring programs for prompt, selective, and differential identification of pathogens. A case in point is the potato crop that serves as a fundamental nutritional source worldwide. Decentralized potato crop and plant protection facilities are pivotal to minimize unnecessary, preemptive use of broad-spectrum fungicides, thus helping to curtail the costs, environmental burden, and the development of resistance in opportunistic human pathogenic fungi. We report here a polymerase chain reaction-restriction fragment length polymorphism approach that is sensitive and adaptable in detection and broad identification of fungal pathogens in potato crops, with a view to future decentralized agrigenomic surveillance programs. Notably, the fingerprinting patterns obtained by the method fully differentiated 12 fungal species examined in silico, with 10 of them also tested in vitro. The method can be scaled up through improvements in electrophoresis and enzyme panel for adaption to other crops and/or pathogens. We suggest that decentralized and integrated agrosurveillance programs and translational agrigenomic programs can inform future innovations in multidomain biosecurity, particularly across omics applications from agriculture and nutrition to clinical medicine and environmental biosafety.

Efficient surveillance for healthcare-associated infections spreading between hospitals

PubMed Central

Ciccolini, Mariano; Donker, Tjibbe; Grundmann, Hajo; Bonten, Marc J. M.; Woolhouse, Mark E. J.

2014-01-01

Early detection of new or novel variants of nosocomial pathogens is a public health priority. We show that, for healthcare-associated infections that spread between hospitals as a result of patient movements, it is possible to design an effective surveillance system based on a relatively small number of sentinel hospitals. We apply recently developed mathematical models to patient admission data from the national healthcare systems of England and The Netherlands. Relatively short detection times are achieved once 10–20% hospitals are recruited as sentinels and only modest reductions are seen as more hospitals are recruited thereafter. Using a heuristic optimization approach to sentinel selection, the same expected time to detection can be achieved by recruiting approximately half as many hospitals. Our study provides a robust evidence base to underpin the design of an efficient sentinel hospital surveillance system for novel nosocomial pathogens, delivering early detection times for reduced expenditure and effort. PMID:24469791

The Evolution of Foodborne Pathogens

NASA Astrophysics Data System (ADS)

Abu-Ali, Galeb S.; Manning, Shannon D.

Despite continuous advances in food safety and disease surveillance, control, and prevention, foodborne bacterial infections remain a major public health concern. Because foodborne pathogens are commonly exposed to multiple environmental stressors, such as low pH and antibiotics, most have evolved specific mechanisms to facilitate survival in adverse environments.

Countering a Bioterrorist Introduction of Pathogen-Infected Mosquitoes through Mosquito Control

USDA-ARS?s Scientific Manuscript database

A workshop titled “Counteracting Bioterrorist Introduction of Pathogen-Infected Vector Mosquitoes” was held in Gainesville, Florida on May 20-22, 2010 to discuss (1) disease and vector surveillance, (2) pre-bioterrorist attack preparations, (3) actions during an ongoing bioterrorist attack, and (4) ...

Migratory and adhesive cues controlling innate-like lymphocyte surveillance of the pathogen-exposed surface of the lymph node

PubMed Central

Zhang, Yang; Roth, Theodore L; Gray, Elizabeth E; Chen, Hsin; Rodda, Lauren B; Liang, Yin; Ventura, Patrick; Villeda, Saul; Crocker, Paul R; Cyster, Jason G

2016-01-01

Lymph nodes (LNs) contain innate-like lymphocytes that survey the subcapsular sinus (SCS) and associated macrophages for pathogen entry. The factors promoting this surveillance behavior have not been defined. Here, we report that IL7RhiCcr6+ lymphocytes in mouse LNs rapidly produce IL17 upon bacterial and fungal challenge. We show that these innate-like lymphocytes are mostly LN resident. Ccr6 is required for their accumulation near the SCS and for efficient IL17 induction. Migration into the SCS intrinsically requires S1pr1, whereas movement from the sinus into the parenchyma involves the integrin LFA1 and its ligand ICAM1. CD169, a sialic acid-binding lectin, helps retain the cells within the sinus, preventing their loss in lymph flow. These findings establish a role for Ccr6 in augmenting innate-like lymphocyte responses to lymph-borne pathogens, and they define requirements for cell movement between parenchyma and SCS in what we speculate is a program of immune surveillance that helps achieve LN barrier immunity. DOI: http://dx.doi.org/10.7554/eLife.18156.001 PMID:27487469

Deep sequencing of H7N8 avian influenza viruses from surveillance zone supports H7N8 high pathogenicity avian influenza was limited to a single outbreak farm in Indiana during 2016.

PubMed

Lee, Dong-Hun; Torchetti, Mia Kim; Killian, Mary Lea; Swayne, David E

2017-07-01

In mid-January 2016, an outbreak of H7N8 high-pathogenicity avian influenza virus (HPAIV) in commercial turkeys occurred in Indiana. Surveillance within the 10km control zone identified H7N8 low-pathogenicity avian influenza virus (LPAIV) in nine surrounding turkey flocks but no other HPAIV-affected premises. We sequenced four of the H7N8 HPAIV isolated from the single farm and nine LPAIV identified during control zone surveillance. Evaluation included phylogenetic network analysis indicating close relatedness across the HPAIV and LPAIV, and that the progenitor H7N8 LPAIV spread among the affected turkey farms in Indiana, followed by spontaneous mutation to HPAIV on a single premise through acquisition of three basic amino acids at the hemagglutinin cleavage site. Deep sequencing of the available viruses failed to identify subpopulations in either the HPAIV or LPAIV suggesting mutation to HPAIV likely occurred on a single farm and the HPAIV did not spread to epidemiologically linked LPAIV-affected farms. Published by Elsevier Inc.

Viral etiology, seasonality and severity of hospitalized patients with severe acute respiratory infections in the Eastern Mediterranean Region, 2007–2014

PubMed Central

Dueger, Erica L.; Kandeel, Amr; Abdallat, Mohamed; El-Kholy, Amani; Al-Awaidy, Salah; Kohlani, Abdul Hakim; Amer, Hanaa; El-Khal, Abel Latif; Said, Mayar; House, Brent; Pimentel, Guillermo; Talaat, Maha

2017-01-01

Introduction Little is known about the role of viral respiratory pathogens in the etiology, seasonality or severity of severe acute respiratory infections (SARI) in the Eastern Mediterranean Region. Methods Sentinel surveillance for SARI was conducted from December 2007 through February 2014 at 20 hospitals in Egypt, Jordan, Oman, Qatar and Yemen. Nasopharyngeal and oropharyngeal swabs were collected from hospitalized patients meeting SARI case definitions and were analyzed for infection with influenza, respiratory syncytial virus (RSV), adenovirus (AdV), human metapneumovirus (hMPV) and human parainfluenza virus types 1–3 (hPIV1-3). We analyzed surveillance data to calculate positivity rates for viral respiratory pathogens, describe the seasonality of those pathogens and determine which pathogens were responsible for more severe outcomes requiring ventilation and/or intensive care and/or resulting in death. Results At least one viral respiratory pathogen was detected in 8,753/28,508 (30.7%) samples tested for at least one pathogen and 3,497/9,315 (37.5%) of samples tested for all pathogens–influenza in 3,345/28,438 (11.8%), RSV in 3,942/24,503 (16.1%), AdV in 923/9,402 (9.8%), hMPV in 617/9,384 (6.6%), hPIV1 in 159/9,402 (1.7%), hPIV2 in 85/9,402 (0.9%) and hPIV3 in 365/9,402 (3.9%). Multiple pathogens were identified in 501/9,316 (5.4%) participants tested for all pathogens. Monthly variation, indicating seasonal differences in levels of infection, was observed for all pathogens. Participants with hMPV infections and participants less than five years of age were significantly less likely than participants not infected with hMPV and those older than five years of age, respectively, to experience a severe outcome, while participants with a pre-existing chronic disease were at increased risk of a severe outcome, compared to those with no reported pre-existing chronic disease. Conclusions Viral respiratory pathogens are common among SARI patients in the Eastern Mediterranean Region. Ongoing surveillance is important to monitor changes in the etiology, seasonality and severity of pathogens of interest. PMID:28704440

Early detection for cases of enterovirus- and influenza-like illness through a newly established school-based syndromic surveillance system in Taipei, January 2010 ~ August 2011.

PubMed

Weng, Ting Chia; Chan, Ta Chien; Lin, Hsien Tang; Chang, Chia Kun Jasper; Wang, Wen Wen; Li, Zheng Rong Tiger; Cheng, Hao-Yuan; Chu, Yu-Roo; Chiu, Allen Wen-Hsiang; Yen, Muh-Yong; King, Chwan-Chuen

2015-01-01

School children may transmit pathogens with cluster cases occurring on campuses and in families. In response to the 2009 influenza A (H1N1) pandemic, Taipei City Government officials developed a School-based Infectious Disease Syndromic Surveillance System (SID-SSS). Teachers and nurses from preschools to universities in all 12 districts within Taipei are required to daily report cases of symptomatic children or sick leave requests through the SID-SSS. The pre-diagnosis at schools is submitted firstly as common pediatric disease syndrome-groups and re-submitted after confirmation by physicians. We retrieved these data from January 2010 to August 2011 for spatio-temporal analysis and evaluated the temporal trends with cases obtained from both the Emergency Department-based Syndromic Surveillance System (ED-SSS) and the Longitudinal Health Insurance Database 2005 (LHID2005). Through the SID-SSS, enterovirus-like illness (EVI) and influenza-like illness (ILI) were the two most reported syndrome groups (77.6% and 15.8% among a total of 19,334 cases, respectively). The pre-diagnosis judgments made by school teachers and nurses showed high consistency with physicians' clinical diagnoses for EVI (97.8%) and ILI (98.9%). Most importantly, the SID-SSS had better timeliness with earlier peaks of EVI and ILI than those in the ED-SSS. Furthermore, both of the syndrome groups in these two surveillance systems had the best correlation reaching 0.98 and 0.95, respectively (p<0.01). Spatio-temporal analysis observed the patterns of EVI and ILI both diffuse from the northern suburban districts to central Taipei, with ILI spreading faster. This novel system can identify early suspected cases of two important pediatric infections occurring at schools, and clusters from schools/families. It was also cost-effective (95.5% of the operation cost reduced and 59.7% processing time saved). The timely surveillance of mild EVI and ILI cases integrated with spatial analysis may help public health decision-makers with where to target for enhancing surveillance and prevention measures to minimize severe cases.

Early Detection for Cases of Enterovirus- and Influenza-Like Illness through a Newly Established School-Based Syndromic Surveillance System in Taipei, January 2010 ~ August 2011

PubMed Central

Weng, Ting Chia; Chan, Ta Chien; Li, Zheng Rong Tiger; Cheng, Hao-Yuan; Chu, Yu-Roo; Chiu, Allen Wen-Hsiang; Yen, Muh-Yong; King, Chwan-Chuen

2015-01-01

School children may transmit pathogens with cluster cases occurring on campuses and in families. In response to the 2009 influenza A (H1N1) pandemic, Taipei City Government officials developed a School-based Infectious Disease Syndromic Surveillance System (SID-SSS). Teachers and nurses from preschools to universities in all 12 districts within Taipei are required to daily report cases of symptomatic children or sick leave requests through the SID-SSS. The pre-diagnosis at schools is submitted firstly as common pediatric disease syndrome-groups and re-submitted after confirmation by physicians. We retrieved these data from January 2010 to August 2011 for spatio-temporal analysis and evaluated the temporal trends with cases obtained from both the Emergency Department-based Syndromic Surveillance System (ED-SSS) and the Longitudinal Health Insurance Database 2005 (LHID2005). Through the SID-SSS, enterovirus-like illness (EVI) and influenza-like illness (ILI) were the two most reported syndrome groups (77.6% and 15.8% among a total of 19,334 cases, respectively). The pre-diagnosis judgments made by school teachers and nurses showed high consistency with physicians’ clinical diagnoses for EVI (97.8%) and ILI (98.9%). Most importantly, the SID-SSS had better timeliness with earlier peaks of EVI and ILI than those in the ED-SSS. Furthermore, both of the syndrome groups in these two surveillance systems had the best correlation reaching 0.98 and 0.95, respectively (p<0.01). Spatio-temporal analysis observed the patterns of EVI and ILI both diffuse from the northern suburban districts to central Taipei, with ILI spreading faster. This novel system can identify early suspected cases of two important pediatric infections occurring at schools, and clusters from schools/families. It was also cost-effective (95.5% of the operation cost reduced and 59.7% processing time saved). The timely surveillance of mild EVI and ILI cases integrated with spatial analysis may help public health decision-makers with where to target for enhancing surveillance and prevention measures to minimize severe cases. PMID:25875080

Low pathogenic avian influenza viruses in wild migratory waterfowl in a region of high poultry production, Delmarva, Maryland

USGS Publications Warehouse

Prosser, Diann J.; Densmore, Christine L.; Hindman, Larry J.; Iwanowicz, Deborah; Ottinger, Christopher A.; Iwanowicz, Luke R.; Driscoll, Cindy P.; Nagel, Jessica L.

2017-01-01

Migratory waterfowl are natural reservoirs for low pathogenic avian influenza viruses (AIVs) and may contribute to the long-distance dispersal of these pathogens as well as spillover into domestic bird populations. Surveillance for AIVs is critical to assessing risks for potential spread of these viruses among wild and domestic bird populations. The Delmarva Peninsula on the east coast of the United States is both a key convergence point for migratory Atlantic waterfowl populations and a region with high poultry production (>4,700 poultry meat facilities). Sampling of key migratory waterfowl species occurred at 20 locations throughout the Delmarva Peninsula in fall and winter of 2013–14. Samples were collected from 400 hunter-harvested or live-caught birds via cloacal and oropharyngeal swabs. Fourteen of the 400 (3.5%) birds sampled tested positive for the AIV matrix gene using real-time reverse transcriptase PCR, all from five dabbling duck species. Further characterization of the 14 viral isolates identified two hemagglutinin (H3 and H4) and four neuraminidase (N2, N6, N8, and N9) subtypes, which were consistent with isolates reported in the Influenza Research Database for this region. Three of 14 isolates contained multiple HA or NA subtypes. This study adds to the limited baseline information available for AIVs in migratory waterfowl populations on the Delmarva Peninsula, particularly prior to the highly pathogenic AIV A(H5N8) and A(H5N2) introductions to the United States in late 2014.

Low Pathogenic Avian Influenza Viruses in Wild Migratory Waterfowl in a Region of High Poultry Production, Delmarva, Maryland.

PubMed

Prosser, Diann J; Densmore, Christine L; Hindman, Larry J; Iwanowicz, Deborah D; Ottinger, Chris A; Iwanowicz, Luke R; Driscoll, Cindy P; Nagel, Jessica L

2017-03-01

Migratory waterfowl are natural reservoirs for low pathogenic avian influenza viruses (AIVs) and may contribute to the long-distance dispersal of these pathogens as well as spillover into domestic bird populations. Surveillance for AIVs is critical to assessing risks for potential spread of these viruses among wild and domestic bird populations. The Delmarva Peninsula on the east coast of the United States is both a key convergence point for migratory Atlantic waterfowl populations and a region with high poultry production (>4,700 poultry meat facilities). Sampling of key migratory waterfowl species occurred at 20 locations throughout the Delmarva Peninsula in fall and winter of 2013-14. Samples were collected from 400 hunter-harvested or live-caught birds via cloacal and oropharyngeal swabs. Fourteen of the 400 (3.5%) birds sampled tested positive for the AIV matrix gene using real-time reverse transcriptase PCR, all from five dabbling duck species. Further characterization of the 14 viral isolates identified two hemagglutinin (H3 and H4) and four neuraminidase (N2, N6, N8, and N9) subtypes, which were consistent with isolates reported in the Influenza Research Database for this region. Three of 14 isolates contained multiple HA or NA subtypes. This study adds to the limited baseline information available for AIVs in migratory waterfowl populations on the Delmarva Peninsula, particularly prior to the highly pathogenic AIV A(H5N8) and A(H5N2) introductions to the United States in late 2014.

Low‐pathogenic notifiable avian influenza serosurveillance and the risk of infection in poultry – a critical review of the European Union active surveillance programme (2005–2007)

PubMed Central

Gonzales, J. L.; Elbers, A. R. W.; Bouma, A.; Koch, G.; De Wit, J. J.; Stegeman, J. A.

2010-01-01

Please cite this paper as: Gonzales et al. (2010) Low‐pathogenic notifiable avian influenza serosurveillance and the risk of infection in poultry – a critical review of the European Union active surveillance programme (2005–2007). Influenza and Other Respiratory Viruses 4(2), 91–99. Background  Since 2003, Member States (MS) of the European Union (EU) have implemented serosurveillance programmes for low pathogenic notifiable avian influenza (LPNAI) in poultry. To date, there is the need to evaluate the surveillance activity in order to optimize the programme’s surveillance design. Objectives  To evaluate MS sampling operations [sample size and targeted poultry types (PTs)] and its relation with the probability of detection and to estimate the PTs relative risk (RR) of being infected. Methods  Reported data of the surveillance carried out from 2005 to 2007 were analyzed using: (i) descriptive indicators to characterize both MS sampling operations and its relation with the probability of detection and the LPNAI epidemiological situation, and (ii) multivariable methods to estimate each PTs RR of being infected. Results  Member States sampling a higher sample size than that recommended by the EU had a significantly higher probability of detection. Poultry types with ducks & geese, game‐birds, ratites and “others” had a significant higher RR of being seropositive than chicken categories. The seroprevalence in duck & geese and game‐bird holdings appears to be higher than 5%, which is the EU‐recommended design prevalence (DP), while in chicken and turkey categories the seroprevalence was considerably lower than 5% and with that there is the risk of missing LPNAI seropositive holdings. Conclusion  It is recommended that the European Commission discusses with its MS whether the results of our evaluation calls for refinement of the surveillance characteristics such as sampling frequency, the between‐holding DP and MS sampling operation strategies. PMID:20167049

Mosquito Surveillance for Prevention and Control of Emerging Mosquito-Borne Diseases in Portugal — 2008–2014

PubMed Central

Osório, Hugo C.; Zé-Zé, Líbia; Amaro, Fátima; Alves, Maria J.

2014-01-01

Mosquito surveillance in Europe is essential for early detection of invasive species with public health importance and prevention and control of emerging pathogens. In Portugal, a vector surveillance national program—REVIVE (REde de VIgilância de VEctores)—has been operating since 2008 under the custody of Portuguese Ministry of Health. The REVIVE is responsible for the nationwide surveillance of hematophagous arthropods. Surveillance for West Nile virus (WNV) and other flaviviruses in adult mosquitoes is continuously performed. Adult mosquitoes—collected mainly with Centre for Disease Control light traps baited with CO2—and larvae were systematically collected from a wide range of habitats in 20 subregions (NUTS III). Around 500,000 mosquitoes were trapped in more than 3,000 trap nights and 3,500 positive larvae surveys, in which 24 species were recorded. The viral activity detected in mosquito populations in these years has been limited to insect specific flaviviruses (ISFs) non-pathogenic to humans. Rather than emergency response, REVIVE allows timely detection of changes in abundance and species diversity providing valuable knowledge to health authorities, which may take control measures of vector populations reducing its impact on public health. This work aims to present the REVIVE operation and to expose data regarding mosquito species composition and detected ISFs. PMID:25396768

An enrichment, amplification, and sequence-based typing (EAST) approach for foodborne pathogen detection and surveillance

USDA-ARS?s Scientific Manuscript database

Introduction: Detection of foodborne pathogens typically involves microbiological enrichment with subsequent isolation and identification of a pure culture. This is typically followed by strain typing, which provides information critical to outbreak and source investigations. In the early 1990’s pul...

DEFENSE MEDICAL SURVEILLANCE SYSTEM (DMSS)

EPA Science Inventory

AMSA operates the Defense Medical Surveillance System (DMSS), an executive information system whose database contains up-to-date and historical data on diseases and medical events (e.g., hospitalizations, ambulatory visits, reportable diseases, HIV tests, acute respiratory diseas...

Travel-associated salmonella and campylobacter gastroenteritis in England: estimation of under-ascertainment through national laboratory surveillance.

PubMed

Zenner, Dominik; Gillespie, Iain

2011-01-01

Increased international travel raises the importance of accurate surveillance of travel-associated gastroenteric pathogens to improve treatment and the investigation of cross-border outbreaks. This study found that 45% of Salmonella and 17% of Campylobacter infections in England were travel-associated, but only 29 and 3% of travel histories were accurately identified by national laboratory surveillance. More structured data collection forms and staff training may be needed to address this. © 2011 International Society of Travel Medicine.

Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis.

PubMed

Wyrsch, Ethan R; Roy Chowdhury, Piklu; Chapman, Toni A; Charles, Ian G; Hammond, Jeffrey M; Djordjevic, Steven P

2016-01-01

Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.

Avian Influenza Vaccination of Poultry and Passive Case Reporting, Egypt

PubMed Central

Grosbois, Vladimir; Jobre, Yilma; Saad, Ahmed; El Nabi, Amira Abd; Galal, Shereen; Kalifa, Mohamed; El Kader, Soheir Abd; Dauphin, Gwenaëlle; Roger, François; Lubroth, Juan; Peyre, Marisa

2012-01-01

We investigated the influence of a mass poultry vaccination campaign on passive surveillance of highly pathogenic avian influenza subtype (H5N1) outbreaks among poultry in Egypt. Passive reporting dropped during the campaign, although probability of infection remained unchanged. Future poultry vaccination campaigns should consider this negative impact on reporting for adapting surveillance strategies. PMID:23171740

Assessing human risk of illness with West Nile virus mosquito surveillance data to improve public health preparedness

USDA-ARS?s Scientific Manuscript database

Surveillance for West Nile virus (WNV) and other mosquito-borne pathogens involves costly and time-consuming collection and testing of mosquito samples. One difficulty faced by public health personnel is how to interpret mosquito data relative to human risk, thus leading to a failure to fully exploi...

Recent Advances in Understanding Enteric Pathogenic Escherichia coli

PubMed Central

Croxen, Matthew A.; Law, Robyn J.; Scholz, Roland; Keeney, Kristie M.; Wlodarska, Marta

2013-01-01

SUMMARY Although Escherichia coli can be an innocuous resident of the gastrointestinal tract, it also has the pathogenic capacity to cause significant diarrheal and extraintestinal diseases. Pathogenic variants of E. coli (pathovars or pathotypes) cause much morbidity and mortality worldwide. Consequently, pathogenic E. coli is widely studied in humans, animals, food, and the environment. While there are many common features that these pathotypes employ to colonize the intestinal mucosa and cause disease, the course, onset, and complications vary significantly. Outbreaks are common in developed and developing countries, and they sometimes have fatal consequences. Many of these pathotypes are a major public health concern as they have low infectious doses and are transmitted through ubiquitous mediums, including food and water. The seriousness of pathogenic E. coli is exemplified by dedicated national and international surveillance programs that monitor and track outbreaks; unfortunately, this surveillance is often lacking in developing countries. While not all pathotypes carry the same public health profile, they all carry an enormous potential to cause disease and continue to present challenges to human health. This comprehensive review highlights recent advances in our understanding of the intestinal pathotypes of E. coli. PMID:24092857

Inactivation of conserved genes induces microbial aversion, drug detoxification, and innate immunity in C.elegans

PubMed Central

Melo, Justine A.; Ruvkun, Gary

2012-01-01

Summary The nematode C. elegans consumes benign bacteria such as E. coli and is repelled by pathogens and toxins. Here we show that RNAi and toxin-mediated disruption of core cellular activities, including translation, respiration, and protein turnover, stimulates behavioral avoidance of attractive E. coli. RNAi of such essential processes also induces expression of detoxification and innate immune response genes in the absence of toxins or pathogens. Disruption of core processes in non-neuronal tissues can stimulate aversion behavior, revealing a neuroendocrine axis of control. Microbial avoidance requires serotonergic and Jnk kinase signaling. We propose that surveillance pathways oversee critical cellular activities to detect pathogens, many of which deploy toxins and virulence factors to disrupt these same host pathways. Variation in cellular surveillance and endocrine pathways controlling behavior, detoxification and immunity selected by past toxin or microbial interactions could underlie aberrant responses to foods, medicines, and microbes. PMID:22500807

Conceptualising the technical relationship of animal disease surveillance to intervention and mitigation as a basis for economic analysis

PubMed Central

2011-01-01

Background Surveillance and intervention are resource-using activities of strategies to mitigate the unwanted effects of disease. Resources are scarce, and allocating them to disease mitigation instead of other uses necessarily involves the loss of alternative sources of benefit to people. For society to obtain the maximum benefits from using resources, the gains from disease mitigation must be compared to the resource costs, guiding decisions made with the objective of achieving the optimal net outcome. Discussion Economics provides criteria to guide decisions aimed at optimising the net benefits from the use of scarce resources. Assessing the benefits of disease mitigation is no exception. However, the technical complexity of mitigation means that economic evaluation is not straightforward because of the technical relationship of surveillance to intervention. We argue that analysis of the magnitudes and distribution of benefits and costs for any given strategy, and hence the outcome in net terms, requires that mitigation is considered in three conceptually distinct stages. In Stage I, 'sustainment', the mitigation objective is to sustain a free or acceptable status by preventing an increase of a pathogen or eliminating it when it occurs. The role of surveillance is to document that the pathogen remains below a defined threshold, giving early warning of an increase in incidence or other significant changes in risk, and enabling early response. If a pathogen is not contained, the situation needs to be assessed as Stage II, 'investigation'. Here, surveillance obtains critical epidemiological information to decide on the appropriate intervention strategy to reduce or eradicate a disease in Stage III, 'implementation'. Stage III surveillance informs the choice, timing, and scale of interventions and documents the progress of interventions directed at prevalence reduction in the population. Summary This article originates from a research project to develop a conceptual framework and practical tool for the economic evaluation of surveillance. Exploring the technical relationship between mitigation as a source of economic value and surveillance and intervention as sources of economic cost is crucial. A framework linking the key technical relationships is proposed. Three conceptually distinct stages of mitigation are identified. Avian influenza, salmonella, and foot and mouth disease are presented to illustrate the framework. PMID:21929812

The Clinical Next-Generation Sequencing Database: A Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification.

PubMed

Nishio, Shin-Ya; Usami, Shin-Ichi

2017-03-01

Recent advances in next-generation sequencing (NGS) have given rise to new challenges due to the difficulties in variant pathogenicity interpretation and large dataset management, including many kinds of public population databases as well as public or commercial disease-specific databases. Here, we report a new database development tool, named the "Clinical NGS Database," for improving clinical NGS workflow through the unified management of variant information and clinical information. This database software offers a two-feature approach to variant pathogenicity classification. The first of these approaches is a phenotype similarity-based approach. This database allows the easy comparison of the detailed phenotype of each patient with the average phenotype of the same gene mutation at the variant or gene level. It is also possible to browse patients with the same gene mutation quickly. The other approach is a statistical approach to variant pathogenicity classification based on the use of the odds ratio for comparisons between the case and the control for each inheritance mode (families with apparently autosomal dominant inheritance vs. control, and families with apparently autosomal recessive inheritance vs. control). A number of case studies are also presented to illustrate the utility of this database. © 2016 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

Surveillance of wild birds for avian influenza virus.

PubMed

Hoye, Bethany J; Munster, Vincent J; Nishiura, Hiroshi; Klaassen, Marcel; Fouchier, Ron A M

2010-12-01

Recent demand for increased understanding of avian influenza virus in its natural hosts, together with the development of high-throughput diagnostics, has heralded a new era in wildlife disease surveillance. However, survey design, sampling, and interpretation in the context of host populations still present major challenges. We critically reviewed current surveillance to distill a series of considerations pertinent to avian influenza virus surveillance in wild birds, including consideration of what, when, where, and how many to sample in the context of survey objectives. Recognizing that wildlife disease surveillance is logistically and financially constrained, we discuss pragmatic alternatives for achieving probability-based sampling schemes that capture this host-pathogen system. We recommend hypothesis-driven surveillance through standardized, local surveys that are, in turn, strategically compiled over broad geographic areas. Rethinking the use of existing surveillance infrastructure can thereby greatly enhance our global understanding of avian influenza and other zoonotic diseases.

Xenosurveillance: A Novel Mosquito-Based Approach for Examining the Human-Pathogen Landscape

PubMed Central

Grubaugh, Nathan D.; Sharma, Supriya; Krajacich, Benjamin J.; Fakoli III, Lawrence S.; Bolay, Fatorma K.; Diclaro II, Joe W.; Johnson, W. Evan; Ebel, Gregory D.; Foy, Brian D.; Brackney, Doug E.

2015-01-01

Background Globally, regions at the highest risk for emerging infectious diseases are often the ones with the fewest resources. As a result, implementing sustainable infectious disease surveillance systems in these regions is challenging. The cost of these programs and difficulties associated with collecting, storing and transporting relevant samples have hindered them in the regions where they are most needed. Therefore, we tested the sensitivity and feasibility of a novel surveillance technique called xenosurveillance. This approach utilizes the host feeding preferences and behaviors of Anopheles gambiae, which are highly anthropophilic and rest indoors after feeding, to sample viruses in human beings. We hypothesized that mosquito bloodmeals could be used to detect vertebrate viral pathogens within realistic field collection timeframes and clinically relevant concentrations. Methodology/Principal Findings To validate this approach, we examined variables influencing virus detection such as the duration between mosquito blood feeding and mosquito processing, the pathogen nucleic acid stability in the mosquito gut and the pathogen load present in the host’s blood at the time of bloodmeal ingestion using our laboratory model. Our findings revealed that viral nucleic acids, at clinically relevant concentrations, could be detected from engorged mosquitoes for up to 24 hours post feeding by qRT-PCR. Subsequently, we tested this approach in the field by examining blood from engorged mosquitoes from two field sites in Liberia. Using next-generation sequencing and PCR we were able to detect the genetic signatures of multiple viral pathogens including Epstein-Barr virus and canine distemper virus. Conclusions/Significance Together, these data demonstrate the feasibility of xenosurveillance and in doing so validated a simple and non-invasive surveillance tool that could be used to complement current biosurveillance efforts. PMID:25775236

Estimating transmission of avian influenza in wild birds from incomplete epizootic data: implications for surveillance and disease spreac

USGS Publications Warehouse

Henaux, Viviane; Jane Parmley,; Catherine Soos,; Samuel, Michael D.

2013-01-01

Synthesis and applications. Our study highlights the potential of integrating incomplete surveillance data with epizootic models to quantify disease transmission and immunity. This modelling approach provides an important tool to understand spatial and temporal epizootic dynamics and inform disease surveillance. Our findings suggest focusing highly pathogenic avian influenza virus (HPAIv) surveillance on postbreeding areas where mortality of immunologically naïve hatch-year birds is most likely to occur, and collecting serology to enhance HPAIv detection. Our modelling approach can integrate various types of disease data facilitating its use with data from other surveillance programs (as illustrated by the estimation of infection rate during an HPAIv outbreak in mute swansCygnus olor in Europe).

Methicillin-resistant Staphylococcus aureus (MRSA) in Iran: A systematic review and meta-analysis.

PubMed

Dadashi, Masoud; Nasiri, Mohammad Javad; Fallah, Fatemeh; Owlia, Parviz; Hajikhani, Bahareh; Emaneini, Mohammad; Mirpour, Mirsasan

2018-03-01

Methicillin-resistant Staphylococcus aureus (MRSA) is among the most prevalent pathogens causing healthcare-associated infections. Accurate and updated data describing the epidemiology of MRSA are crucial for the development of national policies to control MRSA infection in each country. This study aimed to estimate the prevalence of MRSA in different parts of Iran. Several databases, including MEDLINE, Embase, Web of Science and Scientific Information Database (http://www.sid.ir), were searched from 1 January 2000 to 31 March 2016 to identify studies addressing the frequency or prevalence of MRSA in Iran. Comprehensive Meta-Analysis software v.2.2 was used to analyse the data. Of the 725 records identified from the databases, 31 studies fulfilled the eligibility criteria. The analyses showed that the frequency of MRSA infections was 43.0% (95% confidence interval 36.3-50.0%) among confirmed S. aureus isolates. Further stratified analyses indicated that the prevalence of MRSA was higher in studies performed after the year 2000. Since a high rate of MRSA infections was seen in this analysis, regular surveillance of hospital-associated infections, monitoring of antibiotic sensitivity patterns, and formulation of definite antibiotic policy may facilitate more accurate action for the prevention and control of MRSA. Copyright © 2017 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

Evolution of the Sabin vaccine into pathogenic derivatives without appreciable changes in antigenic properties: need for improvement of current poliovirus surveillance.

PubMed

Yakovenko, Maria L; Korotkova, Ekaterina A; Ivanova, Olga E; Eremeeva, Tatyana P; Samoilovich, Elena; Uhova, Iryna; Gavrilin, Gene V; Agol, Vadim I

2009-04-01

The Sabin oral polio vaccine (OPV) may evolve into pathogenic viruses, causing sporadic cases and outbreaks of poliomyelitis. Such vaccine-derived polioviruses (VDPV) generally exhibit altered antigenicity. The current paradigm to distinguish VDPV from OPV and wild polioviruses is to characterize primarily those poliovirus isolates that demonstrate deviations from OPV in antigenic and genetic intratypic differentiation (ITD) tests. Here we report on two independent cases of poliomyelitis caused by VDPVs with "Sabin-like" properties in several ITD assays. The results suggest the existence of diverse pathways of OPV evolution and necessitate improvement of poliovirus surveillance, which currently potentially misses this class of VDPV.

Comparative population genomics of fusarium graminearum reveals adaptive divergence among cereal head blight pathogens

USDA-ARS?s Scientific Manuscript database

During the last decade, a combination of molecular surveillance and population genetic analyses have significantly altered our understanding of Fusarium graminearum, the major FHB pathogen in North America. In addition to the native NA1 population (largely 15ADON toxin type) and the invasive NA2 pop...

Microbial profiling, neural network and semantic web: an integrated information system for human pathogen risk management, prevention and surveillance in food safety

USDA-ARS?s Scientific Manuscript database

It is estimated that food-borne pathogens cause approximately 76 million cases of gastrointestinal illnesses, 325,000 hospitalizations, and 5,000 deaths in the United States annually. Genomic, proteomic, and metabolomic studies, particularly, genome sequencing projects are providing valuable inform...

Genomic Target Database (GTD): A database of potential targets in human pathogenic bacteria

PubMed Central

Barh, Debmalya; Kumar, Anil; Misra, Amarendra Narayana

2009-01-01

A Genomic Target Database (GTD) has been developed having putative genomic drug targets for human bacterial pathogens. The selected pathogens are either drug resistant or vaccines are yet to be developed against them. The drug targets have been identified using subtractive genomics approaches and these are subsequently classified into Drug targets in pathogen specific unique metabolic pathways,Drug targets in host-pathogen common metabolic pathways, andMembrane localized drug targets. HTML code is used to link each target to its various properties and other available public resources. Essential resources and tools for subtractive genomic analysis, sub-cellular localization, vaccine and drug designing are also mentioned. To the best of authors knowledge, no such database (DB) is presently available that has listed metabolic pathways and membrane specific genomic drug targets based on subtractive genomics. Listed targets in GTD are readily available resource in developing drug and vaccine against the respective pathogen, its subtypes, and other family members. Currently GTD contains 58 drug targets for four pathogens. Shortly, drug targets for six more pathogens will be listed. Availability GTD is available at IIOAB website http://www.iioab.webs.com/GTD.htm. It can also be accessed at http://www.iioabdgd.webs.com.GTD is free for academic research and non-commercial use only. Commercial use is strictly prohibited without prior permission from IIOAB. PMID:20011153

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance

PubMed Central

Rand, Hugh; Shumway, Martin; Trees, Eija K.; Simmons, Mustafa; Agarwala, Richa; Davis, Steven; Tillman, Glenn E.; Defibaugh-Chavez, Stephanie; Carleton, Heather A.; Klimke, William A.; Katz, Lee S.

2017-01-01

Background As next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional steps of ortholog determination and multi-gene alignment, instead identifying variants across a set of genomes, then summarizing results in a matrix of single-nucleotide polymorphisms or alleles for standard phylogenetic analysis. However, public health authorities need to document the performance of these methods with appropriate and comprehensive datasets so they can be validated for specific purposes, e.g., outbreak surveillance. Here we propose a set of benchmark datasets to be used for comparison and validation of phylogenomic pipelines. Methods We identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches). These are ideal benchmark datasets, as the trees, WGS data, and epidemiological data for each are all in agreement. We have placed these sequence data, sample metadata, and “known” phylogenetic trees in publicly-accessible databases and developed a standard descriptive spreadsheet format describing each dataset. To facilitate easy downloading of these benchmarks, we developed an automated script that uses the standard descriptive spreadsheet format. Results Our “outbreak” benchmark datasets represent the four major foodborne bacterial pathogens (Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni) and one simulated dataset where the “known tree” can be accurately called the “true tree”. The downloading script and associated table files are available on GitHub: https://github.com/WGS-standards-and-analysis/datasets. Discussion These five benchmark datasets will help standardize comparison of current and future phylogenomic pipelines, and facilitate important cross-institutional collaborations. Our work is part of a global effort to provide collaborative infrastructure for sequence data and analytic tools—we welcome additional benchmark datasets in our recommended format, and, if relevant, we will add these on our GitHub site. Together, these datasets, dataset format, and the underlying GitHub infrastructure present a recommended path for worldwide standardization of phylogenomic pipelines. PMID:29372115

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance.

PubMed

Timme, Ruth E; Rand, Hugh; Shumway, Martin; Trees, Eija K; Simmons, Mustafa; Agarwala, Richa; Davis, Steven; Tillman, Glenn E; Defibaugh-Chavez, Stephanie; Carleton, Heather A; Klimke, William A; Katz, Lee S

2017-01-01

As next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional steps of ortholog determination and multi-gene alignment, instead identifying variants across a set of genomes, then summarizing results in a matrix of single-nucleotide polymorphisms or alleles for standard phylogenetic analysis. However, public health authorities need to document the performance of these methods with appropriate and comprehensive datasets so they can be validated for specific purposes, e.g., outbreak surveillance. Here we propose a set of benchmark datasets to be used for comparison and validation of phylogenomic pipelines. We identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches). These are ideal benchmark datasets, as the trees, WGS data, and epidemiological data for each are all in agreement. We have placed these sequence data, sample metadata, and "known" phylogenetic trees in publicly-accessible databases and developed a standard descriptive spreadsheet format describing each dataset. To facilitate easy downloading of these benchmarks, we developed an automated script that uses the standard descriptive spreadsheet format. Our "outbreak" benchmark datasets represent the four major foodborne bacterial pathogens ( Listeria monocytogenes , Salmonella enterica , Escherichia coli , and Campylobacter jejuni ) and one simulated dataset where the "known tree" can be accurately called the "true tree". The downloading script and associated table files are available on GitHub: https://github.com/WGS-standards-and-analysis/datasets. These five benchmark datasets will help standardize comparison of current and future phylogenomic pipelines, and facilitate important cross-institutional collaborations. Our work is part of a global effort to provide collaborative infrastructure for sequence data and analytic tools-we welcome additional benchmark datasets in our recommended format, and, if relevant, we will add these on our GitHub site. Together, these datasets, dataset format, and the underlying GitHub infrastructure present a recommended path for worldwide standardization of phylogenomic pipelines.

Toward an open-access global database for mapping, control, and surveillance of neglected tropical diseases.

PubMed

Hürlimann, Eveline; Schur, Nadine; Boutsika, Konstantina; Stensgaard, Anna-Sofie; Laserna de Himpsl, Maiti; Ziegelbauer, Kathrin; Laizer, Nassor; Camenzind, Lukas; Di Pasquale, Aurelio; Ekpo, Uwem F; Simoonga, Christopher; Mushinge, Gabriel; Saarnak, Christopher F L; Utzinger, Jürg; Kristensen, Thomas K; Vounatsou, Penelope

2011-12-01

After many years of general neglect, interest has grown and efforts came under way for the mapping, control, surveillance, and eventual elimination of neglected tropical diseases (NTDs). Disease risk estimates are a key feature to target control interventions, and serve as a benchmark for monitoring and evaluation. What is currently missing is a georeferenced global database for NTDs providing open-access to the available survey data that is constantly updated and can be utilized by researchers and disease control managers to support other relevant stakeholders. We describe the steps taken toward the development of such a database that can be employed for spatial disease risk modeling and control of NTDs. With an emphasis on schistosomiasis in Africa, we systematically searched the literature (peer-reviewed journals and 'grey literature'), contacted Ministries of Health and research institutions in schistosomiasis-endemic countries for location-specific prevalence data and survey details (e.g., study population, year of survey and diagnostic techniques). The data were extracted, georeferenced, and stored in a MySQL database with a web interface allowing free database access and data management. At the beginning of 2011, our database contained more than 12,000 georeferenced schistosomiasis survey locations from 35 African countries available under http://www.gntd.org. Currently, the database is expanded to a global repository, including a host of other NTDs, e.g. soil-transmitted helminthiasis and leishmaniasis. An open-access, spatially explicit NTD database offers unique opportunities for disease risk modeling, targeting control interventions, disease monitoring, and surveillance. Moreover, it allows for detailed geostatistical analyses of disease distribution in space and time. With an initial focus on schistosomiasis in Africa, we demonstrate the proof-of-concept that the establishment and running of a global NTD database is feasible and should be expanded without delay.

[Active surveillance of adverse drug reaction in the era of big data: challenge and opportunity for control selection].

PubMed

Wang, S F; Zhan, S Y

2016-07-01

Electronic healthcare databases have become an important source for active surveillance of drug safety in the era of big data. The traditional epidemiology research designs are needed to confirm the association between drug use and adverse events based on these datasets, and the selection of the comparative control is essential to each design. This article aims to explain the principle and application of each type of control selection, introduce the methods and parameters for method comparison, and describe the latest achievements in the batch processing of control selection, which would provide important methodological reference for the use of electronic healthcare databases to conduct post-marketing drug safety surveillance in China.

Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections.

PubMed

McIntyre, K M; Setzkorn, C; Wardeh, M; Hepworth, P J; Radford, A D; Baylis, M

2014-10-01

What are all the species of pathogen that affect our livestock? As 6 out of every 10 human pathogens came from animals, with a good number from livestock and pets, it seems likely that the majority that emerge in the future, and which could threaten or devastate human health, will come from animals. Only 10 years ago, the first comprehensive pathogen list was compiled for humans; we still have no equivalent for animals. Here we describe the creation of a novel pathogen database, and present outputs from the database that demonstrate its value. The ENHanCEd Infectious Diseases database (EID2) is open-access and evidence-based, and it describes the pathogens of humans and animals, their host and vector species, and also their global occurrence. The EID2 systematically collates information on pathogens into a single resource using evidence from the NCBI Taxonomy database, the NCBI Nucleotide database, the NCBI MeSH (Medical Subject Headings) library and PubMed. Information about pathogens is assigned using data-mining of meta-data and semi-automated literature searches. Here we focus on 47 mammalian and avian hosts, including humans and animals commonly used in Europe as food or kept as pets. Currently, the EID2 evidence suggests that: • Within these host species, 793 (30.5%) pathogens were bacteria species, 395 (15.2%) fungi, 705 (27.1%) helminths, 372 (14.3%) protozoa and 332 (12.8%) viruses. • The odds of pathogens being emerging compared to not emerging differed by taxonomic division, and increased when pathogens had greater numbers of host species associated with them, and were zoonotic rather than non-zoonotic. • The odds of pathogens being zoonotic compared to non-zoonotic differed by taxonomic division and also increased when associated with greater host numbers. • The pathogens affecting the greatest number of hosts included: Escherichia coli, Giardia intestinalis, Toxoplasma gondii, Anaplasma phagocytophilum, Cryptosporidium parvum, Rabies virus, Staphylococcus aureus, Neospora caninum and Echinococcus granulosus. • The pathogens of humans and domestic animal hosts are characterised by 4223 interactions between pathogen and host species, with the greatest number found in: humans, sheep/goats, cattle, small mammals, pigs, dogs and equids. • The number of pathogen species varied by European country. The odds of a pathogen being found in Europe compared to the rest of the world differed by taxonomic division, and increased if they were emerging compared to not emerging, or had a larger number of host species associated with them. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

A Web Geographic Information System to share data and explorative analysis tools: The application to West Nile disease in the Mediterranean basin.

PubMed

Savini, Lara; Tora, Susanna; Di Lorenzo, Alessio; Cioci, Daniela; Monaco, Federica; Polci, Andrea; Orsini, Massimiliano; Calistri, Paolo; Conte, Annamaria

2018-01-01

In the last decades an increasing number of West Nile Disease cases was observed in equines and humans in the Mediterranean basin and surveillance systems are set up in numerous countries to manage and control the disease. The collection, storage and distribution of information on the spread of the disease becomes important for a shared intervention and control strategy. To this end, a Web Geographic Information System has been developed and disease data, climatic and environmental remote sensed data, full genome sequences of selected isolated strains are made available. This paper describes the Disease Monitoring Dashboard (DMD) web system application, the tools available for the preliminary analysis on climatic and environmental factors and the other interactive tools for epidemiological analysis. WNV occurrence data are collected from multiple official and unofficial sources. Whole genome sequences and metadata of WNV strains are retrieved from public databases or generated in the framework of the Italian surveillance activities. Climatic and environmental data are provided by NASA website. The Geographical Information System is composed by Oracle 10g Database and ESRI ArcGIS Server 10.03; the web mapping client application is developed with the ArcGIS API for Javascript and Phylocanvas library to facilitate and optimize the mash-up approach. ESRI ArcSDE 10.1 has been used to store spatial data. The DMD application is accessible through a generic web browser at https://netmed.izs.it/networkMediterraneo/. The system collects data through on-line forms and automated procedures and visualizes data as interactive graphs, maps and tables. The spatial and temporal dynamic visualization of disease events is managed by a time slider that returns results on both map and epidemiological curve. Climatic and environmental data can be associated to cases through python procedures and downloaded as Excel files. The system compiles multiple datasets through user-friendly web tools; it integrates entomological, veterinary and human surveillance, molecular information on pathogens and environmental and climatic data. The principal result of the DMD development is the transfer and dissemination of knowledge and technologies to develop strategies for integrated prevention and control measures of animal and human diseases.

The use of animals as a surveillance tool for monitoring environmental health hazards, human health hazards and bioterrorism.

PubMed

Neo, Jacqueline Pei Shan; Tan, Boon Huan

2017-05-01

This review discusses the utilization of wild or domestic animals as surveillance tools for monitoring naturally occurring environmental and human health hazards. Besides providing early warning to natural hazards, animals can also provide early warning to societal hazards like bioterrorism. Animals are ideal surveillance tools to humans because they share the same environment as humans and spend more time outdoors than humans, increasing their exposure risk. Furthermore, the biologically compressed lifespans of some animals may allow them to develop clinical signs more rapidly after exposure to specific pathogens. Animals are an excellent channel for monitoring novel and known pathogens with outbreak potential given that more than 60 % of emerging infectious diseases in humans originate as zoonoses. This review attempts to highlight animal illnesses, deaths, biomarkers or sentinel events, to remind human and veterinary public health programs that animal health can be used to discover, monitor or predict environmental health hazards, human health hazards, or bioterrorism. Lastly, we hope that this review will encourage the implementation of animals as a surveillance tool by clinicians, veterinarians, ecosystem health professionals, researchers and governments. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Locating People Diagnosed With HIV for Public Health Action: Utility of HIV Case Surveillance and Other Data Sources.

PubMed

Padilla, Mabel; Mattson, Christine L; Scheer, Susan; Udeagu, Chi-Chi N; Buskin, Susan E; Hughes, Alison J; Jaenicke, Thomas; Wohl, Amy Rock; Prejean, Joseph; Wei, Stanley C

Human immunodeficiency virus (HIV) case surveillance and other health care databases are increasingly being used for public health action, which has the potential to optimize the health outcomes of people living with HIV (PLWH). However, often PLWH cannot be located based on the contact information available in these data sources. We assessed the accuracy of contact information for PLWH in HIV case surveillance and additional data sources and whether time since diagnosis was associated with accurate contact information in HIV case surveillance and successful contact. The Case Surveillance-Based Sampling (CSBS) project was a pilot HIV surveillance system that selected a random population-based sample of people diagnosed with HIV from HIV case surveillance registries in 5 state and metropolitan areas. From November 2012 through June 2014, CSBS staff members attempted to locate and interview 1800 sampled people and used 22 data sources to search for contact information. Among 1063 contacted PLWH, HIV case surveillance data provided accurate telephone number, address, or HIV care facility information for 239 (22%), 412 (39%), and 827 (78%) sampled people, respectively. CSBS staff members used additional data sources, such as support services and commercial people-search databases, to locate and contact PLWH with insufficient contact information in HIV case surveillance. PLWH diagnosed <1 year ago were more likely to have accurate contact information in HIV case surveillance than were PLWH diagnosed ≥1 year ago ( P = .002), and the benefit from using additional data sources was greater for PLWH with more longstanding HIV infection ( P < .001). When HIV case surveillance cannot provide accurate contact information, health departments can prioritize searching additional data sources, especially for people with more longstanding HIV infection.

Characterizing Lyme Disease Surveillance in an Endemic State.

PubMed

Rutz, H J; Wee, S B; Feldman, K A

2018-03-01

Lyme disease (LD) is the most common vector-borne disease in Maryland and the United States. Surveillance for LD is valuable for understanding the burden of the disease, particularly to assess whether the disease is spreading and to appreciate who is affected. However, not all cases of LD in Maryland are reported, and surveillance practices vary across each of Maryland's 24 local health departments (LHDs). To better understand this variability and to systematically characterize the surveillance process, we surveyed Maryland's LHDs regarding LD surveillance. The Maryland Local Health Department Lyme Disease Surveillance Survey has been administered annually since 2011. Questions asked each year included whether all LD reports are investigated or only a subset, and how many reports are not entered into the surveillance database. Since 2011, Maryland has lost surveillance personnel for LD. Each year from 2009 to 2012, a median 3598 (range 2462 to 5722) reports were not entered into the surveillance database and hence not investigated. These reports represent 43-55% of all reports received for the year. Over time, more LHDs chose to streamline their LD investigation approach by investigating only those reports that met the criteria for laboratory evidence of infection: in 2008, 5 (21%) LHDs investigated only a subset of LD reports; by 2013, this increased to 15 (63%). There is wide variability across LHDs in how LD investigations are conducted. Maryland LHDs have experienced a loss of LD surveillance personnel with a concomitant increase in the number of LHDs adopting a streamlined approach to investigating cases. These findings underscore the tremendous burden of LD on the public health agencies and highlight the need for alternative approaches that can both reduce burden and preserve surveillance data quality. © 2016 Blackwell Verlag GmbH.

Evaluating a surveillance system: live-bird market surveillance for highly pathogenic avian influenza, a case study.

PubMed

Waziri, Ndadilnasiya Endie; Nguku, Patrick; Olayinka, Adebola; Ajayi, Ike; Kabir, Junaidu; Okolocha, Emmanuel; Tseggai, Tesfai; Joannis, Tony; Okewole, Phillip; Kumbish, Peterside; Ahmed, Mohammed; Lombin, Lami; Nsubuga, Peter

2014-01-01

Highly pathogenic avian influenza H5N1 was first reported in poultry in Nigeria in February 2006. The only human case that occurred was linked to contact with poultry in a live bird market (LBM). LBM surveillance was instituted to assess the degree of threat of human exposure to H5N1. The key indicator was detection of H5N1 in LBMs. We evaluated the surveillance system to assess its operations and attributes. We used the US Centers for Disease Control and Prevention (CDC) updated guidelines for evaluating public health surveillance systems. We reviewed and analyzed passive surveillance data for HPAI (January 2006-March 2009) from the Avian Influenza National Reference Laboratory, and live bird market surveillance data from the Food and Agriculture Organization of the United Nations, Nigeria. We interviewed key stakeholders and reviewed reports of live bird market surveillance to obtain additional information on the operations of the system. We assessed the key system attributes. A total of 299 cases occurred in 25 (72%) states and the Federal Capital Territory (FCT). The system detected HPAI H5N1 virus in 7 (9.5%) LBMs; 2 (29%) of which were from 2 (18.2%) states with no previous case. A total of 17,852 (91.5%) of samples arrived at the laboratory within 24 hours but laboratory analysis took over 7 days. The sensitivity and positive predictive value (PPV) were 15.4% and 66.7% respectively. The system is useful, flexible, complex and not timely, but appears to be meeting its objectives. The isolation of HPAI H5N1 virus in some of these markets is an indication that the markets are possible reservoirs of the virus in Nigeria. We recommend that the Federal Government of Nigeria should dedicate more funds for surveillance for HPAI as this will aid early warning and reduce the risk of a pandemic.

HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens.

PubMed

Kosakovsky Pond, Sergei L; Weaver, Steven; Leigh Brown, Andrew J; Wertheim, Joel O

2018-01-31

In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters of transmission in rapidly evolving pathogens, most notably HIV-1. Traditional 'shoeleather' epidemiology infers transmission clusters by tracing chains of partners sharing epidemiological connections (e.g., sexual contact). Here, we present a computational tool for identifying a molecular transmission analog of such clusters: HIV-TRACE (TRAnsmission Cluster Engine). HIV-TRACE implements an approach inspired by traditional epidemiology, by identifying chains of partners whose viral genetic relatedness imply direct or indirect epidemiological connections. Molecular transmission clusters are constructed using codon-aware pairwise alignment to a reference sequence followed by pairwise genetic distance estimation among all sequences. This approach is computationally tractable and is capable of identifying HIV-1 transmission clusters in large surveillance databases comprising tens or hundreds of thousands of sequences in near real time, i.e., on the order of minutes to hours. HIV-TRACE is available at www.hivtrace.org and from github.com/veg/hivtrace, along with the accompanying result visualization module from github.com/veg/hivtrace-viz. Importantly, the approach underlying HIV-TRACE is not limited to the study of HIV-1 and can be applied to study outbreaks and epidemics of other rapidly evolving pathogens. © The Author 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Comparison and optimization of in silico algorithms for predicting the pathogenicity of sodium channel variants in epilepsy.

PubMed

Holland, Katherine D; Bouley, Thomas M; Horn, Paul S

2017-07-01

Variants in neuronal voltage-gated sodium channel α-subunits genes SCN1A, SCN2A, and SCN8A are common in early onset epileptic encephalopathies and other autosomal dominant childhood epilepsy syndromes. However, in clinical practice, missense variants are often classified as variants of uncertain significance when missense variants are identified but heritability cannot be determined. Genetic testing reports often include results of computational tests to estimate pathogenicity and the frequency of that variant in population-based databases. The objective of this work was to enhance clinicians' understanding of results by (1) determining how effectively computational algorithms predict epileptogenicity of sodium channel (SCN) missense variants; (2) optimizing their predictive capabilities; and (3) determining if epilepsy-associated SCN variants are present in population-based databases. This will help clinicians better understand the results of indeterminate SCN test results in people with epilepsy. Pathogenic, likely pathogenic, and benign variants in SCNs were identified using databases of sodium channel variants. Benign variants were also identified from population-based databases. Eight algorithms commonly used to predict pathogenicity were compared. In addition, logistic regression was used to determine if a combination of algorithms could better predict pathogenicity. Based on American College of Medical Genetic Criteria, 440 variants were classified as pathogenic or likely pathogenic and 84 were classified as benign or likely benign. Twenty-eight variants previously associated with epilepsy were present in population-based gene databases. The output provided by most computational algorithms had a high sensitivity but low specificity with an accuracy of 0.52-0.77. Accuracy could be improved by adjusting the threshold for pathogenicity. Using this adjustment, the Mendelian Clinically Applicable Pathogenicity (M-CAP) algorithm had an accuracy of 0.90 and a combination of algorithms increased the accuracy to 0.92. Potentially pathogenic variants are present in population-based sources. Most computational algorithms overestimate pathogenicity; however, a weighted combination of several algorithms increased classification accuracy to >0.90. Wiley Periodicals, Inc. © 2017 International League Against Epilepsy.

Active Surveillance of Birth Defects Among US Department of Defense Beneficiaries: A Feasibility Study

DTIC Science & Technology

1999-05-01

cleft palate / lip , upper alimentary, male reproductive, and urinary tract birth defects than the active surveillance database. Prevalence for the...the passive CEIS surveillance contained a smaller number of cleft palate / lip , upper alimentary, male reproductive, and urinary tract birth defects...Cardiovascular 33 29 8 63 Respiratory 4 3 0 4 Cleft palate / lip 12 4 3 14 Upper alimentary

Using administrative databases in the surveillance of depressive disorders--case definitions.

PubMed

Alaghehbandan, Reza; Macdonald, Don; Barrett, Brendan; Collins, Kayla; Chen, Yue

2012-12-01

The objective of this study was to assess the usefulness of provincial administrative databases in carrying out surveillance on depressive disorders. Electronic medical records (EMRs) at 3 family practice clinics in St. John's, NL, Canada, were audited; 253 depressive disorder cases and 257 patients not diagnosed with a depressive disorder were selected. The EMR served as the "gold standard," which then was compared to these same patients investigated through the use of various case definitions applied against the provincial hospital and physician administrative databases. Variables used in the development of the case definitions were depressive disorder diagnoses (either in hospital or physician claims data), date of diagnosis, and service provider type [general practitioner (GP) vs. psychiatrist]. Of the 120 case definitions investigated, 26 were found to have a kappa statistic greater than 0.6, of which 5 case definitions were considered the most appropriate for surveillance of depressive disorders. Of the 5 definitions, the following case definition, with a 77.5% sensitivity and 93% specificity, was found to be the most valid ([ ≥1 hospitalizations OR ≥1 psychiatrist visit related to depressive disorders any time] OR ≥2 GP visits related to depressive disorders within the first 2 years of diagnosis). This study found that provincial administrative databases may be useful for carrying out surveillance on depressive disorders among the adult population. The approach used in this study was simple and resulted in rather reasonable sensitivity and specificity.

Bacteriological findings in patients with bone marrow transplantation (Karl Marx University Leipzig, 1985-1987).

PubMed

Wonitzki, C; Hoffmann, F A

1989-01-01

The results of the bacteriological surveillance cultures for 26 patients with bone marrow transplantation (Karl Marx University Leipzig, G.D.R., 1985-1987) are presented. 5.9% of all surveillance cultures contained facultatively pathogenic germs (with Pseudomonas aeruginosa as the most frequent representative, which was the reason of a sepsis in two patients). Coagulasenegative Staphylococci and other germs with an obscure pathogenicity were isolated upon a large scale, especially from the mucous membrane regions. There are hints, that above all special strains of coagulasenegative Staphylococci "colonize" the patient's body (also for longer periods) and turn into the blood too. During the total decontamination intestinal anaerobic flora is absent. After closing of total decontamination Clostridium perfringens is the first detectable anaerobic species. During the selective decontamination systemic applications of antibiotics are able to obliterate anaerobic findings for certain periods. Recommendations for an effective arrangement of the surveillance cultures of bone marrow transplantation patients are given.

Targeted surveillance for highly pathogenic avian influenza in migratory waterfowl across the conterminous United States: chapter 12

USGS Publications Warehouse

Farnsworth, Matthew L.; Kendall, William L.; Doherty, Paul F.; Miller, Ryan S.; White, Gary C.; Nichols, James D.; Burnham, Kenneth P.; Franklin, Alan B.; Majumdar, S.; Brenner, F.J.; Huffman, J.E.; McLean, R.G.; Panah, A.I.; Pietrobon, P.J.; Keeler, S.P.; Shive, S.

2011-01-01

Introduction of Asian strain H5N1 Highly Pathogenic avian influenca via waterfowl migration is one potential route of entry into the United States. In conjunction with state, tribe, and laboratory partners, the United States Department of Agriculture collected and tested 124,603 wild bird samples in 2006 as part of a national surveillance effort. A sampling plan was devised to increase the probability fo detecting Asian strain H5N1 at a national scale. Band recovery data were used to identify and prioritize sampling for wild migratory waterfowl, resulting in spatially targeted sampling recommendations focused on reads with high numbers of recoveries. We also compared the spatial and temporal distribution of the 2006 cloacal and fecal waterfowl sampling effort to the bird banding recovery data and found concordance between the two .Finally, we present improvements made to the 2007 fecal sampling component of the surveillance plan and suggest further improvements for future sampling.

A primer of drug safety surveillance: an industry perspective. Part II: Product labeling and product knowledge.

PubMed

Allan, M C

1992-01-01

To place the fundamentals of clinical drug safety surveillance in a conceptual framework that will facilitate understanding and application of adverse drug event data to protect the health of the public and support a market for pharmaceutical manufacturers' products. Part II of this series discusses specific issues regarding product labeling, such as developing the labeling, changing the labeling, and the legal as well as commercial ramifications of the contents of the labeling. An adverse event report scenario is further analyzed and suggestions are offered for maintaining the product labeling as an accurate reflection of the drug safety surveillance data. This article also emphasizes the necessity of product knowledge in adverse event database management. Both scientific and proprietary knowledge are required. Acquiring product knowledge is a part of the day-to-day activities of drug safety surveillance. A knowledge of the history of the product may forestall adverse publicity, as shown in the illustration. This review uses primary sources from the federal laws (regulations), commentaries, and summaries. Very complex topics are briefly summarized in the text. Secondary sources, ranging from newspaper articles to judicial summaries, illustrate the interpretation of adverse drug events and opportunities for drug safety surveillance intervention. The reference materials used were articles theoretically or practically applicable in the day-to-day practice of drug safety surveillance. The role of clinical drug safety surveillance in product monitoring and drug development is described. The process of drug safety surveillance is defined by the Food and Drug Administration regulations, product labeling, product knowledge, and database management. Database management is subdivided into the functions of receipt, retention, retrieval, and review of adverse event reports. Emphasis is placed on the dynamic interaction of the components of the process. Suggestions are offered to facilitate communication of a review of adverse event data for various audiences. Careful drug safety surveillance is beneficial to the health of the public and the commercial well-being of the manufacturer. Attention to the basic principles is essential and, as illustrated, may be sufficient to resolve some problems.

Use of WHONET-SaTScan system for simulated real-time detection of antimicrobial resistance clusters in a hospital in Italy, 2012 to 2014

PubMed Central

Natale, Alessandra; Stelling, John; Meledandri, Marcello; Messenger, Louisa A; D'Ancona, Fortunato

2017-01-01

Resistant pathogens infections cause in healthcare settings, higher patient mortality, longer hospitalisation times and higher costs for treatments. Strengthening and coordinating local, national and international surveillance systems is the cornerstone for the control of antimicrobial resistance (AMR). In this study, the WHONET-SaTScan software was applied in a hospital in Italy to identify potential outbreaks of AMR. Data from San Filippo Neri Hospital in Rome between 2012 and 2014 were extracted from the national surveillance system for antimicrobial resistance (AR-ISS) and analysed using the simulated prospective analysis for real-time cluster detection included in the WHONET-SaTScan software. Results were compared with the hospital infection prevention and control system. The WHONET-SaTScan identified 71 statistically significant clusters, some involving pathogens carrying multiple resistance phenotypes. Of these 71, three were also detected by the hospital system, while a further 15, detected by WHONET-SaTScan only, were considered of relevant importance and worth further investigation by the hospital infection control team. In this study, the WHONET-SaTScan system was applied for the first time to the surveillance of AMR in Italy as a tool to strengthen this surveillance to allow more timely intervention strategies both at local and national level, using data regularly collected by the Italian national surveillance system. PMID:28333615

Lessons learned from research and surveillance directed at highly pathogenic influenza A viruses in wild birds inhabiting North America

USGS Publications Warehouse

Ramey, Andy M.; DeLiberto, Thomas J.; Berhane, Yohannes; Swayne, David E.; Stallknecht, David E.

2018-01-01

Following detections of highly pathogenic (HP) influenza A viruses (IAVs) in wild birds inhabiting East Asia after the turn of the millennium, the intensity of sampling of wild birds for IAVs increased throughout much of North America. The objectives for many research and surveillance efforts were directed towards detecting Eurasian origin HP IAVs and understanding the potential of such viruses to be maintained and dispersed by wild birds. In this review, we highlight five important lessons learned from research and surveillance directed at HP IAVs in wild birds inhabiting North America: (1) Wild birds may disperse IAVs between North America and adjacent regions via migration, (2) HP IAVs can be introduced to wild birds in North America, (3) HP IAVs may cross the wild bird-poultry interface in North America, (4) The probability of encountering and detecting a specific virus may be low, and (5) Population immunity of wild birds may influence HP IAV outbreaks in North America. We review empirical support derived from research and surveillance efforts for each lesson learned and, furthermore, identify implications for future surveillance efforts, biosecurity, and population health. We conclude our review by identifying five additional areas in which we think future mechanistic research relative to IAVs in wild birds in North America are likely to lead to other important lessons learned in the years ahead.

Lessons learned from research and surveillance directed at highly pathogenic influenza A viruses in wild birds inhabiting North America.

PubMed

Ramey, Andrew M; DeLiberto, Thomas J; Berhane, Yohannes; Swayne, David E; Stallknecht, David E

2018-05-01

Following detections of highly pathogenic (HP) influenza A viruses (IAVs) in wild birds inhabiting East Asia after the turn of the millennium, the intensity of sampling of wild birds for IAVs increased throughout much of North America. The objectives for many research and surveillance efforts were directed towards detecting Eurasian origin HP IAVs and understanding the potential of such viruses to be maintained and dispersed by wild birds. In this review, we highlight five important lessons learned from research and surveillance directed at HP IAVs in wild birds inhabiting North America: (1) Wild birds may disperse IAVs between North America and adjacent regions via migration, (2) HP IAVs can be introduced to wild birds in North America, (3) HP IAVs may cross the wild bird-poultry interface in North America, (4) The probability of encountering and detecting a specific virus may be low, and (5) Population immunity of wild birds may influence HP IAV outbreaks in North America. We review empirical support derived from research and surveillance efforts for each lesson learned and, furthermore, identify implications for future surveillance efforts, biosecurity, and population health. We conclude our review by identifying five additional areas in which we think future mechanistic research relative to IAVs in wild birds in North America are likely to lead to other important lessons learned in the years ahead. Published by Elsevier Inc.

Improving Cardiac Surgical Site Infection Reporting and Prevention By Using Registry Data for Case Ascertainment.

PubMed

Nayar, Vaidehi; Kennedy, Andrea; Pappas, Janine; Atchley, Krista D; Field, Cynthia; Smathers, Sarah; Teszner, Eva E; Sammons, Julia S; Coffin, Susan E; Gerber, Jeffrey S; Spray, Thomas L; Steven, James M; Bell, Louis M; Forrer, Joan; Gonzalez, Fernando; Chi, Albert; Nieczpiel, William J; Martin, John N; Gaynor, J William

2016-01-01

The use of administrative data for surgical site infection (SSI) surveillance leads to inaccurate reporting of SSI rates [1]. A quality improvement (QI) initiative was conducted linking clinical registry and administrative databases to improve reporting and reduce the incidence of SSI [2]. At our institution, The Society of Thoracic Surgeons Congenital Heart Surgery Database (STS-CHSD) and infection surveillance database (ISD) were linked to the enterprise data warehouse containing electronic health record (EHR) billing data. A data visualization tool was created to (1) use the STS-CHSD for case ascertainment, (2) resolve discrepancies between the databases, and (3) assess impact of QI initiatives, including wound alert reports, bedside reviews, prevention bundles, and billing coder education. Over the 24-month study period, 1,715 surgical cases were ascertained according to the STS-CHSD clinical criteria, with 23 SSIs identified through the STS-CHSD, 20 SSIs identified through the ISD, and 32 SSIs identified through the billing database. The rolling 12-month STS-CHSD SSI rate decreased from 2.73% (21 of 769 as of January 2013) to 1.11% (9 of 813 as of December 2014). Thirty reporting discrepancies were reviewed to ensure accuracy. Workflow changes facilitated communication and improved adjudication of suspected SSIs. Billing coder education increased coding accuracy and narrowed variation between the 3 SSI sources. The data visualization tool demonstrated temporal relationships between QI initiatives and SSI rate reductions. Linkage of registry and infection control surveillance data with the EHR improves SSI surveillance. The visualization tool and workflow changes facilitated communication, SSI adjudication, and assessment of the QI initiatives. Implementation of these initiatives was associated with decreased SSI rates. Copyright © 2016 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis

PubMed Central

Wyrsch, Ethan R.; Roy Chowdhury, Piklu; Chapman, Toni A.; Charles, Ian G.; Hammond, Jeffrey M.; Djordjevic, Steven P.

2016-01-01

Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance. PMID:27379026

H7N9 Highly Pathogenic Avian Influenza in the United States in 2017

USDA-ARS?s Scientific Manuscript database

In early March of 2017 an outbreak of highly pathogenic avian influenza H7N9 was reported from a broiler-breeder flock Tennessee. A second HPAI case was detected 2 weeks later. Subsequent active and passive surveillance identified several LPAI cases in Alabama, Georgia, Kentucky, and TN that was g...

The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents

PubMed Central

Ecker, David J; Sampath, Rangarajan; Willett, Paul; Wyatt, Jacqueline R; Samant, Vivek; Massire, Christian; Hall, Thomas A; Hari, Kumar; McNeil, John A; Büchen-Osmond, Cornelia; Budowle, Bruce

2005-01-01

Background Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks. Results We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. Conclusion The Microbial Rosetta Stone is available at . The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases. PMID:15850481

From filaments to function: The role of the plant actin cytoskeleton in pathogen perception, signaling and immunity.

PubMed

Porter, Katie; Day, Brad

2016-04-01

The eukaryotic actin cytoskeleton is required for numerous cellular processes, including cell shape, development and movement, gene expression and signal transduction, and response to biotic and abiotic stress. In recent years, research in both plants and animal systems have described a function for actin as the ideal surveillance platform, linking the function and activity of primary physiological processes to the immune system. In this review, we will highlight recent advances that have defined the regulation and breadth of function of the actin cytoskeleton as a network required for defense signaling following pathogen infection. Coupled with an overview of recent work demonstrating specific targeting of the plant actin cytoskeleton by a diversity of pathogens, including bacteria, fungi and viruses, we will highlight the importance of actin as a key signaling hub in plants, one that mediates surveillance of cellular homeostasis and the activation of specific signaling responses following pathogen perception. Based on the studies highlighted herein, we propose a working model that posits changes in actin filament organization is in and of itself a highly specific signal, which induces, regulates and physically directs stimulus-specific signaling processes, most importantly, those associated with response to pathogens. © 2015 Institute of Botany, Chinese Academy of Sciences.

Self/nonself perception in plants in innate immunity and defense

PubMed Central

Sanabria, Natasha M; Huang, Ju-Chi

2010-01-01

The ability to distinguish ‘self’ from ‘nonself’ is the most fundamental aspect of any immune system. The evolutionary solution in plants to the problems of perceiving and responding to pathogens involves surveillance of nonself, damaged-self and altered-self as danger signals. This is reflected in basal resistance or non-host resistance, which is the innate immune response that protects plants against the majority of pathogens. In the case of surveillance of nonself, plants utilize receptor-like proteins or -kinases (RLP/Ks) as pattern recognition receptors (PRRs), which can detect conserved pathogen/microbe-associated molecular pattern (P/MAMP) molecules. P/MAMP detection serves as an early warning system for the presence of a wide range of potential pathogens and the timely activation of plant defense mechanisms. However, adapted microbes express a suite of effector proteins that often interfere or act as suppressors of these defenses. In response, plants have evolved a second line of defense that includes intracellular nucleotide binding leucine-rich repeat (NB-LRR)-containing resistance proteins, which recognize isolate-specific pathogen effectors once the cell wall has been compromised. This host-immunity acts within the species level and is controlled by polymorphic host genes, where resistance protein-mediated activation of defense is based on an ‘altered-self’ recognition mechanism. PMID:21559176

Digital food photography: Dietary surveillance and beyond

USDA-ARS?s Scientific Manuscript database

The method used for creating a database of approximately 20,000 digital images of multiple portion sizes of foods linked to the USDA's Food and Nutrient Database for Dietary Studies (FNDDS) is presented. The creation of this database began in 2002, and its development has spanned 10 years. Initially...

Applying Science: Opportunities to Inform Disease Management Policy with Cooperative Research within a One Health Framework.

PubMed

Blackburn, Jason K; Kracalik, Ian T; Fair, Jeanne Marie

2015-01-01

The ongoing Ebola outbreak in West Africa and the current saiga antelope die off in Kazakhstan each represent very real and difficult to manage public or veterinary health crises. They also illustrate the importance of stable and funded surveillance and sound policy for intervention or disease control. While these two events highlight extreme cases of infectious disease (Ebola) or (possible) environmental exposure (saiga), diseases such as anthrax, brucellosis, tularemia, and plague are all zoonoses that pose risks and present surveillance challenges at the wildlife-livestock-human interfaces. These four diseases are also considered important actors in the threat of biological terror activities and have a long history as legacy biowarfare pathogens. This paper reviews recent studies done cooperatively between American and institutions within nations of the Former Soviet Union (FSU) focused on spatiotemporal, epidemiological, and ecological patterns of these four zoonoses. We examine recent studies and discuss the possible ways in which techniques, including ecological niche modeling, disease risk modeling, and spatiotemporal cluster analysis, can inform disease surveillance, control efforts, and impact policy. Our focus is to posit ways to apply science to disease management policy and actual management or mitigation practices. Across these examples, we illustrate the value of cooperative studies that bring together modern geospatial and epidemiological analyses to improve our understanding of the distribution of pathogens and diseases in livestock, wildlife, and humans. For example, ecological niche modeling can provide national level maps of pathogen distributions for surveillance planning, while space-time models can identify the timing and location of significant outbreak events for defining active control strategies. We advocate for the need to bring the results and the researchers from cooperative studies into the meeting rooms where policy is negotiated and use these results to inform future disease surveillance and control or eradication campaigns.

Comparison of the h-Index Scores Among Pathogens Identified as Emerging Hazards in North America.

PubMed

Cox, R; McIntyre, K M; Sanchez, J; Setzkorn, C; Baylis, M; Revie, C W

2016-02-01

Disease surveillance must assess the relative importance of pathogen hazards. Here, we use the Hirsch index (h-index) as a novel method to identify and rank infectious pathogens that are likely to be a hazard to human health in the North American region. This bibliometric index was developed to quantify an individual's scientific research output and was recently used as a proxy measure for pathogen impact. Analysis of more than 3000 infectious organisms indicated that 651 were human pathogen species that had been recorded in the North American region. The h-index of these pathogens ranged from 0 to 584. The h-index of emerging pathogens was greater than non-emerging pathogens as was the h-index of frequently pathogenic pathogens when compared to non-pathogenic pathogens. As expected, the h-index of pathogens varied over time between 1960 and 2011. We discuss how the h-index can contribute to pathogen prioritization and as an indicator of pathogen emergence. © 2014 Blackwell Verlag GmbH.

PLEXdb: Gene expression resources for plants and plant pathogens

USDA-ARS?s Scientific Manuscript database

PLEXdb (Plant Expression Database), in partnership with community databases, supports comparisons of gene expression across multiple plant and pathogen species, promoting individuals and/or consortia to upload genome-scale data sets to contrast them to previously archived data. These analyses facili...

EuPathDB: the eukaryotic pathogen genomics database resource

PubMed Central

Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.; Brestelli, John; Brunk, Brian P.; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S.; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C.; Lawrence, Cris; Li, Wei; Pinney, Deborah F.; Pulman, Jane A.; Roos, David S.; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J.; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

2017-01-01

The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host–pathogen interactions. PMID:27903906

Opportunities and obstacles to collecting wildlife disease data for public health purposes: Results of a pilot study on Vancouver Island, British Columbia

PubMed Central

Stitt, Tyler; Mountifield, Julie; Stephen, Craig

2007-01-01

Existing sources of wildlife morbidity and mortality data were evaluated and 3 pilot active surveillance projects were undertaken to compare and contrast methods for collecting wildlife disease data on Vancouver Island for public health purposes. Few organizations could collect samples for diagnostic evaluation, fewer still maintained records, and none regularly characterized or reported wildlife disease for public health purposes. Wildlife rehabilitation centers encountered the greatest variety of wildlife from the largest geographic area and frequently received submissions from other organizations. Obstacles to participation included the following: permit restrictions; financial disincentives; staff safety; no mandate to collect relevant data; and lack of contact between wildlife and public health agencies. Despite these obstacles, modest investments in personnel allowed novel pathogens of public health concern to be tracked. Targeted surveillance for known pathogens in specific host species, rather than general surveys for unspecified pathogens, was judged to be a more effective and efficient way to provide useful public health data. PMID:17310627

Antimicrobial resistance surveillance in the AFHSC-GEIS network

PubMed Central

2011-01-01

International infectious disease surveillance has been conducted by the United States (U.S.) Department of Defense (DoD) for many years and has been consolidated within the Armed Forces Health Surveillance Center, Division of Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) since 1998. This includes activities that monitor the presence of antimicrobial resistance among pathogens. AFHSC-GEIS partners work within DoD military treatment facilities and collaborate with host-nation civilian and military clinics, hospitals and university systems. The goals of these activities are to foster military force health protection and medical diplomacy. Surveillance activities include both community-acquired and health care-associated infections and have promoted the development of surveillance networks, centers of excellence and referral laboratories. Information technology applications have been utilized increasingly to aid in DoD-wide global surveillance for diseases significant to force health protection and global public health. This section documents the accomplishments and activities of the network through AFHSC-GEIS partners in 2009. PMID:21388568

Antimicrobial resistance surveillance in the AFHSC-GEIS network.

PubMed

Meyer, William G; Pavlin, Julie A; Hospenthal, Duane; Murray, Clinton K; Jerke, Kurt; Hawksworth, Anthony; Metzgar, David; Myers, Todd; Walsh, Douglas; Wu, Max; Ergas, Rosa; Chukwuma, Uzo; Tobias, Steven; Klena, John; Nakhla, Isabelle; Talaat, Maha; Maves, Ryan; Ellis, Michael; Wortmann, Glenn; Blazes, David L; Lindler, Luther

2011-03-04

International infectious disease surveillance has been conducted by the United States (U.S.) Department of Defense (DoD) for many years and has been consolidated within the Armed Forces Health Surveillance Center, Division of Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) since 1998. This includes activities that monitor the presence of antimicrobial resistance among pathogens. AFHSC-GEIS partners work within DoD military treatment facilities and collaborate with host-nation civilian and military clinics, hospitals and university systems. The goals of these activities are to foster military force health protection and medical diplomacy. Surveillance activities include both community-acquired and health care-associated infections and have promoted the development of surveillance networks, centers of excellence and referral laboratories. Information technology applications have been utilized increasingly to aid in DoD-wide global surveillance for diseases significant to force health protection and global public health. This section documents the accomplishments and activities of the network through AFHSC-GEIS partners in 2009.

Pathogens: raft hijackers.

PubMed

Mañes, Santos; del Real, Gustavo; Martínez-A, Carlos

2003-07-01

Throughout evolution, organisms have developed immune-surveillance networks to protect themselves from potential pathogens. At the cellular level, the signalling events that regulate these defensive responses take place in membrane rafts--dynamic microdomains that are enriched in cholesterol and glycosphingolipids--that facilitate many protein-protein and lipid-protein interactions at the cell surface. Pathogens have evolved many strategies to ensure their own survival and to evade the host immune system, in some cases by hijacking rafts. However, understanding the means by which pathogens exploit rafts might lead to new therapeutic strategies to prevent or alleviate certain infectious diseases, such as those caused by HIV-1 or Ebola virus.

Opportunistic pathogens and elements of the resistome that are common in bottled mineral water support the need for continuous surveillance.

PubMed

Falcone-Dias, Maria Fernanda; Centrón, Daniela; Pavan, Fernando; Moura, Adriana Candido da Silva; Naveca, Felipe Gomes; de Souza, Victor Costa; Farache Filho, Adalberto; Leite, Clarice Queico Fujimura

2015-01-01

Several differences concerning bacterial species, opportunistic pathogens, elements of the resistome as well as variations concerning the CFU/mL counts were identified in some of the five most marketed bottled mineral water from Araraquara city, São Paulo, Brazil. Two out of five brands tested were confirmed as potential source of opportunistic pathogens, including Mycobacterium gordonae, Ralstonia picketti and Burkholderia cepacia complex (Bcc). A total of one hundred and six isolates were recovered from four of these bottled mineral water brands. Betaproteobacteria was predominant followed by Alphaproteobacteria, Gammaproteobacteria and Firmicutes. Ninety percent of the bacteria isolated demonstrated resistance to seventeen of the nineteen antimicrobials tested. These antimicrobials included eight different classes, including 3rd and 4th generation cephalosporins, carbapenems and fluoroquinolones. Multidrug resistant bacteria were detected for fifty-nine percent of isolates in three water brands at counts up to 103 CFU/ml. Of major concern, the two bottled mineral water harboring opportunistic pathogens were also source of elements of the resistome that could be directly transferred to humans. All these differences found among brands highlight the need for continuous bacteriological surveillance of bottled mineral water.

Opportunistic Pathogens and Elements of the Resistome that Are Common in Bottled Mineral Water Support the Need for Continuous Surveillance

PubMed Central

Falcone-Dias, Maria Fernanda; Centrón, Daniela; Pavan, Fernando; Moura, Adriana Candido da Silva; Naveca, Felipe Gomes; de Souza, Victor Costa; Farache Filho, Adalberto; Leite, Clarice Queico Fujimura

2015-01-01

Several differences concerning bacterial species, opportunistic pathogens, elements of the resistome as well as variations concerning the CFU/mL counts were identified in some of the five most marketed bottled mineral water from Araraquara city, São Paulo, Brazil. Two out of five brands tested were confirmed as potential source of opportunistic pathogens, including Mycobacterium gordonae, Ralstonia picketti and Burkholderia cepacia complex (Bcc). A total of one hundred and six isolates were recovered from four of these bottled mineral water brands. Betaproteobacteria was predominant followed by Alphaproteobacteria, Gammaproteobacteria and Firmicutes. Ninety percent of the bacteria isolated demonstrated resistance to seventeen of the nineteen antimicrobials tested. These antimicrobials included eight different classes, including 3rd and 4th generation cephalosporins, carbapenems and fluoroquinolones. Multidrug resistant bacteria were detected for fifty-nine percent of isolates in three water brands at counts up to 103 CFU/ml. Of major concern, the two bottled mineral water harboring opportunistic pathogens were also source of elements of the resistome that could be directly transferred to humans. All these differences found among brands highlight the need for continuous bacteriological surveillance of bottled mineral water. PMID:25803794

DNA variant databases improve test accuracy and phenotype prediction in Alport syndrome.

PubMed

Savige, Judy; Ars, Elisabet; Cotton, Richard G H; Crockett, David; Dagher, Hayat; Deltas, Constantinos; Ding, Jie; Flinter, Frances; Pont-Kingdon, Genevieve; Smaoui, Nizar; Torra, Roser; Storey, Helen

2014-06-01

X-linked Alport syndrome is a form of progressive renal failure caused by pathogenic variants in the COL4A5 gene. More than 700 variants have been described and a further 400 are estimated to be known to individual laboratories but are unpublished. The major genetic testing laboratories for X-linked Alport syndrome worldwide have established a Web-based database for published and unpublished COL4A5 variants ( https://grenada.lumc.nl/LOVD2/COL4A/home.php?select_db=COL4A5 ). This conforms with the recommendations of the Human Variome Project: it uses the Leiden Open Variation Database (LOVD) format, describes variants according to the human reference sequence with standardized nomenclature, indicates likely pathogenicity and associated clinical features, and credits the submitting laboratory. The database includes non-pathogenic and recurrent variants, and is linked to another COL4A5 mutation database and relevant bioinformatics sites. Access is free. Increasing the number of COL4A5 variants in the public domain helps patients, diagnostic laboratories, clinicians, and researchers. The database improves the accuracy and efficiency of genetic testing because its variants are already categorized for pathogenicity. The description of further COL4A5 variants and clinical associations will improve our ability to predict phenotype and our understanding of collagen IV biochemistry. The database for X-linked Alport syndrome represents a model for databases in other inherited renal diseases.

Avian influenza at both ends of a migratory flyway: characterizing viral genomic diversity to optimize surveillance plans for North America

USGS Publications Warehouse

Pearce, John M.; Ramey, Andrew M.; Flint, Paul L.; Koehler, Anson V.; Fleskes, Joseph P.; Franson, J. Christian; Hall, Jeffrey S.; Derksen, Dirk V.; Ip, Hon S.

2009-01-01

Although continental populations of avian influenza viruses are genetically distinct, transcontinental reassortment in low pathogenic avian influenza (LPAI) viruses has been detected in migratory birds. Thus, genomic analyses of LPAI viruses could serve as an approach to prioritize species and regions targeted by North American surveillance activities for foreign origin highly pathogenic avian influenza (HPAI). To assess the applicability of this approach, we conducted a phylogenetic and population genetic analysis of 68 viral genomes isolated from the northern pintail (Anas acuta) at opposite ends of the Pacific migratory flyway in North America. We found limited evidence for Asian LPAI lineages on wintering areas used by northern pintails in California in contrast to a higher frequency on breeding locales of Alaska. Our results indicate that the number of Asian LPAI lineages observed in Alaskan northern pintails, and the nucleotide composition of LPAI lineages, is not maintained through fall migration. Accordingly, our data indicate that surveillance of Pacific Flyway northern pintails to detect foreign avian influenza viruses would be most effective in Alaska. North American surveillance plans could be optimized through an analysis of LPAI genomics from species that demonstrate evolutionary linkages with European or Asian lineages and in regions that have overlapping migratory flyways with areas of HPAI outbreaks.

Filariasis in Travelers Presenting to the GeoSentinel Surveillance Network

PubMed Central

Lipner, Ettie M.; Law, Melissa A.; Barnett, Elizabeth; Keystone, Jay S.; von Sonnenburg, Frank; Loutan, Louis; Prevots, D. Rebecca; Klion, Amy D.; Nutman, Thomas B.

2007-01-01

Background As international travel increases, there is rising exposure to many pathogens not traditionally encountered in the resource-rich countries of the world. Filarial infections, a great problem throughout the tropics and subtropics, are relatively rare among travelers even to filaria-endemic regions of the world. The GeoSentinel Surveillance Network, a global network of medicine/travel clinics, was established in 1995 to detect morbidity trends among travelers. Principal Findings We examined data from the GeoSentinel database to determine demographic and travel characteristics associated with filaria acquisition and to understand the differences in clinical presentation between nonendemic visitors and those born in filaria-endemic regions of the world. Filarial infections comprised 0.62% (n = 271) of all medical conditions reported to the GeoSentinel Network from travelers; 37% of patients were diagnosed with Onchocerca volvulus, 25% were infected with Loa loa, and another 25% were diagnosed with Wuchereria bancrofti. Most infections were reported from immigrants and from those immigrants returning to their county of origin (those visiting friends and relatives); the majority of filarial infections were acquired in sub-Saharan Africa. Among the patients who were natives of filaria-nonendemic regions, 70.6% acquired their filarial infection with exposure greater than 1 month. Moreover, nonendemic visitors to filaria-endemic regions were more likely to present to GeoSentinel sites with clinically symptomatic conditions compared with those who had lifelong exposure. Significance Codifying the filarial infections presenting to the GeoSentinel Surveillance Network has provided insights into the clinical differences seen among filaria-infected expatriates and those from endemic regions and demonstrated that O. volvulus infection can be acquired with short-term travel. PMID:18160987

Prevalence of extended-spectrum-β-lactamase-producing Enterobacteriaceae: first systematic meta-analysis report from Pakistan.

PubMed

Abrar, Samyyia; Hussain, Shahida; Khan, Rehan Ahmad; Ul Ain, Noor; Haider, Hayat; Riaz, Saba

2018-01-01

South-Asia is known as a hub for multidrug-resistant (MDR) bacteria. Unfortunately, proper surveillance and documentation of MDR pathogens is lacking in Pakistan. The alarming increase in the prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is a serious problem. From this perspective, we analysed published data regarding ESBL-producing Enterobacteriaceae in different regions of Pakistan. A meta-analysis was performed to determine the prevalence of ESBL-producing Enterobacteriaceae in Pakistan. A Web-based search was conducted in electronic databases, including PubMed, Scopus and PakMedi Net (for non-indexed Pakistani journals). Articles published (in either indexed or non-indexed journals) between January 2002 and July 2016 were included in the study. Relevant data were extracted, and statistical analysis was performed using the Metaprop command of STATA version 14.1. A total of 68 studies were identified from the electronic data base search, and 55 of these studies met our inclusion criteria. Pakistan's overall pooled proportion of ESBL-producers was 0.40 (95% CI: 0.34-0.47). The overall heterogeneity was significant (I2 = 99.75%, p  < 0.001), and significant ES = 0 (Z = 18.41, p  < 0.001) was found. OXA, SHV, TEM and CTX-M were the most commonly found gene variants for ESBLs in these studies. The prevalence of ESBL-producing Enterobacteriaceae is high in Pakistan. Little is known about the annual frequency of ESBLs and their prevalence in different provinces of Pakistan. No data are available regarding ESBL frequency in Baluchistan. This underscores an urgent demand for regular surveillance to address this antimicrobial resistance problem. Surveillance to better understand the annual ESBL burden is crucial to improve national and regional guidelines.

INTERPOL's Surveillance Network in Curbing Transnational Terrorism

PubMed Central

Gardeazabal, Javier; Sandler, Todd

2015-01-01

Abstract This paper investigates the role that International Criminal Police Organization (INTERPOL) surveillance—the Mobile INTERPOL Network Database (MIND) and the Fixed INTERPOL Network Database (FIND)—played in the War on Terror since its inception in 2005. MIND/FIND surveillance allows countries to screen people and documents systematically at border crossings against INTERPOL databases on terrorists, fugitives, and stolen and lost travel documents. Such documents have been used in the past by terrorists to transit borders. By applying methods developed in the treatment‐effects literature, this paper establishes that countries adopting MIND/FIND experienced fewer transnational terrorist attacks than they would have had they not adopted MIND/FIND. Our estimates indicate that, on average, from 2008 to 2011, adopting and using MIND/FIND results in 0.5 fewer transnational terrorist incidents each year per 100 million people. Thus, a country like France with a population just above 64 million people in 2008 would have 0.32 fewer transnational terrorist incidents per year owing to its use of INTERPOL surveillance. This amounts to a sizeable average proportional reduction of about 30 percent.

Organization of surveillance in GI practice.

PubMed

Senore, Carlo; Bellisario, Cristina; Hassan, Cesare

2016-12-01

Several reports documented an inefficient utilisation of available resources, as well as a suboptimal compliance with surveillance recommendations. Although, evidence suggests that organisational issues can influence the quality of care delivered, surveillance protocols are usually based on non-organized approaches. We conducted a literature search (publication date: 01/2000-06/2016) on PubMed and Cochrane Database of Systematic Reviews, Database of Abstracts of Reviews of Effects and Cochrane Central Register of Controlled Trials for guidelines, or consensus statements, for surveys of practice, reporting information about patients, or providers attitudes and behaviours, for intervention studies to enhance compliance with guidelines. Related articles were also scrutinised. Based on the clinical relevance and burden on endoscopy services this review was focused on surveillance for Barrett's oesophagus, IBD and post-polypectomy surveillance of colonic adenomas. Existing guidelines are generally recognising structure and process requirements influencing delivery of surveillance interventions, while less attention had been devoted to transitions and interfaces in the care process. Available evidence from practice surveys is suggesting the need to design organizational strategies aimed to enable patients to attend and providers to deliver timely and appropriate care. Well designed studies assessing the effectiveness of specific interventions in this setting are however lacking. Indirect evidence from screening settings would suggest that the implementation of automated standardized recall systems, utilisation of clinical registries, removing financial barriers, could improve appropriateness of use and compliance with recommendations. Lack of sound evidence regarding utility and methodology of surveillance can contribute to explain the observed variability in providers and patients attitudes and in compliance with the recommended surveillance. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cell Phone-Based System (Chaak) for Surveillance of Immatures of Dengue Virus Mosquito Vectors

PubMed Central

LOZANO–FUENTES, SAUL; WEDYAN, FADI; HERNANDEZ–GARCIA, EDGAR; SADHU, DEVADATTA; GHOSH, SUDIPTO; BIEMAN, JAMES M.; TEP-CHEL, DIANA; GARCÍA–REJÓN, JULIÁN E.; EISEN, LARS

2014-01-01

Capture of surveillance data on mobile devices and rapid transfer of such data from these devices into an electronic database or data management and decision support systems promote timely data analyses and public health response during disease outbreaks. Mobile data capture is used increasingly for malaria surveillance and holds great promise for surveillance of other neglected tropical diseases. We focused on mosquito-borne dengue, with the primary aims of: 1) developing and field-testing a cell phone-based system (called Chaak) for capture of data relating to the surveillance of the mosquito immature stages, and 2) assessing, in the dengue endemic setting of Mérida, México, the cost-effectiveness of this new technology versus paper-based data collection. Chaak includes a desktop component, where a manager selects premises to be surveyed for mosquito immatures, and a cell phone component, where the surveyor receives the assigned tasks and captures the data. Data collected on the cell phone can be transferred to a central database through different modes of transmission, including near-real time where data are transferred immediately (e.g., over the Internet) or by first storing data on the cell phone for future transmission. Spatial data are handled in a novel, semantically driven, geographic information system. Compared with a pen-and-paper-based method, use of Chaak improved the accuracy and increased the speed of data transcription into an electronic database. The cost-effectiveness of using the Chaak system will depend largely on the up-front cost of purchasing cell phones and the recurring cost of data transfer over a cellular network. PMID:23926788

Active and passive surveillance of yellow fever vaccine 17D or 17DD-associated serious adverse events: systematic review.

PubMed

Thomas, Roger E; Lorenzetti, Diane L; Spragins, Wendy; Jackson, Dave; Williamson, Tyler

2011-06-20

To identify the rate of serious adverse events attributable to yellow fever vaccination with 17D and 17DD strains reported in active and passive surveillance data. We conducted a systematic review of published literature on adverse events associated with yellow fever. We searched 9 electronic databases for peer reviewed and grey literature in all languages. There were no restrictions on date of publication. Reference lists of key studies were also reviewed to identify additional studies. We identified 66 relevant studies: 24 used active, 17 a combination of passive and active (15 of which were pharmacovigilance databases), and 25 passive surveillance. ACTIVE SURVEILLANCE: A total of 2,660,929 patients in general populations were followed for adverse events after vaccination, heavily weighted (97.7%) by one large Brazilian study. There were no observed cases of viscerotropic or neurotropic disease, one of anaphylaxis and 26 cases of urticaria (hypersensitivity). We also identified four studies of infants and children (n=2199), four studies of women (n=1334), and one study of 174 HIV+, and no serious adverse events were observed. PHARMACOVIGILANCE DATABASES: 10 of the 15 databases contributed data to this review, with 107,621,154 patients, heavily weighted (94%) by the Brazilian database. The estimates for Australia were low at 0/210,656 for "severe neurological disease" and 1/210,656 for YEL-AVD, and also low for Brazil with 9 hypersensitivity events, 0.23 anaphylactic shock events, 0.84 neurologic syndrome events and 0.19 viscerotropic events cases/million doses. The five analyses of partly overlapping periods for the US VAERS database provided an estimate of 6.6 YEL-AVD and YEL-AND cases per million, and estimates between 11.1 and 15.6 of overall "serious adverse events" per million. The estimates for the UK were higher at 34 "serious adverse events" and also for Switzerland with 14.6 "neurologic events" and 40 "serious events not neurological"/million doses. PASSIVE SURVEILLANCE: Six studies of campaigns in general populations included 94,500,528 individuals, very heavily weighted (99%) by the Brazilian data, and providing an estimate of 0.51 serious AEFIs/million doses. Five retrospective reviews of hospital or clinic records included 60,698 individuals, and no serious AEFIs were proven. The data are heavily weighted (96%) by the data from the Hospital for Tropical Diseases, London. Two studies included 35,723 children, four studies included 138 pregnant women, six studies included 191 HIV+ patients, and there was one review of patients who were HIV+, and no serious AEFIs were proven. The databases in each country used different definitions, protocols, surveillance mechanisms for the initial identification and reporting of cases, and strategies for the clinical and laboratory follow up of cases. The pharmacovigilance databases provide three sets of estimates: a low estimate from the Brazilian and Australian data, a medium estimate from the US VAERS data, and a higher estimate from the UK and Swiss data. The estimates from the active surveillance data are lower (and strongly influenced by the Brazilian data) and the estimates from the passive surveillance studies are also lower (strongly influenced by the London Hospital for Tropical Diseases data from the early 1950s). Sophisticated pathology, histopathology and tests such as PCR amplicon sequencing are needed to prove that serious adverse events were actually caused by the yellow fever vaccine, and the availability of such diagnostic capability is strongly biased towards recent reports from developed countries. Despite these variations in the estimation of serious harm, overall the 17D and 17DD yellow fever vaccine has proven to be a very safe vaccine and is highly effective against an illness with high potential mortality rates. Copyright © 2011 Elsevier Ltd. All rights reserved.

Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection

PubMed Central

Diaz, Maureen H.; Waller, Jessica L.; Napoliello, Rebecca A.; Islam, Md. Shahidul; Wolff, Bernard J.; Burken, Daniel J.; Holden, Rhiannon L.; Srinivasan, Velusamy; Arvay, Melissa; McGee, Lesley; Oberste, M. Steven; Whitney, Cynthia G.; Schrag, Stephanie J.; Winchell, Jonas M.; Saha, Samir K.

2013-01-01

Identification of etiology remains a significant challenge in the diagnosis of infectious diseases, particularly in resource-poor settings. Viral, bacterial, and fungal pathogens, as well as parasites, play a role for many syndromes, and optimizing a single diagnostic system to detect a range of pathogens is challenging. The TaqMan Array Card (TAC) is a multiple-pathogen detection method that has previously been identified as a valuable technique for determining etiology of infections and holds promise for expanded use in clinical microbiology laboratories and surveillance studies. We selected TAC for use in the Aetiology of Neonatal Infection in South Asia (ANISA) study for identifying etiologies of severe disease in neonates in Bangladesh, India, and Pakistan. Here we report optimization of TAC to improve pathogen detection and overcome technical challenges associated with use of this technology in a large-scale surveillance study. Specifically, we increased the number of assay replicates, implemented a more robust RT-qPCR enzyme formulation, and adopted a more efficient method for extraction of total nucleic acid from blood specimens. We also report the development and analytical validation of ten new assays for use in the ANISA study. Based on these data, we revised the study-specific TACs for detection of 22 pathogens in NP/OP swabs and 12 pathogens in blood specimens as well as two control reactions (internal positive control and human nucleic acid control) for each specimen type. The cumulative improvements realized through these optimization studies will benefit ANISA and perhaps other studies utilizing multiple-pathogen detection approaches. These lessons may also contribute to the expansion of TAC technology to the clinical setting. PMID:23805203

Toward an Open-Access Global Database for Mapping, Control, and Surveillance of Neglected Tropical Diseases

PubMed Central

Hürlimann, Eveline; Schur, Nadine; Boutsika, Konstantina; Stensgaard, Anna-Sofie; Laserna de Himpsl, Maiti; Ziegelbauer, Kathrin; Laizer, Nassor; Camenzind, Lukas; Di Pasquale, Aurelio; Ekpo, Uwem F.; Simoonga, Christopher; Mushinge, Gabriel; Saarnak, Christopher F. L.; Utzinger, Jürg; Kristensen, Thomas K.; Vounatsou, Penelope

2011-01-01

Background After many years of general neglect, interest has grown and efforts came under way for the mapping, control, surveillance, and eventual elimination of neglected tropical diseases (NTDs). Disease risk estimates are a key feature to target control interventions, and serve as a benchmark for monitoring and evaluation. What is currently missing is a georeferenced global database for NTDs providing open-access to the available survey data that is constantly updated and can be utilized by researchers and disease control managers to support other relevant stakeholders. We describe the steps taken toward the development of such a database that can be employed for spatial disease risk modeling and control of NTDs. Methodology With an emphasis on schistosomiasis in Africa, we systematically searched the literature (peer-reviewed journals and ‘grey literature’), contacted Ministries of Health and research institutions in schistosomiasis-endemic countries for location-specific prevalence data and survey details (e.g., study population, year of survey and diagnostic techniques). The data were extracted, georeferenced, and stored in a MySQL database with a web interface allowing free database access and data management. Principal Findings At the beginning of 2011, our database contained more than 12,000 georeferenced schistosomiasis survey locations from 35 African countries available under http://www.gntd.org. Currently, the database is expanded to a global repository, including a host of other NTDs, e.g. soil-transmitted helminthiasis and leishmaniasis. Conclusions An open-access, spatially explicit NTD database offers unique opportunities for disease risk modeling, targeting control interventions, disease monitoring, and surveillance. Moreover, it allows for detailed geostatistical analyses of disease distribution in space and time. With an initial focus on schistosomiasis in Africa, we demonstrate the proof-of-concept that the establishment and running of a global NTD database is feasible and should be expanded without delay. PMID:22180793

Identifying newly acquired cases of hepatitis C using surveillance: a literature review.

PubMed

Sacks-Davis, R; VAN Gemert, C; Bergeri, I; Stoove, M; Hellard, M

2012-11-01

Surveillance of newly acquired hepatitis C virus (HCV) infection is crucial for understanding the epidemiology of HCV and informing public health practice. However, monitoring such infections via surveillance systems is challenging because they are commonly asymptomatic. A literature review was conducted to identify methodologies used by HCV surveillance systems to identify newly acquired infections; relevant surveillance systems in 15 countries were identified. Surveillance systems used three main strategies to identify newly acquired infections: (1) asking physicians to classify cases; (2) identifying symptomatic cases or cases with elevated alanine aminotransferases; and (3) identifying cases with documented evidence of anti-HCV antibody seroconversion within a specific time-frame. Case-ascertainment methods varied with greater completeness of data in enhanced compared to passive surveillance systems. Automated systems that extract and link testing data from multiple laboratory and clinic databases may provide an opportunity for collecting testing histories for individuals that is less resource intensive than enhanced surveillance.

Pathogen occurrence and antimicrobial resistance trends among urinary tract infection isolates in the Asia-Western Pacific Region: report from the SENTRY Antimicrobial Surveillance Program, 1998-1999.

PubMed

Turnidge, John; Bell, Jan; Biedenbach, Douglas J; Jones, Ronald N

2002-07-01

Worldwide surveillance of antimicrobial resistance among urinary tract pathogens is useful to determine important trends and geographical variation for common Gram-positive and -negative species. The most common causative uropathogens often have intrinsic or acquired resistance mechanisms which include ESBL production among enteric bacilli, multi-drug resistant staphylococci and non-fermentative Gram-negative bacilli such as Pseudomonas aeruginosa and Acinetobacter spp. and vancomycin-resistant Enterococcus spp. This study evaluates pathogen frequency and the resistance rates among urinary tract infection (UTI) pathogens in 14 medical centres in the Asia-Pacific region between 1998 and 1999. The isolates were referred to a central monitor for reference NCCLS broth microdilution testing, identification confirmation and patient demographic analysis. Over 50% of the 958 pathogens were Escherichia coli and Klebsiella spp. followed by P. aeruginosa, Enterococcus spp. and Enterobacter spp. Susceptibility for the three enteric bacilli was high for carbapenems (100%), 'fourth-generation' cephalosporins (cefepime 94.9-98.6%) and amikacin (> or = 93.0%). Beta-lactamase inhibitor compounds were more active against E. coli (piperacillin/tazobactam; > 90% susceptible) than the other two enteric species and all other tested agents had a narrower spectra of activity. The rank order of anti-pseudomonal agents was amikacin (91.5% susceptible)> imipenem > piperacillin/tazobactam > tobramycin > ceftazidime and cefepime (77.4 and 76.4% susceptible, respectively). Susceptibility to quinolones for the P. aeruginosa isolates was only 63.2-67.0%. Only one vancomycin-intermediate Enterococcus spp. (van C phenotype) was detected among the 103 strains tested. Newer fluoroquinolones (gatifloxacin; MIC(50), mg/l) were more potent against enterococci than ciprofloxacin (MIC(50), 2 mg/l) and high-level resistance to aminoglycosides was common (41.7%). The data presented are compared to studies of similar design from other areas which are part of the SENTRY surveillance network.

OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture.

PubMed

Gasc, Cyrielle; Constantin, Antony; Jaziri, Faouzi; Peyret, Pierre

2017-01-01

The detection and identification of bacterial pathogens involved in acts of bio- and agroterrorism are essential to avoid pathogen dispersal in the environment and propagation within the population. Conventional molecular methods, such as PCR amplification, DNA microarrays or shotgun sequencing, are subject to various limitations when assessing environmental samples, which can lead to inaccurate findings. We developed a hybridization capture strategy that uses a set of oligonucleotide probes to target and enrich biomarkers of interest in environmental samples. Here, we present Oligonucleotide Capture Probes for Pathogen Identification Database (OCaPPI-Db), an online capture probe database containing a set of 1,685 oligonucleotide probes allowing for the detection and identification of 30 biothreat agents up to the species level. This probe set can be used in its entirety as a comprehensive diagnostic tool or can be restricted to a set of probes targeting a specific pathogen or virulence factor according to the user's needs. : http://ocappidb.uca.works. © The Author(s) 2017. Published by Oxford University Press.

Electronic integrated disease surveillance system and pathogen asset control system.

PubMed

Wahl, Tom G; Burdakov, Aleksey V; Oukharov, Andrey O; Zhilokov, Azamat K

2012-06-20

Electronic Integrated Disease Surveillance System (EIDSS) has been used to strengthen and support monitoring and prevention of dangerous diseases within One Health concept by integrating veterinary and human surveillance, passive and active approaches, case-based records including disease-specific clinical data based on standardised case definitions and aggregated data, laboratory data including sample tracking linked to each case and event with test results and epidemiological investigations. Information was collected and shared in secure way by different means: through the distributed nodes which are continuously synchronised amongst each other, through the web service, through the handheld devices. Electronic Integrated Disease Surveillance System provided near real time information flow that has been then disseminated to the appropriate organisations in a timely manner. It has been used for comprehensive analysis and visualisation capabilities including real time mapping of case events as these unfold enhancing decision making. Electronic Integrated Disease Surveillance System facilitated countries to comply with the IHR 2005 requirements through a data transfer module reporting diseases electronically to the World Health Organisation (WHO) data center as well as establish authorised data exchange with other electronic system using Open Architecture approach. Pathogen Asset Control System (PACS) has been used for accounting, management and control of biological agent stocks. Information on samples and strains of any kind throughout their entire lifecycle has been tracked in a comprehensive and flexible solution PACS.Both systems have been used in a combination and individually. Electronic Integrated Disease Surveillance System and PACS are currently deployed in the Republics of Kazakhstan, Georgia and Azerbaijan as a part of the Cooperative Biological Engagement Program (CBEP) sponsored by the US Defense Threat Reduction Agency (DTRA).

The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain

PubMed Central

Oniciuc, Elena A.; Likotrafiti, Eleni; Alvarez-Molina, Adrián; Alvarez-Ordóñez, Avelino

2018-01-01

Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes. PMID:29789467

Q fever is an old and neglected zoonotic disease in Kenya: a systematic review.

PubMed

Njeru, J; Henning, K; Pletz, M W; Heller, R; Neubauer, H

2016-04-05

Q fever is a neglected zoonosis caused by the bacterium Coxiella burnetii. The knowledge of the epidemiology of Q fever in Kenya is limited with no attention to control and prevention programs. The purpose of this review is to understand the situation of Q fever in human and animal populations in Kenya in the past 60 years, and help identify future research priorities for the country. Databases were searched for national and international scientific studies or reports on Q fever. We included studies and reports published between 1950 and 2015 if they reported on Q fever prevalence, incidence, and infection control programs in Kenya. Data were extracted with respect to studies on prevalence of Coxiella infections, study design, study region, the study populations involved, and sorted according to the year of the study. We identified 15 studies and reports which qualified for data extraction. Human seroprevalence studies revealed evidence of C. burnetii infections ranging from 3 to 35.8% in all regions in which surveys were made and two Q fever outbreak episodes. Coxiella burnetii infections found in cattle 7.4-51.1%, sheep 6.7-20%, camels 20-46%, and goats 20-46% revealed variation based on ecoregions and the year of study. Farming and lack of protective clothing were associated with increased seropositivity among humans. However, high quality data is lacking on Q fever awareness, underlying cultural-economic factors influencing C. burnetii infection, and how the pathogen cycles may be embedded in livestock production and management systems in the economically and ecologically different Kenyan regions. We found no studies on national disease incidence estimates or disease surveillance and control efforts. Coxiella burnetii infections are common in human and in a wide range of animal populations but are still unrecognized and underestimated thus presenting a significant human and animal health threat in Kenya. The factors influencing pathogen transmission, persistence and spread are poorly understood. Integrated disease surveillance and prevention/control programs are needed in Kenya.

Can routine surveillance samples from tracheal aspirate predict bacterial flora in cases of ventilator-associated pneumonia?

PubMed

Lampati, L; Maggioni, E; Langer, M; Malacarne, P; Mozzo, R; Pesenti, A; Fumagalli, R

2009-10-01

The aim of this study was to investigate the hypothesis that periodical sampling of the tracheo-bronchial tree in the absence of clinical suspicion of pneumonia is useful to identify bacteria responsible for subsequent late ventilator associated pneumonia (VAP). This was a retrospective observational human study carried out in two medical-surgical intensive care units of two different hospitals. From January 1999 to December 2000, 559 patients, who received invasive respiratory support for more than 48 hours, were screened. Tracheal aspiration (TA) was performed once or twice weekly in all mechanically ventilated patients. The microbiological findings from TA surveillance cultures done in the eight days before suspicion of VAP were compared to those isolated from the positive diagnostic samples done for late onset VAP (after more than four days of mechanical ventilation). The sensitivity, specificity, and positive/negative predictive values of the ability of the surveillance sample to anticipate the VAP pathogen were calculated. Among the microorganisms isolated from TA, 68% were retrieved from diagnostic samples. All VAP pathogens previously isolated were from 43% of the TA samples. If TA was collected 2-4 days before the clinical diagnosis of VAP, pathogens were detected in 58% of samples. In contrast, only 27% were collected more than four days earlier (P<0.05). The positive predictive values for Pseudomonas aeruginosa and methicillin resistant Staphylococcus aureus from routine TA samples were 92% and 90%, respectively. The negative predictive values for Pseudomonas aeruginosa and methicillin resistant Staphylococcus aureus from routine TA samples were 75% and 89%, respectively. TA cultures in ventilated patients may help to predict pathogens. Early detection may lead to earlier treatment in long term ventilated patients when VAP is suspected.

Model-based evaluation of highly and low pathogenic avian influenza dynamics in wild birds

USGS Publications Warehouse

Hénaux, Viviane; Samuel, Michael D.; Bunck, Christine M.

2010-01-01

There is growing interest in avian influenza (AI) epidemiology to predict disease risk in wild and domestic birds, and prevent transmission to humans. However, understanding the epidemic dynamics of highly pathogenic (HPAI) viruses remains challenging because they have rarely been detected in wild birds. We used modeling to integrate available scientific information from laboratory and field studies, evaluate AI dynamics in individual hosts and waterfowl populations, and identify key areas for future research. We developed a Susceptible-Exposed-Infectious-Recovered (SEIR) model and used published laboratory challenge studies to estimate epidemiological parameters (rate of infection, latency period, recovery and mortality rates), considering the importance of age classes, and virus pathogenicity. Infectious contact leads to infection and virus shedding within 1–2 days, followed by relatively slower period for recovery or mortality. We found a shorter infectious period for HPAI than low pathogenic (LP) AI, which may explain that HPAI has been much harder to detect than LPAI during surveillance programs. Our model predicted a rapid LPAI epidemic curve, with a median duration of infection of 50–60 days and no fatalities. In contrast, HPAI dynamics had lower prevalence and higher mortality, especially in young birds. Based on field data from LPAI studies, our model suggests to increase surveillance for HPAI in post-breeding areas, because the presence of immunologically naïve young birds is predicted to cause higher HPAI prevalence and bird losses during this season. Our results indicate a better understanding of the transmission, infection, and immunity-related processes is required to refine predictions of AI risk and spread, improve surveillance for HPAI in wild birds, and develop disease control strategies to reduce potential transmission to domestic birds and/or humans.

National Infectious Diseases Surveillance data of South Korea.

PubMed

Park, Sunhee; Cho, Eunhee

2014-01-01

The Korea Centers for Disease Control and Prevention (KCDC) operate infectious disease surveillance systems to monitor national disease incidence. Since 1954, Korea has collected data on various infectious diseases in accordance with the Infectious Disease Control and Prevention Act. All physicians (including those working in Oriental medicine) who diagnose a patient with an infectious disease or conduct a postmortem examination of an infectious disease case are obliged to report the disease to the system. These reported data are incorporated into the database of the National Infectious Disease Surveillance System, which has been providing web-based real-time surveillance data on infectious diseases since 2001. In addition, the KCDC analyzes reported data and publishes the Infectious Disease Surveillance Yearbook annually.

Surveillance for highly pathogenic H5 avian influenza virus in synanthropic wildlife associated with poultry farms during an acute outbreak

USDA-ARS?s Scientific Manuscript database

In November 2014, a Eurasian strain H5N8 highly pathogenic avian influenza virus was detected in poultry in Canada. Introduced viruses were soon detected in the United States and within six months had spread to 21 states with more than 48 million poultry affected. In an effort to study potential mec...

Surveillance for highly pathogenic avian influenza virus in wild birds during outbreaks in domestic poultry, Minnesota, 2015

USGS Publications Warehouse

Jennelle, Christopher S.; Carstensen, Michelle; Hildebrand, Erik C.; Cornicelli, Louis; Wolf, Paul C.; Grear, Daniel A.; Ip, Hon S.; VanDalen, Kaci K.; Minicucci, Larissa A.

2016-01-01

In 2015, a major outbreak of highly pathogenic avian influenza virus (HPAIV) infection devastated poultry facilities in Minnesota, USA. To clarify the role of wild birds, we tested 3,139 waterfowl fecal samples and 104 sick and dead birds during March 9–June 4, 2015. HPAIV was isolated from a Cooper’s hawk but not from waterfowl.

The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases.

PubMed

Rabaa, Maia A; Tue, Ngo Tri; Phuc, Tran My; Carrique-Mas, Juan; Saylors, Karen; Cotten, Matthew; Bryant, Juliet E; Nghia, Ho Dang Trung; Cuong, Nguyen Van; Pham, Hong Anh; Berto, Alessandra; Phat, Voong Vinh; Dung, Tran Thi Ngoc; Bao, Long Hoang; Hoa, Ngo Thi; Wertheim, Heiman; Nadjm, Behzad; Monagin, Corina; van Doorn, H Rogier; Rahman, Motiur; Tra, My Phan Vu; Campbell, James I; Boni, Maciej F; Tam, Pham Thi Thanh; van der Hoek, Lia; Simmonds, Peter; Rambaut, Andrew; Toan, Tran Khanh; Van Vinh Chau, Nguyen; Hien, Tran Tinh; Wolfe, Nathan; Farrar, Jeremy J; Thwaites, Guy; Kellam, Paul; Woolhouse, Mark E J; Baker, Stephen

2015-12-01

The effect of newly emerging or re-emerging infectious diseases of zoonotic origin in human populations can be potentially catastrophic, and large-scale investigations of such diseases are highly challenging. The monitoring of emergence events is subject to ascertainment bias, whether at the level of species discovery, emerging disease events, or disease outbreaks in human populations. Disease surveillance is generally performed post hoc, driven by a response to recent events and by the availability of detection and identification technologies. Additionally, the inventory of pathogens that exist in mammalian and other reservoirs is incomplete, and identifying those with the potential to cause disease in humans is rarely possible in advance. A major step in understanding the burden and diversity of zoonotic infections, the local behavioral and demographic risks of infection, and the risk of emergence of these pathogens in human populations is to establish surveillance networks in populations that maintain regular contact with diverse animal populations, and to simultaneously characterize pathogen diversity in human and animal populations. Vietnam has been an epicenter of disease emergence over the last decade, and practices at the human/animal interface may facilitate the likelihood of spillover of zoonotic pathogens into humans. To tackle the scientific issues surrounding the origins and emergence of zoonotic infections in Vietnam, we have established The Vietnam Initiative on Zoonotic Infections (VIZIONS). This countrywide project, in which several international institutions collaborate with Vietnamese organizations, is combining clinical data, epidemiology, high-throughput sequencing, and social sciences to address relevant one-health questions. Here, we describe the primary aims of the project, the infrastructure established to address our scientific questions, and the current status of the project. Our principal objective is to develop an integrated approach to the surveillance of pathogens circulating in both human and animal populations and assess how frequently they are exchanged. This infrastructure will facilitate systematic investigations of pathogen ecology and evolution, enhance understanding of viral cross-species transmission events, and identify relevant risk factors and drivers of zoonotic disease emergence.

Bacterial clonal diagnostics as a tool for evidence-based empiric antibiotic selection

PubMed Central

Tchesnokova, Veronika; Avagyan, Hovhannes; Rechkina, Elena; Chan, Diana; Muradova, Mariya; Haile, Helen Ghirmai; Radey, Matthew; Weissman, Scott; Riddell, Kim; Scholes, Delia; Johnson, James R.

2017-01-01

Despite the known clonal distribution of antibiotic resistance in many bacteria, empiric (pre-culture) antibiotic selection still relies heavily on species-level cumulative antibiograms, resulting in overuse of broad-spectrum agents and excessive antibiotic/pathogen mismatch. Urinary tract infections (UTIs), which account for a large share of antibiotic use, are caused predominantly by Escherichia coli, a highly clonal pathogen. In an observational clinical cohort study of urgent care patients with suspected UTI, we assessed the potential for E. coli clonal-level antibiograms to improve empiric antibiotic selection. A novel PCR-based clonotyping assay was applied to fresh urine samples to rapidly detect E. coli and the urine strain's clonotype. Based on a database of clonotype-specific antibiograms, the acceptability of various antibiotics for empiric therapy was inferred using a 20%, 10%, and 30% allowed resistance threshold. The test's performance characteristics and possible effects on prescribing were assessed. The rapid test identified E. coli clonotypes directly in patients’ urine within 25–35 minutes, with high specificity and sensitivity compared to culture. Antibiotic selection based on a clonotype-specific antibiogram could reduce the relative likelihood of antibiotic/pathogen mismatch by ≥ 60%. Compared to observed prescribing patterns, clonal diagnostics-guided antibiotic selection could safely double the use of trimethoprim/sulfamethoxazole and minimize fluoroquinolone use. In summary, a rapid clonotyping test showed promise for improving empiric antibiotic prescribing for E. coli UTI, including reversing preferential use of fluoroquinolones over trimethoprim/sulfamethoxazole. The clonal diagnostics approach merges epidemiologic surveillance, antimicrobial stewardship, and molecular diagnostics to bring evidence-based medicine directly to the point of care. PMID:28350870

Bacterial clonal diagnostics as a tool for evidence-based empiric antibiotic selection.

PubMed

Tchesnokova, Veronika; Avagyan, Hovhannes; Rechkina, Elena; Chan, Diana; Muradova, Mariya; Haile, Helen Ghirmai; Radey, Matthew; Weissman, Scott; Riddell, Kim; Scholes, Delia; Johnson, James R; Sokurenko, Evgeni V

2017-01-01

Despite the known clonal distribution of antibiotic resistance in many bacteria, empiric (pre-culture) antibiotic selection still relies heavily on species-level cumulative antibiograms, resulting in overuse of broad-spectrum agents and excessive antibiotic/pathogen mismatch. Urinary tract infections (UTIs), which account for a large share of antibiotic use, are caused predominantly by Escherichia coli, a highly clonal pathogen. In an observational clinical cohort study of urgent care patients with suspected UTI, we assessed the potential for E. coli clonal-level antibiograms to improve empiric antibiotic selection. A novel PCR-based clonotyping assay was applied to fresh urine samples to rapidly detect E. coli and the urine strain's clonotype. Based on a database of clonotype-specific antibiograms, the acceptability of various antibiotics for empiric therapy was inferred using a 20%, 10%, and 30% allowed resistance threshold. The test's performance characteristics and possible effects on prescribing were assessed. The rapid test identified E. coli clonotypes directly in patients' urine within 25-35 minutes, with high specificity and sensitivity compared to culture. Antibiotic selection based on a clonotype-specific antibiogram could reduce the relative likelihood of antibiotic/pathogen mismatch by ≥ 60%. Compared to observed prescribing patterns, clonal diagnostics-guided antibiotic selection could safely double the use of trimethoprim/sulfamethoxazole and minimize fluoroquinolone use. In summary, a rapid clonotyping test showed promise for improving empiric antibiotic prescribing for E. coli UTI, including reversing preferential use of fluoroquinolones over trimethoprim/sulfamethoxazole. The clonal diagnostics approach merges epidemiologic surveillance, antimicrobial stewardship, and molecular diagnostics to bring evidence-based medicine directly to the point of care.

Integrating animal health and food safety surveillance data from slaughterhouse control.

PubMed

Lynch, J A; Silva, P

2013-08-01

Surveillance at the slaughterhouse level for animal health and food safety purposes encompasses examination for the presence of pathology, pathogens, drug residues, chemical contaminants and antimicrobial resistance. Government, industry and academia are the primary proponents of such surveillance. A variety of policies and policy instruments from voluntary to legislative may be applied to promote or obligate participation. Efforts to integrate data across such diverse organisations encounter significant legal, logistical and financial challenges. Enhancement of policies to encourage effective integration of animal health and food safety surveillance data from slaughterhouse control should promote: a long-term approach; collaboration among government, industry and academia; application of a risk-based scheme; and transparent public access to data, with generation of consumer-oriented communications derived from the data. A strong case can be made that the complementary pursuit of both sustainable animal health and food safety can continue to be aided by surveillance at the slaughterhouse level.

A searchable database for the genome of Phomopsis longicolla (isolate MSPL 10-6).

PubMed

Darwish, Omar; Li, Shuxian; May, Zane; Matthews, Benjamin; Alkharouf, Nadim W

2016-01-01

Phomopsis longicolla (syn. Diaporthe longicolla) is an important seed-borne fungal pathogen that primarily causes Phomopsis seed decay (PSD) in most soybean production areas worldwide. This disease severely decreases soybean seed quality by reducing seed viability and oil quality, altering seed composition, and increasing frequencies of moldy and/or split beans. To facilitate investigation of the genetic base of fungal virulence factors and understand the mechanism of disease development, we designed and developed a database for P. longicolla isolate MSPL 10-6 that contains information about the genome assemblies (contigs), gene models, gene descriptions and GO functional ontologies. A web-based front end to the database was built using ASP.NET, which allows researchers to search and mine the genome of this important fungus. This database represents the first reported genome database for a seed borne fungal pathogen in the Diaporthe- Phomopsis complex. The database will also be a valuable resource for research and agricultural communities. It will aid in the development of new control strategies for this pathogen. http://bioinformatics.towson.edu/Phomopsis_longicolla/HomePage.aspx.

A searchable database for the genome of Phomopsis longicolla (isolate MSPL 10-6)

PubMed Central

May, Zane; Matthews, Benjamin; Alkharouf, Nadim W.

2016-01-01

Phomopsis longicolla (syn. Diaporthe longicolla) is an important seed-borne fungal pathogen that primarily causes Phomopsis seed decay (PSD) in most soybean production areas worldwide. This disease severely decreases soybean seed quality by reducing seed viability and oil quality, altering seed composition, and increasing frequencies of moldy and/or split beans. To facilitate investigation of the genetic base of fungal virulence factors and understand the mechanism of disease development, we designed and developed a database for P. longicolla isolate MSPL 10-6 that contains information about the genome assemblies (contigs), gene models, gene descriptions and GO functional ontologies. A web-based front end to the database was built using ASP.NET, which allows researchers to search and mine the genome of this important fungus. This database represents the first reported genome database for a seed borne fungal pathogen in the Diaporthe– Phomopsis complex. The database will also be a valuable resource for research and agricultural communities. It will aid in the development of new control strategies for this pathogen. Availability: http://bioinformatics.towson.edu/Phomopsis_longicolla/HomePage.aspx PMID:28197060

Insurance claims data: a possible solution for a national sports injury surveillance system? An evaluation of data information against ASIDD and consensus statements on sports injury surveillance.

PubMed

Aman, Malin; Forssblad, Magnus; Henriksson-Larsén, Karin

2014-06-12

Before preventive actions can be suggested for sports injuries at the national level, a solid surveillance system is required in order to study their epidemiology, risk factors and mechanisms. There are guidelines for sports injury data collection and classifications in the literature for that purpose. In Sweden, 90% of all athletes (57/70 sports federations) are insured with the same insurance company and data from their database could be a foundation for studies on acute sports injuries at the national level. To evaluate the usefulness of sports injury insurance claims data in sports injury surveillance at the national level. A database with 27 947 injuries was exported to an Excel file. Access to the corresponding text files was also obtained. Data were reviewed on available information, missing information and dropouts. Comparison with ASIDD (Australian Sports Injury Data Dictionary) and existing consensus statements in the literature (football (soccer), rugby union, tennis, cricket and thoroughbred horse racing) was performed in a structured manner. Comparison with ASIDD showed that 93% of the suggested data items were present in the database to at least some extent. Compliance with the consensus statements was generally high (13/18). Almost all claims (83%) contained text information concerning the injury. Relatively high-quality sports injury data can be obtained from a specific insurance company at the national level in Sweden. The database has the potential to be a solid base for research on acute sports injuries in different sports at the national level. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Linezolid Surveillance Results for the United States: LEADER Surveillance Program 2011

PubMed Central

Mendes, Rodrigo E.; Ross, James E.; Sader, Helio S.; Jones, Ronald N.

2013-01-01

The LEADER surveillance program monitors the in vitro activity of linezolid and comparator agents against Gram-positive bacteria in the United States. In its eighth consecutive year (2011), a total of 60 medical centers from the United States, including seven medical centers specializing in children's health care contributed a total of 7,303 Gram-positive pathogens. The MIC90 value for Staphylococcus aureus was 2 μg/ml, and for coagulase-negative staphylococci, enterococci, Streptococcus pneumoniae, β-hemolytic streptococci, and viridans group streptococci, the MIC90 was 1 μg/ml. The “all organism” linezolid-resistant and nonsusceptible rate was only 0.19%. PMID:23254424

New insights in the treatment by levofloxacin.

PubMed

File, Thomas M

2004-01-01

Levofloxacin is widely regarded as one of the most important fluoroquinolones available today. It possesses excellent activity against a wide range of important pathogens, including those resistant to many other antimicrobials. While rates of resistance to other previously useful antimicrobial classes has grown, levofloxacin has maintained its efficacy, with generally very low rates of resistance around the world. It is indicated for a wide range of infections including community-acquired respiratory infections in adults, particularly community-acquired pneumonia (CAP), acute bacterial exacerbations of chronic bronchitis (AECB), and acute sinusitis. In addition, it is recommended for infections of skin and soft tissue, and the urinary tract. With postmarketing surveillance data available for the last decade, levofloxacin possesses an unparalleled database to demonstrate its clinical efficacy and safety. Remarkably, levofloxacin continues to expand its list of indications. The development of a new high-dose 750-mg schedule has the potential to decrease the duration of treatment as well as reduce the emergence of resistance.

Factorial analysis of trihalomethanes formation in drinking water.

PubMed

Chowdhury, Shakhawat; Champagne, Pascale; McLellan, P James

2010-06-01

Disinfection of drinking water reduces pathogenic infection, but may pose risks to human health through the formation of disinfection byproducts. The effects of different factors on the formation of trihalomethanes were investigated using a statistically designed experimental program, and a predictive model for trihalomethanes formation was developed. Synthetic water samples with different factor levels were produced, and trihalomethanes concentrations were measured. A replicated fractional factorial design with center points was performed, and significant factors were identified through statistical analysis. A second-order trihalomethanes formation model was developed from 92 experiments, and the statistical adequacy was assessed through appropriate diagnostics. This model was validated using additional data from the Drinking Water Surveillance Program database and was applied to the Smiths Falls water supply system in Ontario, Canada. The model predictions were correlated strongly to the measured trihalomethanes, with correlations of 0.95 and 0.91, respectively. The resulting model can assist in analyzing risk-cost tradeoffs in the design and operation of water supply systems.

Training initiatives within the AFHSC-Global Emerging Infections Surveillance and Response System: support for IHR (2005)

PubMed Central

2011-01-01

Training is a key component of building capacity for public health surveillance and response, but has often been difficult to quantify. During fiscal 2009, the Armed Forces Health Surveillance Center, Division of Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) supported 18 partner organizations in conducting 123 training initiatives in 40 countries for 3,130 U.S. military, civilian and host-country personnel. The training assisted with supporting compliance with International Health Regulations, IHR (2005). Training activities in pandemic preparedness, outbreak investigation and response, emerging infectious disease (EID) surveillance and pathogen diagnostic techniques were expanded significantly. By engaging local health and other government officials and civilian institutions, the U.S. military’s role as a key stakeholder in global public health has been strengthened and has contributed to EID-related surveillance, research and capacity-building initiatives specified elsewhere in this issue. Public health and emerging infections surveillance training accomplished by AFHSC-GEIS and its Department of Defense (DoD) partners during fiscal 2009 will be tabulated and described. PMID:21388565

Pathogen metadata platform: software for accessing and analyzing pathogen strain information.

PubMed

Chang, Wenling E; Peterson, Matthew W; Garay, Christopher D; Korves, Tonia

2016-09-15

Pathogen metadata includes information about where and when a pathogen was collected and the type of environment it came from. Along with genomic nucleotide sequence data, this metadata is growing rapidly and becoming a valuable resource not only for research but for biosurveillance and public health. However, current freely available tools for analyzing this data are geared towards bioinformaticians and/or do not provide summaries and visualizations needed to readily interpret results. We designed a platform to easily access and summarize data about pathogen samples. The software includes a PostgreSQL database that captures metadata useful for disease outbreak investigations, and scripts for downloading and parsing data from NCBI BioSample and BioProject into the database. The software provides a user interface to query metadata and obtain standardized results in an exportable, tab-delimited format. To visually summarize results, the user interface provides a 2D histogram for user-selected metadata types and mapping of geolocated entries. The software is built on the LabKey data platform, an open-source data management platform, which enables developers to add functionalities. We demonstrate the use of the software in querying for a pathogen serovar and for genome sequence identifiers. This software enables users to create a local database for pathogen metadata, populate it with data from NCBI, easily query the data, and obtain visual summaries. Some of the components, such as the database, are modular and can be incorporated into other data platforms. The source code is freely available for download at https://github.com/wchangmitre/bioattribution .

Defining Care Patterns and Outcomes Among Persons Living with HIV in Washington, DC: Linkage of Clinical Cohort and Surveillance Data

PubMed Central

Terzian, Arpi; Opoku, Jenevieve; Happ, Lindsey Powers; Younes, Naji; Kharfen, Michael; Greenberg, Alan

2018-01-01

Background Triangulation of data from multiple sources such as clinical cohort and surveillance data can help improve our ability to describe care patterns, service utilization, comorbidities, and ultimately measure and monitor clinical outcomes among persons living with HIV infection. Objectives The objective of this study was to determine whether linkage of clinical cohort data and routinely collected HIV surveillance data would enhance the completeness and accuracy of each database and improve the understanding of care patterns and clinical outcomes. Methods We linked data from the District of Columbia (DC) Cohort, a large HIV observational clinical cohort, with Washington, DC, Department of Health (DOH) surveillance data between January 2011 and June 2015. We determined percent concordance between select variables in the pre- and postlinked databases using kappa test statistics. We compared retention in care (RIC), viral suppression (VS), sexually transmitted diseases (STDs), and non-HIV comorbid conditions (eg, hypertension) and compared HIV clinic visit patterns determined using the prelinked database (DC Cohort) versus the postlinked database (DC Cohort + DOH) using chi-square testing. Additionally, we compared sociodemographic characteristics, RIC, and VS among participants receiving HIV care at ≥3 sites versus <3 sites using chi-square testing. Results Of the 6054 DC Cohort participants, 5521 (91.19%) were included in the postlinked database and enrolled at a single DC Cohort site. The majority of the participants was male, black, and had men who have sex with men (MSM) as their HIV risk factor. In the postlinked database, 619 STD diagnoses previously unknown to the DC Cohort were identified. Additionally, the proportion of participants with RIC was higher compared with the prelinked database (59.83%, 2678/4476 vs 64.95%, 2907/4476; P<.001) and the proportion with VS was lower (87.85%, 2277/2592 vs 85.15%, 2391/2808; P<.001). Almost a quarter of participants (23.06%, 1279/5521) were identified as receiving HIV care at ≥2 sites (postlinked database). The participants using ≥3 care sites were more likely to achieve RIC (80.7%, 234/290 vs 62.61%, 2197/3509) but less likely to achieve VS (72.3%, 154/213 vs 89.51%, 1869/2088). The participants using ≥3 care sites were more likely to have unstable housing (15.1%, 64/424 vs 8.96%, 380/4242), public insurance (86.1%, 365/424 vs 57.57%, 2442/4242), comorbid conditions (eg, hypertension) (37.7%, 160/424 vs 22.98%, 975/4242), and have acquired immunodeficiency syndrome (77.8%, 330/424 vs 61.20%, 2596/4242) (all P<.001). Conclusions Linking surveillance and clinical data resulted in the improved completeness of each database and a larger volume of available data to evaluate HIV outcomes, allowing for refinement of HIV care continuum estimates. The postlinked database also highlighted important differences between participants who sought HIV care at multiple clinical sites. Our findings suggest that combined datasets can enhance evaluation of HIV-related outcomes across an entire metropolitan area. Future research will evaluate how to best utilize this information to improve outcomes in addition to monitoring them. PMID:29549065

Methods for molecular surveillance of influenza.

PubMed

Wang, Ruixue; Taubenberger, Jeffery K

2010-05-01

Molecular-based techniques for detecting influenza viruses have become an integral component of human and animal surveillance programs in the last two decades. The recent pandemic of the swine-origin influenza A virus (H1N1) and the continuing circulation of highly pathogenic avian influenza A virus (H5N1) further stress the need for rapid and accurate identification and subtyping of influenza viruses for surveillance, outbreak management, diagnosis and treatment. There has been remarkable progress on the detection and molecular characterization of influenza virus infections in clinical, mammalian, domestic poultry and wild bird samples in recent years. The application of these techniques, including reverse transcriptase-PCR, real-time PCR, microarrays and other nucleic acid sequencing-based amplifications, have greatly enhanced the capability for surveillance and characterization of influenza viruses.

[Comparing results of methicillin-resistant Staphylococcus aureus (MRSA) surveillance using the French DRG-based information system (PMSI)].

PubMed

Nuemi, G; Astruc, K; Aho, S; Quantin, C

2013-10-01

The surveillance of methicillin-resistant Staphylococcus aureus (MRSA) is a national priority. The rate of MRSA infections is one of six indicators tracked by the Department of Health. Since 2002, the French institute for public health surveillance (InVS) has monitored MRSA infections to estimate incidence density. Today, the use of the French administrative database (PMSI) could facilitate this surveillance. The aim of this study was to compare MRSA incidence density computed at a national level using PMSI databases with the results from the InVS taken as the reference. PMSI databases for the years 2006 to 2009 were used. The reference results were those published by the InVS from 2006 to 2009. MRSA density defined as the number of MRSA infections recorded per year over 1000 hospital stays was computed. It was then compared with the MRSA incidence density measured by InVS. The time course of MRSA incidence in the PMSI records was modeled using a Poisson regression. The incidence density measured by the InVS was higher than the MRSA density computed using the PMSI, but this difference appeared to decrease over time. The PMSI density/InVS MRSA incidence density ratio was 0.8% in 2006 and about 9.2% in 2009. We observed inverted trends with a growing trend in MRSA density identified by the PMSI. Furthermore, the year of study was significantly associated with incidence density (P=0.01). Using PMSI data as an additional source of information in the hospital MRSA surveillance process makes it possible to detect and analyze patient repeats at the regional and national levels with linkage facilities. Estimation of incidence density for hospitals not participating to this surveillance system will be the next step. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

UMD-USHbases: a comprehensive set of databases to record and analyse pathogenic mutations and unclassified variants in seven Usher syndrome causing genes.

PubMed

Baux, David; Faugère, Valérie; Larrieu, Lise; Le Guédard-Méreuze, Sandie; Hamroun, Dalil; Béroud, Christophe; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

2008-08-01

Using the Universal Mutation Database (UMD) software, we have constructed "UMD-USHbases", a set of relational databases of nucleotide variations for seven genes involved in Usher syndrome (MYO7A, CDH23, PCDH15, USH1C, USH1G, USH3A and USH2A). Mutations in the Usher syndrome type I causing genes are also recorded in non-syndromic hearing loss cases and mutations in USH2A in non-syndromic retinitis pigmentosa. Usher syndrome provides a particular challenge for molecular diagnostics because of the clinical and molecular heterogeneity. As many mutations are missense changes, and all the genes also contain apparently non-pathogenic polymorphisms, well-curated databases are crucial for accurate interpretation of pathogenicity. Tools are provided to assess the pathogenicity of mutations, including conservation of amino acids and analysis of splice-sites. Reference amino acid alignments are provided. Apparently non-pathogenic variants in patients with Usher syndrome, at both the nucleotide and amino acid level, are included. The UMD-USHbases currently contain more than 2,830 entries including disease causing mutations, unclassified variants or non-pathogenic polymorphisms identified in over 938 patients. In addition to data collected from 89 publications, 15 novel mutations identified in our laboratory are recorded in MYO7A (6), CDH23 (8), or PCDH15 (1) genes. Information is given on the relative involvement of the seven genes, the number and distribution of variants in each gene. UMD-USHbases give access to a software package that provides specific routines and optimized multicriteria research and sorting tools. These databases should assist clinicians and geneticists seeking information about mutations responsible for Usher syndrome.

The UCL low-density lipoprotein receptor gene variant database: pathogenicity update

PubMed Central

Futema, Marta; Whittall, Ros; Taylor-Beadling, Alison; Williams, Maggie; den Dunnen, Johan T; Humphries, Steve E

2017-01-01

Background Familial hypercholesterolaemia (OMIM 143890) is most frequently caused by variations in the low-density lipoprotein receptor (LDLR) gene. Predicting whether novel variants are pathogenic may not be straightforward, especially for missense and synonymous variants. In 2013, the Association of Clinical Genetic Scientists published guidelines for the classification of variants, with categories 1 and 2 representing clearly not or unlikely pathogenic, respectively, 3 representing variants of unknown significance (VUS), and 4 and 5 representing likely to be or clearly pathogenic, respectively. Here, we update the University College London (UCL) LDLR variant database according to these guidelines. Methods PubMed searches and alerts were used to identify novel LDLR variants for inclusion in the database. Standard in silico tools were used to predict potential pathogenicity. Variants were designated as class 4/5 only when the predictions from the different programs were concordant and as class 3 when predictions were discordant. Results The updated database (http://www.lovd.nl/LDLR) now includes 2925 curated variants, representing 1707 independent events. All 129 nonsense variants, 337 small frame-shifting and 117/118 large rearrangements were classified as 4 or 5. Of the 795 missense variants, 115 were in classes 1 and 2, 605 in class 4 and 75 in class 3. 111/181 intronic variants, 4/34 synonymous variants and 14/37 promoter variants were assigned to classes 4 or 5. Overall, 112 (7%) of reported variants were class 3. Conclusions This study updates the LDLR variant database and identifies a number of reported VUS where additional family and in vitro studies will be required to confirm or refute their pathogenicity. PMID:27821657

Molecular epidemiological view on Shiga toxin-producing Escherichia coli causing human disease in Germany: Diversity, prevalence, and outbreaks.

PubMed

Fruth, Angelika; Prager, Rita; Tietze, Erhard; Rabsch, Wolfgang; Flieger, Antje

2015-10-01

Infections by intestinal pathogenic Escherichia coli (E. coli) are among those causing a high mortality and morbidity due to diarrheal disease and post infection sequelae worldwide. Since introduction of the Infection Protection Act in Germany 2001, these pathogens rank third among bacterial infections of the gastrointestinal tract. As a major pathovar Shiga toxin-producing E. coli (STEC) which include enterohemorrhagic E. coli (EHEC) play a leading role in occurrence of sporadic cases and disease outbreaks. An outstanding example is the large outbreak in spring 2011 caused by EHEC/EAEC O104:H4. To monitor and trace back STEC infections, national surveillance programs have been implemented including activities of the German National Reference Centre for Salmonella and other Enteric Bacterial Pathogens (NRC). This review highlights advances in our understanding of STEC in the last 20 years of STEC surveillance by the NRC. Here important characteristics of STEC strains from human infections and outbreaks in Germany between 1997 and 2013 are summarized. Copyright © 2015. Published by Elsevier GmbH.

Public Health Surveillance Strategies for Mass Gatherings: Super Bowl XLIX and Related Events, Maricopa County, Arizona, 2015.

PubMed

Ayala, Aurimar; Berisha, Vjollca; Goodin, Kate; Pogreba-Brown, Kristen; Levy, Craig; McKinney, Benita; Koski, Lia; Imholte, Sara

2016-01-01

Super Bowl XLIX took place on February 1, 2015, in Glendale, Arizona. In preparation for this event and associated activities, the Maricopa County Department of Public Health (MCDPH) developed methods for enhanced surveillance, situational awareness, and early detection of public health emergencies. Surveillance strategies implemented from January 22 to February 6, 2015, included enhanced surveillance alerts; animal disease surveillance; review of NFL clinic visits; syndromic surveillance for emergency room visits, urgent care facilities, and hotels; real-time onsite syndromic surveillance; all-hazards mortality surveillance; emergency medical services surveillance, review of poison control center reports; media surveillance; and aberration detection algorithms for notifiable diseases. Surveillance results included increased influenzalike illness activity reported from urgent care centers and a few influenza cases reported in the NFL clinic. A cyanide single event exposure was investigated and determined not to be a public health threat. Real-time field syndromic surveillance documented minor injuries at all events and sporadic cases of gastrointestinal and neurological (mostly headaches) disease. Animal surveillance reports included a cat suspected of carrying plague and tularemia and an investigation of highly pathogenic avian influenza in a backyard chicken flock. Laboratory results in both instances were negative. Aberration detection and syndromic surveillance detected an increase in measles reports associated with a Disneyland exposure, and syndromic surveillance was used successfully during this investigation. Coordinated enhanced epidemiologic surveillance during Super Bowl XLIX increased the response capacity and preparedness of MCDPH to make informed decisions and take public health actions in a timely manner during these mass gathering events.

Acceptance of the Use of HIV Surveillance Data for Care Engagement: National and Local Community Perspectives

PubMed Central

Evans, David; Van Gorder, Dana; Morin, Stephen F.; Steward, Wayne T.; Gaffney, Stuart; Charlebois, Edwin D.

2015-01-01

Background Use of surveillance data including laboratory results (e.g. CD4 and HIV RNA) by public health departments to facilitate linkage, retention, and re-engagement of HIV-infected individuals in health care is on the rise. This is part of the goal of increasing the proportion of infected persons achieving virologic suppression. However, this use of surveillance data is not without controversy, particularly among some providers and people living with HIV. Methods We conducted informal discussions with key stakeholders and a literature search, and held a national think tank in November 2012, bringing together 31 representatives of the federal government, county and state officials, health care providers, and community-based organizations. A follow-up community consultation specific to San Francisco was held January 24, 2014, with 10 participants. Notes from these activities were used as data for this analysis. Results The think tank identified three strategies utilizing HIV surveillance data to aid in care engagement: 1) provider-mediated – where health department staff work with the provider of record on re-engagement, 2) electronic linkages between surveillance databases and medical records databases, and 3) direct outreach – where trained health department staff reach out to persons out of care. Participants also developed recommendations for minimizing harm, guidance on meaningful stakeholder involvement, and a consensus statement in support of the use of HIV surveillance data in care engagement. Conclusions Acceptance of the use of surveillance data for HIV care linkage, retention, and re-engagement is achievable, particularly if stakeholders have been engaged in the design, conduct, and evaluation of programs. PMID:25867776

Novel utilization of the outer membrane proteins for the identification and differentiation of pathogenic versus nonpathogenic microbial strains using mass spectrometry-based proteomics approach

NASA Astrophysics Data System (ADS)

Jabbour, Rabih E.; Wade, Mary; Deshpande, Samir V.; McCubbin, Patrick; Snyder, A. Peter; Bevilacqua, Vicky

2012-06-01

Mass spectrometry based proteomic approaches are showing promising capabilities in addressing various biological and biochemical issues. Outer membrane proteins (OMPs) are often associated with virulence in gram-negative pathogens and could prove to be excellent model biomarkers for strain level differentiation among bacteria. Whole cells and OMP extracts were isolated from pathogenic and non-pathogenic strains of Francisella tularensis, Burkholderia thailandensis, and Burkholderia mallei. OMP extracts were compared for their ability to differentiate and delineate the correct database organism to an experimental sample and for the degree of dissimilarity to the nearest-neighbor database strains. This study addresses the comparative experimental proteome analyses of OMPs vs. whole cell lysates on the strain-level discrimination among gram negative pathogenic and non-pathogenic strains.

Variations in clinicopathologic characteristics of thyroid cancer among racial ethnic groups: analysis of a large public city hospital and the SEER database.

PubMed

Moo-Young, Tricia A; Panergo, Jessel; Wang, Chih E; Patel, Subhash; Duh, Hong Yan; Winchester, David J; Prinz, Richard A; Fogelfeld, Leon

2013-11-01

Clinicopathologic variables influence the treatment and prognosis of patients with thyroid cancer. A retrospective analysis of public hospital thyroid cancer database and the Surveillance, Epidemiology and End Results 17 database was conducted. Demographic, clinical, and pathologic data were compared across ethnic groups. Within the public hospital database, Hispanics versus non-Hispanic whites were younger and had more lymph node involvement (34% vs 17%, P < .001). Median tumor size was not statistically different across ethnic groups. Similar findings were demonstrated within the Surveillance, Epidemiology and End Results database. African Americans aged <45 years had the largest tumors but were least likely to have lymph node involvement. Asians had the most stage IV disease despite having no differences in tumor size, lymph node involvement, and capsular invasion. There is considerable variability in the clinical presentation of thyroid cancer across ethnic groups. Such disparities persist within an equal-access health care system. These findings suggest that factors beyond socioeconomics may contribute to such differences. Copyright © 2013 Elsevier Inc. All rights reserved.

Surveillance for Highly Pathogenic Avian Influenza Virus in Wild Birds during Outbreaks in Domestic Poultry, Minnesota, 2015.

PubMed

Jennelle, Christopher S; Carstensen, Michelle; Hildebrand, Erik C; Cornicelli, Louis; Wolf, Paul; Grear, Daniel A; Ip, Hon S; Vandalen, Kaci K; Minicucci, Larissa A

2016-07-01

In 2015, a major outbreak of highly pathogenic avian influenza virus (HPAIV) infection devastated poultry facilities in Minnesota, USA. To understand the potential role of wild birds, we tested 3,139 waterfowl fecal samples and 104 sick and dead birds during March 9-June 4, 2015. HPAIV was isolated from a Cooper's hawk but not from waterfowl fecal samples.

Highly Pathogenic Avian Influenza Virus (H5N8) Clade 2.3.4.4 Infection in Migratory Birds, Egypt.

PubMed

Selim, Abdullah A; Erfan, Ahmed M; Hagag, Naglaa; Zanaty, Ali; Samir, Abdel-Hafez; Samy, Mohamed; Abdelhalim, Ahmed; Arafa, Abdel-Satar A; Soliman, Mohamed A; Shaheen, Momtaz; Ibraheem, Essam M; Mahrous, Ibrahim; Hassan, Mohamed K; Naguib, Mahmoud M

2017-06-01

We isolated highly pathogenic avian influenza virus (H5N8) of clade 2.3.4.4 from the common coot (Fulica atra) in Egypt, documenting its introduction into Africa through migratory birds. This virus has a close genetic relationship with subtype H5N8 viruses circulating in Europe. Enhanced surveillance to detect newly emerging viruses is warranted.

Immunological and molecular characterization of Leptospira interrogans isolated from a bovine foetus.

PubMed

Monte, Leonardo Garcia; Ridieri, Karine Forster; Jorge, Sérgio; Oliveira, Natasha Rodrigues; Hartwig, Daiane Drawanz; Amaral, Marta Gonçalves; Hartleben, Cláudia Pinho; Dellagostin, Odir Antonio

2015-06-01

Cattle are commonly infected with pathogenic leptospires, and similarly to rodents, they excrete the bacteria in their urine and can transmit the pathogen from animal to animal or animal to human. Thus, surveillance and monitoring systems for detection of new Leptospira serovars are important for the control of leptospirosis. Here, we report the isolation of a spirochete from a stillborn bovine foetus and its characterization by immunological and molecular techniques. A variable number tandem repeat profile using seven discriminatory primers identified the spirochete as belonging to species Leptospira interrogans serogroup Australis serovar Muenchen. A phenotypic analysis using monoclonal antibodies (mAbs) against leptospiral membrane-associated proteins confirmed the expression of important virulence and pathogenicity factors (LipL32 and LigBrep). Out of 120 reference sera tested, 22 positive (36.66%) and 9 negative (15%) also reacted with the new isolate. Furthermore, the serovar Muenchen isolate was virulent in hamster model. The animal inoculated developed acute lethal infection characterized by hepatic, pulmonary and renal lesions. Local isolates exhibited unique characteristics that differed from those of reference strains; therefore, isolation of leptospires is useful in the surveillance of local pathogenic serovars. In conclusion, the data obtained from this study can contribute to the epidemiological understanding and control of leptospirosis in southern Brazil. Copyright © 2015 Elsevier Ltd. All rights reserved.

How Intrusion Detection Can Improve Software Decoy Applications

DTIC Science & Technology

2003-03-01

THIS PAGE INTENTIONALLY LEFT BLANK 41 V. DISCUSSION Military history suggests it is best to employ a layered, defense-in...database: alert, postgresql , user=snort dbname=snort # output database: log, unixodbc, user=snort dbname=snort # output database: log, mssql, dbname...Threat Monitoring and Surveillance, James P. Anderson Co., Fort Washington. PA, April 1980. URL http://csrc.nist.gov/publications/ history /ande80

Surveillance for Asian H5N1 avian influenza in the United States

USGS Publications Warehouse

Ip, Hon S.; Slota, Paul G.

2006-01-01

Increasing concern over the potential for migratory birds to introduce the Asian H5N1 strain of avian influenza to North America prompted the White House Policy Coordinating Committee for Pandemic Influenza Preparedness to request that the U.S. Departments of Agriculture (USDA) and Interior (DOI) develop a plan for the early detection of highly pathogenic avian influenza (HPAI) in the United States. To promote coordination among wildlife, agriculture, and human health agencies on HPAI surveillance efforts, the two Departments worked with representatives from the U.S. Department of Health and Human Services, the International Association of Fish and Wildlife Agencies, and the Alaska Department of Fish and Game to develop the U.S. Interagency Strategic Plan for Early Detection of Asian H5N1 Highly Pathogenic Avian Influenza in Wild Migratory Birds.

[A relational database to store Poison Centers calls].

PubMed

Barelli, Alessandro; Biondi, Immacolata; Tafani, Chiara; Pellegrini, Aristide; Soave, Maurizio; Gaspari, Rita; Annetta, Maria Giuseppina

2006-01-01

Italian Poison Centers answer to approximately 100,000 calls per year. Potentially, this activity is a huge source of data for toxicovigilance and for syndromic surveillance. During the last decade, surveillance systems for early detection of outbreaks have drawn the attention of public health institutions due to the threat of terrorism and high-profile disease outbreaks. Poisoning surveillance needs the ongoing, systematic collection, analysis, interpretation, and dissemination of harmonised data about poisonings from all Poison Centers for use in public health action to reduce morbidity and mortality and to improve health. The entity-relationship model for a Poison Center relational database is extremely complex and not studied in detail. For this reason, not harmonised data collection happens among Italian Poison Centers. Entities are recognizable concepts, either concrete or abstract, such as patients and poisons, or events which have relevance to the database, such as calls. Connectivity and cardinality of relationships are complex as well. A one-to-many relationship exist between calls and patients: for one instance of entity calls, there are zero, one, or many instances of entity patients. At the same time, a one-to-many relationship exist between patients and poisons: for one instance of entity patients, there are zero, one, or many instances of entity poisons. This paper shows a relational model for a poison center database which allows the harmonised data collection of poison centers calls.

Surveillance of Food- and Smear-Transmitted Pathogens in European Soldiers with Diarrhea on Deployment in the Tropics: Experience from the European Union Training Mission (EUTM) Mali

PubMed Central

Frickmann, Hagen; Warnke, Philipp; Frey, Claudia; Schmidt, Salvatore; Janke, Christian; Erkens, Kay; Schotte, Ulrich; Köller, Thomas; Maaßen, Winfried; Podbielski, Andreas; Binder, Alfred; Hinz, Rebecca; Queyriaux, Benjamin; Wiemer, Dorothea; Schwarz, Norbert Georg; Hagen, Ralf Matthias

2015-01-01

Introduction. Since 2013, European soldiers have been deployed on the European Union Training Mission (EUTM) in Mali. From the beginning, diarrhea has been among the most “urgent” concerns. Diarrhea surveillance based on deployable real-time PCR equipment was conducted between December 2013 and August 2014. Material and Methods. In total, 53 stool samples were obtained from 51 soldiers with acute diarrhea. Multiplex PCR panels comprised enteroinvasive bacteria, diarrhea-associated Escherichia coli (EPEC, ETEC, EAEC, and EIEC), enteropathogenic viruses, and protozoa. Noroviruses were characterized by sequencing. Cultural screening for Enterobacteriaceae with extended-spectrum beta-lactamases (ESBL) with subsequent repetitive sequence-based PCR (rep-PCR) typing was performed. Clinical information was assessed. Results. Positive PCR results for diarrhea-associated pathogens were detected in 43/53 samples, comprising EPEC (n = 21), ETEC (n = 19), EAEC (n = 15), Norovirus (n = 10), Shigella spp./EIEC (n = 6), Cryptosporidium parvum (n = 3), Giardia duodenalis (n = 2), Salmonella spp. (n = 1), Astrovirus (n = 1), Rotavirus (n = 1), and Sapovirus (n = 1). ESBL-positive Enterobacteriaceae were grown from 13 out of 48 samples. Simultaneous infections with several enteropathogenic agents were observed in 23 instances. Symptoms were mild to moderate. There were hints of autochthonous transmission. Conclusions. Multiplex real-time PCR proved to be suitable for diarrhea surveillance on deployment. Etiological attribution is challenging in cases of detection of multiple pathogens. PMID:26525953

Detection of the Invasive Mosquito Species Aedes (Stegomyia) albopictus (Diptera: Culicidae) in Portugal.

PubMed

Osório, Hugo Costa; Zé-Zé, Líbia; Neto, Maria; Silva, Sílvia; Marques, Fátima; Silva, Ana Sofia; Alves, Maria João

2018-04-21

The Asian tiger mosquito Aedes albopictus is an invasive mosquito originating from the Asia-Pacific region. This species is of major concern to public and veterinary health because of its vector role in the transmission of several pathogens, such as chikungunya, dengue, and Zika viruses. In Portugal, a National Vector Surveillance Network (REde de VIgilância de VEctores—REVIVE) is responsible for the surveillance of autochthonous, but also invasive, mosquito species at points of entry, such as airports, ports, storage areas, and specific border regions with Spain. At these locations, networks of mosquito traps are set and maintained under surveillance throughout the year. In September 2017, Ae. albopictus was detected for the first time in a tyre company located in the North of Portugal. Molecular typing was performed, and a preliminary phylogenetic analysis indicated a high similarity with sequences of Ae. albopictus collected in Europe. A prompt surveillance response was locally implemented to determine its dispersal and abundance, and adult mosquitoes were screened for the presence of arboviral RNA. A total of 103 specimens, 52 immatures and 51 adults, were collected. No pathogenic viruses were detected. Despite the obtained results suggest low abundance of the population locally introduced, the risk of dispersal and potential establishment of Ae. albopictus in Portugal has raised concern for autochthonous mosquito-borne disease outbreaks.

Syndromic surveillance for West Nile virus using raptors in rehabilitation.

PubMed

Ana, Alba; Perez Andrés, M; Julia, Ponder; Pedro, Puig; Arno, Wünschmann; Kimberly, Vander Waal; Julio, Alvarez; Michelle, Willette

2017-11-29

Wildlife rehabilitation centers routinely gather health-related data from diverse species. Their capability to signal the occurrence of emerging pathogens and improve traditional surveillance remains largely unexplored. This paper assessed the utility for syndromic surveillance of raptors admitted to The Raptor Center (TRC) to signal circulation of West Nile Virus (WNV) in Minnesota between 1990 and 2014. An exhaustive descriptive analysis using grouping time series structures and models of interrupted times series was conducted for indicator subsets. A total of 13,080 raptors were monitored. The most representative species were red-tailed hawks, great horned owls, Cooper's hawks, American kestrels and bald eagles. Results indicated that temporal patterns of accessions at the TRC changed distinctively after the incursion of WNV in 2002. The frequency of hawks showing WNV-like signs increased almost 3 times during July and August, suggesting that monitoring of hawks admitted to TRC with WNV-like signs could serve as an indicator of WNV circulation. These findings were also supported by the results of laboratory diagnosis. This study demonstrates that monitoring of data routinely collected by wildlife rehabilitation centers has the potential to signal the spread of pathogens that may affect wild, domestic animals and humans, thus supporting the early detection of disease incursions in a region and monitoring of disease trends. Ultimately, data collected in rehabilitation centers may provide insights to efficiently allocate financial and human resources on disease prevention and surveillance.

Detection of the Invasive Mosquito Species Aedes (Stegomyia) albopictus (Diptera: Culicidae) in Portugal

PubMed Central

Osório, Hugo Costa; Zé-Zé, Líbia; Neto, Maria; Silva, Sílvia; Marques, Fátima; Silva, Ana Sofia; Alves, Maria João

2018-01-01

The Asian tiger mosquito Aedes albopictus is an invasive mosquito originating from the Asia-Pacific region. This species is of major concern to public and veterinary health because of its vector role in the transmission of several pathogens, such as chikungunya, dengue, and Zika viruses. In Portugal, a National Vector Surveillance Network (REde de VIgilância de VEctores—REVIVE) is responsible for the surveillance of autochthonous, but also invasive, mosquito species at points of entry, such as airports, ports, storage areas, and specific border regions with Spain. At these locations, networks of mosquito traps are set and maintained under surveillance throughout the year. In September 2017, Ae. albopictus was detected for the first time in a tyre company located in the North of Portugal. Molecular typing was performed, and a preliminary phylogenetic analysis indicated a high similarity with sequences of Ae. albopictus collected in Europe. A prompt surveillance response was locally implemented to determine its dispersal and abundance, and adult mosquitoes were screened for the presence of arboviral RNA. A total of 103 specimens, 52 immatures and 51 adults, were collected. No pathogenic viruses were detected. Despite the obtained results suggest low abundance of the population locally introduced, the risk of dispersal and potential establishment of Ae. albopictus in Portugal has raised concern for autochthonous mosquito-borne disease outbreaks. PMID:29690531

Epidemiology of norovirus infections among diarrhea outpatients in a diarrhea surveillance system in Shanghai, China: a cross-sectional study.

PubMed

Xue, Ying; Pan, Hao; Hu, Jiayu; Wu, Huanyu; Li, Jian; Xiao, Wenjia; Zhang, Xi; Yuan, Zheng'an; Wu, Fan

2015-04-15

Norovirus is an important cause of gastroenteritis both in children and adults. In China, few studies have been conducted on adult populations. This study aimed to determine the contribution of norovirus to gastroenteritis, characterize the features of norovirus infections, compare them with other pathogens, and test the effectiveness of the surveillance system. A citywide surveillance network on diarrhea patients was established. Samples were collected with intervals from both children and adults among diarrhea outpatients in hospitals and tested for viruses using rRT-PCR and for bacteria in CDCs. Patient information was acquired through interviews and recorded into a dedicated online system. The Pearson χ2 test, multivariate logistic regression models and discriminant models were fitted into its comparisons with the non-norovirus group and other pathogens. Norovirus was detected in 22.91% of sampled diarrhea patients. The seasonal distribution of norovirus infections was different from non-norovirus patients (p<0.001), with a half-year peak. Higher proportions of males (p=0.001, OR=1.303, 95% CI=1.110-1.529), local citizens (p<0.001) and officials/clerks (p=0.001, OR=1.348, 95% CI=1.124-1.618) were affected with norovirus when compared with non-norovirus patients. Diarrhea patients affected with norovirus featured nausea (p<0.001, OR=1.418, 95% CI=1.176-1.709) and vomiting (p<0.001, OR=1.969, 95% CI=1.618-2.398), while fewer manifested fever (p=0.046, OR=0.758, 95% CI=0.577-0.996) and abdominal pain (p=0.018, OR=0.815, 95% CI=0.689-0.965). Children were more vulnerable to rotavirus (p=0.008, OR=1.637, 95% CI=1.136-2.358) and bacteria (p=0.027, OR=1.511, 95% CI=1.053-2.169) than norovirus. There was a seasonal difference between the GI and GII genotypes (p<0.001). Officials or clerks were more easily affected with GI than GII (p=0.006, OR=1.888, 95% CI=1.205-2.958). This study was based on a citywide hospital-sentinel surveillance system with multiple enteric pathogens included. Norovirus was recognized as the most prevalent enteric pathogen in Shanghai. The seasonal peak was from October to April. Males had a higher prevalence than females. Local citizens and officials/clerks were more vulnerable to norovirus than other pathogens. Compared with rotavirus and bacteria, children were less frequently affected by norovirus. Nausea and vomiting were typical of norovirus, whereas fever and abdominal pain were uncommon symptoms of this pathogen. GI and GII infections were centered in different seasons. Officials and clerks were more easily affected by GI than GII.

Development of an oil spill information system combining remote sensing data and surveillance metadata

NASA Astrophysics Data System (ADS)

Tufte, Lars; Trieschmann, Olaf; Carreau, Philippe; Hunsaenger, Thomas; Clayton, Peter J. S.; Barjenbruch, Ulrich

2004-02-01

The detection of accidentally or illegal marine oil discharges in the German territorial waters of the North Sea and Baltic Sea is of great importance for combating of oil spills and protection of the marine ecosystem. Therefore the German Federal Ministry of Transport set up an airborne surveillance system consisting of two Dornier DO 228-212 aircrafts equipped with a Side-Looking Airborne Radar (SLAR), a IR/UV sensor, a Microwave Radiometer (MWR) for quantification and a Laser-Flurosensor (LFS) for classification purposes of the oil spills. The flight parameters and the remote sensing data are stored in a database during the flight. A Pollution Observation Log is completed by the operator consisting of information about the detected oil spill (e.g. position, length, width) and several other information about the flight (e.g. name of navigator, name of observer). The objective was to develop an oil spill information system which integrates the described data, metadata and includes visualization and spatial analysis capabilities. The metadata are essential for further statistical analysis in spatial and temporal domains of oil spill occurrences and of the surveillance itself. It should facilitate the communication and distribution of metadata between the administrative bodies and partners of the German oil spill surveillance system. A connection between a GIS and the database allows to use the powerful visualization and spatial analysis functionality of the GIS in conjunction with the oil spill database.

Spatio-Temporal Data Comparisons for Global Highly Pathogenic Avian Influenza (HPAI) H5N1 Outbreaks

PubMed Central

Chen, Dongmei; Chen, Yue; Wang, Lei; Zhao, Fei; Yao, Baodong

2010-01-01

Highly pathogenic avian influenza subtype H5N1 is a zoonotic disease and control of the disease is one of the highest priority in global health. Disease surveillance systems are valuable data sources for various researches and management projects, but the data quality has not been paid much attention in previous studies. Based on data from two commonly used databases (Office International des Epizooties (OIE) and Food and Agriculture Organization of the United Nations (FAO)) of global HPAI H5N1 outbreaks during the period of 2003–2009, we examined and compared their patterns of temporal, spatial and spatio-temporal distributions for the first time. OIE and FAO data showed similar trends in temporal and spatial distributions if they were considered separately. However, more advanced approaches detected a significant difference in joint spatio-temporal distribution. Because of incompleteness for both OIE and FAO data, an integrated dataset would provide a more complete picture of global HPAI H5N1 outbreaks. We also displayed a mismatching profile of global HPAI H5N1 outbreaks and found that the degree of mismatching was related to the epidemic severity. The ideas and approaches used here to assess spatio-temporal data on the same disease from different sources are useful for other similar studies. PMID:21187964

Evaluation of the novel respiratory virus surveillance program: Pediatric Early Warning Sentinel Surveillance (PEWSS).

PubMed

Armour, Patricia A; Nguyen, Linh M; Lutman, Michelle L; Middaugh, John P

2013-01-01

Infections caused by respiratory viruses are associated with recurrent epidemics and widespread morbidity and mortality. Routine surveillance of these pathogens is necessary to determine virus activity, monitor for changes in circulating strains, and plan for public health preparedness. The Southern Nevada Health District in Las Vegas, Nevada, recruited five pediatric medical practices to serve as sentinel sites for the Pediatric Early Warning Sentinel Surveillance (PEWSS) program. Sentinel staff collected specimens throughout the year from ill children who met the influenza-like illness case definition and submitted specimens to the Southern Nevada Public Health Laboratory for molecular testing for influenza and six non-influenza viruses. Laboratory results were analyzed and reported to the medical and general communities in weekly bulletins year-round. PEWSS data were also used to establish viral respiratory seasonal baselines and in influenza vaccination campaigns. The surveillance program was evaluated using the Centers for Disease Control and Prevention's (CDC's) Updated Guidelines for Evaluating Public Health Surveillance Systems. PEWSS met three of six program usefulness criteria and seven of nine surveillance system attributes, which exceeded the CDC Guidelines evaluation criteria for a useful and complete public health surveillance program. We found that PEWSS is a useful and complete public health surveillance system that is simple, flexible, accessible, and stable.

Evaluation of the Novel Respiratory Virus Surveillance Program: Pediatric Early Warning Sentinel Surveillance (PEWSS)

PubMed Central

Nguyen, Linh M.; Lutman, Michelle L.; Middaugh, John P.

2013-01-01

Objectives Infections caused by respiratory viruses are associated with recurrent epidemics and widespread morbidity and mortality. Routine surveillance of these pathogens is necessary to determine virus activity, monitor for changes in circulating strains, and plan for public health preparedness. The Southern Nevada Health District in Las Vegas, Nevada, recruited five pediatric medical practices to serve as sentinel sites for the Pediatric Early Warning Sentinel Surveillance (PEWSS) program. Methods Sentinel staff collected specimens throughout the year from ill children who met the influenza-like illness case definition and submitted specimens to the Southern Nevada Public Health Laboratory for molecular testing for influenza and six non-influenza viruses. Results Laboratory results were analyzed and reported to the medical and general communities in weekly bulletins year-round. PEWSS data were also used to establish viral respiratory seasonal baselines and in influenza vaccination campaigns. The surveillance program was evaluated using the Centers for Disease Control and Prevention's (CDC's) Updated Guidelines for Evaluating Public Health Surveillance Systems. PEWSS met three of six program usefulness criteria and seven of nine surveillance system attributes, which exceeded the CDC Guidelines evaluation criteria for a useful and complete public health surveillance program. Conclusion We found that PEWSS is a useful and complete public health surveillance system that is simple, flexible, accessible, and stable. PMID:23997308

Integration of Surveillance for STDs, HIV, Hepatitis, and TB: A Survey of U.S. STD Control Programs.

PubMed

Dowell, Deborah; Gaffga, Nicholas H; Weinstock, Hillard; Peterman, Thomas A

2009-01-01

Integration of surveillance for sexually transmitted diseases (STDs), human immunodeficiency virus (HIV), hepatitis, and tuberculosis (TB) may improve disease prevention and control. We determined the extent of surveillance integration in these programs, the benefits of integration, and barriers to increased integration. We e-mailed a survey to the 58 federally funded local and state STD control programs and followed up with phone interviews of nine program representatives. The response rate was 81%. Many had compared infections by population subgroup for STDs and HIV (89%), STDs and hepatitis (53%), or STDs and TB (28%). Most (74%) had examined co-infections with HIV and STDs at the individual level and entered STD and HIV surveillance data into the same database (54%). All respondents thought some integration would be useful. Many (72%) used integrated data to disseminate information or change program strategies. The most commonly reported barriers to integration were policies preventing work with HIV data (85%) and incompatible databases (59%). Most STD control programs in the United States have some experience integrating surveillance data, but the degree of integration varies widely. Specific barriers to further integration were identified. The Centers for Disease Control and Prevention can help address these barriers by facilitating access to information and sharing technical solutions. Local and state programs can continue advancing surveillance integration by improving understanding of where integrated data are needed, increasing the use of available data, and pressing for appropriate and secure data sharing.

A general temporal data model and the structured population event history register

PubMed Central

Clark, Samuel J.

2010-01-01

At this time there are 37 demographic surveillance system sites active in sub-Saharan Africa, Asia and Central America, and this number is growing continuously. These sites and other longitudinal population and health research projects generate large quantities of complex temporal data in order to describe, explain and investigate the event histories of individuals and the populations they constitute. This article presents possible solutions to some of the key data management challenges associated with those data. The fundamental components of a temporal system are identified and both they and their relationships to each other are given simple, standardized definitions. Further, a metadata framework is proposed to endow this abstract generalization with specific meaning and to bind the definitions of the data to the data themselves. The result is a temporal data model that is generalized, conceptually tractable, and inherently contains a full description of the primary data it organizes. Individual databases utilizing this temporal data model can be customized to suit the needs of their operators without modifying the underlying design of the database or sacrificing the potential to transparently share compatible subsets of their data with other similar databases. A practical working relational database design based on this general temporal data model is presented and demonstrated. This work has arisen out of experience with demographic surveillance in the developing world, and although the challenges and their solutions are more general, the discussion is organized around applications in demographic surveillance. An appendix contains detailed examples and working prototype databases that implement the examples discussed in the text. PMID:20396614

Resistance among Gram-negative ESKAPE pathogens isolated from hospitalized patients with intra-abdominal and urinary tract infections in Latin American countries: SMART 2013-2015.

PubMed

Karlowsky, James A; Hoban, Daryl J; Hackel, Meredith A; Lob, Sibylle H; Sahm, Daniel F

Gram-negative ESKAPE pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are important etiologic agents of nosocomial infection that are frequently resistant to broad-spectrum antimicrobial agents. Gram-negative ESKAPE pathogens were collected from hospitalized patients in 11 Latin American countries from 2013 to 2015 as part of the Study for Monitoring Antimicrobial Resistance Trends (SMART) global surveillance program. In total, 2113 isolates from intra-abdominal infections (IAI) and 970 isolates from urinary tract infections (UTI) were tested against antimicrobial agents using standardized CLSI broth microdilution methodology. Of the agents tested, amikacin demonstrated the highest rates of susceptibility (%) for K. pneumoniae (92.2, 92.3), Enterobacter spp. (97.5, 92.1), and P. aeruginosa (85.3, 75.2) isolates from both IAI and UTI, respectively. Ertapenem (68.5, 62.6) and imipenem (79.2, 75.9) showed substantially higher rates of susceptibility (%) than other β-lactams, including piperacillin-tazobactam (35.9, 37.4) against ESBL-positive isolates of K. pneumoniae from IAI and UTI, respectively. Rates of susceptibility to all agents tested against A. baumannii were ≤30.9%. Gram-negative ESKAPE pathogens isolated from Latin America demonstrated compromised in vitro susceptibility to commonly prescribed broad-spectrum, parenteral antimicrobial agents. Continued surveillance is warranted. New antimicrobial agents with potent activity against Gram-negative ESKAPE pathogens are urgently needed. Copyright © 2017 Sociedade Brasileira de Infectologia. Published by Elsevier Editora Ltda. All rights reserved.

Microbial properties database editor tutorial

USDA-ARS?s Scientific Manuscript database

A Microbial Properties Database Editor (MPDBE) has been developed to help consolidate microbialrelevant data to populate a microbial database and support a database editor by which an authorized user can modify physico-microbial properties related to microbial indicators and pathogens. Physical prop...

Effector-triggered versus pattern-triggered immunity: how animals sense virulent pathogens

PubMed Central

Stuart, Lynda M.; Paquette, Nicholas; Boyer, Laurent

2014-01-01

A fundamental question of any immune system is how it can discriminate between pathogens and non-pathogens. Here, we discuss that this can be mediated by a surveillance system distinct from pattern recognition receptors that recognize conserved microbial patterns and can be based instead on the host’s ability to sense perturbations in host cells induced by bacterial toxins or ‘effectors’ that are exclusively encoded by virulent microorganisms. Such ‘effector-triggered immunity’ was previously thought to be restricted to plants, but recent data indicate that animals also use this strategy. PMID:23411798

DBSecSys: a database of Burkholderia mallei secretion systems.

PubMed

Memišević, Vesna; Kumar, Kamal; Cheng, Li; Zavaljevski, Nela; DeShazer, David; Wallqvist, Anders; Reifman, Jaques

2014-07-16

Bacterial pathogenicity represents a major public health concern worldwide. Secretion systems are a key component of bacterial pathogenicity, as they provide the means for bacterial proteins to penetrate host-cell membranes and insert themselves directly into the host cells' cytosol. Burkholderia mallei is a Gram-negative bacterium that uses multiple secretion systems during its host infection life cycle. To date, the identities of secretion system proteins for B. mallei are not well known, and their pathogenic mechanisms of action and host factors are largely uncharacterized. We present the Database of Burkholderia malleiSecretion Systems (DBSecSys), a compilation of manually curated and computationally predicted bacterial secretion system proteins and their host factors. Currently, DBSecSys contains comprehensive experimentally and computationally derived information about B. mallei strain ATCC 23344. The database includes 143 B. mallei proteins associated with five secretion systems, their 1,635 human and murine interacting targets, and the corresponding 2,400 host-B. mallei interactions. The database also includes information about 10 pathogenic mechanisms of action for B. mallei secretion system proteins inferred from the available literature. Additionally, DBSecSys provides details about 42 virulence attenuation experiments for 27 B. mallei secretion system proteins. Users interact with DBSecSys through a Web interface that allows for data browsing, querying, visualizing, and downloading. DBSecSys provides a comprehensive, systematically organized resource of experimental and computational data associated with B. mallei secretion systems. It provides the unique ability to study secretion systems not only through characterization of their corresponding pathogen proteins, but also through characterization of their host-interacting partners.The database is available at https://applications.bhsai.org/dbsecsys.

Surveillance for Highly Pathogenic Avian Influenza Virus in Wild Birds during Outbreaks in Domestic Poultry, Minnesota, 2015

PubMed Central

Carstensen, Michelle; Hildebrand, Erik C.; Cornicelli, Louis; Wolf, Paul; Grear, Daniel A.; Ip, Hon S.; Vandalen, Kaci K.; Minicucci, Larissa A.

2016-01-01

In 2015, a major outbreak of highly pathogenic avian influenza virus (HPAIV) infection devastated poultry facilities in Minnesota, USA. To understand the potential role of wild birds, we tested 3,139 waterfowl fecal samples and 104 sick and dead birds during March 9–June 4, 2015. HPAIV was isolated from a Cooper’s hawk but not from waterfowl fecal samples. PMID:27064759

Highly pathogenic influenza H5N1 virus of clade 2.3.2.1c in Western Siberia.

PubMed

Marchenko, V Y; Susloparov, I M; Kolosova, N P; Goncharova, N I; Shipovalov, A V; Ilyicheva, T N; Durymanov, A G; Chernyshova, O A; Kozlovskiy, L I; Chernyshova, T V; Pryadkina, E N; Karimova, T V; Mikheev, V N; Ryzhikov, A B

2016-06-01

In the spring of 2015, avian influenza virus surveillance in Western Siberia resulted in isolation of several influenza H5N1 virus strains. The strains were isolated from several wild bird species. Investigation of biological features of those strains demonstrated their high pathogenicity for mammals. Phylogenetic analysis of the HA gene showed that the strains belong to clade 2.3.2.1c.

[Surveillance and control of methicillin-resistant Staphylococcus aureus in Spanish hospitals. A GEIH-SEIMC and SEMPSPH consensus document].

PubMed

Rodríguez-Baño, Jesús; Bischofberger, Cornelia; Alvarez-Lerma, Francisco; Asensio, Angel; Delgado, Teresa; García-Arcal, Dolores; García-Ortega, Lola; Hernández, M Jesús; Molina-Cabrillana, Jesús; Pérez-Canosa, Carmen; Pujol, Miquel

2008-05-01

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen, both in-hospital and in the community. Although there are several guidelines with recommendations for the control of this microorganism, the measures proposed are not uniformly implemented in Spanish hospitals. The objective of this document is to provide evidence-based recommendations that are applicable to Spanish hospitals, with the aim of reducing transmission of MRSA in our health care centers. The recommendations are divided into the following groups: surveillance, active detection of colonization in patients and health care workers, control measures for colonized or infected patients, decolonization therapy, environmental cleaning and disinfection, antimicrobial consumption, measures for non-hospitalized patients, and others. The main measures recommended include appropriate surveillance, hand hygiene, and implementation of active surveillance, contact precautions, and environmental cleaning.

Pathogen Research Databases

Science.gov Websites

Hepatitis C Virus (HCV) database project is funded by the Division of Microbiology and Infectious Diseases of the National Institute of Allergies and Infectious Diseases (NIAID). The HCV database project started as a spin-off from the HIV database project. There are two databases for HCV, a sequence database

Towards pathogenomics: a web-based resource for pathogenicity islands

PubMed Central

Yoon, Sung Ho; Park, Young-Kyu; Lee, Soohyun; Choi, Doil; Oh, Tae Kwang; Hur, Cheol-Goo; Kim, Jihyun F.

2007-01-01

Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at . PMID:17090594

In silico analysis of cacao (Theobroma cacao L.) genes that involved in pathogen and disease responses

NASA Astrophysics Data System (ADS)

Agung, Muhammad Budi; Budiarsa, I. Made; Suwastika, I. Nengah

2017-02-01

Cocoa bean is one of the main commodities from Indonesia for the world, which still have problem regarding yield degradation due to pathogens and disease attack. Developing robust cacao plant that genetically resistant to pathogen and disease attack is an ideal solution in over taking on this problem. The aim of this study was to identify Theobroma cacao genes on database of cacao genome that homolog to response genes of pathogen and disease attack in other plant, through in silico analysis. Basic information survey and gene identification were performed in GenBank and The Arabidopsis Information Resource database. The In silico analysis contains protein BLAST, homology test of each gene's protein candidates, and identification of homologue gene in Cacao Genome Database using data source "Theobroma cacao cv. Matina 1-6 v1.1" genome. Identification found that Thecc1EG011959t1 (EDS1), Thecc1EG006803t1 (EDS5), Thecc1EG013842t1 (ICS1), and Thecc1EG015614t1 (BG_PPAP) gene of Cacao Genome Database were Theobroma cacao genes that homolog to plant's resistance genes which highly possible to have similar functions of each gene's homologue gene.

MPD: a pathogen genome and metagenome database

PubMed Central

Zhang, Tingting; Miao, Jiaojiao; Han, Na; Qiang, Yujun; Zhang, Wen

2018-01-01

Abstract Advances in high-throughput sequencing have led to unprecedented growth in the amount of available genome sequencing data, especially for bacterial genomes, which has been accompanied by a challenge for the storage and management of such huge datasets. To facilitate bacterial research and related studies, we have developed the Mypathogen database (MPD), which provides access to users for searching, downloading, storing and sharing bacterial genomics data. The MPD represents the first pathogenic database for microbial genomes and metagenomes, and currently covers pathogenic microbial genomes (6604 genera, 11 071 species, 41 906 strains) and metagenomic data from host, air, water and other sources (28 816 samples). The MPD also functions as a management system for statistical and storage data that can be used by different organizations, thereby facilitating data sharing among different organizations and research groups. A user-friendly local client tool is provided to maintain the steady transmission of big sequencing data. The MPD is a useful tool for analysis and management in genomic research, especially for clinical Centers for Disease Control and epidemiological studies, and is expected to contribute to advancing knowledge on pathogenic bacteria genomes and metagenomes. Database URL: http://data.mypathogen.org PMID:29917040

MALDI-TOF mass spectrometry-based identification of group A Streptococcus isolated from areas of the 2011 scarlet fever outbreak in china.

PubMed

Xiao, Di; You, Yuanhai; Bi, Zhenwang; Wang, Haibin; Zhang, Yongchan; Hu, Bin; Song, Yanyan; Zhang, Huifang; Kou, Zengqiang; Yan, Xiaomei; Zhang, Menghan; Jin, Lianmei; Jiang, Xihong; Su, Peng; Bi, Zhenqiang; Luo, Fengji; Zhang, Jianzhong

2013-03-01

There was a dramatic increase in scarlet fever cases in China from March to July 2011. Group A Streptococcus (GAS) is the only pathogen known to cause scarlet fever. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) coupled to Biotyper system was used for GAS identification in 2011. A local reference database (LRD) was constructed, evaluated and used to identify GAS isolates. The 75 GAS strains used to evaluate the LRD were all identified correctly. Of the 157 suspected β-hemolytic strains isolated from 298 throat swab samples, 127 (100%) and 120 (94.5%) of the isolates were identified as GAS by the MALDI-TOF MS system and the conventional bacitracin sensitivity test method, respectively. All 202 (100%) isolates were identified at the species level by searching the LRD, while 182 (90.1%) were identified by searching the original reference database (ORD). There were statistically significant differences with a high degree of credibility at species level (χ(2)=6.052, P<0.05 between the LRD and ORD). The test turnaround time was shortened 36-48h, and the cost of each sample is one-tenth of the cost of conventional methods. Establishing a domestic database is the most effective way to improve the identification efficiency using a MALDI-TOF MS system. MALDI-TOF MS is a viable alternative to conventional methods and may aid in the diagnosis and surveillance of GAS. Copyright © 2013 Elsevier B.V. All rights reserved.

Modeling the Ecological Niche of Bacillus anthracis to Map Anthrax Risk in Kyrgyzstan

PubMed Central

Blackburn, Jason K.; Matakarimov, Saitbek; Kozhokeeva, Sabira; Tagaeva, Zhyldyz; Bell, Lindsay K.; Kracalik, Ian T.; Zhunushov, Asankadyr

2017-01-01

Anthrax, caused by the environmental bacterium Bacillus anthracis, is an important zoonosis nearly worldwide. In Central Asia, anthrax represents a major veterinary and public health concern. In the Republic of Kyrgyzstan, ongoing anthrax outbreaks have been reported in humans associated with handling infected livestock and contaminated animal by-products such as meat or hides. The current anthrax situation has prompted calls for improved insights into the epidemiology, ecology, and spatial distribution of the disease in Kyrgyzstan to better inform control and surveillance. Disease control for both humans and livestock relies on annual livestock vaccination ahead of outbreaks. Toward this, we used a historic database of livestock anthrax reported from 1932 to 2006 mapped at high resolution to develop an ecological niche model–based prediction of B. anthracis across Kyrgyzstan and identified spatial clusters of livestock anthrax using a cluster morphology statistic. We also defined the seasonality of outbreaks in livestock. Cattle were the most frequently reported across the time period, with the greatest number of cases in late summer months. Our niche models defined four areas as suitable to support pathogen persistence, the plateaus near Talas and Bishkek, the valleys of western Kyrgyzstan along the Fergana Valley, and the low-lying areas along the shore of Lake Isyk-Kul. These areas should be considered “at risk” for livestock anthrax and subsequent human cases. Areas defined by the niche models can be used to prioritize anthrax surveillance and inform efforts to target livestock vaccination campaigns. PMID:28115677

Modeling the Ecological Niche of Bacillus anthracis to Map Anthrax Risk in Kyrgyzstan.

PubMed

Blackburn, Jason K; Matakarimov, Saitbek; Kozhokeeva, Sabira; Tagaeva, Zhyldyz; Bell, Lindsay K; Kracalik, Ian T; Zhunushov, Asankadyr

2017-03-01

AbstractAnthrax, caused by the environmental bacterium Bacillus anthracis , is an important zoonosis nearly worldwide. In Central Asia, anthrax represents a major veterinary and public health concern. In the Republic of Kyrgyzstan, ongoing anthrax outbreaks have been reported in humans associated with handling infected livestock and contaminated animal by-products such as meat or hides. The current anthrax situation has prompted calls for improved insights into the epidemiology, ecology, and spatial distribution of the disease in Kyrgyzstan to better inform control and surveillance. Disease control for both humans and livestock relies on annual livestock vaccination ahead of outbreaks. Toward this, we used a historic database of livestock anthrax reported from 1932 to 2006 mapped at high resolution to develop an ecological niche model-based prediction of B. anthracis across Kyrgyzstan and identified spatial clusters of livestock anthrax using a cluster morphology statistic. We also defined the seasonality of outbreaks in livestock. Cattle were the most frequently reported across the time period, with the greatest number of cases in late summer months. Our niche models defined four areas as suitable to support pathogen persistence, the plateaus near Talas and Bishkek, the valleys of western Kyrgyzstan along the Fergana Valley, and the low-lying areas along the shore of Lake Isyk-Kul. These areas should be considered "at risk" for livestock anthrax and subsequent human cases. Areas defined by the niche models can be used to prioritize anthrax surveillance and inform efforts to target livestock vaccination campaigns.

Regional seroreactivity and vector-borne disease co-exposures in dogs in the United States from 2004-2010: utility of canine surveillance.

PubMed

Yancey, Caroline B; Hegarty, Barbara C; Qurollo, Barbara A; Levy, Michael G; Birkenheuer, Adam J; Weber, David J; Diniz, Pedro P V P; Breitschwerdt, Edward B

2014-10-01

Vector-borne disease (VBD) pathogens remain an emerging health concern for animals and humans throughout the world. Surveillance studies of ticks and humans have made substantial contributions to our knowledge of VBD epidemiology trends, but long-term VBD surveillance data of dogs in the United States is limited. This seroreactivity study assessed US temporal and regional trends and co-exposures to Anaplasma, Babesia, Bartonella, Borrelia burgdorferi, Dirofilaria immitis, Ehrlichia spp., and spotted fever group Rickettsia in dogs from 2004-2010. Dog serum samples (N=14,496) were submitted to the North Carolina State University, College of Veterinary Medicine, Vector Borne Disease Diagnostic Laboratory for vector-borne pathogens diagnostic testing using immunofluorescent antibody (IFA) and enzyme-linked immunosorbent assay (ELISA) assays. These convenience samples were retrospectively reviewed and analyzed. The largest proportion of samples originated from the South (47.6%), with the highest percent of seroreactive samples observed in the Midatlantic (43.4%), compared to other US regions. The overall seroreactivity of evaluated VBD antigens were Rickettsia rickettsia (10.4%), B. burgdorferi (5.2%), Ehrlichia spp. (4.3%), Bartonella henselae (3.8%), Anaplasma spp. (1.9%), Bartonella vinsonii subsp. berkhoffii (1.5%), Babesia canis (1.1%), and D. immitis (0.8%). Significant regional and annual seroreactivity variation was observed with B. burgdorferi, Ehrlichia, and Rickettsia exposures. Seasonal seroreactivity variation was evident with Rickettsia. Seroreactivity to more than one antigen was present in 16.5% of exposed dogs. Nationally, the most prevalent co-exposure was Rickettsia with Ehrlichia spp. (5.3%), and the highest odds of co-exposure was associated with Anaplasma spp. and B. burgdorferi (odds ratio=6.6; 95% confidence interval 5.0, 8.8). Notable annual and regional seroreactivity variation was observed with certain pathogens over 7 years of study, suggesting canine surveillance studies may have value in contributing to future VBD knowledge.

Surveillance of antibiotic resistance

PubMed Central

Johnson, Alan P.

2015-01-01

Surveillance involves the collection and analysis of data for the detection and monitoring of threats to public health. Surveillance should also inform as to the epidemiology of the threat and its burden in the population. A further key component of surveillance is the timely feedback of data to stakeholders with a view to generating action aimed at reducing or preventing the public health threat being monitored. Surveillance of antibiotic resistance involves the collection of antibiotic susceptibility test results undertaken by microbiology laboratories on bacteria isolated from clinical samples sent for investigation. Correlation of these data with demographic and clinical data for the patient populations from whom the pathogens were isolated gives insight into the underlying epidemiology and facilitates the formulation of rational interventions aimed at reducing the burden of resistance. This article describes a range of surveillance activities that have been undertaken in the UK over a number of years, together with current interventions being implemented. These activities are not only of national importance but form part of the international response to the global threat posed by antibiotic resistance. PMID:25918439

A meta-analysis of patient outcomes with subcentimeter disease after chemotherapy for metastatic non-seminomatous germ cell tumor

PubMed Central

Ravi, P.; Gray, K. P.; O'Donnell, E. K.; Sweeney, C. J.

2014-01-01

Background Approximately a quarter of men with metastatic non-seminomatous germ cell tumor (NSGCT) have a residual mass, typically in the retroperitoneum, after chemotherapy. The management of small residual masses (≤1 cm) is controversial, with good outcomes seen with either post-chemotherapy retroperitoneal lymph node dissection (PC-RPLND) or surveillance. We sought to review our experience of surveillance and synthesize the cumulative findings with the current literature in the form of a meta-analysis. Patients and methods We searched PubMed, EMBASE and abstracts from ASCO and AUA to identify relevant, English-language studies for the meta-analysis. The DFCI (Dana Farber Cancer Institute) database was constructed from a database of men undergoing cisplatin-based chemotherapy for metastatic NSGCT. The outcomes of interest were the proportion with necrosis, teratoma or active cancer on histology at PC-RPLND (literature) and the total number of relapses, RP-only relapses and overall survival in men undergoing surveillance (literature and DFCI cohort). Results Three of 47 men undergoing post-chemotherapy surveillance at our institution relapsed over a median follow-up of 5.4 years. All three were alive at a median of 4.2 years after relapse. On meta-analysis, the pooled estimates of necrosis, teratoma and active cancer in the 588 men who underwent PC-RPLND were 71, 24 and 4%, respectively. Of the combined 455 men who underwent surveillance, the pooled estimate of the relapse rate was 5%, with an RP-only relapse rate of 3%. Of the 15 men who suffered an RP-only relapse on surveillance, two died of disease. Conclusion Surveillance is a reasonable strategy for men with minimal residual RP disease after chemotherapy and avoids an RPLND in ∼97% of men who are cured with chemotherapy alone. PMID:24276027

Bistatic and Multistatic Radar: Surveillance, Countermeasures, and Radar Cross Sections. (Latest citations from the Aerospace Database)

NASA Technical Reports Server (NTRS)

1998-01-01

The bibliography contains citations concerning the design, development, testing, and evaluation of bistatic and multistatic radar used in surveillance and countermeasure technology. Citations discuss radar cross sections, target recognition and characteristics, ghost recognition, motion image compensation, and wavelet analysis. Stealth aircraft design, stealth target tracking, synthetic aperture radar, and space applications are examined.

Bistatic and Multistatic Radar: Surveillance, Countermeasures, and Radar Cross Sections. (Latest Citations from the Aerospace Database)

NASA Technical Reports Server (NTRS)

1997-01-01

The bibliography contains citations concerning the design, development, testing, and evaluation of bistatic and multistatic radar used in surveillance and countermeasure technology. Citations discuss radar cross sections, target recognition and characteristics, ghost recognition, motion image compensation, and wavelet analysis. Stealth aircraft design, stealth target tracking, synthetic aperture radar, and space applications are examined.

An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

PubMed

Zhang, C; Crasta, O; Cammer, S; Will, R; Kenyon, R; Sullivan, D; Yu, Q; Sun, W; Jha, R; Liu, D; Xue, T; Zhang, Y; Moore, M; McGarvey, P; Huang, H; Chen, Y; Zhang, J; Mazumder, R; Wu, C; Sobral, B

2008-01-01

The NIAID-funded Biodefense Proteomics Resource Center (RC) provides storage, dissemination, visualization and analysis capabilities for the experimental data deposited by seven Proteomics Research Centers (PRCs). The data and its publication is to support researchers working to discover candidates for the next generation of vaccines, therapeutics and diagnostics against NIAID's Category A, B and C priority pathogens. The data includes transcriptional profiles, protein profiles, protein structural data and host-pathogen protein interactions, in the context of the pathogen life cycle in vivo and in vitro. The database has stored and supported host or pathogen data derived from Bacillus, Brucella, Cryptosporidium, Salmonella, SARS, Toxoplasma, Vibrio and Yersinia, human tissue libraries, and mouse macrophages. These publicly available data cover diverse data types such as mass spectrometry, yeast two-hybrid (Y2H), gene expression profiles, X-ray and NMR determined protein structures and protein expression clones. The growing database covers over 23 000 unique genes/proteins from different experiments and organisms. All of the genes/proteins are annotated and integrated across experiments using UniProt Knowledgebase (UniProtKB) accession numbers. The web-interface for the database enables searching, querying and downloading at the level of experiment, group and individual gene(s)/protein(s) via UniProtKB accession numbers or protein function keywords. The system is accessible at http://www.proteomicsresource.org/.

Molecular characterization of avian influenza H5N1 virus in Egypt and the emergence of a novel endemic subclade

PubMed Central

El-Shesheny, Rabeh; Kandeil, Ahmed; Bagato, Ola; Maatouq, Asmaa M.; Moatasim, Yassmin; Rubrum, Adam; Song, Min-Suk; Webby, Richard J.

2014-01-01

Clade 2.2 highly pathogenic H5N1 viruses have been in continuous circulation in Egyptian poultry since 2006. Their persistence caused significant genetic drift that led to the reclassification of these viruses into subclades 2.2.1 and 2.2.1.1. Here, we conducted full-genome sequence and phylogenetic analyses of 45 H5N1 isolated during 2006–2013 through systematic surveillance in Egypt, and 53 viruses that were sequenced previously and available in the public domain. Results indicated that H5N1 viruses in Egypt continue to evolve and a new distinct cluster has emerged. Mutations affecting viral virulence, pathogenicity, transmission, receptor-binding preference and drug resistance were studied. In light of our findings that H5N1 in Egypt continues to evolve, surveillance and molecular studies need to be sustained. PMID:24722680

Internet-based biosurveillance methods for vector-borne diseases: Are they novel public health tools or just novelties?

PubMed

Pollett, Simon; Althouse, Benjamin M; Forshey, Brett; Rutherford, George W; Jarman, Richard G

2017-11-01

Internet-based surveillance methods for vector-borne diseases (VBDs) using "big data" sources such as Google, Twitter, and internet newswire scraping have recently been developed, yet reviews on such "digital disease detection" methods have focused on respiratory pathogens, particularly in high-income regions. Here, we present a narrative review of the literature that has examined the performance of internet-based biosurveillance for diseases caused by vector-borne viruses, parasites, and other pathogens, including Zika, dengue, other arthropod-borne viruses, malaria, leishmaniasis, and Lyme disease across a range of settings, including low- and middle-income countries. The fundamental features, advantages, and drawbacks of each internet big data source are presented for those with varying familiarity of "digital epidemiology." We conclude with some of the challenges and future directions in using internet-based biosurveillance for the surveillance and control of VBD.

Internet-based biosurveillance methods for vector-borne diseases: Are they novel public health tools or just novelties?

PubMed Central

Pollett, Simon; Althouse, Benjamin M.; Forshey, Brett; Rutherford, George W.; Jarman, Richard G.

2017-01-01

Internet-based surveillance methods for vector-borne diseases (VBDs) using “big data” sources such as Google, Twitter, and internet newswire scraping have recently been developed, yet reviews on such “digital disease detection” methods have focused on respiratory pathogens, particularly in high-income regions. Here, we present a narrative review of the literature that has examined the performance of internet-based biosurveillance for diseases caused by vector-borne viruses, parasites, and other pathogens, including Zika, dengue, other arthropod-borne viruses, malaria, leishmaniasis, and Lyme disease across a range of settings, including low- and middle-income countries. The fundamental features, advantages, and drawbacks of each internet big data source are presented for those with varying familiarity of “digital epidemiology.” We conclude with some of the challenges and future directions in using internet-based biosurveillance for the surveillance and control of VBD. PMID:29190281

Infectious Disease Surveillance in the Big Data Era: Towards Faster and Locally Relevant Systems

PubMed Central

Simonsen, Lone; Gog, Julia R.; Olson, Don; Viboud, Cécile

2016-01-01

While big data have proven immensely useful in fields such as marketing and earth sciences, public health is still relying on more traditional surveillance systems and awaiting the fruits of a big data revolution. A new generation of big data surveillance systems is needed to achieve rapid, flexible, and local tracking of infectious diseases, especially for emerging pathogens. In this opinion piece, we reflect on the long and distinguished history of disease surveillance and discuss recent developments related to use of big data. We start with a brief review of traditional systems relying on clinical and laboratory reports. We then examine how large-volume medical claims data can, with great spatiotemporal resolution, help elucidate local disease patterns. Finally, we review efforts to develop surveillance systems based on digital and social data streams, including the recent rise and fall of Google Flu Trends. We conclude by advocating for increased use of hybrid systems combining information from traditional surveillance and big data sources, which seems the most promising option moving forward. Throughout the article, we use influenza as an exemplar of an emerging and reemerging infection which has traditionally been considered a model system for surveillance and modeling. PMID:28830112

The Toxic Exposure Surveillance System (TESS): Risk assessment and real-time toxicovigilance across United States poison centers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Watson, William A.; Litovitz, Toby L.; Belson, Martin G.

2005-09-01

The Toxic Exposure Surveillance System (TESS) is a uniform data set of US poison centers cases. Categories of information include the patient, the caller, the exposure, the substance(s), clinical toxicity, treatment, and medical outcome. The TESS database was initiated in 1985, and provides a baseline of more than 36.2 million cases through 2003. The database has been utilized for a number of safety evaluations. Consideration of the strengths and limitations of TESS data must be incorporated into data interpretation. Real-time toxicovigilance was initiated in 2003 with continuous uploading of new cases from all poison centers to a central database. Real-timemore » toxicovigilance utilizing general and specific approaches is systematically run against TESS, further increasing the potential utility of poison center experiences as a means of early identification of potential public health threats.« less

Surveillance of bloodstream infections in pediatric cancer centers – what have we learned and how do we move on?

PubMed Central

Simon, Arne; Furtwängler, Rhoikos; Graf, Norbert; Laws, Hans Jürgen; Voigt, Sebastian; Piening, Brar; Geffers, Christine; Agyeman, Philipp; Ammann, Roland A.

2016-01-01

Pediatric patients receiving conventional chemotherapy for malignant disease face an increased risk of bloodstream infection (BSI). Since BSI may represent an acute life-threatening event in patients with profound immunosuppression, and show further negative impact on quality of life and anticancer treatment, the prevention of BSI is of paramount importance to improve and guarantee patients’ safety during intensive treatment. The great majority of all pediatric cancer patients (about 85%) have a long-term central venous access catheter in use (type Broviac or Port; CVAD). Referring to the current surveillance definitions a significant proportion of all BSI in pediatric patients with febrile neutropenia is categorized as CVAD-associated BSI. This state of the art review summarizes the epidemiology and the distinct pathogen profile of BSI in pediatric cancer patients from the perspective of infection surveillance. Problems in executing the current surveillance definition in this patient population are discussed and a new concept for the surveillance of BSI in pediatric cancer patients is outlined. PMID:27274442

Surveillance of bloodstream infections in pediatric cancer centers - what have we learned and how do we move on?

PubMed

Simon, Arne; Furtwängler, Rhoikos; Graf, Norbert; Laws, Hans Jürgen; Voigt, Sebastian; Piening, Brar; Geffers, Christine; Agyeman, Philipp; Ammann, Roland A

2016-01-01

Pediatric patients receiving conventional chemotherapy for malignant disease face an increased risk of bloodstream infection (BSI). Since BSI may represent an acute life-threatening event in patients with profound immunosuppression, and show further negative impact on quality of life and anticancer treatment, the prevention of BSI is of paramount importance to improve and guarantee patients' safety during intensive treatment. The great majority of all pediatric cancer patients (about 85%) have a long-term central venous access catheter in use (type Broviac or Port; CVAD). Referring to the current surveillance definitions a significant proportion of all BSI in pediatric patients with febrile neutropenia is categorized as CVAD-associated BSI. This state of the art review summarizes the epidemiology and the distinct pathogen profile of BSI in pediatric cancer patients from the perspective of infection surveillance. Problems in executing the current surveillance definition in this patient population are discussed and a new concept for the surveillance of BSI in pediatric cancer patients is outlined.

A MLVA Genotyping Scheme for Global Surveillance of the Citrus Pathogen Xanthomonas citri pv. citri Suggests a Worldwide Geographical Expansion of a Single Genetic Lineage

PubMed Central

Boyer, Karine; Leduc, Alice; Tourterel, Christophe; Drevet, Christine; Ravigné, Virginie; Gagnevin, Lionel; Guérin, Fabien; Chiroleu, Frédéric; Koebnik, Ralf; Verdier, Valérie; Vernière, Christian

2014-01-01

MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epidemics on a global scale. Xanthomonas citri pv. citri is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of Xanthomonas citri pv. citri strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these in silico data, an optimized MLVA scheme was developed to assess the global diversity of this monomorphic bacterium. Thirty-one minisatellite loci (MLVA-31) were selected to assess the genetic structure of 129 strains representative of the worldwide pathological and genetic diversity of X. citri pv. citri. Based on Discriminant Analysis of Principal Components (DAPC), four pathotype-specific clusters were defined. DAPC cluster 1 comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31. MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the Xanthomonas citri genotyping database (http://www.biopred.net/MLVA/). PMID:24897119

[Etiological surveillance and analysis of infectious diarrhea in Beijing in year 2010].

PubMed

Huang, Fang; Deng, Ying; Qu, Mei; Liu, Gui-Rong; Liu, Yuan; Zhang, Xin; Li, Jie; Yan, Han-Qiu; Gao, Zhi-Yong; Liu, Bai-Wei; Li, Xi-Tai; Li, Xin-Yu

2011-09-01

To explore the pathogenic form, epidemic features and serotype distribution of the pathogenic bacteria causing infectious diarrhea in Beijing. A total of 2118 samples of rectal swabs and stool specimens of diarrheal patients were collected from 6 surveillant intestinal tract clinics during the period between April and October, 2010. Enteric multiple pathogens including Vibrio cholerae, Vibrio parahaemolyticus, Salmonella, Shigella and diarrheagenic Escherichia coli were detected by the isolation culture, biochemical identification and serotyping methods. The population distribution, temporal distribution and serotype distribution of the above pathogenic bacteria were analyzed by descriptive statistical methods. 478 strains isolated from the total 2118 specimens were positive for pathogen detection, accounting to 22.6%. Among the 478 strains of pathogenic bacteria, Shigella accounting for 40.8% (195/478) was the most frequent pathogen, followed by Vibrio parahaemolyticus accouting for 23.8% (114/478), Salmonella accounting for 19.0% (91/478) and diarrheagenic Escherichia coli accounting for 4.8% (23/478). Enteric pathogenic bacteria spread mainly among adults aging between 20 and 39; and the distribution was different among different age groups, while the highest detected rate was in 30 - 39 age group, accounting for 27.2% (92/338). The detected rate of pathogenic bacteria showed evident seasonal variations, with a peak from July to October, whose detected rates were 23.5% (114/486), 32.8% (176/536), 36.1% (90/249) and 25.9% (29/112) respectively. The detected rates in other months were all under 16.0%. Shigella Sonnei was the dominant serotype, accounting for 83.1% (162/195). O3:K6 was the dominant serotype among Vibrio parahaemolyticus, accounting for 63.2% (72/114). Salmonella Enteritidis and Salmonella Typhimurium were dominant serotypes among Salmonella, accounting for 13.2% (12/91) and 12.1% (11/91) separately. Enterpathogenic Escherichia coli and enterotoxigenic Escherichia coli were the dominant serotypes among Diarrheagenic Escherichia coli, accounting for 69.6% (16/23) and 30.4% (7/23) respectively. The three main pathogenic bacteria causing infectious diarrhea in Beijing are Shigella, Vibrio parahaemolyticus, Salmonella; and there are obvious changes in the serotype distribution of Shigella and Samonella compared to previous years.

Use of wildlife rehabilitation centres in pathogen surveillance: A case study in white storks (Ciconia ciconia).

PubMed

Camacho, MariaCruz; Hernández, Jose Manuel; Lima-Barbero, Jose Francisco; Höfle, Ursula

2016-08-01

More than 70% of new human pathogens are zoonotic and many originate from the wildlife reservoir. Wildlife rehabilitation centres (WRC) are an easily accessible source for sample and data collection for preventive surveillance, but data collected this way may be biased. We use white storks (Ciconia ciconia) as a model to compare pathogen prevalence obtained in the field and WRC. We address factors that may affect disease prevalence data like origin, the age group and the "diseased" state of WRC admissions. In this study we compared prevalence of Escherichia coli and Salmonella spp. in the digestive tract; antibodies against West Nile virus, avian influenza and Newcastle disease virus, and antimicrobial resistance patterns of E. coli between nestling and adult wild storks established in different habitats (n=90) and storks admitted to two different WRC (n=30) in the same region. When age groups and colonies of origin were disregarded, the mean enterobacteria (E. coli, Salmonella) and viral antibody prevalence of the wild population (n=90) were similar to prevalence observed in the individuals admitted to WRC (n=30). However, in fledgling juvenile storks admitted to WRC, the prevalence of Salmonella spp. (13.3%), E. coli showing resistance to cefotaxime (37.9%) and against two antimicrobials at once (41.4%) were more similar to the prevalence in stork nestlings from landfill-associated colonies (7.9%, 37.1% and 48.6%, respectively for prevalence of Salmonella spp. and E. coli displaying, cefotaxime resistance and resistance against two antimicrobials), and significantly higher than in colonies located in natural habitats (0%; 10.5% and 15.8%, respectively). Thus, pathogen surveillance in individuals from an abundant species admitted to WRC is useful to monitor overall mean prevalence, but for certain pathogens may not be sufficient to detect differences between local populations. In addition, the ecology of the tested species and the specific temporal, spatial and age group distribution of WRC admissions have to be taken into account. Copyright © 2016 Elsevier B.V. All rights reserved.

Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

PubMed Central

Scheutz, Flemming; Lund, Ole; Hasman, Henrik; Kaas, Rolf S.; Nielsen, Eva M.; Aarestrup, Frank M.

2014-01-01

Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all suspected VTEC isolates. During a 7-week period in the fall of 2012, all incoming isolates were concurrently subjected to WGS using IonTorrent PGM. Real-time bioinformatics analysis was performed using web-tools (www.genomicepidemiology.org) for species determination, multilocus sequence type (MLST) typing, and determination of phylogenetic relationship, and a specific VirulenceFinder for detection of E. coli virulence genes was developed as part of this study. In total, 46 suspected VTEC isolates were characterized in parallel during the study. VirulenceFinder proved successful in detecting virulence genes included in routine typing, explicitly verocytotoxin 1 (vtx1), verocytotoxin 2 (vtx2), and intimin (eae), and also detected additional virulence genes. VirulenceFinder is also a robust method for assigning verocytotoxin (vtx) subtypes. A real-time clustering of isolates in agreement with the epidemiology was established from WGS, enabling discrimination between sporadic and outbreak isolates. Overall, WGS typing produced results faster and at a lower cost than the current routine. Therefore, WGS typing is a superior alternative to conventional typing strategies. This approach may also be applied to typing and surveillance of other pathogens. PMID:24574290

The Perceived Value of Passive Animal Health Surveillance: The Case of Highly Pathogenic Avian Influenza in Vietnam.

PubMed

Delabouglise, A; Antoine-Moussiaux, N; Phan, T D; Dao, D C; Nguyen, T T; Truong, B D; Nguyen, X N T; Vu, T D; Nguyen, K V; Le, H T; Salem, G; Peyre, M

2016-03-01

Economic evaluations are critical for the assessment of the efficiency and sustainability of animal health surveillance systems and the improvement of their efficiency. Methods identifying and quantifying costs and benefits incurred by public and private actors of passive surveillance systems (i.e. actors of veterinary authorities and private actors who may report clinical signs) are needed. This study presents the evaluation of perceived costs and benefits of highly pathogenic avian influenza (HPAI) passive surveillance in Vietnam. Surveys based on participatory epidemiology methods were conducted in three provinces in Vietnam to collect data on costs and benefits resulting from the reporting of HPAI suspicions to veterinary authorities. A quantitative tool based on stated preference methods and participatory techniques was developed and applied to assess the non-monetary costs and benefits. The study showed that poultry farmers are facing several options regarding the management of HPAI suspicions, besides reporting the following: treatment, sale or destruction of animals. The option of reporting was associated with uncertain outcome and transaction costs. Besides, actors anticipated the release of health information to cause a drop of markets prices. This cost was relevant at all levels, including farmers, veterinary authorities and private actors of the upstream sector (feed, chicks and medicine supply). One benefit associated with passive surveillance was the intervention of public services to clean farms and the environment to limit the disease spread. Private actors of the poultry sector valued information on HPAI suspicions (perceived as a non-monetary benefit) which was mainly obtained from other private actors and media. © 2015 The Authors. Zoonoses and Public Health Published by Blackwell Verlag GmbH.

Genomic interplay in bacterial communities: implications for growth promoting practices in animal husbandry

PubMed Central

Roy Chowdhury, Piklu; McKinnon, Jessica; Wyrsch, Ethan; Hammond, Jeffrey M.; Charles, Ian G.; Djordjevic, Steven P.

2014-01-01

The discovery of antibiotics heralded the start of a “Golden Age” in the history of medicine. Over the years, the use of antibiotics extended beyond medical practice into animal husbandry, aquaculture and agriculture. Now, however, we face the worldwide threat of diseases caused by pathogenic bacteria that are resistant to all existing major classes of antibiotic, reflecting the possibility of an end to the antibiotic era. The seriousness of the threat is underscored by the severely limited production of new classes of antibiotics. Evolution of bacteria resistant to multiple antibiotics results from the inherent genetic capability that bacteria have to adapt rapidly to changing environmental conditions. Consequently, under antibiotic selection pressures, bacteria have acquired resistance to all classes of antibiotics, sometimes very shortly after their introduction. Arguably, the evolution and rapid dissemination of multiple drug resistant genes en-masse across microbial pathogens is one of the most serious threats to human health. In this context, effective surveillance strategies to track the development of resistance to multiple antibiotics are vital to managing global infection control. These surveillance strategies are necessary for not only human health but also for animal health, aquaculture and plant production. Shortfalls in the present surveillance strategies need to be identified. Raising awareness of the genetic events that promote co-selection of resistance to multiple antimicrobials is an important prerequisite to the design and implementation of molecular surveillance strategies. In this review we will discuss how lateral gene transfer (LGT), driven by the use of low-dose antibiotics in animal husbandry, has likely played a significant role in the evolution of multiple drug resistance (MDR) in Gram-negative bacteria and has complicated molecular surveillance strategies adopted for predicting imminent resistance threats. PMID:25161648

Visual Analytics of Surveillance Data on Foodborne Vibriosis, United States, 1973–2010

PubMed Central

Sims, Jennifer N.; Isokpehi, Raphael D.; Cooper, Gabrielle A.; Bass, Michael P.; Brown, Shyretha D.; St John, Alison L.; Gulig, Paul A.; Cohly, Hari H.P.

2011-01-01

Foodborne illnesses caused by microbial and chemical contaminants in food are a substantial health burden worldwide. In 2007, human vibriosis (non-cholera Vibrio infections) became a notifiable disease in the United States. In addition, Vibrio species are among the 31 major known pathogens transmitted through food in the United States. Diverse surveillance systems for foodborne pathogens also track outbreaks, illnesses, hospitalization and deaths due to non-cholera vibrios. Considering the recognition of vibriosis as a notifiable disease in the United States and the availability of diverse surveillance systems, there is a need for the development of easily deployed visualization and analysis approaches that can combine diverse data sources in an interactive manner. Current efforts to address this need are still limited. Visual analytics is an iterative process conducted via visual interfaces that involves collecting information, data preprocessing, knowledge representation, interaction, and decision making. We have utilized public domain outbreak and surveillance data sources covering 1973 to 2010, as well as visual analytics software to demonstrate integrated and interactive visualizations of data on foodborne outbreaks and surveillance of Vibrio species. Through the data visualization, we were able to identify unique patterns and/or novel relationships within and across datasets regarding (i) causative agent; (ii) foodborne outbreaks and illness per state; (iii) location of infection; (iv) vehicle (food) of infection; (v) anatomical site of isolation of Vibrio species; (vi) patients and complications of vibriosis; (vii) incidence of laboratory-confirmed vibriosis and V. parahaemolyticus outbreaks. The additional use of emerging visual analytics approaches for interaction with data on vibriosis, including non-foodborne related disease, can guide disease control and prevention as well as ongoing outbreak investigations. PMID:22174586

Surveillance bronchoscopy in children during the first year after lung transplantation: Is it worth it?

PubMed

Benden, C; Harpur-Sinclair, O; Ranasinghe, A S; Hartley, J C; Elliott, M J; Aurora, P

2007-01-01

Since January 2002, routine surveillance bronchoscopy with bronchoalveolar lavage (BAL) and transbronchial biopsy has been performed in all paediatric recipients of lung and heart-lung transplants at the Great Ormond Street Hospital for Children, London, UK, using a newly revised treatment protocol. To report the prevalence of rejection and bacterial, viral or fungal pathogens in asymptomatic children and compare this with the prevalence in children with symptoms. The study population included all paediatric patients undergoing single lung transplantation (SLTx), double lung transplantation (DLTx) or heart-lung transplantation between January 2002 and December 2005. Surveillance bronchoscopies were performed at 1 week, and 1, 3, 6 and 12 months after transplant. Bronchoscopies were classified according to whether subjects had symptoms, defined as the presence of cough, sputum production, dyspnoea, malaise, decrease in lung function or chest radiograph changes. Results of biopsies and BAL were collected, and procedural complications recorded. 23 lung-transplant operations were performed, 12 DLTx, 10 heart-lung transplants and 1 SLTx (15 female patients). The median (range) age of patients was 14.0 (4.9-17.3) years. 17 patients had cystic fibrosis. 95 surveillance bronchoscopies were performed. Rejection (> or =A2) was diagnosed in 4% of biopsies of asymptomatic recipients, and in 12% of biopsies of recipients with symptoms. Potential pathogens were detected in 29% of asymptomatic patients and in 69% of patients with symptoms. The overall diagnostic yield was 35% for asymptomatic children, and 85% for children with symptoms (p < 0.001). The complication rate for bronchoscopies was 3.2%. Many children have silent rejection or subclinical infection in the first year after lung transplantation. Routine surveillance bronchoscopy allows detection and targeted treatment of these complications.

Distribution and Diversity of Pathogenic Leptospira Species in Peri-domestic Surface Waters from South Central Chile.

PubMed

Mason, Meghan R; Encina, Carolina; Sreevatsan, Srinand; Muñoz-Zanzi, Claudia

2016-08-01

Leptospirosis is a neglected zoonosis affecting animals and humans caused by infection with Leptospira. The bacteria can survive outside of hosts for long periods of time in soil and water. While identification of Leptospira species from human cases and animal reservoirs are increasingly reported, little is known about the diversity of pathogenic Leptospira species in the environment and how surveillance of the environment might be used for monitoring and controlling disease. Water samples (n = 104) were collected from the peri-domestic environment of 422 households from farms, rural villages, and urban slums participating in a broader study on the eco-epidemiology of leptospirosis in the Los Rios Region, Chile, between October 2010 and April 2012. The secY region of samples, previously detected as pathogenic Leptospira by PCR, was amplified and sequenced. Sequences were aligned using ClustalW in MEGA, and a minimum spanning tree was created in PHYLOViZ using the goeBURST algorithm to assess sequence similarity. Sequences from four clinical isolates, 17 rodents, and 20 reference strains were also included in the analysis. Overall, water samples contained L. interrogans, L. kirschneri, and L. weilii, with descending frequency. All species were found in each community type. The distribution of the species differed by the season in which the water samples were obtained. There was no evidence that community-level prevalence of Leptospira in dogs, rodents, or livestock influenced pathogen diversity in the water samples. This study reports the presence of pathogenic Leptospira in the peri-domestic environment of households in three community types and the differences in Leptospira diversity at the community level. Systematic environmental surveillance of Leptospira can be used for detecting changes in pathogen diversity and to identify and monitor contaminated areas where an increased risk of human infection exists.

Incidence and etiology of hospitalized acute respiratory infections in the Egyptian Delta.

PubMed

Rowlinson, Emily; Dueger, Erica; Mansour, Adel; Azzazy, Nahed; Mansour, Hoda; Peters, Lisa; Rosenstock, Summer; Hamid, Sarah; Said, Mayar M; Geneidy, Mohamed; Abd Allah, Monier; Kandeel, Amr

2017-01-01

Acute Respiratory Infections (ARI) are responsible for nearly two million childhood deaths worldwide. A limited number of studies have been published on the epidemiology of viral respiratory pathogens in Egypt. A total of 6113 hospitalized patients >1 month of age with suspected ARI were enrolled between June 23, 2009 and December 31, 2013. Naso- and oropharyngeal specimens were collected and tested for influenza A and B, respiratory syncytial virus, human metapneumovirus, adenovirus, and parainfluenza viruses 1-3. Blood specimens from children 1-11 months were cultured and bacterial growth was identified by polymerase chain reaction. Results from a healthcare utilization survey on the proportion of persons seeking care for ARI was used to calculate adjusted ARI incidence rates in the surveillance population. The proportion of patients with a viral pathogen detected decreased with age from 67% in patients age 1-11 months to 19% in patients ≥65 years of age. Influenza was the dominant viral pathogen detected in patients ≥1 year of age (13.9%). The highest incidence rates for hospitalized ARI were observed in children 1-11 months (1757.9-5537.5/100 000 population) and RSV was the most commonly detected pathogen in this age group. In this study population, influenza is the largest viral contributor to hospitalized ARIs and children 1-11 months of age experience a high rate of ARI hospitalizations. This study highlights a need for surveillance of additional viral pathogens and alternative detection methods for bacterial pathogens, which may reveal a substantial proportion of as yet unidentified etiologies in adults. © 2016 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

Genetic evolution of H5 highly pathogenic avian influenza virus in domestic poultry in Vietnam between 2011 and 2013.

PubMed

Lee, Eun-Kyoung; Kang, Hyun-Mi; Kim, Kwang-Il; Choi, Jun-Gu; To, Thanh Long; Nguyen, Tho Dang; Song, Byung-Min; Jeong, Jipseol; Choi, Kang-Seuk; Kim, Ji-Ye; Lee, Hee-Soo; Lee, Youn-Jeong; Kim, Jae-Hong

2015-04-01

In spite of highly pathogenic avian influenza H5N1 vaccination campaigns for domestic poultry, H5N1 viruses continue to circulate in Vietnam. To estimate the prevalence of avian influenza virus in Vietnam, surveillance was conducted between November 2011 and February 2013. Genetic analysis of 312 highly pathogenic avian influenza H5 viruses isolated from poultry in Vietnam was conducted and possible genetic relationships with strains from neighboring countries were investigated. As previously reported, phylogenetic analysis of the avian influenza virus revealed two H5N1 HPAI clades that were circulating in Vietnam. Clade 1.1, related to Cambodian strains, was predominant in the southern provinces, while clade 2.3.2.1 viruses were predominant in the northern and central provinces. Sequence analysis revealed evidence of active genetic evolution. In the gene constellation of clade 2.3.2.1, genotypes A, B, and B(II) existed during the 2011/2012 winter season. In June 2012, new genotype C emerged by reassortment between genotype A and genotype B(II), and this genotype was predominant in 2013 in the northern and central provinces. Interestingly, enzootic Vietnamese clade 2.3.2.1C H5 virus subsequently reassorted with N2, which originated from wild birds, to generate H5N2 highly pathogenic avian influenza, which was isolated from duck in the northeast region. This investigation indicated that H5N1 outbreaks persist in Vietnam and cause genetic reassortment with circulating viruses. It is necessary to strengthen active influenza surveillance to eradicate highly pathogenic avian influenza viruses and sever the link between highly pathogenic avian influenza and other circulating influenza viruses. © 2015 Poultry Science Association Inc.

History and Medicine: ex voto as a tool for health and epidemiological surveillance.

PubMed

Nante, N; Azzolini, E; Troiano, G; Serafini, A; Gentile, A; Messina, G

2016-01-01

Ex voto is a donation for a divinity, a Saint or to Virgin Mary for a received mercy. From the analysis of an ex voto it's possible to obtain lots of information and therefore it can be used as a tool for health and epidemiological surveillance, to study morbidity in the past. The aim of this study was the creation of a database to rebuild epidemiological events and diseases, using ex voto as a source of health surveillance. We chose to study votive pictures using three types of sources: photographed alive, on-line archives, books and photographic collections. Ex voto have been saved in an Hard Disk, numbered and inserted in a database, then analyzed using Stata®. total of 6231 ex voto were collected and catalogued in our database. Ex voto referring to diseases are the most represented (41%), but they have decreased with the time. Road accidents (21.4%) have a constant increase, especially with the appearance of cars and motorcycles. Aggressions (5.45%) decrease constantly; warlike accidents (4.44%) had a peak in the period including both world wars; non professional accidents (10.60%) and accidents at work (3.79%) increase without peaks; maritime accidents (8.88%) have not uniform ups and downs during the time. The database let us rebuild epidemiological events of the past, which are not deductible from other sources. Our purpose is to expand in the space-time our source data in order to perform an interesting comparison between past and present.

Avian influenza surveillance in wild birds in the European Union in 2006.

PubMed

Hesterberg, Uta; Harris, Kate; Stroud, David; Guberti, Vittorio; Busani, Luca; Pittman, Maria; Piazza, Valentina; Cook, Alasdair; Brown, Ian

2009-01-01

Infections of wild birds with highly pathogenic avian influenza (AI) subtype H5N1 virus were reported for the first time in the European Union in 2006. To capture epidemiological information on H5N1 HPAI in wild bird populations through large-scale surveillance and extensive data collection. Records were analysed at bird level to explore the epidemiology of AI with regard to species of wild birds involved, timing and location of infections as well as the applicability of different surveillance types for the detection of infections. In total, 120,706 records of birds were sent to the Community Reference Laboratory for analysis. Incidents of H5N1 HPAI in wild birds were detected in 14 EU Member States during 2006. All of these incidents occurred between February and May, with the exception of two single cases during the summer months in Germany and Spain. For the detection of H5N1 HPAI virus, passive surveillance of dead or diseased birds appeared the most effective approach, whilst active surveillance offered better detection of low pathogenic avian influenza (LPAI) viruses. No carrier species for H5N1 HPAI virus could be identified and almost all birds infected with H5N1 HPAI virus were either dead or showed clinical signs. A very large number of Mallards (Anas platyrhynchos) were tested in 2006 and while a high proportion of LPAI infections were found in this species, H5N1 HPAI virus was rarely identified in these birds. Orders of species that appeared to be very clinically susceptible to H5N1 HPAI virus were swans, diving ducks, mergansers and grebes, supporting experimental evidence. Surveillance results indicate that H5N1 HPAI virus did not establish itself successfully in the EU wild bird population in 2006.

Mild Respiratory Illness Among Young Children Caused by Highly Pathogenic Avian Influenza A (H5N1) Virus Infection in Dhaka, Bangladesh, 2011.

PubMed

Chakraborty, Apurba; Rahman, Mahmudur; Hossain, M Jahangir; Khan, Salah Uddin; Haider, M Sabbir; Sultana, Rebeca; Ali Rimi, Nadia; Islam, M Saiful; Haider, Najmul; Islam, Ausraful; Sultana Shanta, Ireen; Sultana, Tahmina; Al Mamun, Abdullah; Homaira, Nusrat; Goswami, Doli; Nahar, Kamrun; Alamgir, A S M; Rahman, Mustafizur; Mahbuba Jamil, Khondokar; Azziz-Baumgartner, Eduardo; Simpson, Natosha; Shu, Bo; Lindstrom, Stephen; Gerloff, Nancy; Davis, C Todd; Katz, Jaqueline M; Mikolon, Andrea; Uyeki, Timothy M; Luby, Stephen P; Sturm-Ramirez, Katharine

2017-09-15

In March 2011, a multidisciplinary team investigated 2 human cases of highly pathogenic avian influenza A(H5N1) virus infection, detected through population-based active surveillance for influenza in Bangladesh, to assess transmission and contain further spread. We collected clinical and exposure history of the case patients and monitored persons coming within 1 m of a case patient during their infectious period. Nasopharyngeal wash specimens from case patients and contacts were tested with real-time reverse-transcription polymerase chain reaction, and virus culture and isolates were characterized. Serum samples were tested with microneutralization and hemagglutination inhibition assays. We tested poultry, wild bird, and environmental samples from case patient households and surrounding areas for influenza viruses. Two previously healthy case patients, aged 13 and 31 months, had influenzalike illness and fully recovered. They had contact with poultry 7 and 10 days before illness onset, respectively. None of their 57 contacts were subsequently ill. Clade 2.2.2.1 highly pathogenic avian influenza H5N1 viruses were isolated from the case patients and from chicken fecal samples collected at the live bird markets near the patients' dwellings. Identification of H5N1 cases through population-based surveillance suggests possible additional undetected cases throughout Bangladesh and highlights the importance of surveillance for mild respiratory illness among populations frequently exposed to infected poultry. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

In vitro activity of Ceftaroline against bacterial pathogens isolated from patients with skin and soft tissue and respiratory tract infections in African and Middle Eastern countries: AWARE global surveillance program 2012-2014.

PubMed

Karlowsky, James A; Biedenbach, Douglas J; Bouchillon, Samuel K; Hackel, Meredith; Iaconis, Joseph P; Sahm, Daniel F

2016-10-01

The objective of this report was to document antimicrobial susceptibility testing surveillance data for ceftaroline and comparative agents from the AWARE (Assessing Worldwide Antimicrobial Resistance Evaluation) global surveillance program for bacterial pathogens causing skin and soft tissue and respiratory tract infections in African and Middle Eastern countries from 2012 through 2014. Pathogen identities were confirmed by MALDI-TOF and antimicrobial susceptibility testing performed by CLSI broth microdilution methodology in a central laboratory. All methicillin-susceptible Staphylococcus aureus (MSSA) (n= 923; MIC90, 0.25 μg/mL) and 91.8% of methicillin-resistant S. aureus (MRSA) (n= 1161; MIC90, 1 μg/mL) tested were susceptible to ceftaroline. The maximum ceftaroline MIC observed for isolates of MRSA was 2 μg/mL. All Streptococcus pyogenes (n= 174; MIC90, 0.008 μg/mL), Streptococcus agalactiae (n= 44; MIC90, 0.015 μg/mL), Streptococcus pneumoniae (n= 351; MIC90, 0.25 μg/mL), and Haemophilus influenzae (n= 84; MIC90, ≤0.015 μg/mL) were susceptible to ceftaroline. Rates of susceptibility to ceftaroline among ESBL-negative Escherichia coli (n= 338), Klebsiella pneumoniae (n= 241), and Klebsiella oxytoca (n= 97) were 89.1% (MIC90, 1 μg/mL), 94.2% (MIC90, 0.5 μg/mL), and 99.0% (MIC90, 0.5 μg/mL), respectively. Copyright © 2016. Published by Elsevier Inc.

An investigation of the factors effecting high-risk individuals’ decision-making about prophylactic total gastrectomy and surveillance for hereditary diffuse gastric cancer (HDGC)

PubMed Central

Hallowell, Nina; Badger, Shirlene; Richardson, Sue; Caldas, Carlos; Hardwick, Richard H.; Fitzgerald, Rebecca C.; Lawton, Julia

2018-01-01

Because Hereditary Diffuse Gastric Cancer (HDGC) has an early onset and poor prognosis, individuals who carry a pathogenic (CDH1) mutation in the E-cadherin gene (CDH1) are offered endoscopic surveillance and advised to undergo prophylactic total gastrectomy (PTG) in their early to mid-twenties. Patients not ready or fit to undergo gastrectomy, or in whom the genetic testing result is unknown or ambiguous, are offered surveillance. Little is known about the factors that influence decisions to undergo or decline PTG, making it difficult to provide optimal support for those facing these decisions. Qualitative interviews were carried out with 35 high-risk individuals from the Familial Gastric Cancer Study in the UK. Twenty-seven had previously undergone PTG and eight had been identified as carrying a pathogenic CDH1 mutation but had declined surgery at the time of interview. The interviews explored the experience of decision-making and factors influencing risk-management decisions. The data suggest that decisions to proceed with PTG are influenced by a number of potentially competing factors: objective risk confirmation by genetic testing and/or receiving a positive biopsy; perceived familial cancer burden and associated risk perceptions; perceptions of post-surgical life; an increasing inability to tolerate endoscopic procedures; a concern that surveillance could miss a cancer developing and individual’s life stage. These findings have implications for advising this patient group. PMID:27256430

Exploiting mosquito sugar feeding to detect mosquito-borne pathogens

PubMed Central

Hall-Mendelin, Sonja; Ritchie, Scott A.; Johansen, Cheryl A.; Zborowski, Paul; Cortis, Giles; Dandridge, Scott; Hall, Roy A.; van den Hurk, Andrew F.

2010-01-01

Arthropod-borne viruses (arboviruses) represent a global public health problem, with dengue viruses causing millions of infections annually, while emerging arboviruses, such as West Nile, Japanese encephalitis, and chikungunya viruses have dramatically expanded their geographical ranges. Surveillance of arboviruses provides vital data regarding their prevalence and distribution that may be utilized for biosecurity measures and the implementation of disease control strategies. However, current surveillance methods that involve detection of virus in mosquito populations or sero-conversion in vertebrate hosts are laborious, expensive, and logistically problematic. We report a unique arbovirus surveillance system to detect arboviruses that exploits the process whereby mosquitoes expectorate virus in their saliva during sugar feeding. In this system, infected mosquitoes captured by CO2-baited updraft box traps are allowed to feed on honey-soaked nucleic acid preservation cards within the trap. The cards are then analyzed for expectorated virus using real-time reverse transcription-PCR. In field trials, this system detected the presence of Ross River and Barmah Forest viruses in multiple traps deployed at two locations in Australia. Viral RNA was preserved for at least seven days on the cards, allowing for long-term placement of traps and continuous collection of data documenting virus presence in mosquito populations. Furthermore no mosquito handling or processing was required and cards were conveniently shipped to the laboratory overnight. The simplicity and efficacy of this approach has the potential to transform current approaches to vector-borne disease surveillance by streamlining the monitoring of pathogens in vector populations. PMID:20534559

Identification of pathogens for differential diagnosis of fever with jaundice in the Central African Republic: a retrospective assessment, 2008-2010.

PubMed

Gadia, Christelle Luce Bobossi; Manirakiza, Alexandre; Tekpa, Gaspard; Konamna, Xavier; Vickos, Ulrich; Nakoune, Emmanuel

2017-11-29

Febrile jaundice results clinically in generalized yellow coloration of the teguments and mucous membranes due to excess plasma bilirubin, accompanied by fever. Two types are found: conjugated and unconjugated bilirubin jaundice. Jaundice is a sign in several diseases due to viruses (viral hepatitis and arbovirus), parasites (malaria) and bacteria (leptospirosis). In the Central African Republic (CAR), only yellow fever is included on the list of diseases for surveillance. The aim of this study was to identify the other pathogens that can cause febrile jaundice, for better management of patients. Between 2008 and 2010, 198 sera negative for yellow fever IgM were randomly selected from 2177 samples collected during yellow fever surveillance. Laboratory analyses targeted four groups of pathogens: hepatitis B, C, delta and E viruses; dengue, chikungunya, Zika, Crimean-Congo haemorrhagic fever, West Nile and Rift Valley arboviruses; malaria parasites; and bacteria (leptospirosis). Overall, 30.9% sera were positive for hepatitis B, 20.2% for hepatitis E, 12.3% for hepatitis C and 8.2% for malaria. The majority of positive sera (40.4%) were from people aged 16-30 years. Co-infection with at least two of these pathogens was also found. These findings suggest that a systematic investigation should be undertaken of infectious agents that cause febrile jaundice in the CAR.

Comparing transfusion reaction risks for various plasma products - an analysis of 7 years of ISTARE haemovigilance data.

PubMed

Saadah, Nicholas H; van der Bom, Johanna G; Wiersum-Osselton, Johanna C; Richardson, Clive; Middelburg, Rutger A; Politis, Constantina; Renaudier, Philippe; Robillard, Pierre; Schipperus, Martin R

2018-03-01

Plasma transfusions may result in transfusion reactions. We used the International Surveillance of Transfusion-Associated Reactions and Events (ISTARE) database, containing yearly reported national annual aggregate data on transfusion reactions from participating countries, to investigate risks of plasma transfusion reactions and compare transfusion reaction risks for different plasma types. We calculated risks for plasma transfusion reactions and compared transfusion reaction risks between plasma types using random effects regression on repeated measures. The ISTARE database contains data from 23 countries, reporting units issued and/or transfused and transfusion reactions observed for some portion of 7 years (2006-2012). Interquartile ranges (IQRs) of plasma transfusion reaction risks were: allergic reactions (5·6-72·2 reactions/10 5 units transfused); febrile non-haemolytic transfusion reactions (0-9·1); transfusion-associated circulatory overload (0-1·9); transfusion related acute lung injury (TRALI) (0-1·2); and hypotensive reactions (0-0·6). Apheresis plasma was associated with more allergic reactions [odds ratio (OR) = 1·29 (95% confidence interval: 1·19-1·40)] and hypotensive reactions [OR = 2·17 (1·38-3·41)] than whole blood-derived plasma. Pathogen-inactivated plasma was associated with fewer transfusion reactions than untreated plasma. © 2018 John Wiley & Sons Ltd.

A concept for routine emergency-care data-based syndromic surveillance in Europe.

PubMed

Ziemann, A; Rosenkötter, N; Garcia-Castrillo Riesgo, L; Schrell, S; Kauhl, B; Vergeiner, G; Fischer, M; Lippert, F K; Krämer, A; Brand, H; Krafft, T

2014-11-01

We developed a syndromic surveillance (SyS) concept using emergency dispatch, ambulance and emergency-department data from different European countries. Based on an inventory of sub-national emergency data availability in 12 countries, we propose framework definitions for specific syndromes and a SyS system design. We tested the concept by retrospectively applying cumulative sum and spatio-temporal cluster analyses for the detection of local gastrointestinal outbreaks in four countries and comparing the results with notifiable disease reporting. Routine emergency data was available daily and electronically in 11 regions, following a common structure. We identified two gastrointestinal outbreaks in two countries; one was confirmed as a norovirus outbreak. We detected 1/147 notified outbreaks. Emergency-care data-based SyS can supplement local surveillance with near real-time information on gastrointestinal patients, especially in special circumstances, e.g. foreign tourists. It most likely cannot detect the majority of local gastrointestinal outbreaks with few, mild or dispersed cases.

Omics approaches in food safety: fulfilling the promise?

PubMed Central

Bergholz, Teresa M.; Moreno Switt, Andrea I.; Wiedmann, Martin

2014-01-01

Genomics, transcriptomics, and proteomics are rapidly transforming our approaches to detection, prevention and treatment of foodborne pathogens. Microbial genome sequencing in particular has evolved from a research tool into an approach that can be used to characterize foodborne pathogen isolates as part of routine surveillance systems. Genome sequencing efforts will not only improve outbreak detection and source tracking, but will also create large amounts of foodborne pathogen genome sequence data, which will be available for data mining efforts that could facilitate better source attribution and provide new insights into foodborne pathogen biology and transmission. While practical uses and application of metagenomics, transcriptomics, and proteomics data and associated tools are less prominent, these tools are also starting to yield practical food safety solutions. PMID:24572764

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi.

PubMed

Irinyi, Laszlo; Serena, Carolina; Garcia-Hermoso, Dea; Arabatzis, Michael; Desnos-Ollivier, Marie; Vu, Duong; Cardinali, Gianluigi; Arthur, Ian; Normand, Anne-Cécile; Giraldo, Alejandra; da Cunha, Keith Cassia; Sandoval-Denis, Marcelo; Hendrickx, Marijke; Nishikaku, Angela Satie; de Azevedo Melo, Analy Salles; Merseguel, Karina Bellinghausen; Khan, Aziza; Parente Rocha, Juliana Alves; Sampaio, Paula; da Silva Briones, Marcelo Ribeiro; e Ferreira, Renata Carmona; de Medeiros Muniz, Mauro; Castañón-Olivares, Laura Rosio; Estrada-Barcenas, Daniel; Cassagne, Carole; Mary, Charles; Duan, Shu Yao; Kong, Fanrong; Sun, Annie Ying; Zeng, Xianyu; Zhao, Zuotao; Gantois, Nausicaa; Botterel, Françoise; Robbertse, Barbara; Schoch, Conrad; Gams, Walter; Ellis, David; Halliday, Catriona; Chen, Sharon; Sorrell, Tania C; Piarroux, Renaud; Colombo, Arnaldo L; Pais, Célia; de Hoog, Sybren; Zancopé-Oliveira, Rosely Maria; Taylor, Maria Lucia; Toriello, Conchita; de Almeida Soares, Célia Maria; Delhaes, Laurence; Stubbe, Dirk; Dromer, Françoise; Ranque, Stéphane; Guarro, Josep; Cano-Lira, Jose F; Robert, Vincent; Velegraki, Aristea; Meyer, Wieland

2015-05-01

Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Evaluation of a National Call Center and a Local Alerts System for Detection of New Cases of Ebola Virus Disease - Guinea, 2014-2015.

PubMed

Lee, Christopher T; Bulterys, Marc; Martel, Lise D; Dahl, Benjamin A

2016-03-11

The epidemic of Ebola virus disease (Ebola) in West Africa began in Guinea in late 2013 (1), and on August 8, 2014, the World Health Organization (WHO) declared the epidemic a Public Health Emergency of International Concern (2). Guinea was declared Ebola-free on December 29, 2015, and is under a 90 day period of enhanced surveillance, following 3,351 confirmed and 453 probable cases of Ebola and 2,536 deaths (3). Passive surveillance for Ebola in Guinea has been conducted principally through the use of a telephone alert system. Community members and health facilities report deaths and suspected Ebola cases to local alert numbers operated by prefecture health departments or to a national toll-free call center. The national call center additionally functions as a source of public health information by responding to questions from the public about Ebola. To evaluate the sensitivity of the two systems and compare the sensitivity of the national call center with the local alerts system, the CDC country team performed probabilistic record linkage of the combined prefecture alerts database, as well as the national call center database, with the national viral hemorrhagic fever (VHF) database; the VHF database contains records of all known confirmed Ebola cases. Among 17,309 alert calls analyzed from the national call center, 71 were linked to 1,838 confirmed Ebola cases in the VHF database, yielding a sensitivity of 3.9%. The sensitivity of the national call center was highest in the capital city of Conakry (11.4%) and lower in other prefectures. In comparison, the local alerts system had a sensitivity of 51.1%. Local public health infrastructure plays an important role in surveillance in an epidemic setting.

An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids.

PubMed

Barrero, Roberto A; Napier, Kathryn R; Cunnington, James; Liefting, Lia; Keenan, Sandi; Frampton, Rebekah A; Szabo, Tamas; Bulman, Simon; Hunter, Adam; Ward, Lisa; Whattam, Mark; Bellgard, Matthew I

2017-01-11

Detection and preventing entry of exotic viruses and viroids at the border is critical for protecting plant industries trade worldwide. Existing post entry quarantine screening protocols rely on time-consuming biological indicators and/or molecular assays that require knowledge of infecting viral pathogens. Plants have developed the ability to recognise and respond to viral infections through Dicer-like enzymes that cleave viral sequences into specific small RNA products. Many studies reported the use of a broad range of small RNAs encompassing the product sizes of several Dicer enzymes involved in distinct biological pathways. Here we optimise the assembly of viral sequences by using specific small RNA subsets. We sequenced the small RNA fractions of 21 plants held at quarantine glasshouse facilities in Australia and New Zealand. Benchmarking of several de novo assembler tools yielded SPAdes using a kmer of 19 to produce the best assembly outcomes. We also found that de novo assembly using 21-25 nt small RNAs can result in chimeric assemblies of viral sequences and plant host sequences. Such non-specific assemblies can be resolved by using 21-22 nt or 24 nt small RNAs subsets. Among the 21 selected samples, we identified contigs with sequence similarity to 18 viruses and 3 viroids in 13 samples. Most of the viruses were assembled using only 21-22 nt long virus-derived siRNAs (viRNAs), except for one Citrus endogenous pararetrovirus that was more efficiently assembled using 24 nt long viRNAs. All three viroids found in this study were fully assembled using either 21-22 nt or 24 nt viRNAs. Optimised analysis workflows were customised within the Yabi web-based analytical environment. We present a fully automated viral surveillance and diagnosis web-based bioinformatics toolkit that provides a flexible, user-friendly, robust and scalable interface for the discovery and diagnosis of viral pathogens. We have implemented an automated viral surveillance and diagnosis (VSD) bioinformatics toolkit that produces improved viruses and viroid sequence assemblies. The VSD toolkit provides several optimised and reusable workflows applicable to distinct viral pathogens. We envisage that this resource will facilitate the surveillance and diagnosis viral pathogens in plants, insects and invertebrates.

The commercial impact of pig Salmonella spp. infections in border-free markets during an economic recession

PubMed Central

Evangelopoulou, G.; Kritas, S.; Christodoulopoulos, G.; Burriel, A. R.

2015-01-01

The genus Salmonella, a group of important zoonotic pathogens, is having global economic and political importance. Its main political importance results from the pathogenicity of many of its serovars for man. Serovars Salmonella Enteritidis and Salmonella Typhimurium are currently the most frequently associated to foodborne infections, but they are not the only ones. Animal food products contaminated from subclinically infected animals are a risk to consumers. In border free markets, an example is the EU, these consumers at risk are international. This is why, economic competition could use the risk of consumer infection either to restrict or promote free border trade in animals and their products. Such use of public health threats increases during economic recessions in nations economically weak to effectively enforce surveillance. In free trade conditions, those unable to pay the costs of pathogen control are unable to effectively implement agreed regulations, centrally decided, but leaving their enforcement to individual states. Free trade of animal food products depends largely on the promotion of safety, included in “quality,” when traders target foreign markets. They will overtake eventually the markets of those ineffectively implementing agreed safety regulations, if their offered prices are also attractive for recession hit consumers. Nations unable to effectively enforce safety regulations become disadvantaged partners unequally competing with producers of economically robust states when it comes to public health. Thus, surveillance and control of pathogens like Salmonella are not only quantitative. They are also political issues upon which states base national trade decisions. Hence, the quantitative calculation of costs incurring from surveillance and control of animal salmonelloses, should not only include the cost for public health protection, but also the long term international economic and political costs for an individual state. These qualitative and qualitative costs of man and animal Salmonella infections should be calculated in the light of free trade and open borders. Understandably, accurate calculation of the economic and political costs requires knowledge of the many factors influencing nationally the quality and safety of pork products and internationally free trade. Thus, how Salmonella pig infections affect commerce and public health across open borders depends on a state’s ability to accurately calculate costs for the surveillance and control of animal salmonelloses in general, and pig infections as a particular example. PMID:27047083

Is methicillin-resistant Staphylococcus aureus an emerging community pathogen? A review of the literature

PubMed Central

Gardam, Michael A

2000-01-01

OBJECTIVES: To discuss the historical epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) and review the literature suggesting that MRSA has become a community pathogen. DATA SOURCES: A search of the MEDLINE database was performed, encompassing all English or French language citations from 1966 to 1999 and containing the subjects and/or text words: 'Staphylococcus aureus', 'methicillin resistance', 'endocarditis', 'cellulites', 'pneumonia' and 'community-acquired'. Articles published in other languages that provided English or French abstracts were included. All relevant references cited in articles obtained from the MEDLINE database and book chapters were also included. DATA EXTRACTION: All articles obtained from the above sources were examined and were included in the review if a laboratory or epidemiological study of community-acquired MRSA was presented. DATA SYNTHESIS AND CONCLUSIONS: MRSA has emerged over the past 30 years to become a worldwide nosocomial pathogen and has recently been reported as a cause of community-acquired infections. The changing epidemiology of MRSA is likely because of two mechanisms: the movement of nosocomial MRSA strains into the community and the de novo appearance of community strains resulting from the transfer of genetic material from methicillin-resistant Gram-positive organisms to sensitive S aureus strains. The emergence of MRSA as a community pathogen has occurred at a slower rate than it did for penicillin-resistant S aureus (PRSA) in the 1950s and 1960s, possibly because the mechanism of methicillin resistance does not exhibit the same ease of transferability as that of penicillin resistance. Four case reports, seven case series, 10 case-control studies and two cohort studies on community-acquired MRSA were analyzed. Determining whether these reports involve new community-acquired strains rather than previously acquired nosocomial strains can be problematic. It appears, however, that MRSA strains of both nosocomial and community origin are now endemic in certain communities in different parts of the world. Few surveillance studies of nonhospitalized patient populations have been performed to date; thus, the true prevalence of MRSA in the community at large is essentially unknown, although it appears to be low. At present, the empirical treatment of community-acquired S aureus infections with a beta-lactamase-stable beta-lactam antibiotic is appropriate for most populations. However, empirical vancomycin therapy for serious S aureus infections should be strongly considered for patients with significant risk factors for previously-acquired nosocomial MRSA or for patients belonging to outpatient populations with a proven high prevalence of MRSA. Increasing vancomycin use will likely have a significant impact on the development of resistance in Gram-positive organisms. PMID:18159291

Towards an integrated approach in surveillance of vector-borne diseases in Europe

PubMed Central

2011-01-01

Vector borne disease (VBD) emergence is a complex and dynamic process. Interactions between multiple disciplines and responsible health and environmental authorities are often needed for an effective early warning, surveillance and control of vectors and the diseases they transmit. To fully appreciate this complexity, integrated knowledge about the human and the vector population is desirable. In the current paper, important parameters and terms of both public health and medical entomology are defined in order to establish a common language that facilitates collaboration between the two disciplines. Special focus is put on the different VBD contexts with respect to the current presence or absence of the disease, the pathogen and the vector in a given location. Depending on the context, whether a VBD is endemic or not, surveillance activities are required to assess disease burden or threat, respectively. Following a decision for action, surveillance activities continue to assess trends. PMID:21967706

Benefits of using heterologous polyclonal antibodies and potential applications to new and undertreated infectious pathogens.

PubMed

Dixit, Rashmi; Herz, Jenny; Dalton, Richard; Booy, Robert

2016-02-24

Passive immunotherapy using polyclonal antibodies (immunoglobulins) has been used for over a century in the treatment and post-exposure prophylaxis of various infections and toxins. Heterologous polyclonal antibodies are obtained from animals hyperimmunised with a pathogen or toxin. The aims of this review are to examine the history of animal polyclonal antibody therapy use, their development into safe and effective products and the potential application to humans for emerging and neglected infectious diseases. A literature search of OVID Medline and OVID Embase databases was undertaken to identify articles on the safety, efficacy and ongoing development of polyclonal antibodies. The search contained database-specific MeSH and EMTREE terms in combination with pertinent text-words: polyclonal antibodies and rare/neglected diseases, antivenins, immunoglobulins, serum sickness, anaphylaxis, drug safety, post marketing surveillance, rabies, human influenza, Dengue, West Nile, Nipah, Hendra, Marburg, MERS, Hemorrhagic Fever Virus, and Crimean-Congo. No language limits were applied. The final search was completed on 20.06.2015. Of 1960 articles, title searches excluded many irrelevant articles, yielding 303 articles read in full. Of these, 179 are referenced in this study. Serum therapy was first used in the 1890s against diphtheria. Early preparation techniques yielded products contaminated with reactogenic animal proteins. The introduction of enzymatic digestion, and purification techniques substantially improved their safety profile. The removal of the Fc fragment of antibodies further reduces hypersensitivity reactions. Clinical studies have demonstrated the efficacy of polyclonal antibodies against various infections, toxins and venoms. Products are being developed against infections for which prophylactic and therapeutic options are currently limited, such as avian influenza, Ebola and other zoonotic viruses. Polyclonal antibodies have been successfully applied to rabies, envenomation and intoxication. Polyclonal production provides an exciting opportunity to revolutionise the prognosis of both longstanding neglected tropical diseases as well as emerging infectious threats to humans. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

The Israeli National Genetic database: a 10-year experience.

PubMed

Zlotogora, Joël; Patrinos, George P

2017-03-16

The Israeli National and Ethnic Mutation database ( http://server.goldenhelix.org/israeli ) was launched in September 2006 on the ETHNOS software to include clinically relevant genomic variants reported among Jewish and Arab Israeli patients. In 2016, the database was reviewed and corrected according to ClinVar ( https://www.ncbi.nlm.nih.gov/clinvar ) and ExAC ( http://exac.broadinstitute.org ) database entries. The present article summarizes some key aspects from the development and continuous update of the database over a 10-year period, which could serve as a paradigm of successful database curation for other similar resources. In September 2016, there were 2444 entries in the database, 890 among Jews, 1376 among Israeli Arabs, and 178 entries among Palestinian Arabs, corresponding to an ~4× data content increase compared to when originally launched. While the Israeli Arab population is much smaller than the Jewish population, the number of pathogenic variants causing recessive disorders reported in the database is higher among Arabs (934) than among Jews (648). Nevertheless, the number of pathogenic variants classified as founder mutations in the database is smaller among Arabs (175) than among Jews (192). In 2016, the entire database content was compared to that of other databases such as ClinVar and ExAC. We show that a significant difference in the percentage of pathogenic variants from the Israeli genetic database that were present in ExAC was observed between the Jewish population (31.8%) and the Israeli Arab population (20.6%). The Israeli genetic database was launched in 2006 on the ETHNOS software and is available online ever since. It allows querying the database according to the disorder and the ethnicity; however, many other features are not available, in particular the possibility to search according to the name of the gene. In addition, due to the technical limitations of the previous ETHNOS software, new features and data are not included in the present online version of the database and upgrade is currently ongoing.

Epidemiology of low pathogenic avian influenza viruses in wild birds.

PubMed

Fouchier, R A M; Munster, V J

2009-04-01

Although extensive data are available on low pathogenic avian influenza (LPAI) virus surveillance in wild birds in North America and Europe, data are scarce for other parts of the world, and our understanding of LPAI virus ecology in the natural reservoir is still far from complete. The outbreak of highly pathogenic avian influenza (HPAI) of the H5N1 subtype in the eastern hemisphere has put an increased focus on the role of wild birds in influenza virus transmission. Here, the authors review the current knowledge of the (molecular) epidemiology, genetics and evolution of LPAI viruses in wild birds, and identify some important gaps in current knowledge.

OIE Collaborating Centre for Biorisk Management Strategic Plan.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brass, Van Hildren

Due to efforts by individual nations and the international community to monitor and control natural occurring outbreaks of animal and zoonotic diseases, any number and variety of select agents and especially dangerous pathogens can be found at diagnostic laboratories around the world. Diagnostic testing is a crucial aspect of disease surveillance, but the organized collection and testing of diagnostic samples from the animal and human population at laboratories has created a repository of disease agents and toxins that could cause serious harm if released or acquired by nefarious means. The delicate balance between public health disease surveillance and the managementmore » of biorisks at facilities utilized in surveillance is a necessary goal of veterinary public health.« less

New technologies in predicting, preventing and controlling emerging infectious diseases.

PubMed

Christaki, Eirini

2015-01-01

Surveillance of emerging infectious diseases is vital for the early identification of public health threats. Emergence of novel infections is linked to human factors such as population density, travel and trade and ecological factors like climate change and agricultural practices. A wealth of new technologies is becoming increasingly available for the rapid molecular identification of pathogens but also for the more accurate monitoring of infectious disease activity. Web-based surveillance tools and epidemic intelligence methods, used by all major public health institutions, are intended to facilitate risk assessment and timely outbreak detection. In this review, we present new methods for regional and global infectious disease surveillance and advances in epidemic modeling aimed to predict and prevent future infectious diseases threats.

New technologies in predicting, preventing and controlling emerging infectious diseases

PubMed Central

Christaki, Eirini

2015-01-01

Surveillance of emerging infectious diseases is vital for the early identification of public health threats. Emergence of novel infections is linked to human factors such as population density, travel and trade and ecological factors like climate change and agricultural practices. A wealth of new technologies is becoming increasingly available for the rapid molecular identification of pathogens but also for the more accurate monitoring of infectious disease activity. Web-based surveillance tools and epidemic intelligence methods, used by all major public health institutions, are intended to facilitate risk assessment and timely outbreak detection. In this review, we present new methods for regional and global infectious disease surveillance and advances in epidemic modeling aimed to predict and prevent future infectious diseases threats. PMID:26068569

DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems.

PubMed

Memišević, Vesna; Kumar, Kamal; Zavaljevski, Nela; DeShazer, David; Wallqvist, Anders; Reifman, Jaques

2016-09-20

Burkholderia mallei and B. pseudomallei are the causative agents of glanders and melioidosis, respectively, diseases with high morbidity and mortality rates. B. mallei and B. pseudomallei are closely related genetically; B. mallei evolved from an ancestral strain of B. pseudomallei by genome reduction and adaptation to an obligate intracellular lifestyle. Although these two bacteria cause different diseases, they share multiple virulence factors, including bacterial secretion systems, which represent key components of bacterial pathogenicity. Despite recent progress, the secretion system proteins for B. mallei and B. pseudomallei, their pathogenic mechanisms of action, and host factors are not well characterized. We previously developed a manually curated database, DBSecSys, of bacterial secretion system proteins for B. mallei. Here, we report an expansion of the database with corresponding information about B. pseudomallei. DBSecSys 2.0 contains comprehensive literature-based and computationally derived information about B. mallei ATCC 23344 and literature-based and computationally derived information about B. pseudomallei K96243. The database contains updated information for 163 B. mallei proteins from the previous database and 61 additional B. mallei proteins, and new information for 281 B. pseudomallei proteins associated with 5 secretion systems, their 1,633 human- and murine-interacting targets, and 2,400 host-B. mallei interactions and 2,286 host-B. pseudomallei interactions. The database also includes information about 13 pathogenic mechanisms of action for B. mallei and B. pseudomallei secretion system proteins inferred from the available literature or computationally. Additionally, DBSecSys 2.0 provides details about 82 virulence attenuation experiments for 52 B. mallei secretion system proteins and 98 virulence attenuation experiments for 61 B. pseudomallei secretion system proteins. We updated the Web interface and data access layer to speed-up users' search of detailed information for orthologous proteins related to secretion systems of the two pathogens. The updates of DBSecSys 2.0 provide unique capabilities to access comprehensive information about secretion systems of B. mallei and B. pseudomallei. They enable studies and comparisons of corresponding proteins of these two closely related pathogens and their host-interacting partners. The database is available at http://dbsecsys.bhsai.org .

The Free Trade Area of the Americas: Can Regional Economic Integration Lead to Greater Cooperation on Security?

DTIC Science & Technology

2002-12-01

Brazilian Air Force has been testing a new surveillance system called Sistema de Vigilancia da Amazonia (SIVAM), designed to...2000 Online Database, 23 April 1998 and “Plan de seguridad para la triple frontera,” Ser en el 2000 Online Database, 01 June...Plan de seguridad para la triple frontera,” Ser en el 2000 Online Database, 01 June 1998. 64 Robert Devlin, Antoni Estevadeordal

EMERGING WATERBORNE PATHOGENS

EPA Science Inventory

In 1971, the U.S. Environmental Protection Agency (EPA) entered into a long term agreement with the Centers for Disease Control and Prevention (CDC) to gather data on the occurrence of waterborne illness. It is difficult however to know what effects increases in surveillance hav...

Dengue and Chikungunya Vector Control Pocket Guide

USDA-ARS?s Scientific Manuscript database

This technical guide consolidates information and procedures for surveillance and control of mosquitoes that transmit dengue and chikungunya viruses. The guide focuses on mosquitoes that transmit dengue but also makes reference to chikungunya and yellow fever because the pathogens that cause these ...

Avian influenza surveillance and diagnosis

USDA-ARS?s Scientific Manuscript database

Rapid detection and accurate identification of low (LPAI) and high pathogenicity avian influenza (HPAI) is critical to controlling infections and disease in poultry. Test selection and algorithms for the detection and diagnosis of avian influenza virus (AIV) in poultry may vary somewhat among differ...

Methodological comparisons for antimicrobial resistance surveillance in feedlot cattle

PubMed Central

2013-01-01

Background The purpose of this study was to objectively compare methodological approaches that might be utilized in designing an antimicrobial resistance (AMR) surveillance program in beef feedlot cattle. Specifically, four separate comparisons were made to investigate their potential impact on estimates for prevalence of AMR. These included investigating potential differences between 2 different susceptibility testing methods (broth microdilution and disc diffusion), between 2 different target bacteria (non-type-specific E. coli [NTSEC] and Mannheimia haemolytica), between 2 strategies for sampling feces (individual samples collected per rectum and pooled samples collected from the pen floor), and between 2 strategies for determining which cattle to sample (cattle that were culture-positive for Mannheimia haemolytica and those that were culture-negative). Results Comparing two susceptibility testing methods demonstrated differences in the likelihood of detecting resistance between automated disk diffusion (BioMIC®) and broth microdilution (Sensititre®) for both E. coli and M. haemolytica. Differences were also detected when comparing resistance between two bacterial organisms within the same cattle; there was a higher likelihood of detecting resistance in E. coli than in M. haemolytica. Differences in resistance prevalence were not detected when using individual animal or composite pen sampling strategies. No differences in resistance prevalences were detected in E. coli recovered from cattle that were culture-positive for M. haemolytica compared to those that were culture-negative, suggesting that sampling strategies which targeted recovery of E. coli from M. haemolytica-positive cattle would not provide biased results. Conclusions We found that for general purposes, the susceptibility test selected for AMR surveillance must be carefully chosen considering the purpose of the surveillance since the ability to detect resistance appears to vary between these tests depending upon the population where they are applied. Continued surveillance of AMR in M. haemolytica recovered by nasopharyngeal swab is recommended if monitoring an animal health pathogen is an objective of the surveillance program as results of surveillance using fecal E. coli cannot be extrapolated to this important respiratory pathogen. If surveillance of E. coli was pursued in the same population, study populations could target animals that were culture-positive for M. haemolytica without biasing estimates for AMR in E. coli. Composite pen-floor sampling or sampling of individuals per-rectum could possibly be used interchangeably for monitoring resistance in E. coli. PMID:24144185

Development of a prototype system for statewide asthma surveillance.

PubMed

Deprez, Ronald D; Asdigian, Nancy L; Oliver, L Christine; Anderson, Norman; Caldwell, Edgar; Baggott, Lee Ann

2002-12-01

We developed and evaluated a statewide and community-level asthma surveillance system. Databases and measures included a community prevalence survey, hospital admissions data, emergency department/outpatient clinic visit records, and a physician survey of diagnosis and treatment practices. We evaluated the system in 5 Maine communities varying in population and income. Asthma hospitalizations were high in the rural/low-socioeconomic-status communities studied, although diagnosed asthma was low. Males were more likely than females to experience asthma symptoms, although they were less likely to have been diagnosed with asthma or to have used hospital-based asthma care. Databases were useful for estimating asthma burden and identifying service needs as well as high-risk groups. They were less useful in estimating severity or in identifying environmental risks.

How Quickly Do Asymptomatic Infrarenal Abdominal Aortic Aneurysms Grow and What Factors Affect Aneurysm Growth Rates? Analysis of a Single Centre Surveillance Cohort Database.

PubMed

Ahmad, Mehtab; Mistry, Rakesh; Hodson, James; Bradbury, Andrew W

2017-11-01

Abdominal aortic aneurysm (AAA) maximum antero-posterior diameter (MAPD) is the parameter most commonly used to inform the timing of surgical intervention. However, other factors, such as growth rates and patient comorbidities are likely to be important considerations as they may influence AAA related complications including rupture, operative outcomes, and the clinical and cost effectiveness of continued surveillance. This was a retrospective analysis of a 20 year period of a single centre AAA surveillance database. In total, 5363 AAA measurements in 692 patients were analysed for patient demographics, including comorbidity and drug history, growth and rupture rates, and cause of death. A significant proportion of patients (n = 73; 11%) were kept under surveillance despite having a MAPD < 30 mm. Overall, mean aneurysm growth rate was 2.3 mm/year. Elective repair was undertaken in 20.1% and those who required surgical intervention had significantly faster growth rates. Only 3.9% of patients in surveillance ruptured, 40.7% of whom had a MAPD <55 mm at their last scan. Of the 214 deaths recorded, only 11.7% were related to AAA. The majority of patients who died in surveillance did so from malignancy. Patients with larger AAA (MAPD > 40 mm) on entry into surveillance were significantly more likely to receive surgical intervention, as were those whose AAA expanded >4 mm/year. Females had significantly higher growth rates, and those with diabetes had significantly smaller growth rates. Other comorbidities and drug history were not associated with AAA growth, or 5 and 10 year surgery free survival. The results highlight several areas for service improvement. Specifically, it is important not to maintain surveillance in patients who are very unlikely to ever grow to a point where AAA surgery would be contemplated on grounds or age and/or comorbidity. Similarly, patients should be discharged from surveillance when this likelihood becomes apparent. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Post-treatment surveillance testing of patients with colorectal cancer and the association with survival: protocol for a retrospective cohort study of the Surveillance, Epidemiology, and End Results (SEER)-Medicare database.

PubMed

Hines, Robert B; Jiban, Md Jibanul Haque; Choudhury, Kanak; Loerzel, Victoria; Specogna, Adrian V; Troy, Steven P; Zhang, Shunpu

2018-04-28

Although the colorectal cancer (CRC) mortality rate has significantly improved over the past several decades, many patients will have a recurrence following curative treatment. Despite this high risk of recurrence, adherence to CRC surveillance testing guidelines is poor which increases cancer-related morbidity and potentially, mortality. Several randomised controlled trials (RCTs) with varying surveillance strategies have yielded conflicting evidence regarding the survival benefit associated with surveillance testing. However, due to differences in study protocols and limitations of sample size and length of follow-up, the RCT may not be the best study design to evaluate this relationship. An observational comparative effectiveness research study can overcome the sample size/follow-up limitations of RCT designs while assessing real-world variability in receipt of surveillance testing to provide much needed evidence on this important clinical issue. The gap in knowledge that this study will address concerns whether adherence to National Comprehensive Cancer Network CRC surveillance guidelines improves survival. Patients with colon and rectal cancer aged 66-84 years, who have been diagnosed between 2002 and 2008 and have been included in the Surveillance, Epidemiology, and End Results-Medicare database, are eligible for this retrospective cohort study. To minimise bias, patients had to survive at least 12 months following the completion of treatment. Adherence to surveillance testing up to 5 years post-treatment will be assessed in each year of follow-up and overall. Binomial regression will be used to assess the association between patients' characteristics and adherence. Survival analysis will be conducted to assess the association between adherence and 5-year survival. This study was approved by the National Cancer Institute and the Institutional Review Board of the University of Central Florida. The results of this study will be disseminated by publishing in the peer-reviewed scientific literature, presentation at national/international scientific conferences and posting through social media. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Application of Species Distribution Modeling for Avian Influenza surveillance in the United States considering the North America Migratory Flyways

NASA Astrophysics Data System (ADS)

Belkhiria, Jaber; Alkhamis, Moh A.; Martínez-López, Beatriz

2016-09-01

Highly Pathogenic Avian Influenza (HPAI) has recently (2014-2015) re-emerged in the United States (US) causing the largest outbreak in US history with 232 outbreaks and an estimated economic impact of $950 million. This study proposes to use suitability maps for Low Pathogenic Avian Influenza (LPAI) to identify areas at high risk for HPAI outbreaks. LPAI suitability maps were based on wild bird demographics, LPAI surveillance, and poultry density in combination with environmental, climatic, and socio-economic risk factors. Species distribution modeling was used to produce high-resolution (cell size: 500m x 500m) maps for Avian Influenza (AI) suitability in each of the four North American migratory flyways (NAMF). Results reveal that AI suitability is heterogeneously distributed throughout the US with higher suitability in specific zones of the Midwest and coastal areas. The resultant suitability maps adequately predicted most of the HPAI outbreak areas during the 2014-2015 epidemic in the US (i.e. 89% of HPAI outbreaks were located in areas identified as highly suitable for LPAI). Results are potentially useful for poultry producers and stakeholders in designing risk-based surveillance, outreach and intervention strategies to better prevent and control future HPAI outbreaks in the US.

Online Databases for Taxonomy and Identification of Pathogenic Fungi and Proposal for a Cloud-Based Dynamic Data Network Platform

PubMed Central

Prakash, Peralam Yegneswaran; Irinyi, Laszlo; Halliday, Catriona; Chen, Sharon; Robert, Vincent

2017-01-01

ABSTRACT The increase in public online databases dedicated to fungal identification is noteworthy. This can be attributed to improved access to molecular approaches to characterize fungi, as well as to delineate species within specific fungal groups in the last 2 decades, leading to an ever-increasing complexity of taxonomic assortments and nomenclatural reassignments. Thus, well-curated fungal databases with substantial accurate sequence data play a pivotal role for further research and diagnostics in the field of mycology. This minireview aims to provide an overview of currently available online databases for the taxonomy and identification of human and animal-pathogenic fungi and calls for the establishment of a cloud-based dynamic data network platform. PMID:28179406

Clothing hanger injuries: pediatric head and neck traumas in the United States, 2002-2012.

PubMed

Walls, Andrew; Pierce, Matthew; Wang, Hongkun; Harley, Earl H

2014-02-01

To discuss pediatric clothing hanger injuries and review the National Electronic Injury Surveillance System to elucidate frequency and promote increased public awareness among pediatric otolaryngologists. Cross-sectional analysis of a national database. National Electronic Injury Surveillance System Database. A retrospective review of the National Electronic Injury Surveillance System provided a nationally weighted sampling estimate of 394 pediatric incident reports involving clothing hangers. Each incident report was analyzed for impalement, facial laceration, and contusion injuries to the mouth, face, and head. In addition, hospital disposition and location of the described incident were also obtained. Upon review of the National Electronic Injury Surveillance System, incident rates of pediatric oral impalement (95% confidence interval [CI], 0.10-0.41), facial laceration (95% CI, 0.22-0.41), and facial abrasion injuries (95% CI, 0.15-0.44) frequently involved the metal clothing hanger design. In addition, most of the reported injuries occurred within the home and involved lacerations to the oral cavity. This is the first multiyear, nationally representative study to analyze clothing hanger injuries in the pediatric population. We demonstrate that these injuries occur more frequently than the medical literature currently reports and also elucidate that children are more likely to obtain laceration injuries by metal clothing hangers within the home. Furthermore, we provide a recommendation for standardization of the National Electronic Injury Surveillance System such that product safety analysis may occur and reduce further pediatric incidents.

The Danish Microbiology Database (MiBa) 2010 to 2013.

PubMed

Voldstedlund, M; Haarh, M; Mølbak, K

2014-01-09

The Danish Microbiology Database (MiBa) is a national database that receives copies of reports from all Danish departments of clinical microbiology. The database was launched in order to provide healthcare personnel with nationwide access to microbiology reports and to enable real-time surveillance of communicable diseases and microorganisms. The establishment and management of MiBa has been a collaborative process among stakeholders, and the present paper summarises lessons learned from this nationwide endeavour which may be relevant to similar projects in the rapidly changing landscape of health informatics.

Viral Metagenomics on Blood-Feeding Arthropods as a Tool for Human Disease Surveillance

PubMed Central

Brinkmann, Annika; Nitsche, Andreas; Kohl, Claudia

2016-01-01

Surveillance and monitoring of viral pathogens circulating in humans and wildlife, together with the identification of emerging infectious diseases (EIDs), are critical for the prediction of future disease outbreaks and epidemics at an early stage. It is advisable to sample a broad range of vertebrates and invertebrates at different temporospatial levels on a regular basis to detect possible candidate viruses at their natural source. However, virus surveillance systems can be expensive, costly in terms of finances and resources and inadequate for sampling sufficient numbers of different host species over space and time. Recent publications have presented the concept of a new virus surveillance system, coining the terms “flying biological syringes”, “xenosurveillance” and “vector-enabled metagenomics”. According to these novel and promising surveillance approaches, viral metagenomics on engorged mosquitoes might reflect the viral diversity of numerous mammals, birds and humans, combined in the mosquitoes’ blood meal during feeding on the host. In this review article, we summarize the literature on vector-enabled metagenomics (VEM) techniques and its application in disease surveillance in humans. Furthermore, we highlight the combination of VEM and “invertebrate-derived DNA” (iDNA) analysis to identify the host DNA within the mosquito midgut. PMID:27775568

Laboratory-based Salmonella surveillance in Fiji, 2004-2005.

PubMed

Dunn, John; Pryor, Jan; Saketa, Salanieta; Delai, Wasale; Buadromo, Eka; Kishore, Kamal; Naidu, Shakila; Greene, Sharon; Varma, Jay; Chiller, Tom

2005-09-01

Although foodborne diseases are an important public health problem worldwide, the burden of foodborne illness is not well described in most Pacific Island Countries and Territories. Laboratory-based surveillance programs can detect trends and outbreaks, estimate burden of illness, and allow subtyping of enteric pathogens (e.g. Salmonella serotyping), which is critical for linking illness to food vehicles and animal reservoirs. To enhance public health capacity in Fiji for foodborne disease surveillance, we developed the Salmonella Surveillance Project (SSP), a collaboration to pilot laboratory-based surveillance for Salmonella. A network of national and international partners was formed including epidemiologists, microbiologists, and environmental health personnel. Ministry of Health personnel were trained in foodborne disease surveillance and outbreak investigation. Three clinical microbiology laboratories from different parts of the country functioned as sentinel sites, reporting all laboratory-confirmed Salmonella infections using a standardized case report form. Non-Typhi Salmonella isolates were collected for serotyping. In 2004-2005, 86 non-Typhi Salmonella and 275 S. Typhi laboratory-confirmed infections were reported. Salmonella enterica serotype I 3,10: r:- and Salmonella enterica serotype Weltevreden were the most commonly isolated non-Typhi serotypes. In Fiji, the SSP utilized international partnerships to facilitate training, and to enhance laboratory capacity and surveillance for salmonellosis. Incorporating laboratory-based foodborne disease reporting into national disease surveillance will enable public health officials to describe the burden of foodborne illness, identify outbreaks, conduct analytic epidemiology studies, and improve food safety.

Future challenges in the elimination of bacterial meningitis.

PubMed

Bottomley, Matthew J; Serruto, Davide; Sáfadi, Marco Aurélio Palazzi; Klugman, Keith P

2012-05-30

Despite the widespread implementation of several effective vaccines over the past few decades, bacterial meningitis caused by Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis and Group B Streptococcus (GBS) still results in unacceptably high levels of human mortality and morbidity. A residual disease burden due to bacterial meningitis is also apparent due to a number of persistent or emerging pathogens, including Mycobacterium tuberculosis, Escherichia coli, Staphylococcus aureus, Salmonella spp. and Streptococcus suis. Here, we review the current status of bacterial meningitis caused by these pathogens, highlighting how past and present vaccination programs have attempted to counter these pathogens. We discuss how improved pathogen surveillance, implementation of current vaccines, and development of novel vaccines may be expected to further reduce bacterial meningitis and related diseases in the future. Copyright © 2011 Elsevier Ltd. All rights reserved.

The Naval Health Research Center Respiratory Disease Laboratory.

PubMed

Ryan, M; Gray, G; Hawksworth, A; Malasig, M; Hudspeth, M; Poddar, S

2000-07-01

Concern about emerging and reemerging respiratory pathogens prompted the development of a respiratory disease reference laboratory at the Naval Health Research Center. Professionals working in this laboratory have instituted population-based surveillance for pathogens that affect military trainees and responded to threats of increased respiratory disease among high-risk military groups. Capabilities of this laboratory that are unique within the Department of Defense include adenovirus testing by viral shell culture and microneutralization serotyping, influenza culture and hemagglutination inhibition serotyping, and other special testing for Streptococcus pneumoniae, Streptococcus pyogenes, Mycoplasma pneumonia, and Chlamydia pneumoniae. Projected capabilities of this laboratory include more advanced testing for these pathogens and testing for other emerging pathogens, including Bordetella pertussis, Legionella pneumoniae, and Haemophilus influenzae type B. Such capabilities make the laboratory a valuable resource for military public health.

The ecology of emerging infectious diseases in migratory birds: an assessment of the role of climate change and priorities for future research.

PubMed

Fuller, Trevon; Bensch, Staffan; Müller, Inge; Novembre, John; Pérez-Tris, Javier; Ricklefs, Robert E; Smith, Thomas B; Waldenström, Jonas

2012-03-01

Pathogens that are maintained by wild birds occasionally jump to human hosts, causing considerable loss of life and disruption to global commerce. Preliminary evidence suggests that climate change and human movements and commerce may have played a role in recent range expansions of avian pathogens. Since the magnitude of climate change in the coming decades is predicted to exceed climatic changes in the recent past, there is an urgent need to determine the extent to which climate change may drive the spread of disease by avian migrants. In this review, we recommend actions intended to mitigate the impact of emergent pathogens of migratory birds on biodiversity and public health. Increased surveillance that builds upon existing bird banding networks is required to conclusively establish a link between climate and avian pathogens and to prevent pathogens with migratory bird reservoirs from spilling over to humans.

Sequential Learning and Recognition of Comprehensive Behavioral Patterns Based on Flow of People

NASA Astrophysics Data System (ADS)

Gibo, Tatsuya; Aoki, Shigeki; Miyamoto, Takao; Iwata, Motoi; Shiozaki, Akira

Recently, surveillance cameras have been set up everywhere, for example, in streets and public places, in order to detect irregular situations. In the existing surveillance systems, as only a handful of surveillance agents watch a large number of images acquired from surveillance cameras, there is a possibility that they may miss important scenes such as accidents or abnormal incidents. Therefore, we propose a method for sequential learning and the recognition of comprehensive behavioral patterns in crowded places. First, we comprehensively extract a flow of people from input images by using optical flow. Second, we extract behavioral patterns on the basis of change-point detection of the flow of people. Finally, in order to recognize an observed behavioral pattern, we draw a comparison between the behavioral pattern and previous behavioral patterns in the database. We verify the effectiveness of our approach by placing a surveillance camera on a campus.

Detection of Upscale-Crop and Partial Manipulation in Surveillance Video Based on Sensor Pattern Noise

PubMed Central

Hyun, Dai-Kyung; Ryu, Seung-Jin; Lee, Hae-Yeoun; Lee, Heung-Kyu

2013-01-01

In many court cases, surveillance videos are used as significant court evidence. As these surveillance videos can easily be forged, it may cause serious social issues, such as convicting an innocent person. Nevertheless, there is little research being done on forgery of surveillance videos. This paper proposes a forensic technique to detect forgeries of surveillance video based on sensor pattern noise (SPN). We exploit the scaling invariance of the minimum average correlation energy Mellin radial harmonic (MACE-MRH) correlation filter to reliably unveil traces of upscaling in videos. By excluding the high-frequency components of the investigated video and adaptively choosing the size of the local search window, the proposed method effectively localizes partially manipulated regions. Empirical evidence from a large database of test videos, including RGB (Red, Green, Blue)/infrared video, dynamic-/static-scene video and compressed video, indicates the superior performance of the proposed method. PMID:24051524

[Post-marketing surveillance systems for psychoactive prescription drug abuse].

PubMed

Nordmann, Sandra; Frauger, Elisabeth; Pauly, Vanessa; Rouby, Frank; Mallaret, Michel; Micallef, Joëlle; Thirion, Xavier

2011-01-01

Drugs affecting the central nervous system form a unique group of products for surveillance because they could be misused, abused or diverted. Considering the characteristics of this behaviour that is often concealed, specific post-marketing surveillance systems have been developed to monitor abuse of prescription drugs in some countries. The purpose of this review is to list and to describe post-marketing surveillance systems, according their methodology, in France and in foreign countries. These programs are based on adverse effect notifications, medical or legal consequences of abuse, general or specific population-based survey, professional networks or medication databases. Some programs use simultaneously several information sources. In conclusion, the multifaceted nature, the diversity and the inventiveness of post-marketing surveillance systems reflects the complexity of the abuse issue. © 2011 Société Française de Pharmacologie et de Thérapeutique.

Integrating Remote Sensing and Disease Surveillance to Forecast Malaria Epidemics

NASA Astrophysics Data System (ADS)

Wimberly, M. C.; Beyane, B.; DeVos, M.; Liu, Y.; Merkord, C. L.; Mihretie, A.

2015-12-01

Advance information about the timing and locations of malaria epidemics can facilitate the targeting of resources for prevention and emergency response. Early detection methods can detect incipient outbreaks by identifying deviations from expected seasonal patterns, whereas early warning approaches typically forecast future malaria risk based on lagged responses to meteorological factors. A critical limiting factor for implementing either of these approaches is the need for timely and consistent acquisition, processing and analysis of both environmental and epidemiological data. To address this need, we have developed EPIDEMIA - an integrated system for surveillance and forecasting of malaria epidemics. The EPIDEMIA system includes a public health interface for uploading and querying weekly surveillance reports as well as algorithms for automatically validating incoming data and updating the epidemiological surveillance database. The newly released EASTWeb 2.0 software application automatically downloads, processes, and summaries remotely-sensed environmental data from multiple earth science data archives. EASTWeb was implemented as a component of the EPIDEMIA system, which combines the environmental monitoring data and epidemiological surveillance data into a unified database that supports both early detection and early warning models. Dynamic linear models implemented with Kalman filtering were used to carry out forecasting and model updating. Preliminary forecasts have been disseminated to public health partners in the Amhara Region of Ethiopia and will be validated and refined as the EPIDEMIA system ingests new data. In addition to continued model development and testing, future work will involve updating the public health interface to provide a broader suite of outbreak alerts and data visualization tools that are useful to our public health partners. The EPIDEMIA system demonstrates a feasible approach to synthesizing the information from epidemiological surveillance systems and remotely-sensed environmental monitoring systems to improve malaria epidemic detection and forecasting.

SilkPathDB: a comprehensive resource for the study of silkworm pathogens

PubMed Central

Pan, Guo-Qing; Vossbrinck, Charles R.; Xu, Jin-Shan; Li, Chun-Feng; Chen, Jie; Long, Meng-Xian; Yang, Ming; Xu, Xiao-Fei; Xu, Chen; Debrunner-Vossbrinck, Bettina A.

2017-01-01

Silkworm pathogens have been heavily impeding the development of sericultural industry and play important roles in lepidopteran ecology, and some of which are used as biological insecticides. Rapid advances in studies on the omics of silkworm pathogens have produced a large amount of data, which need to be brought together centrally in a coherent and systematic manner. This will facilitate the reuse of these data for further analysis. We have collected genomic data for 86 silkworm pathogens from 4 taxa (fungi, microsporidia, bacteria and viruses) and from 4 lepidopteran hosts, and developed the open-access Silkworm Pathogen Database (SilkPathDB) to make this information readily available. The implementation of SilkPathDB involves integrating Drupal and GBrowse as a graphic interface for a Chado relational database which houses all of the datasets involved. The genomes have been assembled and annotated for comparative purposes and allow the search and analysis of homologous sequences, transposable elements, protein subcellular locations, including secreted proteins, and gene ontology. We believe that the SilkPathDB will aid researchers in the identification of silkworm parasites, understanding the mechanisms of silkworm infections, and the developmental ecology of silkworm parasites (gene expression) and their hosts. Database URL: http://silkpathdb.swu.edu.cn PMID:28365723

Possibility of Database Research as a Means of Pharmacovigilance in Japan Based on a Comparison with Sertraline Postmarketing Surveillance.

PubMed

Hirano, Yoko; Asami, Yuko; Kuribayashi, Kazuhiko; Kitazaki, Shigeru; Yamamoto, Yuji; Fujimoto, Yoko

2018-05-01

Many pharmacoepidemiologic studies using large-scale databases have recently been utilized to evaluate the safety and effectiveness of drugs in Western countries. In Japan, however, conventional methodology has been applied to postmarketing surveillance (PMS) to collect safety and effectiveness information on new drugs to meet regulatory requirements. Conventional PMS entails enormous costs and resources despite being an uncontrolled observational study method. This study is aimed at examining the possibility of database research as a more efficient pharmacovigilance approach by comparing a health care claims database and PMS with regard to the characteristics and safety profiles of sertraline-prescribed patients. The characteristics of sertraline-prescribed patients recorded in a large-scale Japanese health insurance claims database developed by MinaCare Co. Ltd. were scanned and compared with the PMS results. We also explored the possibility of detecting signals indicative of adverse reactions based on the claims database by using sequence symmetry analysis. Diabetes mellitus, hyperlipidemia, and hyperthyroidism served as exploratory events, and their detection criteria for the claims database were reported by the Pharmaceuticals and Medical Devices Agency in Japan. Most of the characteristics of sertraline-prescribed patients in the claims database did not differ markedly from those in the PMS. There was no tendency for higher risks of the exploratory events after exposure to sertraline, and this was consistent with sertraline's known safety profile. Our results support the concept of using database research as a cost-effective pharmacovigilance tool that is free of selection bias . Further investigation using database research is required to confirm our preliminary observations. Copyright © 2018. Published by Elsevier Inc.

Colonoscopic surveillance improves survival after colorectal cancer diagnosis in inflammatory bowel disease.

PubMed

Lutgens, M W M D; Oldenburg, B; Siersema, P D; van Bodegraven, A A; Dijkstra, G; Hommes, D W; de Jong, D J; Stokkers, P C F; van der Woude, C J; Vleggaar, F P

2009-11-17

Colonoscopic surveillance provides the best practical means for preventing colorectal cancer (CRC) in inflammatory bowel disease (IBD) patients. Strong evidence for improved survival from surveillance programmes is sparse. The aim of this study was to compare tumour stage and survival of IBD patients with CRC who were a part of a surveillance programme with those who were not. A nationwide pathology database (PALGA (pathologisch anatomisch landelijk geautomatiseerd archief)) was consulted to identify IBD patients with CRC treated in all eight university hospitals in The Netherlands over a period of 15 years. Patients were assigned to the surveillance group when they had undergone one or more surveillance colonoscopies before a diagnosis of CRC. Patients who had not undergone surveillance served as controls. Tumour stage and survival were compared between the two groups. A total of 149 patients with IBD-associated CRC were identified. Twenty-three had had colonoscopic surveillance before CRC was discovered. The 5-year CRC-related survival rate of patients in the surveillance group was 100% compared with 74% in the non-surveillance group (P=0.042). In the surveillance group, only one patient died as a consequence of CRC compared with 29 patients in the control group (P=0.047). In addition, more early tumour stages were found in the surveillance group (P=0.004). These results provide evidence for improved survival from colonoscopic surveillance in IBD patients by detecting CRC at a more favourable tumour stage.

High rates of detection of Clade 2.3.4.4 Highly Pathogenic Avian Influenza H5 viruses in wild birds in the Pacific Northwest during the winter of 2014-2015

USGS Publications Warehouse

Ip, Hon S.; Dusek, Robert J.; Bodenstein, Barbara L.; Kim Torchetti, Mia; DeBruyn, Paul; Mansfield, Kristin G.; DeLiberto, Thomas; Sleeman, Jonathan M.

2016-01-01

In 2014, Clade 2.3.4.4 H5N8 highly pathogenic avian influenza (HPAI) viruses spread across the Republic of Korea and ultimately were reported in China, Japan, Russia and Europe. Mortality associated with a reassortant HPAI H5N2 virus was detected in poultry farms in Western Canada at the end of November. The same strain (with identical genetic structure) was then detected in free-living wild birds that had died prior to December 8 of unrelated causes in Whatcom County, Washington, USA in an area contiguous with the index Canadian location. A gyrfalcon (Falco rusticolus) that had hunted and fed on an American wigeon (Anas americana) on December 6 in the same area and died two days later, tested positive for the Eurasian origin HPAI H5N8. Subsequently, an Active Surveillance Program using hunter-harvest waterfowl in Washington and Oregon detected ten HPAI H5 viruses, of three different subtypes (four H5N2, three H5N8 and three H5N1) with 4 segments in common (HA, PB2, NP and MA). In addition, a mortality-based Passive Surveillance Program detected 18 HPAI (14 H5N2 and four H5N8) cases from Idaho, Kansas, Oregon, Minnesota, Montana, Washington and Wisconsin. Comparatively, mortality-based passive surveillance appears to be detecting these HPAI infections at a higher rate than active surveillance during the period following initial introduction into the US.

High Rates of Detection of Clade 2.3.4.4 Highly Pathogenic Avian Influenza H5 Viruses in Wild Birds in the Pacific Northwest During the Winter of 2014-15.

PubMed

Ip, Hon S; Dusek, Robert J; Bodenstein, Barbara; Torchetti, Mia Kim; DeBruyn, Paul; Mansfield, Kristin G; DeLiberto, Thomas; Sleeman, Jonathan M

2016-05-01

In 2014, clade 2.3.4.4 H5N8 highly pathogenic avian influenza (HPAI) viruses spread across the Republic of Korea and ultimately were reported in China, Japan, Russia, and Europe. Mortality associated with a reassortant HPAI H5N2 virus was detected in poultry farms in western Canada at the end of November. The same strain (with identical genetic structure) was then detected in free-living wild birds that had died prior to December 8, 2014, of unrelated causes in Whatcom County, Washington, U. S. A., in an area contiguous with the index Canadian location. A gyrfalcon (Falco rusticolus) that had hunted and fed on an American wigeon (Anas americana) on December 6, 2014, in the same area, and died 2 days later, tested positive for the Eurasian-origin HPAI H5N8. Subsequently, an active surveillance program using hunter-harvested waterfowl in Washington and Oregon detected 10 HPAI H5 viruses, of three different subtypes (four H5N2, three H5N8, and three H5N1) with four segments in common (HA, PB2, NP, and MA). In addition, a mortality-based passive surveillance program detected 18 HPAI (14 H5N2 and four H5N8) cases from Idaho, Kansas, Oregon, Minnesota, Montana, Washington, and Wisconsin. Comparatively, mortality-based passive surveillance appears to have detected these HPAI infections at a higher rate than active surveillance during the period following initial introduction into the United States.

SEER Bibliography

Cancer.gov

Search this database of articles and other publications produced by cancer registry staff and Surveillance Research Program staff. Search by author, title, date, and organization. Provides links to PubMed and abstracts.

Prospective surveillance of device-associated health care-associated infection in an intensive care unit of a tertiary care hospital in New Delhi, India.

PubMed

Kumar, Shilpee; Sen, Poornima; Gaind, Rajni; Verma, Pardeep Kumar; Gupta, Poonam; Suri, Prem Rose; Nagpal, Sunita; Rai, Anil Kumar

2018-02-01

Surveillance of health care-associated infections (HAIs) plays a key role in the hospital infection control program and reduction of HAIs. In India, most of the surveillance of HAIs is reported from private sector hospitals that do not depict the situation of government sector hospitals. Other studies do not confirm with the Centers for Disease Control and Prevention's (CDC) National Healthcare Safety Network (NHSN) surveillance criterion, or deal with ventilator-associated pneumonia (VAP) instead of ventilator-associated event (VAE). The aim of this study was to identify the incidences of 3 device-associated HAIs (DA-HAIs) (VAE, central line-associated bloodstream infection [CLABSI], and catheter-associated urinary tract infection [CAUTI]) by active surveillance using CDC's NHSN surveillance criteria and to identify the pathogens associated with these DA-HAIs. This was a prospective surveillance study (January 2015-December 2016) conducted in an intensive care unit (ICU) of a large, tertiary care, government hospital situated in Delhi, India. Targeted surveillance was done as per the CDC's NHSN 2016 surveillance criteria. There were 343 patients admitted to the ICU that were included in the study. The surveillance data was reported over 3,755 patient days. A DA-HAIs attack rate of 20.1 per 100 admissions and incidence of 18.3 per 1,000 patient days was observed. The duration of use for each device for patients with DA-HAIs was significantly longer than for patients without DA-HAIs. The device utilization ratios of central line, ventilator, and urinary catheters were 0.57, 0.85, and 0.72, respectively. The crude excess length of stay for patients with DA-HAI was 13 days, and crude excess mortality rate was 11.8%. VAE, CLABSI, and CAUTI rates were 11.8, 7.4, and 9.7 per 1,000 device days, respectively. Among 69 DA-HAIs reported, pathogens could be identified for 49 DA-HAI cases. Klebsiella spp was the most common organism isolated, accounting 28.5% for all DA-HAI cases, followed by Enterococcus spp (24.4%). The most common organisms causing VAE, CAUTI, and CLABSI were Acinetobacter (6/15, 40%), Enterococcus spp (11/31, 35.4%), and Candida spp (5/19, 26.3%), respectively. Most of the gram-negative organisms were carbapenem resistant; however, none of the isolates were colistin resistant. To reduce the risk of infection in hospitalized patients, DA-HAI surveillance is of primary importance because it effectively describes and addresses the importance and characteristics of the threatening situation created by DA-HAIs. The present surveillance shows high rates of ICU-onset DA-HAIs and high resistance patterns of organisms causing HAIs, representing a major risk to patient safety. Copyright © 2018 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Epidemiology, microbiology and mortality associated with community-acquired bacteremia in northeast Thailand: a multicenter surveillance study.

PubMed

Kanoksil, Manas; Jatapai, Anchalee; Peacock, Sharon J; Limmathurotsakul, Direk

2013-01-01

National statistics in developing countries are likely to underestimate deaths due to bacterial infections. Here, we calculated mortality associated with community-acquired bacteremia (CAB) in a developing country using routinely available databases. Information was obtained from the microbiology and hospital database of 10 provincial hospitals in northeast Thailand, and compared with the national death registry from the Ministry of Interior, Thailand for the period between 2004 and 2010. CAB was defined in patients who had pathogenic organisms isolated from blood taken within 2 days of hospital admission without a prior inpatient episode in the preceding 30 days. A total of 15,251 CAB patients identified, of which 5,722 (37.5%) died within 30 days of admission. The incidence rate of CAB between 2004 and 2010 increased from 16.7 to 38.1 per 100,000 people per year, and the mortality rate associated with CAB increased from 6.9 to 13.7 per 100,000 people per year. In 2010, the mortality rate associated with CAB was lower than that from respiratory tract infection, but higher than HIV disease or tuberculosis. The most common causes of CAB were Escherichia coli (23.1%), Burkholderia pseudomallei (19.3%), and Staphylococcus aureus (8.2%). There was an increase in the proportion of Extended-Spectrum Beta-Lactamases (ESBL) producing E. coli and Klebsiella pneumoniae over time. This study has demonstrated that national statistics on causes of death in developing countries could be improved by integrating information from readily available databases. CAB is neglected as an important cause of death, and specific prevention and intervention is urgently required to reduce its incidence and mortality.

Epidemiology, Microbiology and Mortality Associated with Community-Acquired Bacteremia in Northeast Thailand: A Multicenter Surveillance Study

PubMed Central

Kanoksil, Manas; Jatapai, Anchalee; Peacock, Sharon J.; Limmathurotsakul, Direk

2013-01-01

Background National statistics in developing countries are likely to underestimate deaths due to bacterial infections. Here, we calculated mortality associated with community-acquired bacteremia (CAB) in a developing country using routinely available databases. Methods/Principal Findings Information was obtained from the microbiology and hospital database of 10 provincial hospitals in northeast Thailand, and compared with the national death registry from the Ministry of Interior, Thailand for the period between 2004 and 2010. CAB was defined in patients who had pathogenic organisms isolated from blood taken within 2 days of hospital admission without a prior inpatient episode in the preceding 30 days. A total of 15,251 CAB patients identified, of which 5,722 (37.5%) died within 30 days of admission. The incidence rate of CAB between 2004 and 2010 increased from 16.7 to 38.1 per 100,000 people per year, and the mortality rate associated with CAB increased from 6.9 to 13.7 per 100,000 people per year. In 2010, the mortality rate associated with CAB was lower than that from respiratory tract infection, but higher than HIV disease or tuberculosis. The most common causes of CAB were Escherichia coli (23.1%), Burkholderia pseudomallei (19.3%), and Staphylococcus aureus (8.2%). There was an increase in the proportion of Extended-Spectrum Beta-Lactamases (ESBL) producing E. coli and Klebsiella pneumoniae over time. Conclusions This study has demonstrated that national statistics on causes of death in developing countries could be improved by integrating information from readily available databases. CAB is neglected as an important cause of death, and specific prevention and intervention is urgently required to reduce its incidence and mortality. PMID:23349954

Analysis of sepsis in allogeneic bone marrow transplant recipients: a single-center study.

PubMed

Mitsui, Hideki; Karasuno, Takahiro; Santo, Taisuke; Fukushima, Kentaro; Matsunaga, Hitomi; Nakamura, Hiroyuki; Hiraoka, Akira

2003-09-01

We reviewed the records of 235 consecutive recipients of allogeneic bone marrow transplantation (allo-BMT) at our center between February 1983 and October 2000. Sepsis occurred in 25 patients (10.6%) at a median of 10 days (range, 1-280 days) after BMT. Five of the 25 patients (20%) died of sepsis. Pathogens isolated from blood culture were gram-positive cocci in 19 patients, gram-negative rods in 7, fungi in 2, and others in 1 patient. Two pathogens were detected concomitantly in 4 patients. Univariate analysis revealed that risk factors for sepsis were selective gut decontamination using lomefloxacin hydrochloride and nystatin, an unrelated donor, HLA mismatched BMT, and stomatitis. Multivariate logistic regression analysis revealed that an unrelated donor was the only significant independent risk factor, with a relative risk of 5.432. In 12 of 25 patients with sepsis, the pathogens of sepsis were sensitive to antibiotics used for gut decontamination. Selective gut decontamination significantly increased the incidence of sepsis, especially that with gram-positive cocci, but not the mortality rate of sepsis, compared with total gut decontamination using vancomycin. We also found a significant relationship between pathogens isolated from blood culture and those isolated from surveillance cultures of stool, urine, and gargled water in the period before sepsis occurred. The present study revealed an independent risk factor for sepsis (unrelated donor), the feasibility of selective gut decontamination, and the importance of surveillance culture.

Estimated Annual Numbers of Foodborne Pathogen-Associated Illnesses, Hospitalizations, and Deaths, France, 2008-2013.

PubMed

Van Cauteren, Dieter; Le Strat, Yann; Sommen, Cécile; Bruyand, Mathias; Tourdjman, Mathieu; Da Silva, Nathalie Jourdan; Couturier, Elisabeth; Fournet, Nelly; de Valk, Henriette; Desenclos, Jean-Claude

2017-09-01

Estimates of the annual numbers of foodborne illnesses and associated hospitalizations and deaths are needed to set priorities for surveillance, prevention, and control strategies. The objective of this study was to determine such estimates for 2008-2013 in France. We considered 15 major foodborne pathogens (10 bacteria, 3 viruses, and 2 parasites) and estimated that each year, the pathogens accounted for 1.28-2.23 million illnesses, 16,500-20,800 hospitalizations, and 250 deaths. Campylobacter spp., nontyphoidal Salmonella spp., and norovirus accounted for >70% of all foodborne pathogen-associated illnesses and hospitalizations; nontyphoidal Salmonella spp. and Listeria monocytogenes were the main causes of foodborne pathogen-associated deaths; and hepatitis E virus appeared to be a previously unrecognized foodborne pathogen causing ≈68,000 illnesses in France every year. The substantial annual numbers of foodborne illnesses and associated hospitalizations and deaths in France highlight the need for food-safety policymakers to prioritize foodborne disease prevention and control strategies.

[Current aspects of the definition and diagnosis of sepsis and antibiotic resistance].

PubMed

Brunkhorst, Frank M; Gastmeier, Petra; Abu Sin, Muna

2018-05-01

Hospital mortality of patients with secondary sepsis remains high at around 40%. Because of the methodological deficiencies of the definitions used so far, valid epidemiological data on secondary sepsis that allow for national and international comparisons are lacking. Since 2016, new clinical diagnostic tools that are also suitable for sepsis screening outside of intensive care units have been available. To counteract the high mortality of nosocomial sepsis, new approaches to the early identification of at-risk patients are needed. An adequate blood culture sampling rate and a high preanalytical quality should be established as a basis for quality assurance, especially in the field of nosocomial bloodstream infections; otherwise, there is a risk of surveillance bias. Data from laboratory-based antibiotic resistance surveillance on MRSA in blood culture isolates have shown a downward trend over the last 4 years. In Gram-negative pathogens, a relatively stable resistance situation has been observed over this period for many of the pathogen-antibiotic combinations.

Respiratory Infections in the U.S. Military: Recent Experience and Control

PubMed Central

Cooper, Michael J.; Myers, Christopher A.; Cummings, James F.; Vest, Kelly G.; Russell, Kevin L.; Sanchez, Joyce L.; Hiser, Michelle J.; Gaydos, Charlotte A.

2015-01-01

SUMMARY This comprehensive review outlines the impact of military-relevant respiratory infections, with special attention to recruit training environments, influenza pandemics in 1918 to 1919 and 2009 to 2010, and peacetime operations and conflicts in the past 25 years. Outbreaks and epidemiologic investigations of viral and bacterial infections among high-risk groups are presented, including (i) experience by recruits at training centers, (ii) impact on advanced trainees in special settings, (iii) morbidity sustained by shipboard personnel at sea, and (iv) experience of deployed personnel. Utilizing a pathogen-by-pathogen approach, we examine (i) epidemiology, (ii) impact in terms of morbidity and operational readiness, (iii) clinical presentation and outbreak potential, (iv) diagnostic modalities, (v) treatment approaches, and (vi) vaccine and other control measures. We also outline military-specific initiatives in (i) surveillance, (ii) vaccine development and policy, (iii) novel influenza and coronavirus diagnostic test development and surveillance methods, (iv) influenza virus transmission and severity prediction modeling efforts, and (v) evaluation and implementation of nonvaccine, nonpharmacologic interventions. PMID:26085551

Developing a database management system to support birth defects surveillance in Florida.

PubMed

Salemi, Jason L; Hauser, Kimberlea W; Tanner, Jean Paul; Sampat, Diana; Correia, Jane A; Watkins, Sharon M; Kirby, Russell S

2010-01-01

The value of any public health surveillance program is derived from the ways in which data are managed and used to improve the public's health. Although birth defects surveillance programs vary in their case volume, budgets, staff, and objectives, the capacity to operate efficiently and maximize resources remains critical to long-term survival. The development of a fully-integrated relational database management system (DBMS) can enrich a surveillance program's data and improve efficiency. To build upon the Florida Birth Defects Registry--a statewide registry relying solely on linkage of administrative datasets and unconfirmed diagnosis codes-the Florida Department of Health provided funding to the University of South Florida to develop and pilot an enhanced surveillance system in targeted areas with a more comprehensive approach to case identification and diagnosis confirmation. To manage operational and administrative complexities, a DBMS was developed, capable of managing transmission of project data from multiple sources, tracking abstractor time during record reviews, offering tools for defect coding and case classification, and providing reports to DBMS users. Since its inception, the DBMS has been used as part of our surveillance projects to guide the receipt of over 200 case lists and review of 12,924 fetuses and infants (with associated maternal records) suspected of having selected birth defects in over 90 birthing and transfer facilities in Florida. The DBMS has provided both anticipated and unexpected benefits. Automation of the processes for managing incoming case lists has reduced clerical workload considerably, while improving accuracy of working lists for field abstraction. Data quality has improved through more effective use of internal edits and comparisons with values for other data elements, while simultaneously increasing abstractor efficiency in completion of case abstraction. We anticipate continual enhancement to the DBMS in the future. While we have focused on enhancing the capacity of our DBMS for birth defects surveillance, many of the tools and approaches we have developed translate directly to other public health and clinical registries.

Epidemiology of human infections with highly pathogenic avian influenza A(H7N9) virus in Guangdong, 2016 to 2017.

PubMed

Kang, Min; Lau, Eric H Y; Guan, Wenda; Yang, Yuwei; Song, Tie; Cowling, Benjamin J; Wu, Jie; Peiris, Malik; He, Jianfeng; Mok, Chris Ka Pun

2017-07-06

We describe the epidemiology of highly pathogenic avian influenza (HPAI) A(H7N9) based on poultry market environmental surveillance and laboratory-confirmed human cases (n = 9) in Guangdong, China. We also compare the epidemiology between human cases of high- and low-pathogenic avian influenza A(H7N9) (n = 51) in Guangdong. Case fatality and severity were similar. Touching sick or dead poultry was the most important risk factor for HPAI A(H7N9) infections and should be highlighted for the control of future influenza A(H7N9) epidemics. This article is copyright of The Authors, 2017.

Humans and Cattle: A Review of Bovine Zoonoses

PubMed Central

Cardwell, Diana M.; Moeller, Robert B.; Gray, Gregory C.

2014-01-01

Abstract Infectious disease prevention and control has been among the top public health objectives during the last century. However, controlling disease due to pathogens that move between animals and humans has been challenging. Such zoonotic pathogens have been responsible for the majority of new human disease threats and a number of recent international epidemics. Currently, our surveillance systems often lack the ability to monitor the human–animal interface for emergent pathogens. Identifying and ultimately addressing emergent cross-species infections will require a “One Health” approach in which resources from public veterinary, environmental, and human health function as part of an integrative system. Here we review the epidemiology of bovine zoonoses from a public health perspective. PMID:24341911

The KIzSS network, a sentinel surveillance system for infectious diseases in day care centers: study protocol.

PubMed

Enserink, Remko; Noel, Harold; Friesema, Ingrid H M; de Jager, Carolien M; Kooistra-Smid, Anna M D; Kortbeek, Laetitia M; Duizer, Erwin; van der Sande, Marianne A B; Smit, Henriette A; Pelt, Wilfrid van

2012-10-15

Day care-associated infectious diseases are widely recognized as a public health problem but rarely studied. Insights into their dynamics and their association with the day care setting are important for effective decision making in management of infectious disease control. This paper describes the purpose, design and potential of our national multi-center, day care-based sentinel surveillance network for infectious diseases (the KIzSS network). The aim of the KIzSS network is to acquire a long-term insight into the syndromic and microbiological aspects of day care-related infectious diseases and associated disease burden and to model these aspects with day care setting characteristics. The KIzSS network applies a prospective cohort design, following day care centers rather than individual children or staff members over time. Data on infectious disease symptoms and related morbidity (children and staff), medical consumption, absenteeism and circulating enteric pathogens (children) are collected on a daily, weekly or monthly basis. Every two years, a survey is performed to assess the characteristics of participating day care centers. The KIzSS network offers a unique potential to study infectious disease dynamics in the day care setting over a sustained period of time. The created (bio)databases will help us to assess day care-related disease burden of infectious diseases among attending children and staff and their relation with the day care setting. This will support the much needed development of evidence-based and pragmatic guidelines for infectious disease control in day care centers.

The KIzSS network, a sentinel surveillance system for infectious diseases in day care centers: study protocol

PubMed Central

2012-01-01

Background Day care-associated infectious diseases are widely recognized as a public health problem but rarely studied. Insights into their dynamics and their association with the day care setting are important for effective decision making in management of infectious disease control. This paper describes the purpose, design and potential of our national multi-center, day care-based sentinel surveillance network for infectious diseases (the KIzSS network). The aim of the KIzSS network is to acquire a long-term insight into the syndromic and microbiological aspects of day care-related infectious diseases and associated disease burden and to model these aspects with day care setting characteristics. Methods/design The KIzSS network applies a prospective cohort design, following day care centers rather than individual children or staff members over time. Data on infectious disease symptoms and related morbidity (children and staff), medical consumption, absenteeism and circulating enteric pathogens (children) are collected on a daily, weekly or monthly basis. Every two years, a survey is performed to assess the characteristics of participating day care centers. Discussion The KIzSS network offers a unique potential to study infectious disease dynamics in the day care setting over a sustained period of time. The created (bio)databases will help us to assess day care-related disease burden of infectious diseases among attending children and staff and their relation with the day care setting. This will support the much needed development of evidence-based and pragmatic guidelines for infectious disease control in day care centers. PMID:23066727

Bacterial community dynamics in a cooling tower with emphasis on pathogenic bacteria and Legionella species using universal and genus-specific deep sequencing.

PubMed

Pereira, Rui P A; Peplies, Jörg; Höfle, Manfred G; Brettar, Ingrid

2017-10-01

Cooling towers are the major source of outbreaks of legionellosis in Europe and worldwide. These outbreaks are mostly associated with Legionella species, primarily L. pneumophila, and its surveillance in cooling tower environments is of high relevance to public health. In this study, a combined NGS-based approach was used to study the whole bacterial community, specific waterborne and water-based bacterial pathogens, especially Legionella species, targeting the 16S rRNA gene. This approach was applied to water from a cooling tower obtained by monthly sampling during two years. The studied cooling tower was an open circuit cooling tower with lamellar cooling situated in Braunschweig, Germany. A highly diverse bacterial community was observed with 808 genera including 25 potentially pathogenic taxa using universal 16S rRNA primers. Sphingomonas and Legionella were the most abundant pathogenic genera. By applying genus-specific primers for Legionella, a diverse community with 85 phylotypes, and a representative core community with substantial temporal heterogeneity was observed. A high percentage of sequences (65%) could not be affiliated to an acknowledged species. L. pneumophila was part of the core community and the most abundant Legionella species reinforcing the importance of cooling towers as its environmental reservoir. Major temperature shifts (>10 °C) were the key environmental factor triggering the reduction or dominance of the Legionella species in the Legionella community dynamics. In addition, interventions by chlorine dioxide had a strong impact on the Legionella community composition but not on the whole bacterial community. Overall, the presented results demonstrated the value of a combined NGS approach for the molecular monitoring and surveillance of health related pathogens in man-made freshwater systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Role of domestic ducks in the emergence of a new genotype of highly pathogenic H5N1 avian influenza A viruses in Bangladesh

PubMed Central

Barman, Subrata; Marinova-Petkova, Atanaska; Hasan, M Kamrul; Akhtar, Sharmin; El-Shesheny, Rabeh; Turner, Jasmine CM; Franks, John; Walker, David; Seiler, Jon; Friedman, Kimberly; Kercher, Lisa; Jeevan, Trushar; Darnell, Daniel; Kayali, Ghazi; Jones-Engel, Lisa; McKenzie, Pamela; Krauss, Scott; Webby, Richard J; Webster, Robert G; Feeroz, Mohammed M

2017-01-01

Highly pathogenic avian influenza H5N1 viruses were first isolated in Bangladesh in February 2007. Subsequently, clades 2.2.2, 2.3.4.2 and 2.3.2.1a were identified in Bangladesh, and our previous surveillance data revealed that by the end of 2014, the circulating viruses exclusively comprised clade 2.3.2.1a. We recently determined the status of circulating avian influenza viruses in Bangladesh by conducting surveillance of live poultry markets and waterfowl in wetland areas from February 2015 through February 2016. Until April 2015, clade 2.3.2.1a persisted without any change in genotype. However, in June 2015, we identified a new genotype of H5N1 viruses, clade 2.3.2.1a, which quickly became predominant. These newly emerged H5N1 viruses contained the hemagglutinin, neuraminidase and matrix genes of circulating 2.3.2.1a Bangladeshi H5N1 viruses and five other genes of low pathogenic Eurasian-lineage avian influenza A viruses. Some of these internal genes were closely related to those of low pathogenic viruses isolated from ducks in free-range farms and wild birds in a wetland region of northeastern Bangladesh, where commercially raised domestic ducks have frequent contact with migratory birds. These findings indicate that migratory birds of the Central Asian flyway and domestic ducks in the free-range farms in Tanguar haor-like wetlands played an important role in the emergence of this novel genotype of highly pathogenic H5N1 viruses. PMID:28790460

Pan-European resistance monitoring programmes encompassing food-borne bacteria and target pathogens of food-producing and companion animals.

PubMed

de Jong, A; Thomas, V; Klein, U; Marion, H; Moyaert, H; Simjee, S; Vallé, M

2013-05-01

Antimicrobial resistance is a concern both for animal and human health. Veterinary programmes monitoring resistance of animal and zoonotic pathogens are therefore essential. Various European countries have implemented national surveillance programmes, particularly for zoonotic and commensal bacteria, and the European Food Safety Authority (EFSA) is compiling the data. However, harmonisation is identified as a weakness and an essential need in order to compare data across countries. Comparisons of resistance monitoring data among national programmes are hampered by differences between programmes, such as sampling and testing methodology, and different epidemiological cut-off values or clinical breakpoints. Moreover, only very few valid data are available regarding target pathogens both of farm and companion animals. The European Animal Health Study Centre (CEESA) attempts to fill these gaps. The resistance monitoring programmes of CEESA have been a collaboration of veterinary pharmaceutical companies for over a decade and include two different projects: the European Antimicrobial Susceptibility Surveillance in Animals (EASSA) programme, which collects food-borne bacteria at slaughter from healthy animals, and the pathogen programmes that collect first-intention target pathogens from acutely diseased animals. The latter comprises three subprogrammes: VetPath; MycoPath; and ComPath. All CEESA projects include uniform sample collection and bacterial identification to species level in various European Union (EU) member states. A central laboratory conducts quantitative susceptibility testing to antimicrobial agents either important in human medicine or commonly used in veterinary medicine. This 'methodology harmonisation' allows easy comparisons among EU member states and makes the CEESA programmes invaluable to address food safety and antibiotic efficacy. Copyright © 2012 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Longitudinal surveillance on antibiogram of important Gram-positive pathogens in Southern China, 2001 to 2015.

PubMed

Xu, Zhenbo; Xie, Jinhong; Peters, Brian M; Li, Bing; Li, Lin; Yu, Guangchao; Shirtliff, Mark E

2017-02-01

A longitudinal surveillance aimed to investigate the antibiogram of three genus of important Gram-positive pathogens in Southern China during 2001-2015. A total of 3849 Staphylococcus, Enterococcus and Streptococcus strains were isolated from Southern China during 2001-2015. Bacteria identification was performed by colony morphology, Gram staining, the API commercial kit and the Vitek 2 automated system. Antimicrobial susceptibility testing was determined by disk diffusion method and MIC method. As sampling site was concerned, 51.4% of Staphylococcus strains were isolated from sputum, whereas urinary tract remained the dominant infection site among Enterococcus and Streptococcus. According to the antimicrobial susceptibility, three genus of important Gram-positive pathogens showed high resistance against erythromycin, tetracycline, ciprofloxacin and clindamycin. Resistance rates to penicillins (penicillin, oxacillin, ampicillin) were high as well, with the exception of E. faecalis and Streptococcus. Overall, resistance rates against methicillin (oxacillin) were 63.2% in S. aureus and 76.2% in coagulase-negative Staphylococcus (CNS), along with continuous increases during the study. VRSA and vancomycin-resistant coagulase-negative Staphylococcus only appeared in 2011-2015. Sight decline was obtained for the vancomycin resistance of E. faecalis, while vancomycin-resistant E. faecium only appeared in 2011-2015, with its intermediate rate decreasing. Significant decrease in penicillin-resistant Streptococcus pneumonia (PRSP) was observed during studied period. Glycopeptide antibiotic remained highly effective to Staphylococcus, Enterococcus and Streptococcus (resistance rates <5%). Despite decline obtained for some antibiotic agents resistance during 2001-2015, antimicrobial resistance among Gram-positive pathogens still remained high in Southern China. This study may aid in the guidance for appropriate therapeutic strategy of infections caused by nosocomial pathogens. Copyright © 2016 Elsevier Ltd. All rights reserved.

Prevalence and Functioning of Children with Cerebral Palsy in Four Areas of the United States in 2006: A Report from the Autism and Developmental Disabilities Monitoring Network

ERIC Educational Resources Information Center

Kirby, Russell S.; Wingate, Martha S.; Van Naarden Braun, Kim; Doernberg, Nancy S.; Arneson, Carrie L.; Benedict, Ruth E.; Mulvihill, Beverly; Durkin, Maureen S.; Fitzgerald, Robert T.; Maenner, Matthew J.; Patz, Jean A.; Yeargin-Allsopp, Marshalyn

2011-01-01

Aim: To estimate the prevalence of cerebral palsy (CP) and the frequency of co-occurring developmental disabilities (DDs), gross motor function (GMF), and walking ability using the largest surveillance DD database in the US. Methods: We conducted population-based surveillance of 8-year-old children in 2006 (N = 142,338), in areas of Alabama,…

Implementing GermWatcher, an enterprise infection control application.

PubMed

Doherty, Joshua; Noirot, Laura A; Mayfield, Jennie; Ramiah, Sridhar; Huang, Christine; Dunagan, Wm Claiborne; Bailey, Thomas C

2006-01-01

Automated surveillance tools can provide significant advantages to infection control practitioners. When stored in a relational database, the data collected can also be used to support numerous research and quality improvement opportunities. A previously described electronic infection control surveillance system was remodeled to provide multi-hospital support, an XML based rule set, and interoperability with an enterprise terminology server. This paper describes the new architecture being used at hospitals across BJC HealthCare.

Automated graphic image generation system for effective representation of infectious disease surveillance data.

PubMed

Inoue, Masashi; Hasegawa, Shinsaku; Suyama, Akihiko; Meshitsuka, Shunsuke

2003-11-01

Infectious disease surveillance schemes have been established to detect infectious disease outbreak in the early stages, to identify the causative viral strains, and to rapidly assess related morbidity and mortality. To make a scheme function well, two things are required. Firstly, it must have sufficient sensitivity and be timely to guarantee as short a delay as possible from collection to redistribution of information. Secondly, it must provide a good representation of the results of the surveillance. To do this, we have developed a database system that can redistribute the information via the Internet. The feature of this system is to automatically generate the graphic images based on the numerical data stored in the database by using Hypertext Preprocessor (PHP) script and Graphics Drawing (GD) library. It dynamically displays the information as a map or bar chart as well as a numerical impression according to the real time demand of the users. This system will be a useful tool for medical personnel and researchers working on infectious disease problems and will save significant time in the redistribution of information.

Online Databases for Taxonomy and Identification of Pathogenic Fungi and Proposal for a Cloud-Based Dynamic Data Network Platform.

PubMed

Prakash, Peralam Yegneswaran; Irinyi, Laszlo; Halliday, Catriona; Chen, Sharon; Robert, Vincent; Meyer, Wieland

2017-04-01

The increase in public online databases dedicated to fungal identification is noteworthy. This can be attributed to improved access to molecular approaches to characterize fungi, as well as to delineate species within specific fungal groups in the last 2 decades, leading to an ever-increasing complexity of taxonomic assortments and nomenclatural reassignments. Thus, well-curated fungal databases with substantial accurate sequence data play a pivotal role for further research and diagnostics in the field of mycology. This minireview aims to provide an overview of currently available online databases for the taxonomy and identification of human and animal-pathogenic fungi and calls for the establishment of a cloud-based dynamic data network platform. Copyright © 2017 American Society for Microbiology.

Surveillance of laboratory exposures to human pathogens and toxins: Canada 2016.

PubMed

Bienek, A; Heisz, M; Su, M

2017-11-02

Canada recently enacted legislation to authorize the collection of data on laboratory incidents involving a biological agent. This is done by the Public Health Agency of Canada (PHAC) as part of a comprehensive national program that protects Canadians from the health and safety risks posed by human and terrestrial animal pathogens and toxins. To describe the first year of data on laboratory exposure incidents and/or laboratory-acquired infections in Canada since the Human Pathogens and Toxins Regulations came into effect. Incidents that occurred between January 1 and December 31, 2016 were self-reported by federally-regulated parties across Canada using a standardized form from the Laboratory Incident Notification Canada (LINC) surveillance system. Exposure incidents were described by sector, frequency of occurrence, timeliness of reporting, number of affected persons, human pathogens and toxins involved, causes and corrective actions taken. Microsoft Excel 2010 was used for basic descriptive analyses. In 2016, 46 exposure incidents were reported by holders of 835 active licences in Canada representing 1,352 physical areas approved for work involving a biological agent, for an overall incidence of 3.4%. The number of incidents was highest in the academic (n=16; 34.8%) and hospital (n=12; 26.1%) sectors, while the number of reported incidents was relatively low in the private industry sector. An average of four to five incidents occurred each month; the month of September presented as an outlier with 10 incidents. ​: A total of 100 people were exposed, with no reports of secondary exposure. Four incidents led to suspected (n=3) or confirmed (n=1) cases of laboratory-acquired infection. Most incidents involved pathogens classified at a risk group 2 level that were manipulated in a containment level 2 laboratory (91.3%). Over 22 different species of human pathogens and toxins were implicated, with bacteria the most frequent (34.8%), followed by viruses (26.1%). Eleven (23.9%) incidents involved a security sensitive biologic agent. Procedure breaches (n=15) and sharps-related incidents (n=14) were the most common antecedents to an exposure. In 10 (21.7%) cases, inadvertent possession (i.e., isolation of an unexpected biological agent during routine work) played a role. Possible improvements to standard operating procedures were cited in 71.7% of incidents. Improvements were also indicated for communication (26.1%) and management (23.9%). The Laboratory Incident Notification Canada is one of the first surveillance systems in the world to gather comprehensive data on laboratory incidents involving human pathogens and toxins. Exposure incidents reported in the first year were relatively rare, occurring in less than 4% of containment zones within laboratory settings.

Surveillance of laboratory exposures to human pathogens and toxins: Canada 2016

PubMed Central

Bienek, A; Heisz, M; Su, M

2017-01-01

Background Canada recently enacted legislation to authorize the collection of data on laboratory incidents involving a biological agent. This is done by the Public Health Agency of Canada (PHAC) as part of a comprehensive national program that protects Canadians from the health and safety risks posed by human and terrestrial animal pathogens and toxins. Objective To describe the first year of data on laboratory exposure incidents and/or laboratory-acquired infections in Canada since the Human Pathogens and Toxins Regulations came into effect. Methods Incidents that occurred between January 1 and December 31, 2016 were self-reported by federally-regulated parties across Canada using a standardized form from the Laboratory Incident Notification Canada (LINC) surveillance system. Exposure incidents were described by sector, frequency of occurrence, timeliness of reporting, number of affected persons, human pathogens and toxins involved, causes and corrective actions taken. Microsoft Excel 2010 was used for basic descriptive analyses. Results In 2016, 46 exposure incidents were reported by holders of 835 active licences in Canada representing 1,352 physical areas approved for work involving a biological agent, for an overall incidence of 3.4%. The number of incidents was highest in the academic (n=16; 34.8%) and hospital (n=12; 26.1%) sectors, while the number of reported incidents was relatively low in the private industry sector. An average of four to five incidents occurred each month; the month of September presented as an outlier with 10 incidents. ​ A total of 100 people were exposed, with no reports of secondary exposure. Four incidents led to suspected (n=3) or confirmed (n=1) cases of laboratory-acquired infection. Most incidents involved pathogens classified at a risk group 2 level that were manipulated in a containment level 2 laboratory (91.3%). Over 22 different species of human pathogens and toxins were implicated, with bacteria the most frequent (34.8%), followed by viruses (26.1%). Eleven (23.9%) incidents involved a security sensitive biologic agent. Procedure breaches (n=15) and sharps-related incidents (n=14) were the most common antecedents to an exposure. In 10 (21.7%) cases, inadvertent possession (i.e., isolation of an unexpected biological agent during routine work) played a role. Possible improvements to standard operating procedures were cited in 71.7% of incidents. Improvements were also indicated for communication (26.1%) and management (23.9%). Conclusions The Laboratory Incident Notification Canada is one of the first surveillance systems in the world to gather comprehensive data on laboratory incidents involving human pathogens and toxins. Exposure incidents reported in the first year were relatively rare, occurring in less than 4% of containment zones within laboratory settings. PMID:29770052

Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units

PubMed Central

Schürch, Anita C.; Schipper, Debby; Bijl, Maarten A.; Dau, Jim; Beckmen, Kimberlee B.; Schapendonk, Claudia M. E.; Raj, V. Stalin; Osterhaus, Albert D. M. E.; Haagmans, Bart L.; Tryland, Morten; Smits, Saskia L.

2014-01-01

Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae. PMID:25140520

Evaluation of a commercial ELISA for H5 low pathogenic avian influenza virus antibody detection in duck sera using Bayesian methods.

PubMed

Schmitz, Audrey; Le Bras, Marie-Odile; Guillemoto, Carole; Pierre, Isabelle; Rose, Nicolas; Bougeard, Stéphanie; Jestin, Véronique

2013-10-01

Following the emergence of highly pathogenic avian influenza (AI), active surveillance of infections due to the H5 and H7 subtypes in poultry has increased and been made compulsory in Europe since 2002, by means of annual serological surveys using the haemagglutination inhibition (HI) test. Domestic anseriforms, particularly ducks and geese, are more frequently infected by H5 low pathogenic AI virus, often subclinically, and represent a threat for other terrestrial poultry. 1783 sera, mainly from ducks, have been used to evaluate and compare a commercial ELISA kit detecting H5 antibodies with the currently recommended HI test. Different approaches to calculating specificity and sensitivity have been used, including the original Bayesian method. Results were similar when data were analyzed at the individual and batch levels, and when using different methods of calculation. However, results showed that H5 ELISA had both a higher sensitivity and a lower specificity than the HI test. Given that sensitivity is the most important factor for a screening test, H5 ELISA could therefore be recommended for AI surveillance, followed in cases of positivity by molecular tests aimed at detecting the virus gene. Copyright © 2013 Elsevier B.V. All rights reserved.

Influenza virus isolation.

PubMed

Krauss, Scott; Walker, David; Webster, Robert G

2012-01-01

The isolation of influenza viruses is important for the diagnosis of respiratory diseases in lower animals and humans, for the detection of the infecting agent in surveillance programs, and is an essential element in the development and production of vaccine. Since influenza is caused by a zoonotic virus it is necessary to do surveillance in the reservoir species (aquatic waterfowls), intermediate hosts (quails, pigs), and in affected mammals including humans. Two of the hemagglutinin (HA) subtypes of influenza A viruses (H5 and H7) can evolve into highly pathogenic (HP) strains for gallinaceous poultry; some HP H5 and H7 strains cause lethal infection of humans. In waterfowls, low pathogenic avian influenza (LPAI) isolates are obtained primarily from the cloaca (or feces); in domestic poultry, the virus is more often recovered from the respiratory tract than from cloacal samples; in mammals, the virus is most often isolated from the respiratory tract, and in cases of high pathogenic avian influenza (HPAI) from the blood and internal organs of infected birds. Virus isolation procedures are performed by inoculation of clinical specimens into embryonated eggs (primarily chicken eggs) or onto a variety of primary or continuous tissue culture systems. Successful isolation of influenza virus depends on the quality of the sample and matching the appropriate culture method to the sample type.

Receptor-mediated signalling in plants: molecular patterns and programmes

PubMed Central

Tör, Mahmut; Lotze, Michael T.; Holton, Nicholas

2009-01-01

A highly evolved surveillance system in plants is able to detect a broad range of signals originating from pathogens, damaged tissues, or altered developmental processes, initiating sophisticated molecular mechanisms that result in defence, wound healing, and development. Microbe-associated molecular pattern molecules (MAMPs), damage-associated molecular pattern molecules (DAMPs), virulence factors, secreted proteins, and processed peptides can be recognized directly or indirectly by this surveillance system. Nucleotide binding-leucine rich repeat proteins (NB-LRR) are intracellular receptors and have been targeted by breeders for decades to elicit resistance to crop pathogens in the field. Receptor-like kinases (RLKs) or receptor like proteins (RLPs) are membrane bound signalling molecules with an extracellular receptor domain. They provide an early warning system for the presence of potential pathogens and activate protective immune signalling in plants. In addition, they act as a signal amplifier in the case of tissue damage, establishing symbiotic relationships and effecting developmental processes. The identification of several important ligands for the RLK-type receptors provided an opportunity to understand how plants differentiate, how they distinguish beneficial and detrimental stimuli, and how they co-ordinate the role of various types of receptors under varying environmental conditions. The diverse roles of extra-and intracellular plant receptors are examined here and the recent findings on how they promote defence and development is reviewed. PMID:19628572

The burden of seasonal respiratory infections on a national telehealth service in England.

PubMed

Morbey, R A; Harcourt, S; Pebody, R; Zambon, M; Hutchison, J; Rutter, J; Thomas, H; Smith, G E; Elliot, A J

2017-07-01

Seasonal respiratory illnesses present a major burden on primary care services. We assessed the burden of respiratory illness on a national telehealth system in England and investigated the potential for providing early warning of respiratory infection. We compared weekly laboratory reports for respiratory pathogens with telehealth calls (NHS 111) between week 40 in 2013 and week 29 in 2015. Multiple linear regression was used to identify which pathogens had a significant association with respiratory calls. Children aged <5 and 5-14 years, and adults over 65 years were modelled separately as were time lags of up to 4 weeks between calls and laboratory specimen dates. Associations with respiratory pathogens explained over 83% of the variation in cold/flu, cough and difficulty breathing calls. Based on the first two seasons available, the greatest burden was associated with respiratory syncytial virus (RSV) and influenza, with associations found in all age bands. The most sensitive signal for influenza was calls for 'cold/flu', whilst for RSV it was calls for cough. The best-fitting models showed calls increasing a week before laboratory specimen dates. Daily surveillance of these calls can provide early warning of seasonal rises in influenza and RSV, contributing to the national respiratory surveillance programme.

Development of the ageing management database of PUSPATI TRIGA reactor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramli, Nurhayati, E-mail: nurhayati@nm.gov.my; Tom, Phongsakorn Prak; Husain, Nurfazila

Since its first criticality in 1982, PUSPATI TRIGA Reactor (RTP) has been operated for more than 30 years. As RTP become older, ageing problems have been seen to be the prominent issues. In addressing the ageing issues, an Ageing Management (AgeM) database for managing related ageing matters was systematically developed. This paper presents the development of AgeM database taking into account all RTP major Systems, Structures and Components (SSCs) and ageing mechanism of these SSCs through the system surveillance program.

Turkish meteor surveillance systems and network: Impact craters and meteorites database

NASA Astrophysics Data System (ADS)

Unsalan, O.; Ozel, M. E.; Derman, I. E.; Terzioglu, Z.; Kaygisiz, E.; Temel, T.; Topoyan, D.; Solmaz, A.; Yilmaz Kocahan, O.; Esenoglu, H. H.; Emrahoglu, N.; Yilmaz, A.; Yalcinkaya, B. O.

2014-07-01

In our project, we aim toward constructing Turkish Meteor Surveillance Systems and Network in Turkey. For this goal, video observational systems from SonotaCo (Japan) were chosen. Meteors are going to be observed with the specific cameras, their orbits will be calculated by the software from SonotaCo, and the places where they will be falling / impacting will be examined by field trips. The collected meteorites will be investigated by IR-Raman Spectroscopic techniques and SEM-EDX analyses in order to setup a database. On the other hand, according to our Prime Ministry Ottoman Archives, there are huge amounts of reports of falls for the past centuries. In order to treat these data properly, it is obvious that processing systems should be constructed and developed.

Arizona Hospital Discharge and Emergency Department Database: Implications for Occupational Health Surveillance.

PubMed

Harber, Philip; Ha, Jennifer; Roach, Matthew

2017-04-01

The objective of the project was to identify trends in emergency department visits and inpatient admissions for occupational injury and disease frequency and describe the financial impact from specific clinical groups known to have occupational risk factors. Workers compensation cases among 19 million records in the Arizona statewide hospital discharge database (HDD) were assessed for seven clinical groups from 2008 to 2014, including back, cardiac, carpal tunnel syndrome, heat-related, psychiatric, pulmonary, and trauma. Cases with cardiac, psychiatric, and pulmonary diagnoses were both frequent and expensive. Although incidence was generally stable, charges per case rose significantly over the time period. Inpatient and emergency department records provide valuable data that complement other surveillance approaches for both occupational illnesses and injuries. Tracking charge as well as incidence data is useful.

Herpes zoster surveillance using electronic databases in the Valencian Community (Spain)

PubMed Central

2013-01-01

Background Epidemiologic data of Herpes Zoster (HZ) disease in Spain are scarce. The objective of this study was to assess the epidemiology of HZ in the Valencian Community (Spain), using outpatient and hospital electronic health databases. Methods Data from 2007 to 2010 was collected from computerized health databases of a population of around 5 million inhabitants. Diagnoses were recorded by physicians using the International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM). A sample of medical records under different criteria was reviewed by a general practitioner, to assess the reliability of codification. Results The average annual incidence of HZ was 4.60 per 1000 persons-year (PY) for all ages (95% CI: 4.57-4.63), is more frequent in women [5.32/1000PY (95% CI: 5.28-5.37)] and is strongly age-related, with a peak incidence at 70-79 years. A total of 7.16/1000 cases of HZ required hospitalization. Conclusions Electronic health database used in the Valencian Community is a reliable electronic surveillance tool for HZ disease and will be useful to define trends in disease burden before and after HZ vaccine introduction. PMID:24094135

epiPATH: an information system for the storage and management of molecular epidemiology data from infectious pathogens.

PubMed

Amadoz, Alicia; González-Candelas, Fernando

2007-04-20

Most research scientists working in the fields of molecular epidemiology, population and evolutionary genetics are confronted with the management of large volumes of data. Moreover, the data used in studies of infectious diseases are complex and usually derive from different institutions such as hospitals or laboratories. Since no public database scheme incorporating clinical and epidemiological information about patients and molecular information about pathogens is currently available, we have developed an information system, composed by a main database and a web-based interface, which integrates both types of data and satisfies requirements of good organization, simple accessibility, data security and multi-user support. From the moment a patient arrives to a hospital or health centre until the processing and analysis of molecular sequences obtained from infectious pathogens in the laboratory, lots of information is collected from different sources. We have divided the most relevant data into 12 conceptual modules around which we have organized the database schema. Our schema is very complete and it covers many aspects of sample sources, samples, laboratory processes, molecular sequences, phylogenetics results, clinical tests and results, clinical information, treatments, pathogens, transmissions, outbreaks and bibliographic information. Communication between end-users and the selected Relational Database Management System (RDMS) is carried out by default through a command-line window or through a user-friendly, web-based interface which provides access and management tools for the data. epiPATH is an information system for managing clinical and molecular information from infectious diseases. It facilitates daily work related to infectious pathogens and sequences obtained from them. This software is intended for local installation in order to safeguard private data and provides advanced SQL-users the flexibility to adapt it to their needs. The database schema, tool scripts and web-based interface are free software but data stored in our database server are not publicly available. epiPATH is distributed under the terms of GNU General Public License. More details about epiPATH can be found at http://genevo.uv.es/epipath.

HPIDB 2.0: a curated database for host–pathogen interactions

PubMed Central

Ammari, Mais G.; Gresham, Cathy R.; McCarthy, Fiona M.; Nanduri, Bindu

2016-01-01

Identification and analysis of host–pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host–pathogen systems. Therefore, resources that annotate, predict and display the HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB 2.0 (http://www.agbase.msstate.edu/hpi/main.html) is a resource for HPI data, and contains 45, 238 manually curated entries in the current release. Since the first description of the database in 2010, multiple enhancements to HPIDB data and interface services were made that are described here. Notably, HPIDB 2.0 now provides targeted biocuration of molecular interaction data. As a member of the International Molecular Exchange consortium, annotations provided by HPIDB 2.0 curators meet community standards to provide detailed contextual experimental information and facilitate data sharing. Moreover, HPIDB 2.0 provides access to rapidly available community annotations that capture minimum molecular interaction information to address immediate researcher needs for HPI network analysis. In addition to curation, HPIDB 2.0 integrates HPI from existing external sources and contains tools to infer additional HPI where annotated data are scarce. Compared to other interaction databases, our data collection approach ensures HPIDB 2.0 users access the most comprehensive HPI data from a wide range of pathogens and their hosts (594 pathogen and 70 host species, as of February 2016). Improvements also include enhanced search capacity, addition of Gene Ontology functional information, and implementation of network visualization. The changes made to HPIDB 2.0 content and interface ensure that users, especially agricultural researchers, are able to easily access and analyse high quality, comprehensive HPI data. All HPIDB 2.0 data are updated regularly, are publically available for direct download, and are disseminated to other molecular interaction resources. Database URL: http://www.agbase.msstate.edu/hpi/main.html PMID:27374121

The application of epidemiology in aquatic animal health -opportunities and challenges

PubMed Central

2011-01-01

Over recent years the growth in aquaculture, accompanied by the emergence of new and transboundary diseases, has stimulated epidemiological studies of aquatic animal diseases. Great potential exists for both observational and theoretical approaches to investigate the processes driving emergence but, to date, compared to terrestrial systems, relatively few studies exist in aquatic animals. Research using risk methods has assessed routes of introduction of aquatic animal pathogens to facilitate safe trade (e.g. import risk analyses) and support biosecurity. Epidemiological studies of risk factors for disease in aquaculture (most notably Atlantic salmon farming) have effectively supported control measures. Methods developed for terrestrial livestock diseases (e.g. risk-based surveillance) could improve the capacity of aquatic animal surveillance systems to detect disease incursions and emergence. The study of disease in wild populations presents many challenges and the judicious use of theoretical models offers some solutions. Models, parameterised from observational studies of host pathogen interactions, have been used to extrapolate estimates of impacts on the individual to the population level. These have proved effective in estimating the likely impact of parasite infections on wild salmonid populations in Switzerland and Canada (where the importance of farmed salmon as a reservoir of infection was investigated). A lack of data is often the key constraint in the application of new approaches to surveillance and modelling. The need for epidemiological approaches to protect aquatic animal health will inevitably increase in the face of the combined challenges of climate change, increasing anthropogenic pressures, limited water sources and the growth in aquaculture. Table of contents 1 Introduction 4 2 The development of aquatic epidemiology 7 3 Transboundary and emerging diseases 9 3.1 Import risk analysis (IRA) 10 3.2 Aquaculture and disease emergence 11 3.3 Climate change and disease emergence 13 3.4 Outbreak investigations 13 4 Surveillance and surveys 15 4.1 Investigation of disease prevalence 15 4.2 Developments in surveillance methodology 16 4.2.1 Risk-based surveillance and scenario tree modelling 16 4.2.2 Spatial and temporal analysis 16 4.3 Test validation 17 5 Spread, establishment and impact of pathogens 18 5.1 Identifying routes of spread 18 5.1.1 Ex-ante studies of disease spread 19 5.1.2 Ex-post observational studies 21 5.2 Identifying risk factors for disease establishment 23 5.3 Assessing impact at the population level 24 5.3.1 Recording mortality 24 5.3.2 Farm health and production records 26 5.3.3 Assessing the impact of disease in wild populations 27 6 Conclusions 31 7 Competing interests 32 8 Authors' contributions 32 9 Acknowledgements 33 10 References 33 PMID:21834990

The Pathogen-Host Interactions database (PHI-base): additions and future developments

PubMed Central

Urban, Martin; Pant, Rashmi; Raghunath, Arathi; Irvine, Alistair G.; Pedro, Helder; Hammond-Kosack, Kim E.

2015-01-01

Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens. Mutant phenotypes are associated with gene information. The included pathogens infect a wide range of hosts including humans, animals, plants, insects, fish and other fungi. The current version, PHI-base 3.6, available at http://www.phi-base.org, stores information on 2875 genes, 4102 interactions, 110 host species, 160 pathogenic species (103 plant, 3 fungal and 54 animal infecting species) and 181 diseases drawn from 1243 references. Phenotypic and gene function information has been obtained by manual curation of the peer-reviewed literature. A controlled vocabulary consisting of nine high-level phenotype terms permits comparisons and data analysis across the taxonomic space. PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes. Virulence genes and hotspots can be visualized directly in genome browsers. Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s). PMID:25414340

Fructose 1,6-Bisphosphate aldolase, a novel immunogenic surface protein on Listeria species

USDA-ARS?s Scientific Manuscript database

Listeria monocytogenes is a ubiquitous food-borne pathogen, and its presence in food or production facilities highlights the importance of surveillance. Increased understanding of the surface exposed antigens on Listeria would provide potential diagnostic and therapeutic targets. In the present work...

Circulating Mycobacterium bovis peptides and host response proteins as biomarkers for unambiguous detection of subclinical infection

USDA-ARS?s Scientific Manuscript database

Background: Bovine tuberculosis remains one of the most damaging zoonotic diseases. A critical need exists for rapid and inexpensive diagnostics capable of detecting and differentiating M. bovis infection from other pathogenic and environmental mycobacteria at multiple surveillance levels. Method...

Trends in Drug Resistance of Acinetobacter baumannii over a 10-year Period: Nationwide Data from the China Surveillance of Antimicrobial Resistance Program.

PubMed

Gao, Lei; Lyu, Yuan; Li, Yun

2017-03-20

Acinetobacter baumannii has emerged as an important pathogen causing a variety of infections. Using data from the China Surveillance of Antimicrobial Resistance Program conducted biennially, we investigated the secular changes in the resistance of 2917 isolates of A. baumannii from 2004 to 2014 to differ antimicrobial agents. Pathogen samples were collected from 17 to 20 hospitals located in the eastern, central, and western regions of China. Minimum inhibitory concentrations (MICs) were determined by a 2-fold agar dilution method, and antimicrobial susceptibility was established using the 2014 Clinical Laboratory Standards Institute-approved breakpoints. Isolates not susceptible to all the tested aminoglycosides, fluoroquinolones, β-lactams, β-lactam/β-lactam inhibitors and carbapenems were defined as extensively drug resistant. The rates of nonsusceptibility to common antimicrobial agents remained high (>65%) over the years with some fluctuations to certain agents. The prevalence of imipenem-resistant A. baumannii (IRAB) increased from 13.3% in 2004 to 70.5% in 2014 and that of extensively drug-resistant A. baumannii (XDRAB) increased from 11.1% in 2004 to 60.4% in 2014. The activity of tigecycline was stable with MIC90 ≤4 mg/L against A. baumannii from 2009 to 2014. Susceptibility to colistin remained high (97.0%) from 2009 to 2014. The prevalence of XDRAB increased in all the three surveillance regions over the years and was significantly higher in Intensive Care Unit (ICU) wards than non-ICU wards. This longitudinal multicenter surveillance program revealed the nationwide emergence of A. baumannii in China and showed a significant increase in prevalence from 2004 to 2014. High levels of bacterial resistance were detected among samples collected from clinical settings in China, with IRAB and XDRAB being especially prevalent. This study will help to guide empirical therapy and identify at-risk groups requiring more intense interventional infection control measures, while also helping to focus surveillance efforts.

Distribution and Diversity of Pathogenic Leptospira Species in Peri-domestic Surface Waters from South Central Chile

PubMed Central

Mason, Meghan R.; Encina, Carolina; Sreevatsan, Srinand; Muñoz-Zanzi, Claudia

2016-01-01

Background Leptospirosis is a neglected zoonosis affecting animals and humans caused by infection with Leptospira. The bacteria can survive outside of hosts for long periods of time in soil and water. While identification of Leptospira species from human cases and animal reservoirs are increasingly reported, little is known about the diversity of pathogenic Leptospira species in the environment and how surveillance of the environment might be used for monitoring and controlling disease. Methods and Findings Water samples (n = 104) were collected from the peri-domestic environment of 422 households from farms, rural villages, and urban slums participating in a broader study on the eco-epidemiology of leptospirosis in the Los Rios Region, Chile, between October 2010 and April 2012. The secY region of samples, previously detected as pathogenic Leptospira by PCR, was amplified and sequenced. Sequences were aligned using ClustalW in MEGA, and a minimum spanning tree was created in PHYLOViZ using the goeBURST algorithm to assess sequence similarity. Sequences from four clinical isolates, 17 rodents, and 20 reference strains were also included in the analysis. Overall, water samples contained L. interrogans, L. kirschneri, and L. weilii, with descending frequency. All species were found in each community type. The distribution of the species differed by the season in which the water samples were obtained. There was no evidence that community-level prevalence of Leptospira in dogs, rodents, or livestock influenced pathogen diversity in the water samples. Conclusions This study reports the presence of pathogenic Leptospira in the peri-domestic environment of households in three community types and the differences in Leptospira diversity at the community level. Systematic environmental surveillance of Leptospira can be used for detecting changes in pathogen diversity and to identify and monitor contaminated areas where an increased risk of human infection exists. PMID:27529550

Novel Rickettsia and emergent tick-borne pathogens: A molecular survey of ticks and tick-borne pathogens in Shimba Hills National Reserve, Kenya.

PubMed

Mwamuye, Micky M; Kariuki, Edward; Omondi, David; Kabii, James; Odongo, David; Masiga, Daniel; Villinger, Jandouwe

2017-02-01

Ticks are important vectors of emerging and re-emerging zoonoses, the majority of which originate from wildlife. In recent times, this has become a global public health concern that necessitates surveillance of both known and unknown tick-borne pathogens likely to be future disease threats, as well as their tick vectors. We carried out a survey of the diversity of ticks and tick-borne pathogens in Kenya's Shimba Hills National Reserve (SHNR), an area with intensified human-livestock-wildlife interactions, where we collected 4297 questing ticks (209 adult ticks, 586 nymphs and 3502 larvae). We identified four tick species of two genera (Amblyomma eburneum, Amblyomma tholloni, Rhipicephalus maculatus and a novel Rhipicephalus sp.) based on both morphological characteristics and molecular analysis of 16S rRNA, internal transcribed spacer 2 (ITS 2) and cytochrome oxidase subunit 1 (CO1) genes. We pooled the ticks (3-8 adults, 8-15 nymphs or 30 larvae) depending on species and life-cycle stages, and screened for bacterial, arboviral and protozoal pathogens using PCR with high-resolution melting analysis and sequencing of unique melt profiles. We report the first molecular detection of Anaplasma phagocytophilum, a novel Rickettsia-like and Ehrlichia-like species, in Rh. maculatus ticks. We also detected Ehrlichia chaffeensis, Coxiella sp., Rickettsia africae and Theileria velifera in Am. eburneum ticks for the first time. Our findings demonstrate previously unidentified tick-pathogen relationships and a unique tick diversity in the SHNR that may contribute to livestock, and possibly human, morbidity in the region. This study highlights the importance of routine surveillance in similar areas to elucidate disease transmission dynamics, as a critical component to inform the development of better tick-borne disease diagnosis, prevention and control measures. Copyright © 2016 Elsevier GmbH. All rights reserved.

Coronavirus and paramyxovirus in bats from Northwest Italy.

PubMed

Rizzo, Francesca; Edenborough, Kathryn M; Toffoli, Roberto; Culasso, Paola; Zoppi, Simona; Dondo, Alessandro; Robetto, Serena; Rosati, Sergio; Lander, Angelika; Kurth, Andreas; Orusa, Riccardo; Bertolotti, Luigi; Mandola, Maria Lucia

2017-12-22

Bat-borne virus surveillance is necessary for determining inter-species transmission risks and is important due to the wide-range of bat species which may harbour potential pathogens. This study aimed to monitor coronaviruses (CoVs) and paramyxoviruses (PMVs) in bats roosting in northwest Italian regions. Our investigation was focused on CoVs and PMVs due to their proven ability to switch host and their zoonotic potential. Here we provide the phylogenetic characterization of the highly conserved polymerase gene fragments. Family-wide PCR screenings were used to test 302 bats belonging to 19 different bat species. Thirty-eight animals from 12 locations were confirmed as PCR positive, with an overall detection rate of 12.6% [95% CI: 9.3-16.8]. CoV RNA was found in 36 bats belonging to eight species, while PMV RNA in three Pipistrellus spp. Phylogenetic characterization have been obtained for 15 alpha- CoVs, 5 beta-CoVs and three PMVs; moreover one P. pipistrellus resulted co-infected with both CoV and PMV. A divergent alpha-CoV clade from Myotis nattereri SpA is also described. The compact cluster of beta-CoVs from R. ferrumequinum roosts expands the current viral sequence database, specifically for this species in Europe. To our knowledge this is the first report of CoVs in Plecotus auritus and M. oxygnathus, and of PMVs in P. kuhlii. This study identified alpha and beta-CoVs in new bat species and in previously unsurveyed Italian regions. To our knowledge this represents the first and unique report of PMVs in Italy. The 23 new bat genetic sequences presented will expand the current molecular bat-borne virus databases. Considering the amount of novel bat-borne PMVs associated with the emergence of zoonotic infections in animals and humans in the last years, the definition of viral diversity within European bat species is needed. Performing surveillance studies within a specific geographic area can provide awareness of viral burden where bats roost in close proximity to spillover hosts, and form the basis for the appropriate control measures against potential threats for public health and optimal management of bats and their habitats.

Analysis of the full genome of human group C rotaviruses reveals lineage diversification and reassortment.

PubMed

Medici, Maria Cristina; Tummolo, Fabio; Martella, Vito; Arcangeletti, Maria Cristina; De Conto, Flora; Chezzi, Carlo; Fehér, Enikő; Marton, Szilvia; Calderaro, Adriana; Bányai, Krisztián

2016-08-01

Group C rotaviruses (RVC) are enteric pathogens of humans and animals. Whole-genome sequences are available only for few RVCs, leaving gaps in our knowledge about their genetic diversity. We determined the full-length genome sequence of two human RVCs (PR2593/2004 and PR713/2012), detected in Italy from hospital-based surveillance for rotavirus infection in 2004 and 2012. In the 11 RNA genomic segments, the two Italian RVCs segregated within separate intra-genotypic lineages showed variation ranging from 1.9 % (VP6) to 15.9 % (VP3) at the nucleotide level. Comprehensive analysis of human RVC sequences available in the databases allowed us to reveal the existence of at least two major genome configurations, defined as type I and type II. Human RVCs of type I were all associated with the M3 VP3 genotype, including the Italian strain PR2593/2004. Conversely, human RVCs of type II were all associated with the M2 VP3 genotype, including the Italian strain PR713/2012. Reassortant RVC strains between these major genome configurations were identified. Although only a few full-genome sequences of human RVCs, mostly of Asian origin, are available, the analysis of human RVC sequences retrieved from the databases indicates that at least two intra-genotypic RVC lineages circulate in European countries. Gathering more sequence data is necessary to develop a standardized genotype and intra-genotypic lineage classification system useful for epidemiological investigations and avoiding confusion in the literature.

Infectious Disease Surveillance in the Big Data Era: Towards Faster and Locally Relevant Systems.

PubMed

Simonsen, Lone; Gog, Julia R; Olson, Don; Viboud, Cécile

2016-12-01

While big data have proven immensely useful in fields such as marketing and earth sciences, public health is still relying on more traditional surveillance systems and awaiting the fruits of a big data revolution. A new generation of big data surveillance systems is needed to achieve rapid, flexible, and local tracking of infectious diseases, especially for emerging pathogens. In this opinion piece, we reflect on the long and distinguished history of disease surveillance and discuss recent developments related to use of big data. We start with a brief review of traditional systems relying on clinical and laboratory reports. We then examine how large-volume medical claims data can, with great spatiotemporal resolution, help elucidate local disease patterns. Finally, we review efforts to develop surveillance systems based on digital and social data streams, including the recent rise and fall of Google Flu Trends. We conclude by advocating for increased use of hybrid systems combining information from traditional surveillance and big data sources, which seems the most promising option moving forward. Throughout the article, we use influenza as an exemplar of an emerging and reemerging infection which has traditionally been considered a model system for surveillance and modeling. Published by Oxford University Press for the Infectious Diseases Society of America 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Health Information-Seeking Patterns of the General Public and Indications for Disease Surveillance: Register-Based Study Using Lyme Disease.

PubMed

Pesälä, Samuli; Virtanen, Mikko J; Sane, Jussi; Mustonen, Pekka; Kaila, Minna; Helve, Otto

2017-11-06

People using the Internet to find information on health issues, such as specific diseases, usually start their search from a general search engine, for example, Google. Internet searches such as these may yield results and data of questionable quality and reliability. Health Library is a free-of-charge medical portal on the Internet providing medical information for the general public. Physician's Databases, an Internet evidence-based medicine source, provides medical information for health care professionals (HCPs) to support their clinical practice. Both databases are available throughout Finland, but the latter is used only by health professionals and pharmacies. Little is known about how the general public seeks medical information from medical sources on the Internet, how this behavior differs from HCPs' queries, and what causes possible differences in behavior. The aim of our study was to evaluate how the general public's and HCPs' information-seeking trends from Internet medical databases differ seasonally and temporally. In addition, we aimed to evaluate whether the general public's information-seeking trends could be utilized for disease surveillance and whether media coverage could affect these seeking trends. Lyme disease, serving as a well-defined disease model with distinct seasonal variation, was chosen as a case study. Two Internet medical databases, Health Library and Physician's Databases, were used. We compared the general public's article openings on Lyme disease from Health Library to HCPs' article openings on Lyme disease from Physician's Databases seasonally across Finland from 2011 to 2015. Additionally, media publications related to Lyme disease were searched from the largest and most popular media websites in Finland. Both databases, Health Library and Physician's Databases, show visually similar patterns in temporal variations of article openings on Lyme disease in Finland from 2011 to 2015. However, Health Library openings show not only an increasing trend over time but also greater fluctuations, especially during peak opening seasons. Outside these seasons, publications in the media coincide with Health Library article openings only occasionally. Lyme disease-related information-seeking behaviors between the general public and HCPs from Internet medical portals share similar temporal variations, which is consistent with the trend seen in epidemiological data. Therefore, the general public's article openings could be used as a supplementary source of information for disease surveillance. The fluctuations in article openings appeared stronger among the general public, thus, suggesting that different factors such as media coverage, affect the information-seeking behaviors of the public versus professionals. However, media coverage may also have an influence on HCPs. Not every publication was associated with an increase in openings, but the higher the media coverage by some publications, the higher the general public's access to Health Library. ©Samuli Pesälä, Mikko J Virtanen, Jussi Sane, Pekka Mustonen, Minna Kaila, Otto Helve. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 06.11.2017.

An emerging cyberinfrastructure for biodefense pathogen and pathogen–host data

PubMed Central

Zhang, C.; Crasta, O.; Cammer, S.; Will, R.; Kenyon, R.; Sullivan, D.; Yu, Q.; Sun, W.; Jha, R.; Liu, D.; Xue, T.; Zhang, Y.; Moore, M.; McGarvey, P.; Huang, H.; Chen, Y.; Zhang, J.; Mazumder, R.; Wu, C.; Sobral, B.

2008-01-01

The NIAID-funded Biodefense Proteomics Resource Center (RC) provides storage, dissemination, visualization and analysis capabilities for the experimental data deposited by seven Proteomics Research Centers (PRCs). The data and its publication is to support researchers working to discover candidates for the next generation of vaccines, therapeutics and diagnostics against NIAID's Category A, B and C priority pathogens. The data includes transcriptional profiles, protein profiles, protein structural data and host–pathogen protein interactions, in the context of the pathogen life cycle in vivo and in vitro. The database has stored and supported host or pathogen data derived from Bacillus, Brucella, Cryptosporidium, Salmonella, SARS, Toxoplasma, Vibrio and Yersinia, human tissue libraries, and mouse macrophages. These publicly available data cover diverse data types such as mass spectrometry, yeast two-hybrid (Y2H), gene expression profiles, X-ray and NMR determined protein structures and protein expression clones. The growing database covers over 23 000 unique genes/proteins from different experiments and organisms. All of the genes/proteins are annotated and integrated across experiments using UniProt Knowledgebase (UniProtKB) accession numbers. The web-interface for the database enables searching, querying and downloading at the level of experiment, group and individual gene(s)/protein(s) via UniProtKB accession numbers or protein function keywords. The system is accessible at http://www.proteomicsresource.org/. PMID:17984082

Public health surveillance and infectious disease detection.

PubMed

Morse, Stephen S

2012-03-01

Emerging infectious diseases, such as HIV/AIDS, SARS, and pandemic influenza, and the anthrax attacks of 2001, have demonstrated that we remain vulnerable to health threats caused by infectious diseases. The importance of strengthening global public health surveillance to provide early warning has been the primary recommendation of expert groups for at least the past 2 decades. However, despite improvements in the past decade, public health surveillance capabilities remain limited and fragmented, with uneven global coverage. Recent initiatives provide hope of addressing this issue, and new technological and conceptual advances could, for the first time, place capability for global surveillance within reach. Such advances include the revised International Health Regulations (IHR 2005) and the use of new data sources and methods to improve global coverage, sensitivity, and timeliness, which show promise for providing capabilities to extend and complement the existing infrastructure. One example is syndromic surveillance, using nontraditional and often automated data sources. Over the past 20 years, other initiatives, including ProMED-mail, GPHIN, and HealthMap, have demonstrated new mechanisms for acquiring surveillance data. In 2009 the U.S. Agency for International Development (USAID) began the Emerging Pandemic Threats (EPT) program, which includes the PREDICT project, to build global capacity for surveillance of novel infections that have pandemic potential (originating in wildlife and at the animal-human interface) and to develop a framework for risk assessment. Improved understanding of factors driving infectious disease emergence and new technological capabilities in modeling, diagnostics and pathogen identification, and communications, such as using the increasing global coverage of cellphones for public health surveillance, can further enhance global surveillance.

Ante- and postmortem diagnostic techniques for anthrax: rethinking pathogen exposure and the geographic extent of the disease in wildlife.

PubMed

Bagamian, Karoun H; Alexander, Kathleen A; Hadfield, Ted L; Blackburn, Jason K

2013-10-01

Although antemortem approaches in wildlife disease surveillance are common for most zoonoses, they have been used infrequently in anthrax surveillance. Classically, anthrax is considered a disease with extremely high mortality. This is because anthrax outbreaks are often detected ex post facto through wildlife or livestock fatalities or spillover transmission to humans. As a result, the natural prevalence of anthrax infection in animal populations is largely unknown. However, in the past 20 yr, antemortem serologic surveillance in wildlife has indicated that not all species exposed succumb to infection, and anthrax exposure may be more widespread than originally appreciated. These studies brought about a multitude of new questions, many of which can be addressed by increased antemortem serologic surveillance in wildlife populations. To fully understand anthrax transmission dynamics and geographic extent, it is important to identify exposure in wildlife hosts and associated factors and, in turn, understand how these influences may drive environmental reservoir dynamics and concurrent disease risk in livestock and humans. Here we review our current understanding of the serologic response to anthrax among wildlife hosts and serologic diagnostic assays used to augment traditional postmortem anthrax surveillance strategies. We also provide recommendations for the use of serology and sentinel species surveillance approaches in anthrax research and management.

Clinical Microbiology Laboratories' Adoption of Culture-Independent Diagnostic Tests Is a Threat to Foodborne-Disease Surveillance in the United States.

PubMed

Shea, Shari; Kubota, Kristy A; Maguire, Hugh; Gladbach, Stephen; Woron, Amy; Atkinson-Dunn, Robyn; Couturier, Marc Roger; Miller, Melissa B

2017-01-01

INTRODUCTIONIn November 2015, the Centers for Disease Control and Prevention (CDC) sent a letter to state and territorial epidemiologists, state and territorial public health laboratory directors, and state and territorial health officials. In this letter, culture-independent diagnostic tests (CIDTs) for detection of enteric pathogens were characterized as "a serious and current threat to public health surveillance, particularly for Shiga toxin-producing Escherichia coli (STEC) and Salmonella" The document says CDC and its public health partners are approaching this issue, in part, by "reviewing regulatory authority in public health agencies to require culture isolates or specimen submission if CIDTs are used." Large-scale foodborne outbreaks are a continuing threat to public health, and tracking these outbreaks is an important tool in shortening them and developing strategies to prevent them. It is clear that the use of CIDTs for enteric pathogen detection, including both antigen detection and multiplex nucleic acid amplification techniques, is becoming more widespread. Furthermore, some clinical microbiology laboratories will resist the mandate to require submission of culture isolates, since it will likely not improve patient outcomes but may add significant costs. Specimen submission would be less expensive and time-consuming for clinical laboratories; however, this approach would be burdensome for public health laboratories, since those laboratories would need to perform culture isolation prior to typing. Shari Shea and Kristy Kubota from the Association of Public Health Laboratories, along with state public health laboratory officials from Colorado, Missouri, Tennessee, and Utah, will explain the public health laboratories' perspective on why having access to isolates of enteric pathogens is essential for public health surveillance, detection, and tracking of outbreaks and offer potential workable solutions which will allow them to do this. Marc Couturier of ARUP Laboratories and Melissa Miller of the University of North Carolina will explain the advantages of CIDTs for enteric pathogens and discuss practical solutions for clinical microbiology laboratories to address these public health needs. Copyright © 2016 American Society for Microbiology.

Epidemiologic analysis of respiratory viral infections among Singapore military servicemen in 2016.

PubMed

Lau, Yuk-Fai; Koh, Wee-Hong Victor; Kan, Clement; Dua, Poh-Choo Alethea; Lim, Ai-Sim Elizabeth; Liaw, Chin-Wen Jasper; Gao, Qiu-Han; Chng, Jeremiah; Lee, Vernon J; Tan, Boon-Huan; Loh, Jin-Phang

2018-03-12

Respiratory illnesses have been identified as a significant factor leading to lost training time and morbidity among Singapore military recruits. A surveillance programme has been put in place to determine etiological agents responsible for febrile, as well as afebrile respiratory illnesses in a military camp. The goal of the study is to better understand the epidemiology of these diseases and identify potential countermeasures to protect military recruits against them. From Jan 2016 - Jan 2017, a total of 2647 respiratory cases were enrolled into the surveillance programme. The cases were further stratified into Febrile Respiratory Illness (FRI, with body temperature > 37.5 °C) or Acute Respiratory Illness (ARI, with body temperature < 37.5 °C). Nasal washes were collected and tested by multiplex PCR to detect 26 different pathogens. One thousand ninety five cases (41% of total cases) met the criteria of FRI in which 932 cases (85% of FRI cases) were screened positive for at least one virus. The most common etiological agents for FRI mono-infection cases were Adenovirus E and Rhinovirus. Recruits infected with H3N2 influenza, Influenza B and Adenovirus E viruses were most likely presented as FRI cases. Notably, H3N2 influenza resulted in the greatest rise in body temperature. The remaining 1552 cases (59% of total cases) met the criteria of ARI in which 1198 cases (77% of ARI cases) were screened positive for at least one virus. The most common etiological agent for ARI mono-infection was Rhinovirus. The distribution pattern for dual infections was different for ARI and FRI cases. Maximum number of pathogens detected in a sample was five for both groups. Previous studies on respiratory diseases in military focused largely on FRI cases. With the expanded surveillance to ARI cases, this study allows unbiased evaluation of the impact of respiratory disease pathogens among recruits in a military environment. The results show that several pathogens have a much bigger role in causing respiratory diseases in this cohort.

Multiplex tests to identify gastrointestinal bacteria, viruses and parasites in people with suspected infectious gastroenteritis: a systematic review and economic analysis.

PubMed

Freeman, Karoline; Mistry, Hema; Tsertsvadze, Alexander; Royle, Pam; McCarthy, Noel; Taylor-Phillips, Sian; Manuel, Rohini; Mason, James

2017-04-01

Gastroenteritis is a common, transient disorder usually caused by infection and characterised by the acute onset of diarrhoea. Multiplex gastrointestinal pathogen panel (GPP) tests simultaneously identify common bacterial, viral and parasitic pathogens using molecular testing. By providing test results more rapidly than conventional testing methods, GPP tests might positively influence the treatment and management of patients presenting in hospital or in the community. To systematically review the evidence for GPP tests [xTAG ® (Luminex, Toronto, ON, Canada), FilmArray (BioFire Diagnostics, Salt Lake City, UT, USA) and Faecal Pathogens B (AusDiagnostics, Beaconsfield, NSW, Australia)] and to develop a de novo economic model to compare the cost-effectiveness of GPP tests with conventional testing in England and Wales. Multiple electronic databases including MEDLINE, EMBASE, Web of Science and the Cochrane Database were searched from inception to January 2016 (with supplementary searches of other online resources). Eligible studies included patients with acute diarrhoea; comparing GPP tests with standard microbiology techniques; and patient, management, test accuracy or cost-effectiveness outcomes. Quality assessment of eligible studies used tailored Quality Assessment of Diagnostic Accuracy Studies-2, Consolidated Health Economic Evaluation Reporting Standards and Philips checklists. The meta-analysis included positive and negative agreement estimated for each pathogen. A de novo decision tree model compared patients managed with GPP testing or comparable coverage with patients managed using conventional tests, within the Public Health England pathway. Economic models included hospital and community management of patients with suspected gastroenteritis. The model estimated costs (in 2014/15 prices) and quality-adjusted life-year losses from a NHS and Personal Social Services perspective. Twenty-three studies informed the review of clinical evidence (17 xTAG, four FilmArray, two xTAG and FilmArray, 0 Faecal Pathogens B). No study provided an adequate reference standard with which to compare the test accuracy of GPP with conventional tests. A meta-analysis (of 10 studies) found considerable heterogeneity; however, GPP testing produces a greater number of pathogen-positive findings than conventional testing. It is unclear whether or not these additional 'positives' are clinically important. The review identified no robust evidence to inform consequent clinical management of patients. There is considerable uncertainty about the cost-effectiveness of GPP panels used to test for suspected infectious gastroenteritis in hospital and community settings. Uncertainties in the model include length of stay, assumptions about false-positive findings and the costs of tests. Although there is potential for cost-effectiveness in both settings, key modelling assumptions need to be verified and model findings remain tentative. No test-treat trials were retrieved. The economic model reflects one pattern of care, which will vary across the NHS. The systematic review and cost-effectiveness model identify uncertainties about the adoption of GPP tests within the NHS. GPP testing will generally correctly identify pathogens identified by conventional testing; however, these tests also generate considerable additional positive results of uncertain clinical importance. An independent reference standard may not exist to evaluate alternative approaches to testing. A test-treat trial might ascertain whether or not additional GPP 'positives' are clinically important or result in overdiagnoses, whether or not earlier diagnosis leads to earlier discharge in patients and what the health consequences of earlier intervention are. Future work might also consider the public health impact of different testing treatments, as test results form the basis for public health surveillance. This study is registered as PROSPERO CRD2016033320. The National Institute for Health Research Health Technology Assessment programme.

Implications of the cattle trade network in Cameroon for regional disease prevention and control

PubMed Central

Motta, Paolo; Porphyre, Thibaud; Handel, Ian; Hamman, Saidou M.; Ngu Ngwa, Victor; Tanya, Vincent; Morgan, Kenton; Christley, Rob; Bronsvoort, Barend M. deC.

2017-01-01

Movement of live animals is a major risk factor for the spread of livestock diseases and zoonotic infections. Understanding contact patterns is key to informing cost-effective surveillance and control strategies. In West and Central Africa some of the most rapid urbanization globally is expected to increase the demand for animal-source foods and the need for safer and more efficient animal production. Livestock trading points represent a strategic contact node in the dissemination of multiple pathogens. From October 2014 to May 2015 official transaction records were collected and a questionnaire-based survey was carried out in cattle markets throughout Western and Central-Northern Cameroon. The data were used to analyse the cattle trade network including a total of 127 livestock markets within Cameroon and five neighboring countries. This study explores for the first time the influence of animal trade on infectious disease spread in the region. The investigations showed that national borders do not present a barrier against pathogen dissemination and that non-neighbouring countries are epidemiologically connected, highlighting the importance of a regional approach to disease surveillance, prevention and control. Furthermore, these findings provide evidence for the benefit of strategic risk-based approaches for disease monitoring, surveillance and control, as well as for communication and training purposes through targeting key regions, highly connected livestock markets and central trading links. PMID:28266589

Antimicrobial resistance in human and animal pathogens in Zambia, Democratic Republic of Congo, Mozambique and Tanzania: an urgent need of a sustainable surveillance system.

PubMed

Mshana, Stephen E; Matee, Mecky; Rweyemamu, Mark

2013-10-12

A review of the published and unpublished literature on bacterial resistance in human and animals was performed. Sixty-eight articles/reports from the Democratic Republic of Congo (DRC), Mozambique, Tanzania and Zambia were reviewed. The majority of these articles were from Tanzania. There is an increasing trend in the incidence of antibiotic resistance; of major concern is the increase in multidrug- resistant Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Vibrio cholera, non-typhoid Salmonella and other pathogens responsible for nosocomial infections. The increase in methicillin- resistant Staphylococcus aureus and extended-spectrum beta-lactamase (ESBL) producers in the countries under review confirms the spread of these clones worldwide. Clinical microbiology services in these countries need to be strengthened in order to allow a coordinated surveillance for antimicrobial resistance and provide data for local treatment guidelines and for national policies to control antimicrobial resistance. While the present study does not provide conclusive evidence to associate the increasing trend in antibiotic resistance in humans with the use of antibiotics in animals, either as feed additives or veterinary prescription, we strongly recommend a one-health approach of systematic surveillance across the public and animal health sectors, as well as the adherence to the FAO (Food and Agriculture Organization)-OIE (World Organization of animal Health) -WHO(World Health Organization) recommendations for non-human antimicrobial usage.

Implications of the cattle trade network in Cameroon for regional disease prevention and control

NASA Astrophysics Data System (ADS)

Motta, Paolo; Porphyre, Thibaud; Handel, Ian; Hamman, Saidou M.; Ngu Ngwa, Victor; Tanya, Vincent; Morgan, Kenton; Christley, Rob; Bronsvoort, Barend M. Dec.

2017-03-01

Movement of live animals is a major risk factor for the spread of livestock diseases and zoonotic infections. Understanding contact patterns is key to informing cost-effective surveillance and control strategies. In West and Central Africa some of the most rapid urbanization globally is expected to increase the demand for animal-source foods and the need for safer and more efficient animal production. Livestock trading points represent a strategic contact node in the dissemination of multiple pathogens. From October 2014 to May 2015 official transaction records were collected and a questionnaire-based survey was carried out in cattle markets throughout Western and Central-Northern Cameroon. The data were used to analyse the cattle trade network including a total of 127 livestock markets within Cameroon and five neighboring countries. This study explores for the first time the influence of animal trade on infectious disease spread in the region. The investigations showed that national borders do not present a barrier against pathogen dissemination and that non-neighbouring countries are epidemiologically connected, highlighting the importance of a regional approach to disease surveillance, prevention and control. Furthermore, these findings provide evidence for the benefit of strategic risk-based approaches for disease monitoring, surveillance and control, as well as for communication and training purposes through targeting key regions, highly connected livestock markets and central trading links.

Waterborne Pathogens: Detection Methods and Challenges

PubMed Central

Ramírez-Castillo, Flor Yazmín; Loera-Muro, Abraham; Jacques, Mario; Garneau, Philippe; Avelar-González, Francisco Javier; Harel, Josée; Guerrero-Barrera, Alma Lilián

2015-01-01

Waterborne pathogens and related diseases are a major public health concern worldwide, not only by the morbidity and mortality that they cause, but by the high cost that represents their prevention and treatment. These diseases are directly related to environmental deterioration and pollution. Despite the continued efforts to maintain water safety, waterborne outbreaks are still reported globally. Proper assessment of pathogens on water and water quality monitoring are key factors for decision-making regarding water distribution systems’ infrastructure, the choice of best water treatment and prevention waterborne outbreaks. Powerful, sensitive and reproducible diagnostic tools are developed to monitor pathogen contamination in water and be able to detect not only cultivable pathogens but also to detect the occurrence of viable but non-culturable microorganisms as well as the presence of pathogens on biofilms. Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. This review aims to present a research outlook on waterborne outbreaks that have occurred in recent years. This review also focuses in the main molecular techniques for detection of waterborne pathogens and the use of QMRA approach to protect public health. PMID:26011827

A bootstrap based space-time surveillance model with an application to crime occurrences

NASA Astrophysics Data System (ADS)

Kim, Youngho; O'Kelly, Morton

2008-06-01

This study proposes a bootstrap-based space-time surveillance model. Designed to find emerging hotspots in near-real time, the bootstrap based model is characterized by its use of past occurrence information and bootstrap permutations. Many existing space-time surveillance methods, using population at risk data to generate expected values, have resulting hotspots bounded by administrative area units and are of limited use for near-real time applications because of the population data needed. However, this study generates expected values for local hotspots from past occurrences rather than population at risk. Also, bootstrap permutations of previous occurrences are used for significant tests. Consequently, the bootstrap-based model, without the requirement of population at risk data, (1) is free from administrative area restriction, (2) enables more frequent surveillance for continuously updated registry database, and (3) is readily applicable to criminology and epidemiology surveillance. The bootstrap-based model performs better for space-time surveillance than the space-time scan statistic. This is shown by means of simulations and an application to residential crime occurrences in Columbus, OH, year 2000.

Surveillance of adverse effects following vaccination and safety of immunization programs.

PubMed

Waldman, Eliseu Alves; Luhm, Karin Regina; Monteiro, Sandra Aparecida Moreira Gomes; Freitas, Fabiana Ramos Martin de

2011-02-01

The aim of the review was to analyze conceptual and operational aspects of systems for surveillance of adverse events following immunization. Articles available in electronic format were included, published between 1985 and 2009, selected from the PubMed/Medline databases using the key words "adverse events following vaccine surveillance", "post-marketing surveillance", "safety vaccine" and "Phase IV clinical trials". Articles focusing on specific adverse events were excluded. The major aspects underlying the Public Health importance of adverse events following vaccination, the instruments aimed at ensuring vaccine safety, and the purpose, attributes, types, data interpretation issues, limitations, and further challenges in adverse events following immunization were describe, as well as strategies to improve sensitivity. The review was concluded by discussing the challenges to be faced in coming years with respect to ensuring the safety and reliability of vaccination programs.

Salmonella Enteritidis organ invasion and egg contamination in experimentally infected laying hens housed in conventional or enriched cages.

USDA-ARS?s Scientific Manuscript database

Both disease surveillance and epidemiologic analyses have confirmed a strong association between human salmonellosis and the prevalence of Salmonella Enteritidis (SE) in commercial egg flocks. The majority of human illnesses caused by this pathogen are attributed to contaminated eggs. Animal welfare...

Contamination of eggs by Salmonella Enteritidis in experimentally infected laying hens housed in conventional or enriched cages

USDA-ARS?s Scientific Manuscript database

Both epidemiologic analyses and active disease surveillance confirm an ongoing strong association between human salmonellosis and the prevalence of Salmonella Enteritidis in commercial egg flocks. The majority of human illnesses caused by this pathogen are attributed to the consumption of contaminat...

Development of a two-step, non-probed multiplex real-time PCR for surveilling Vibrio anguillarum in seawater

USDA-ARS?s Scientific Manuscript database

Vibrio anguillarum is an aggressive and halophilic bacterial pathogen commonly found in seawater. Its presence in aquaculture facilities causes significant morbidity and mortality among aquaculture species primarily from hemorrhaging of the body and skin of the infected fish that eventually leads t...

Biological agents database in the armed forces.

PubMed

Niemcewicz, Marcin; Kocik, Janusz; Bielecka, Anna; Wierciński, Michał

2014-10-01

Rapid detection and identification of the biological agent during both, natural or deliberate outbreak is crucial for implementation of appropriate control measures and procedures in order to mitigate the spread of disease. Determination of pathogen etiology may not only support epidemiological investigation and safety of human beings, but also enhance forensic efforts in pathogen tracing, collection of evidences and correct inference. The article presents objectives of the Biological Agents Database, which was developed for the purpose of the Ministry of National Defense of the Republic of Poland under the European Defence Agency frame. The Biological Agents Database is an electronic catalogue of genetic markers of highly dangerous pathogens and biological agents of weapon of mass destruction concern, which provides full identification of biological threats emerging in Poland and in locations of activity of Polish troops. The Biological Agents Database is a supportive tool used for tracing biological agents' origin as well as rapid identification of agent causing the disease of unknown etiology. It also provides support in diagnosis, analysis, response and exchange of information between institutions that use information contained in it. Therefore, it can be used not only for military purposes, but also in a civilian environment.

Design and Implementation of an Operational Database for the Fleet Area Control and Surveillance Facility, NAS North Island, San Diego, California

DTIC Science & Technology

1989-03-01

deficiencies of the present system. Specific objectives critical in de,’cloping an under- standing of the system are: " Identify all knowledge workers who use...to be negligible. The limited training require- ments are primarily due to the users existing knowledge of tK2 Oracle database system, the Users

A Meta-Analysis of the Prevalence of Influenza A H5N1 and H7N9 Infection in Birds.

PubMed

Bui, C; Rahman, B; Heywood, A E; MacIntyre, C R

2017-06-01

Despite a much higher rate of human influenza A (H7N9) infection compared to influenza A (H5N1), and the assumption that birds are the source of human infection, detection rates of H7N9 in birds are lower than those of H5N1. This raises a question about the role of birds in the spread and transmission of H7N9 to humans. We conducted a meta-analysis of overall prevalence of H5N1 and H7N9 in different bird populations (domestic poultry, wild birds) and different environments (live bird markets, commercial poultry farms, wild habitats). The electronic database, Scopus, was searched for published papers, and Google was searched for country surveillance reports. A random effect meta-analysis model was used to produce pooled estimates of the prevalence of H5N1 and H7N9 for various subcategories. A random effects logistic regression model was used to compare prevalence rates between H5N1 and H7N9. Both viruses have low prevalence across all bird populations. Significant differences in prevalence rates were observed in domestic birds, farm settings, for pathogen and antibody testing, and during routine surveillance. Random effects logistic regression analyses show that among domestic birds, the prevalence of H5N1 is 47.48 (95% CI: 17.15-133.13, P < 0.001) times higher than H7N9. In routine surveillance (where surveillance was not conducted in response to human infections or bird outbreaks), the prevalence of H5N1 is still higher than H7N9 with an OR of 43.02 (95% CI: 16.60-111.53, P < 0.001). H7N9 in humans has occurred at a rate approximately four times higher than H5N1, and for both infections, birds are postulated to be the source. Much lower rates of H7N9 in birds compared to H5N1 raise doubts about birds as the sole source of high rates of human H7N9 infection. Other sources of transmission of H7N9 need to be considered and explored. © 2016 The Authors. Transboundary and Emerging Diseases Published by Blackwell Verlag GmbH.

Surveillance for foodborne disease outbreaks - United States, 1998-2008.

PubMed

Gould, L Hannah; Walsh, Kelly A; Vieira, Antonio R; Herman, Karen; Williams, Ian T; Hall, Aron J; Cole, Dana

2013-06-28

Foodborne diseases cause an estimated 48 million illnesses each year in the United States, including 9.4 million caused by known pathogens. Foodborne disease outbreak surveillance provides valuable insights into the agents and foods that cause illness and the settings in which transmission occurs. CDC maintains a surveillance program for collection and periodic reporting of data on the occurrence and causes of foodborne disease outbreaks in the United States. This surveillance system is the primary source of national data describing the numbers of illnesses, hospitalizations, and deaths; etiologic agents; implicated foods; contributing factors; and settings of food preparation and consumption associated with recognized foodborne disease outbreaks in the United States. 1998-2008. The Foodborne Disease Outbreak Surveillance System collects data on foodborne disease outbreaks, defined as the occurrence of two or more cases of a similar illness resulting from the ingestion of a common food. Public health agencies in all 50 states, the District of Columbia, U.S. territories, and Freely Associated States have primary responsibility for identifying and investigating outbreaks and use a standard form to report outbreaks voluntarily to CDC. During 1998-2008, reporting was made through the electronic Foodborne Outbreak Reporting System (eFORS). During 1998-2008, CDC received reports of 13,405 foodborne disease outbreaks, which resulted in 273,120 reported cases of illness, 9,109 hospitalizations, and 200 deaths. Of the 7,998 outbreaks with a known etiology, 3,633 (45%) were caused by viruses, 3,613 (45%) were caused by bacteria, 685 (5%) were caused by chemical and toxic agents, and 67 (1%) were caused by parasites. Among the 7,724 (58%) outbreaks with an implicated food or contaminated ingredient reported, 3,264 (42%) could be assigned to one of 17 predefined commodity categories: fish, crustaceans, mollusks, dairy, eggs, beef, game, pork, poultry, grains/beans, oils/sugars, fruits/nuts, fungi, leafy vegetables, root vegetables, sprouts, and vegetables from a vine or stalk. The commodities implicated most commonly were poultry (18.9%; 95% confidence interval [CI] = 17.4-20.3) and fish (18.6%; CI = 17.2-20), followed by beef (11.9%; CI = 10.8-13.1). The pathogen-commodity pairs most commonly responsible for outbreaks were scombroid toxin/histamine and fish (317 outbreaks), ciguatoxin and fish (172 outbreaks), Salmonella and poultry (145 outbreaks), and norovirus and leafy vegetables (141 outbreaks). The pathogen-commodity pairs most commonly responsible for outbreak-related illnesses were norovirus and leafy vegetables (4,011 illnesses), Clostridium perfringens and poultry (3,452 illnesses), Salmonella and vine-stalk vegetables (3,216 illnesses), and Clostridium perfringens and beef (2,963 illnesses). Compared with the first 2 years of the study (1998-1999), the percentage of outbreaks associated with leafy vegetables and dairy increased substantially during 2006-2008, while the percentage of outbreaks associated with eggs decreased. Outbreak reporting rates and implicated foods varied by state and year, respectively; analysis of surveillance data for this 11-year period provides important information regarding changes in sources of illness over time. A substantial percentage of foodborne disease outbreaks were associated with poultry, fish, and beef, whereas many outbreak-related illnesses were associated with poultry, leafy vegetables, beef, and fruits/nuts. The percentage of outbreaks associated with leafy vegetables and dairy increased during the surveillance period, while the percentage associated with eggs decreased. Outbreak surveillance data highlight the etiologic agents, foods, and settings involved most often in foodborne disease outbreaks and can help to identify food commodities and preparation settings in which interventions might be most effective. Analysis of data collected over several years of surveillance provides a means to assess changes in the food commodities associated most frequently with outbreaks that might occur following improvements in food safety or changes in consumption patterns or food preparation practices. Prevention of foodborne disease depends on targeted interventions at appropriate points from food production to food preparation. Efforts to reduce foodborne illness should focus on the pathogens and food commodities causing the most outbreaks and outbreak-associated illnesses, including beef, poultry, fish, and produce.

Practice databases and their uses in clinical research.

PubMed

Tierney, W M; McDonald, C J

1991-04-01

A few large clinical information databases have been established within larger medical information systems. Although they are smaller than claims databases, these clinical databases offer several advantages: accurate and timely data, rich clinical detail, and continuous parameters (for example, vital signs and laboratory results). However, the nature of the data vary considerably, which affects the kinds of secondary analyses that can be performed. These databases have been used to investigate clinical epidemiology, risk assessment, post-marketing surveillance of drugs, practice variation, resource use, quality assurance, and decision analysis. In addition, practice databases can be used to identify subjects for prospective studies. Further methodologic developments are necessary to deal with the prevalent problems of missing data and various forms of bias if such databases are to grow and contribute valuable clinical information.

Sensitivity and Specificity Estimation for the Clinical Diagnosis of Highly Pathogenic Avian Influenza in the Egyptian Participatory Disease Surveillance Program.

PubMed

Verdugo, C; El Masry, I; Makonnen, Y; Hannah, H; Unger, F; Soliman, M; Galal, S; Lubroth, J; Grace, D

2016-12-01

Many developing countries lack sufficient resources to conduct animal disease surveillance. In recent years, participatory epidemiology has been used to increase the cover and decrease the costs of surveillance. However, few diagnostic performance assessments have been carried out on participatory methods. The objective of the present study was to estimate the diagnostic performance of practitioners working for the Community-Based Animal Health and Outreach (CAHO) program, which is a participatory disease surveillance system for the detection of highly pathogenic avian influenza outbreaks in Egypt. CAHO practitioners' diagnostic assessment of inspected birds was compared with real-time reverse-transcriptase polymerase chain reaction (RRT-PCR) test results at the household level. Diagnostic performance was estimated directly from two-by-two tables using RRT-PCR as a reference test in two different scenarios. In the first scenario, only results from chickens were considered. In the second scenario, results for all poultry species were analyzed. Poultry flocks in 916 households located in 717 villages were inspected by CAHO practitioners, who collected 3458 bird samples. In the first scenario, CAHO practitioners presented sensitivity (Se) and specificity (Sp) estimates of 40% (95% confidence interval [CI]: 21%-59%) and 92% (95% CI: 91%-94%), respectively. In the second scenario, diagnostic performance estimates were Se = 47% (95% CI: 29%-65%) and Sp = 88% (95% CI: 86%-90%). A significant difference was observed only between Sp estimates (P < 0.01). Practitioners' diagnostics and RRT-PCR results were in very poor agreement with kappa values of 0.16 and 0.14 for scenarios 1 and 2, respectively. However, the use of a broad case definition, the possible presence of immunity against the virus in replacement birds, and the low prevalence observed during the survey would negatively affect the practitioners' performance.

Surveillance of avian influenza virus type A in semi-scavenging ducks in Bangladesh

PubMed Central

2013-01-01

Background Ducks are the natural reservoir of influenza A virus and the central host for highly pathogenic avian influenza (H5N1), while domestic ducks rearing in semi-scavenging system could serve as re-assortment vessels for re-emerging new subtypes of influenza viruses between birds to human. Avian influenza virus (AIV) surveillance in Bangladesh has been passive, relying on poultry farmers to report suspected outbreaks of highly pathogenic H5N1 influenza. Here, the results of an active surveillance effort focusing on the semi-scavenging ducks are presented. Result A total of 2100 cloacal swabs and 2100 sera were collected from semi-scavenging ducks from three wintering-sites of Bangladesh during three successive winter seasons, December through February in the years between 2009 and 2012. Virus isolation and identification were carried out from the cloacal swabs by virus propagation in embryonated hen eggs followed by amplification of viral RNA using Avian influenza virus (AIV) specific RT-PCR. The overall prevalence of avian influenza type A was 22.05% for swab samples and 39.76% ducks were sero-positive for avian influenza type A antibody. Extremely low sero-prevalence (0.09%) of AIV H5N1 was detected. Conclusions Based on our surveillance results, we conclude that semi-scavenging ducks in Bangladesh might play important role in transmitting Avian Influenza virus (AIV) type A. However, the current risk of infection for humans from domestic ducks in Bangladesh is negligible. We believe that this relatively large dataset over three winters in Bangladesh might create a strong foundation for future studies of AIV prevalence, evolution, and ecology in wintering sites around the globe. PMID:24099526

Capacity of the national influenza surveillance system in Afghanistan, a chronic conflict setting.

PubMed

Rasooly, M H; Sahak, M N; Saeed, K I; Krishnan, S K; Khan, W; Hassounah, S

2016-10-02

Influenza surveillance is needed to monitor potential public health threats from the emergence of novel influenza viruses. This study assessed the capacity and performance of the national influenza surveillance system in Afghanistan from 2007 to 2014. Data were collected by review of hospital registers and the National Influenza Centre (NIC) database, interviews with influenza focal points at 9 influenza sentinel surveillance sites and the Centre staff, and observation of the sites. Out of 6900 specimens collected, influenza virus was detected in 253 (3.6%), predominantly H1N1 (63%); most of these cases were detected during the 2009 pandemic. The NIC had the capacity for virus isolation and PCR identification and performed reasonably until 2011 when support of the Naval American Medical Research Unit 3 was withdrawn. The limitations identified in the system indicated the need for: more complete data, improved technical competence and trained human resources, updating of the infrastructure/facilities, and the presence of standard operating procedures throughout surveillance.

Global Avian Influenza Surveillance in Wild Birds: A Strategy to Capture Viral Diversity

PubMed Central

Machalaba, Catherine C.; Elwood, Sarah E.; Forcella, Simona; Smith, Kristine M.; Hamilton, Keith; Jebara, Karim B.; Swayne, David E.; Webby, Richard J.; Mumford, Elizabeth; Mazet, Jonna A.K.; Gaidet, Nicolas; Daszak, Peter

2015-01-01

Wild birds play a major role in the evolution, maintenance, and spread of avian influenza viruses. However, surveillance for these viruses in wild birds is sporadic, geographically biased, and often limited to the last outbreak virus. To identify opportunities to optimize wild bird surveillance for understanding viral diversity, we reviewed responses to a World Organisation for Animal Health–administered survey, government reports to this organization, articles on Web of Knowledge, and the Influenza Research Database. At least 119 countries conducted avian influenza virus surveillance in wild birds during 2008–2013, but coordination and standardization was lacking among surveillance efforts, and most focused on limited subsets of influenza viruses. Given high financial and public health burdens of recent avian influenza outbreaks, we call for sustained, cost-effective investments in locations with high avian influenza diversity in wild birds and efforts to promote standardized sampling, testing, and reporting methods, including full-genome sequencing and sharing of isolates with the scientific community. PMID:25811221

Improving surveillance for injuries associated with potential motor vehicle safety defects

PubMed Central

Whitfield, R; Whitfield, A

2004-01-01

Objective: To improve surveillance for deaths and injuries associated with potential motor vehicle safety defects. Design: Vehicles in fatal crashes can be studied for indications of potential defects using an "early warning" surveillance statistic previously suggested for screening reports of adverse drug reactions. This statistic is illustrated with time series data for fatal, tire related and fire related crashes. Geographic analyses are used to augment the tire related statistics. Results: A statistical criterion based on the Poisson distribution that tests the likelihood of an expected number of events, given the number of events that actually occurred, is a promising method that can be readily adapted for use in injury surveillance. Conclusions: Use of the demonstrated techniques could have helped to avert a well known injury surveillance failure. This method is adaptable to aid in the direction of engineering and statistical reviews to prevent deaths and injuries associated with potential motor vehicle safety defects using available databases. PMID:15066972

Research Methods in Healthcare Epidemiology and Antimicrobial Stewardship: Use of Administrative and Surveillance Databases.

PubMed

Drees, Marci; Gerber, Jeffrey S; Morgan, Daniel J; Lee, Grace M

2016-11-01

Administrative and surveillance data are used frequently in healthcare epidemiology and antimicrobial stewardship (HE&AS) research because of their wide availability and efficiency. However, data quality issues exist, requiring careful consideration and potential validation of data. This methods paper presents key considerations for using administrative and surveillance data in HE&AS, including types of data available and potential use, data limitations, and the importance of validation. After discussing these issues, we review examples of HE&AS research using administrative data with a focus on scenarios when their use may be advantageous. A checklist is provided to help aid study development in HE&AS using administrative data. Infect Control Hosp Epidemiol 2016;1-10.

Strategies for Improving Polio Surveillance Performance in the Security-Challenged Nigerian States of Adamawa, Borno, and Yobe During 2009-2014.

PubMed

Hamisu, Abdullahi Walla; Johnson, Ticha Muluh; Craig, Kehinde; Mkanda, Pascal; Banda, Richard; Tegegne, Sisay G; Oyetunji, Ajiboye; Ningi, Nuhu; Mohammed, Said M; Adamu, Mohammed Isa; Abdulrahim, Khalid; Nsubuga, Peter; Vaz, Rui G; Muhammed, Ado J G

2016-05-01

The security-challenged states of Adamawa, Borno, and Yobe bear most of the brunt of the Boko Haram insurgency in Nigeria. The security challenge has led to the killing of health workers, destruction of health facilities, and displacement of huge populations. To identify areas of polio transmission and promptly detect possible cases of importation in these states, polio surveillance must be very sensitive. We conducted a retrospective review of acute flaccid paralysis surveillance in the security-compromised states between 2009 and 2014, using the acute flaccid paralysis database at the World Health Organization Nigeria Country Office. We also reviewed the reports of surveillance activities conducted in these security-challenged states, to identify strategies that were implemented to improve polio surveillance. Environmental surveillance was implemented in Borno in 2013 and in Yobe in 2014. All disease surveillance and notification officers in the 3 security-challenged states now receive annual training, and the number of community informants in these states has dramatically increased. Media-based messaging (via radio and television) is now used to sensitize the public to the importance of surveillance, and contact samples have been regularly collected in both states since 2014. The strategies implemented in the security-challenged states improved the quality of polio surveillance during the review period. © 2016 World Health Organization; licensee Oxford Journals.

Strategies for Improving Polio Surveillance Performance in the Security-Challenged Nigerian States of Adamawa, Borno, and Yobe During 2009–2014

PubMed Central

Hamisu, Abdullahi Walla; Johnson, Ticha Muluh; Craig, Kehinde; Mkanda, Pascal; Banda, Richard; Tegegne, Sisay G.; Oyetunji, Ajiboye; Ningi, Nuhu; Mohammed, Said M.; Adamu, Mohammed Isa; Abdulrahim, Khalid; Nsubuga, Peter; Vaz, Rui G.; Muhammed, Ado J. G.

2016-01-01

Background. The security-challenged states of Adamawa, Borno, and Yobe bear most of the brunt of the Boko Haram insurgency in Nigeria. The security challenge has led to the killing of health workers, destruction of health facilities, and displacement of huge populations. To identify areas of polio transmission and promptly detect possible cases of importation in these states, polio surveillance must be very sensitive. Methods. We conducted a retrospective review of acute flaccid paralysis surveillance in the security-compromised states between 2009 and 2014, using the acute flaccid paralysis database at the World Health Organization Nigeria Country Office. We also reviewed the reports of surveillance activities conducted in these security-challenged states, to identify strategies that were implemented to improve polio surveillance. Results. Environmental surveillance was implemented in Borno in 2013 and in Yobe in 2014. All disease surveillance and notification officers in the 3 security-challenged states now receive annual training, and the number of community informants in these states has dramatically increased. Media-based messaging (via radio and television) is now used to sensitize the public to the importance of surveillance, and contact samples have been regularly collected in both states since 2014. Conclusions. The strategies implemented in the security-challenged states improved the quality of polio surveillance during the review period. PMID:26655842

Global Measles and Rubella Laboratory Network Support for Elimination Goals, 2010-2015.

PubMed

Mulders, Mick N; Rota, Paul A; Icenogle, Joseph P; Brown, Kevin E; Takeda, Makoto; Rey, Gloria J; Ben Mamou, Myriam C; Dosseh, Annick R G A; Byabamazima, Charles R; Ahmed, Hinda J; Pattamadilok, Sirima; Zhang, Yan; Gacic-Dobo, Marta; Strebel, Peter M; Goodson, James L

2016-05-06

In 2012, the World Health Assembly endorsed the Global Vaccine Action Plan (GVAP)* with the objective to eliminate measles and rubella in five World Health Organization (WHO) regions by 2020. In September 2013, countries in all six WHO regions had established measles elimination goals, and additional goals for elimination of rubella and congenital rubella syndrome were established in three regions (1). Capacity for surveillance, including laboratory confirmation, is fundamental to monitoring and verifying elimination. The 2012-2020 Global Measles and Rubella Strategic Plan of the Measles and Rubella Initiative(†) calls for effective case-based surveillance with laboratory testing for case confirmation (2). In 2000, the WHO Global Measles and Rubella Laboratory Network (GMRLN) was established to provide high quality laboratory support for surveillance (3). The GMRLN is the largest globally coordinated laboratory network, with 703 laboratories supporting surveillance in 191 countries. During 2010-2015, 742,187 serum specimens were tested, and 27,832 viral sequences were reported globally. Expansion of the capacity of the GMRLN will support measles and rubella elimination efforts as well as surveillance for other vaccine-preventable diseases (VPDs), including rotavirus, and for emerging pathogens of public health concern.

The role of surveillance cultures in guiding ventilator-associated pneumonia therapy.

PubMed

Luna, Carlos M; Bledel, Ignacio; Raimondi, Alejandro

2014-04-01

Ventilator-associated pneumonia (VAP) is the most frequent cause of death among the nosocomial infections acquired in the ICU. Routine surveillance endotracheal aspirate (ETA) cultures in patients on mechanical ventilation have been proposed to predict the cause of VAP. Our aim is to review the available experience regarding the role of surveillance ETA cultures in guiding VAP antimicrobial therapy. Microorganisms arrive in the lower respiratory tract by aspiration from the oropharynx or gastric reflux, extension from a contiguous infection, air contamination or by hematogenous seeding. Bacterial colonization of the airway leads to the development of VAP and may result from the aspiration of oropharyngeal or gastric secretions. Recent studies have suggested that surveillance cultures could provide a rationale for prescribing appropriate antibiotics, while waiting for culture results, in up to 95% of patients in whom VAP is ultimately diagnosed by bronchoalveolar lavage fluid culture. However, some authors observed that guiding therapy with those routine surveillance cultures leads to unacceptably low coverage of the pathogens producing VAP. This article describes the evidence supporting the use of routine ETA cultures to prescribe appropriate initial empirical therapy compared with the current practice dictated by guidelines.

Radiation Embrittlement Archive Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klasky, Hilda B; Bass, Bennett Richard; Williams, Paul T

2013-01-01

The Radiation Embrittlement Archive Project (REAP), which is being conducted by the Probabilistic Integrity Safety Assessment (PISA) Program at Oak Ridge National Laboratory under funding from the U.S. Nuclear Regulatory Commission s (NRC) Office of Nuclear Regulatory Research, aims to provide an archival source of information about the effect of neutron radiation on the properties of reactor pressure vessel (RPV) steels. Specifically, this project is an effort to create an Internet-accessible RPV steel embrittlement database. The project s website, https://reap.ornl.gov, provides information in two forms: (1) a document archive with surveillance capsule(s) reports and related technical reports, in PDF format,more » for the 104 commercial nuclear power plants (NPPs) in the United States, with similar reports from other countries; and (2) a relational database archive with detailed information extracted from the reports. The REAP project focuses on data collected from surveillance capsule programs for light-water moderated, nuclear power reactor vessels operated in the United States, including data on Charpy V-notch energy testing results, tensile properties, composition, exposure temperatures, neutron flux (rate of irradiation damage), and fluence, (Fast Neutron Fluence a cumulative measure of irradiation for E>1 MeV). Additionally, REAP contains data from surveillance programs conducted in other countries. REAP is presently being extended to focus on embrittlement data analysis, as well. This paper summarizes the current status of the REAP database and highlights opportunities to access the data and to participate in the project.« less

Childhood asthma surveillance using administrative data: consistency between medical billing and hospital discharge diagnoses.

PubMed

Labrèche, France; Kosatsky, Tom; Przybysz, Raymond

2008-01-01

The absence of ongoing surveillance for childhood asthma in Montreal, Quebec, prompted the present investigation to assess the validity and practicality of administrative databases as a foundation for surveillance. To explore the consistency between cases of asthma identified through physician billings compared with hospital discharge summaries. Rates of service use for asthma in 1998 among Montreal children aged one, four and eight years were estimated. Correspondence between the two databases (physician billing claims versus medical billing claims) were explored during three different time periods: the first day of hospitalization, during the entire hospital stay, and during the hospital stay plus a one-day margin before admission and after discharge ('hospital stay +/- 1 day'). During 1998, 7.6% of Montreal children consulted a physician for asthma at least once and 0.6% were hospitalized with a principal diagnosis of asthma. There were no contemporaneous physician billings for asthma 'in hospital' during hospital stay +/- 1 day for 22% of hospitalizations in which asthma was the primary diagnosis recorded at discharge. Conversely, among children with a physician billing for asthma 'in hospital', 66% were found to have a contemporaneous in-hospital record of a stay for 'asthma'. Both databases of hospital and medical billing claims are useful for estimating rates of hospitalization for asthma in children. The potential for diagnostic imprecision is of concern, especially if capturing the exact number of uses is more important than establishing patterns of use.

Immune subversion by chromatin manipulation: a 'new face' of host-bacterial pathogen interaction.

PubMed

Arbibe, Laurence

2008-08-01

Bacterial pathogens have evolved various strategies to avoid immune surveillance, depending of their in vivo'lifestyle'. The identification of few bacterial effectors capable to enter the nucleus and modifying chromatin structure in host raises the fascinating questions of how pathogens modulate chromatin structure and why. Chromatin is a dynamic structure that maintains the stability and accessibility of the host DNA genome to the transcription machinery. This review describes the various strategies used by pathogens to interface with host chromatin. In some cases, chromatin injury can be a strategy to take control of major cellular functions, such as the cell cycle. In other cases, manipulation of chromatin structure at specific genomic locations by modulating epigenetic information provides a way for the pathogen to impose its own transcriptional signature onto host cells. This emerging field should strongly influence our understanding of chromatin regulation at interphase nucleus and may provide invaluable openings to the control of immune gene expression in inflammatory and infectious diseases.

Effects of landscape anthropization on mosquito community composition and abundance

NASA Astrophysics Data System (ADS)

Ferraguti, Martina; Martínez-de La Puente, Josué; Roiz, David; Ruiz, Santiago; Soriguer, Ramón; Figuerola, Jordi

2016-07-01

Anthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control.

Effects of landscape anthropization on mosquito community composition and abundance

PubMed Central

Ferraguti, Martina; Martínez-de la Puente, Josué; Roiz, David; Ruiz, Santiago; Soriguer, Ramón; Figuerola, Jordi

2016-01-01

Anthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control. PMID:27373794

Spatial variation in risk and consequence of Batrachochytrium salamandrivorans introduction in the USA

USGS Publications Warehouse

Richgels, Katherine L. D.; Russell, Robin E.; Adams, Michael J.; White, C. LeAnn; Campbell Grant, Evan H.

2016-01-01

A newly identified fungal pathogen, Batrachochytrium salamandrivorans (Bsal), is responsible for mass mortality events and severe population declines in European salamanders. The eastern USA has the highest diversity of salamanders in the world and the introduction of this pathogen is likely to be devastating. Although data are inevitably limited for new pathogens, disease-risk assessments use best available data to inform management decisions. Using characteristics of Bsal ecology, spatial data on imports and pet trade establishments, and salamander species diversity, we identify high-risk areas with both a high likelihood of introduction and severe consequences for local salamanders. We predict that the Pacific coast, southern Appalachian Mountains and mid-Atlantic regions will have the highest relative risk from Bsal. Management of invasive pathogens becomes difficult once they are established in wildlife populations; therefore, import restrictions to limit pathogen introduction and early detection through surveillance of high-risk areas are priorities for preventing the next crisis for North American salamanders.

The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts.

PubMed

Monteiro, Pedro Tiago; Pais, Pedro; Costa, Catarina; Manna, Sauvagya; Sá-Correia, Isabel; Teixeira, Miguel Cacho

2017-01-04

We present the PATHOgenic YEAst Search for Transcriptional Regulators And Consensus Tracking (PathoYeastract - http://pathoyeastract.org) database, a tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in the pathogenic yeasts Candida albicans and C. glabrata Upon data retrieval from hundreds of publications, followed by curation, the database currently includes 28 000 unique documented regulatory associations between transcription factors (TF) and target genes and 107 DNA binding sites, considering 134 TFs in both species. Following the structure used for the YEASTRACT database, PathoYeastract makes available bioinformatics tools that enable the user to exploit the existing information to predict the TFs involved in the regulation of a gene or genome-wide transcriptional response, while ranking those TFs in order of their relative importance. Each search can be filtered based on the selection of specific environmental conditions, experimental evidence or positive/negative regulatory effect. Promoter analysis tools and interactive visualization tools for the representation of TF regulatory networks are also provided. The PathoYeastract database further provides simple tools for the prediction of gene and genomic regulation based on orthologous regulatory associations described for other yeast species, a comparative genomics setup for the study of cross-species evolution of regulatory networks. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The dimensions of nursing surveillance: a concept analysis.

PubMed

Kelly, Lesly; Vincent, Deborah

2011-03-01

This paper is a report of an analysis of the concept of nursing surveillance. Nursing surveillance, a primary function of acute care nurses, is critical to patient safety and outcomes. Although it has been associated with patient outcomes and organizational context of care, little knowledge has been generated about the conceptual and operational process of surveillance. A search using the CINAHL, Medline and PubMed databases was used to compile an international data set of 18 papers and 4 book chapters published from 1985 to 2009. Rodger's evolutionary concept analysis techniques were used to analyse surveillance in a systems framework. This method focused the search to nursing surveillance (as opposed to other medical uses of the term) and used a theoretical framework to guide the analysis. The examination of the literature clarifies the multifaceted nature of nursing surveillance in the acute care setting. Surveillance involves purposeful and ongoing acquisition, interpretation and synthesis of patient data for clinical decision-making. Behavioural activities and multiple cognitive processes are used in surveillance in order for the nurse to make decisions for patient safety and health maintenance. A systems approach to the analysis also demonstrates how organizational characteristics and contextual factors influence the process in the acute care environment. This conceptual analysis describes the nature of the surveillance process and clarifies the concept for effective communication and future use in health services research. © 2010 The Authors. Journal of Advanced Nursing © 2010 Blackwell Publishing Ltd.

Systematic review of electronic surveillance of infectious diseases with emphasis on antimicrobial resistance surveillance in resource-limited settings.

PubMed

Rattanaumpawan, Pinyo; Boonyasiri, Adhiratha; Vong, Sirenda; Thamlikitkul, Visanu

2018-02-01

Electronic surveillance of infectious diseases involves rapidly collecting, collating, and analyzing vast amounts of data from interrelated multiple databases. Although many developed countries have invested in electronic surveillance for infectious diseases, the system still presents a challenge for resource-limited health care settings. We conducted a systematic review by performing a comprehensive literature search on MEDLINE (January 2000-December 2015) to identify studies relevant to electronic surveillance of infectious diseases. Study characteristics and results were extracted and systematically reviewed by 3 infectious disease physicians. A total of 110 studies were included. Most surveillance systems were developed and implemented in high-income countries; less than one-quarter were conducted in low-or middle-income countries. Information technologies can be used to facilitate the process of obtaining laboratory, clinical, and pharmacologic data for the surveillance of infectious diseases, including antimicrobial resistance (AMR) infections. These novel systems require greater resources; however, we found that using electronic surveillance systems could result in shorter times to detect targeted infectious diseases and improvement of data collection. This study highlights a lack of resources in areas where an effective, rapid surveillance system is most needed. The availability of information technology for the electronic surveillance of infectious diseases, including AMR infections, will facilitate the prevention and containment of such emerging infectious diseases. Copyright © 2018 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

The dimensions of nursing surveillance: a concept analysis

PubMed Central

Kelly, Lesly; Vincent, Deborah

2011-01-01

Aim This paper is a report of an analysis of the concept of nursing surveillance. Background Nursing surveillance, a primary function of acute care nurses, is critical to patient safety and outcomes. Although it has been associated with patient outcomes and organizational context of care, little knowledge has been generated about the conceptual and operational process of surveillance. Data sources A search using the CINAHL, Medline and PubMed databases was used to compile an international data set of 18 papers and 4 book chapters published from 1985 to 2009. Review methods Rodger’s evolutionary concept analysis techniques were used to analyse surveillance in a systems framework. This method focused the search to nursing surveillance (as opposed to other medical uses of the term) and used a theoretical framework to guide the analysis. Results The examination of the literature clarifies the multifaceted nature of nursing surveillance in the acute care setting. Surveillance involves purposeful and ongoing acquisition, interpretation and synthesis of patient data for clinical decision- making. Behavioural activities and multiple cognitive processes are used in surveillance in order for the nurse to make decisions for patient safety and health maintenance. A systems approach to the analysis also demonstrates how organizational characteristics and contextual factors influence the process in the acute care environment. Conclusion This conceptual analysis describes the nature of the surveillance process and clarifies the concept for effective communication and future use in health services research. PMID:21129007

The Pathogen-Host Interactions database (PHI-base): additions and future developments.

PubMed

Urban, Martin; Pant, Rashmi; Raghunath, Arathi; Irvine, Alistair G; Pedro, Helder; Hammond-Kosack, Kim E

2015-01-01

Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens. Mutant phenotypes are associated with gene information. The included pathogens infect a wide range of hosts including humans, animals, plants, insects, fish and other fungi. The current version, PHI-base 3.6, available at http://www.phi-base.org, stores information on 2875 genes, 4102 interactions, 110 host species, 160 pathogenic species (103 plant, 3 fungal and 54 animal infecting species) and 181 diseases drawn from 1243 references. Phenotypic and gene function information has been obtained by manual curation of the peer-reviewed literature. A controlled vocabulary consisting of nine high-level phenotype terms permits comparisons and data analysis across the taxonomic space. PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes. Virulence genes and hotspots can be visualized directly in genome browsers. Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s). © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Geographical distribution of Culicoides (DIPTERA: CERATOPOGONIDAE) in mainland Portugal: Presence/absence modelling of vector and potential vector species.

PubMed

Ramilo, David W; Nunes, Telmo; Madeira, Sara; Boinas, Fernando; da Fonseca, Isabel Pereira

2017-01-01

Vector-borne diseases are not only accounted responsible for their burden on human health-care systems, but also known to cause economic constraints to livestock and animal production. Animals are affected directly by the transmitted pathogens and indirectly when animal movement is restricted. Distribution of such diseases depends on climatic and social factors, namely, environmental changes, globalization, trade and unplanned urbanization. Culicoides biting midges are responsible for the transmission of several pathogenic agents with relevant economic impact. Due to a fragmentary knowledge of their ecology, occurrence is difficult to predict consequently, limiting the control of these arthropod vectors. In order to understand the distribution of Culicoides species, in mainland Portugal, data collected during the National Entomologic Surveillance Program for Bluetongue disease (2005-2013), were used for statistical evaluation. Logistic regression analysis was preformed and prediction maps (per season) were obtained for vector and potentially vector species. The variables used at the present study were selected from WorldClim (two climatic variables) and CORINE databases (twenty-two land cover variables). This work points to an opposite distribution of C. imicola and species from the Obsoletus group within mainland Portugal. Such findings are evidenced in autumn, with the former appearing in Central and Southern regions. Although appearing northwards, on summer and autumn, C. newsteadi reveals a similar distribution to C. imicola. The species C. punctatus appears in all Portuguese territory throughout the year. Contrary, C. pulicaris is poorly caught in all areas of mainland Portugal, being paradoxical present near coastal areas and higher altitude regions.

Geographical distribution of Culicoides (DIPTERA: CERATOPOGONIDAE) in mainland Portugal: Presence/absence modelling of vector and potential vector species

PubMed Central

Madeira, Sara; Boinas, Fernando; da Fonseca, Isabel Pereira

2017-01-01

Vector-borne diseases are not only accounted responsible for their burden on human health-care systems, but also known to cause economic constraints to livestock and animal production. Animals are affected directly by the transmitted pathogens and indirectly when animal movement is restricted. Distribution of such diseases depends on climatic and social factors, namely, environmental changes, globalization, trade and unplanned urbanization. Culicoides biting midges are responsible for the transmission of several pathogenic agents with relevant economic impact. Due to a fragmentary knowledge of their ecology, occurrence is difficult to predict consequently, limiting the control of these arthropod vectors. In order to understand the distribution of Culicoides species, in mainland Portugal, data collected during the National Entomologic Surveillance Program for Bluetongue disease (2005–2013), were used for statistical evaluation. Logistic regression analysis was preformed and prediction maps (per season) were obtained for vector and potentially vector species. The variables used at the present study were selected from WorldClim (two climatic variables) and CORINE databases (twenty-two land cover variables). This work points to an opposite distribution of C. imicola and species from the Obsoletus group within mainland Portugal. Such findings are evidenced in autumn, with the former appearing in Central and Southern regions. Although appearing northwards, on summer and autumn, C. newsteadi reveals a similar distribution to C. imicola. The species C. punctatus appears in all Portuguese territory throughout the year. Contrary, C. pulicaris is poorly caught in all areas of mainland Portugal, being paradoxical present near coastal areas and higher altitude regions. PMID:28683145

National Communicable Disease Surveillance System: A review on Information and Organizational Structures in Developed Countries.

PubMed

Bagherian, Hossein; Farahbakhsh, Mohammad; Rabiei, Reza; Moghaddasi, Hamid; Asadi, Farkhondeh

2017-12-01

To obtain necessary information for managing communicable diseases, different countries have developed national communicable diseases surveillance systems (NCDSS). Exploiting the lesson learned from the leading countries in development of surveillance systems provides the foundation for developing these systems in other countries. In this study, the information and organizational structure of NCDSS in developed countries were reviewed. The study reviewed publications found on the organizational structure, content and data flow of NCDSS in the United States of America (USA), Australia and Germany that were published in English between 2000 and 2016. The publications were identified by searching the CINAHL, Science Direct, ProQuest, PubMed, Google Scholar databases and the related databases in selected countries. Thirty-four studies were investigated. All of the reviewed countries have implemented the NCDSS. In majority of countries the department of health (DoH) is responsible for managing this system. The reviewed countries have created a minimum data set for reporting communicable diseases data and information. For developing NCDSS, establishing coordinator centers, setting the effective policies and procedures, providing appropriate communication infrastructures for data exchange and defining a communicable diseases minimum data set are essential.

Connecting the study of wild influenza with the potential for pandemic disease

PubMed Central

Runstadler, Jonathan; Hill, Nichola; Hussein, Islam T.M.; Puryear, Wendy; Keogh, Mandy

2013-01-01

Continuing outbreaks of pathogenic (H5N1) and pandemic (SOIVH1N1) influenza have underscored the need to understand the origin, characteristics, and evolution of novel influenza A virus (IAV) variants that pose a threat to human health. In the last 4–5 years, focus has been placed on the organization of large-scale surveillance programs to examine the phylogenetics of avian influenza virus (AIV) and host-virus relationships in domestic and wild animals. Here we review the current gaps in wild animal and environmental surveillance and the current understanding of genetic signatures in potentially pandemic strains. PMID:23541413

Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens

PubMed Central

Sosa, Ezequiel J; Burguener, Germán; Lanzarotti, Esteban; Radusky, Leandro; Pardo, Agustín M; Marti, Marcelo

2018-01-01

Abstract Available genomic data for pathogens has created new opportunities for drug discovery and development to fight them, including new resistant and multiresistant strains. In particular structural data must be integrated with both, gene information and experimental results. In this sense, there is a lack of an online resource that allows genome wide-based data consolidation from diverse sources together with thorough bioinformatic analysis that allows easy filtering and scoring for fast target selection for drug discovery. Here, we present Target-Pathogen database (http://target.sbg.qb.fcen.uba.ar/patho), designed and developed as an online resource that allows the integration and weighting of protein information such as: function, metabolic role, off-targeting, structural properties including druggability, essentiality and omic experiments, to facilitate the identification and prioritization of candidate drug targets in pathogens. We include in the database 10 genomes of some of the most relevant microorganisms for human health (Mycobacterium tuberculosis, Mycobacterium leprae, Klebsiella pneumoniae, Plasmodium vivax, Toxoplasma gondii, Leishmania major, Wolbachia bancrofti, Trypanosoma brucei, Shigella dysenteriae and Schistosoma Smanosoni) and show its applicability. New genomes can be uploaded upon request. PMID:29106651

Seasonal dynamics of bacterial meningitis: a time-series analysis.

PubMed

Paireau, Juliette; Chen, Angelica; Broutin, Helene; Grenfell, Bryan; Basta, Nicole E

2016-06-01

Bacterial meningitis, which is caused mainly by Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae, inflicts a substantial burden of disease worldwide. Yet, the temporal dynamics of this disease are poorly characterised and many questions remain about the ecology of the disease. We aimed to comprehensively assess seasonal trends in bacterial meningitis on a global scale. We developed the first bacterial meningitis global database by compiling monthly incidence data as reported by country-level surveillance systems. Using country-level wavelet analysis, we identified whether a 12 month periodic component (annual seasonality) was detected in time-series that had at least 5 years of data with at least 40 cases reported per year. We estimated the mean timing of disease activity by computing the centre of gravity of the distribution of cases and investigated whether synchrony exists between the three pathogens responsible for most cases of bacterial meningitis. We used country-level data from 66 countries, including from 47 countries outside the meningitis belt in sub-Saharan Africa. A persistent seasonality was detected in 49 (96%) of the 51 time-series from 38 countries eligible for inclusion in the wavelet analyses. The mean timing of disease activity had a latitudinal trend, with bacterial meningitis seasons peaking during the winter months in countries in both the northern and southern hemispheres. The three pathogens shared similar seasonality, but time-shifts differed slightly by country. Our findings provide key insight into the seasonal dynamics of bacterial meningitis and add to knowledge about the global epidemiology of meningitis and the host, environment, and pathogen characteristics driving these patterns. Comprehensive understanding of global seasonal trends in meningitis could be used to design more effective prevention and control strategies. Princeton University Health Grand Challenge, US National Institutes of Health (NIH), NIH Fogarty International Center Research and Policy for Infectious Disease Dynamics programme (RAPIDD), Bill & Melinda Gates Foundation. Copyright © 2016 Paireau et al. Open Access article distributed under the terms of CC BY NC-ND. Published by Elsevier Ltd.. All rights reserved.

Seasonal dynamics of bacterial meningitis: a time-series analysis

PubMed Central

Paireau, Juliette; Chen, Angelica; Broutin, Helene; Grenfell, Bryan; Basta, Nicole E

2017-01-01

Summary Background Bacterial meningitis, which is caused mainly by Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae, inflicts a substantial burden of disease worldwide. Yet, the temporal dynamics of this disease are poorly characterised and many questions remain about the ecology of the disease. We aimed to comprehensively assess seasonal trends in bacterial meningitis on a global scale. Methods We developed the first bacterial meningitis global database by compiling monthly incidence data as reported by country-level surveillance systems. Using country-level wavelet analysis, we identified whether a 12 month periodic component (annual seasonality) was detected in time-series that had at least 5 years of data with at least 40 cases reported per year. We estimated the mean timing of disease activity by computing the centre of gravity of the distribution of cases and investigated whether synchrony exists between the three pathogens responsible for most cases of bacterial meningitis. Findings We used country-level data from 66 countries, including from 47 countries outside the meningitis belt in sub-Saharan Africa. A persistent seasonality was detected in 49 (96%) of the 51 time-series from 38 countries eligible for inclusion in the wavelet analyses. The mean timing of disease activity had a latitudinal trend, with bacterial meningitis seasons peaking during the winter months in countries in both the northern and southern hemispheres. The three pathogens shared similar seasonality, but time-shifts differed slightly by country. Interpretation Our findings provide key insight into the seasonal dynamics of bacterial meningitis and add to knowledge about the global epidemiology of meningitis and the host, environment, and pathogen characteristics driving these patterns. Comprehensive understanding of global seasonal trends in meningitis could be used to design more effective prevention and control strategies. Funding Princeton University Health Grand Challenge, US National Institutes of Health (NIH), NIH Fogarty International Center Research and Policy for Infectious Disease Dynamics programme (RAPIDD), Bill & Melinda Gates Foundation. PMID:27198841

Cancer of the nasal cavity in the pediatric population.

PubMed

Benoit, Margo McKenna; Bhattacharyya, Neil; Faquin, William; Cunningham, Michael

2008-01-01

The purpose of this work was to investigate the clinical manifestations and diagnostic range of malignant entities presenting as a nasal mass in the pediatric population. A retrospective cohort analysis was conducted at a specialty hospital and a tertiary care university hospital. Patients aged between birth and 18 years and diagnosed with a malignancy that arose within the nasal cavity between the years 1991 and 2006 were included. This institution-specific patient group was compared with a similar cohort of patients extracted from the national Surveillance Epidemiology and End Results database. The main outcome measures were the incidence, presentation, and diagnoses of nasal cancer presenting in this population. Sixteen patients with nasal malignancies presented institutionally in the defined pediatric age group. Patient age at the time of diagnosis ranged from 7 months to 17 years, with a slight male predominance. The main presenting symptoms were unilateral nasal congestion and ophthalmologic complaints. The median time from presentation to diagnosis was 7 weeks; patients who presented with nonspecific complaints, such as nasal obstruction, headache, and fatigue, were given a diagnosis, on average, later than those who presented with focal manifestations. Nationwide, 47 patients were identified from the Surveillance Epidemiology and End Results database. In both subject groups, the most common diagnoses were rhabdomyosarcoma (37.5% institutionally and 23% in the Surveillance Epidemiology and End Results group) and esthesioneuroblastoma (25% institutionally and 28% Surveillance Epidemiology and End Results). In the Surveillance Epidemiology and End Results cohort, the overall mean survival rate was 188 months. Nasal cancer in the pediatric population often presents with nonspecific signs and symptoms, and a high index of suspicion is necessary for a timely diagnosis. Soft tissue sarcomas are expectedly common. The relative high frequency of esthesioneuroblastoma is particularly noteworthy.

The design and evaluation of an antimicrobial resistance surveillance system for neonatal intensive care units in Iran.

PubMed

Rezaei-Hachesu, Peyman; Samad-Soltani, Taha; Yaghoubi, Sajad; GhaziSaeedi, Marjan; Mirnia, Kayvan; Masoumi-Asl, Hossein; Safdari, Reza

2018-07-01

Neonatal intensive care units (NICUs) have complex patients in terms of their diagnoses and required treatments. Antimicrobial treatment is a common therapy for patients in NICUs. To solve problems pertaining to empirical therapy, antimicrobial stewardship programs have recently been introduced. Despite the success of these programs in terms of data collection, there is still inefficiency in terms of analyzing and reporting the data. Thus, to successfully implement these stewardship programs, the design of antimicrobial resistance (AMR) surveillance systems is recommended as a first step. As a result, this study aimed to design an AMR surveillance system for use in the NICUs in northwestern Iranian hospitals to cover these information gaps. The recommended system is compatible with the World Health Organization (WHO) guidelines. The business intelligence (BI) requirements were extracted in an interview with a product owner (PO) using a valid and reliable checklist. Following this, an AMR surveillance system was designed and evaluated in relation to user experiences via a user experience questionnaire (UEQ). Finally, an association analysis was performed on the database, and the results were reported by identifying the important multidrug resistances in the database. A customized software development methodology was proposed. The three major modules of the AMR surveillance are the data registry, dashboard, and decision support modules. The data registry module was implemented based on a three-tier architecture, and the Clinical Decision Support System (CDSS) and dashboard modules were designed based on the BI requirements of the Scrum product owner (PO). The mean values of UEQ measures were in a good range. This measures showed the suitable usability of the AMR surveillance system. Applying efficient software development methodologies allows for the systems' compatibility with users' opinions and requirements. In addition, the construction of interdisciplinary communication models for research and software engineering allows for research and development concepts to be used in operational environments. Copyright © 2018 Elsevier B.V. All rights reserved.

Bayesian evidence and epidemiological implications of environmental contamination from acute respiratory infection in long-term care facilities.

PubMed

Diaz-Decaro, J D; Launer, B; Mckinnell, J A; Singh, R; Dutciuc, T D; Green, N M; Bolaris, M; Huang, S S; Miller, L G

2018-05-01

Skilled nursing home facilities (SNFs) house a vulnerable population frequently exposed to respiratory pathogens. Our study aims to gain a better understanding of the transmission of nursing home-acquired viral respiratory infections in non-epidemic settings. Symptomatic surveillance was performed in three SNFs for residents exhibiting acute respiratory symptoms. Environmental surveillance of five high-touch areas was performed to assess possible transmission. All resident and environmental samples were screened using a commercial multiplex polymerase chain reaction platform. Bayesian methods were used to evaluate environmental contamination. Among nursing home residents with respiratory symptoms, 19% had a detectable viral pathogen (parainfluenza-3, rhinovirus/enterovirus, RSV, or influenza B). Environmental contamination was found in 20% of total room surface swabs of symptomatic residents. Environmental and resident results were all concordant. Target period prevalence among symptomatic residents ranged from 5.5 to 13.3% depending on target. Bayesian analysis quantifies the probability of environmental shedding due to parainfluenza-3 as 92.4% (95% CI: 86.8-95.8%) and due to rhinovirus/enterovirus as 65.6% (95% CI: 57.9-72.5%). Our findings confirm that non-epidemic viral infections are common among SNF residents exhibiting acute respiratory symptoms and that environmental contamination may facilitate further spread with considerable epidemiological implications. Findings further emphasise the importance of environmental infection control for viral respiratory pathogens in long-term care facilities.

Greasy tactics in the plant-pathogen molecular arms race.

PubMed

Boyle, Patrick C; Martin, Gregory B

2015-03-01

The modification of proteins by the attachment of fatty acids is a targeting tactic involved in mechanisms of both plant immunity and bacterial pathogenesis. The plant plasma membrane (PM) is a key battleground in the war against disease-causing microbes. This membrane is armed with an array of sensor proteins that function as a surveillance system to detect invading pathogens. Several of these sensor proteins are directed to the plasma membrane through the covalent addition of fatty acids, a process termed fatty acylation. Phytopathogens secrete effector proteins into the plant cell to subvert these surveillance mechanisms, rendering the host susceptible to infection. The targeting of effectors to specific locales within plant cells, particularly the internal face of the host PM, is critical for their virulence function. Several bacterial effectors hijack the host fatty acylation machinery to be modified and directed to this contested locale. To find and fight these fatty acylated effectors the plant leverages lipid-modified intracellular sensors. This review provides examples featuring how fatty acylation is a battle tactic used by both combatants in the molecular arms race between plants and pathogens. Also highlighted is the exploitation of a specific form of host-mediated fatty acid modification, which appears to be exclusively employed by phytopathogenic effector proteins. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Genetic and biological characterization of three poultry-origin H5N6 avian influenza viruses with all internal genes from genotype S H9N2 viruses.

PubMed

Liu, Kaituo; Gu, Min; Hu, Shunlin; Gao, Ruyi; Li, Juan; Shi, Liwei; Sun, Wenqi; Liu, Dong; Gao, Zhao; Xu, Xiulong; Hu, Jiao; Wang, Xiaoquan; Liu, Xiaowen; Chen, Sujuan; Peng, Daxin; Jiao, Xinan; Liu, Xiufan

2018-04-01

During surveillance for avian influenza viruses, three H5N6 viruses were isolated in chickens obtained from live bird markets in eastern China, between January 2015 and April 2016. Sequence analysis revealed a high genomic homology between these poultry isolates and recent human H5N6 variants whose internal genes were derived from genotype S H9N2 avian influenza viruses. Glycan binding assays revealed that all avian H5N6 viruses were capable of binding to both human-type SAα-2,6Gal receptors and avian-type SAα-2,3Gal receptors. Their biological characteristics were further studied in BALB/c mice, specific-pathogen-free chickens, and mallard ducks. All three isolates had low pathogenicity in mice but were highly pathogenic to chickens, as evidenced by 100% mortality 36-120 hours post infection at a low dose of 10 3.0 EID 50 and through effective contact transmission. Moreover, all three poultry H5N6 isolates caused asymptomatic infections in ducks, which may serve as a reservoir host for their maintenance and dissemination; these migrating waterfowl could cause a potential global pandemic. Our study suggests that continuous epidemiological surveillance in poultry should be implemented for the early prevention of future influenza outbreaks.

Geographic Risk for Lyme Disease and Human Granulocytic Ehrlichiosis in Southern New York State†

PubMed Central

Daniels, Thomas J.; Boccia, Theresa M.; Varde, Shobha; Marcus, Jonathan; Le, Jianhua; Bucher, Doris J.; Falco, Richard C.; Schwartz, Ira

1998-01-01

Ixodes scapularis, the tick vector of Lyme disease and human granulocytic ehrlichiosis (HGE), is prevalent in much of southern New York state. The distribution of this species has increased, as have reported cases of both Lyme disease and HGE. The unreliability of case reports, however, demonstrates the need for tick and pathogen surveillance in order to accurately define areas of high risk. In this study, a total of 89,550 m2 at 34 study sites was drag sampled in 1995 and a total of 51,540 m2 at 40 sites was sampled in 1996 to determine tick and pathogen distribution in southern New York state. I. scapularis was collected from 90% of the sites sampled, and regionally, a 2.5-fold increase in nymphal abundance occurred from 1995 to 1996. I. scapularis individuals from all sites were infected with Borrelia burgdorferi in 1995, while an examination of ticks for both B. burgdorferi and the agent of HGE in 1996 confirmed that these organisms were present in all counties; the average coinfection rate was 1.9%. No correlation was found between estimated risk and reported cases of Lyme disease. The geographic disparity of risk observed among sites in this study underscores the need for vector and pathogen surveillance on a regional level. An entomologic risk index can help identify sites for targeted tick control efforts. PMID:9835546

National Surveillance of Spotted Fever Group Rickettsioses in the United States, 2008-2012.

PubMed

Drexler, Naomi A; Dahlgren, F Scott; Heitman, Kristen Nichols; Massung, Robert F; Paddock, Christopher D; Behravesh, Casey Barton

2016-01-01

Spotted fever group (SFG) rickettsioses are notifiable conditions in the United States caused by the highly pathogenic Rickettsia rickettsii and less pathogenic rickettsial species such as Rickettsia parkeri and Rickettsia sp. 364D. Surveillance data from 2008 to 2012 for SFG rickettsioses are summarized. Incidence increased from 1.7 cases per million person-years (PY) in 2000 to 14.3 cases per million PY in 2012. During 2008-2012, cases of SFG rickettsiosis were more frequently reported among males, persons of white race, and non-Hispanic ethnicity. Overall, case fatality rate (CFR) was low (0.4%), however, risk of death was significantly higher for American Indian/Alaska Natives (relative risk [RR] = 5.4) and Asian/Pacific Islanders (RR = 5.7) compared with persons of white race. Children aged < 10 years continue to experience the highest CFR (1.6%). Higher incidence of SFG rickettsioses and decreased CFR likely result from increased reporting of tick-borne disease including those caused by less pathogenic species. Recently, fewer cases have been confirmed using species-specific laboratory methods (such as cell culture and DNA detection using polymerase chain reaction [PCR] assays), causing a clouded epidemiological picture. Use of PCR and improved documentation of clinical signs, such as eschars, will better differentiate risk factors, incidence, and clinical outcomes of specific rickettsioses in the future. © The American Society of Tropical Medicine and Hygiene.

Integration of animal health, food pathogen and foodborne disease surveillance in the Americas.

PubMed

Hulebak, K; Rodricks, J; Smith DeWaal, C

2013-08-01

This paper describes the characteristics of surveillance and the attempts made in the Americas to institute truly integrated surveillance systems that bring together disease surveillance of medically treated clinical populations with disease surveillance for food-production animals. Characteristics of an ideal, integrated food safety system are described. Systematic surveillance programmes in the Americas vary widely in scope and reliability, and none is fully integrated. Estimates of foodborne disease rates, particularly in North America, are becoming increasingly accurate, and programmes such as those promoted by the Pan American Health Organization are gradually leading to improvements in estimates of the foodborne disease burden in Latin America. Linking foodborne diseases to their sources is necessary for reducing disease incidence, and the World Health Organization's Global Foodborne Infections Network is building global capacity in this area. Activities in these areas in the Americas are described in detail. There is now clear recognition that there are dynamic links between infectious diseases occurring in wildlife and livestock and those occurring in humans, and this has led to calls from organisations such as the US National Academy of Sciences and the American Veterinary Medical Association to integrate surveillance programmes for zoonotic and human diseases. Models for the development of such integrated programmes, at local, national and international levels, are described. To be effective, such models must incorporate programmes to capture information from numerous, discrete surveillance systems in a way that allows rapid analysis to identify zoonotic and human disease connections. No effective integration now exists, but there are signals that governments in the Americas are working together towards this goal.

Epidemiological surveillance methods for vector-borne diseases.

PubMed

Thompson, P N; Etter, E

2015-04-01

Compared with many other diseases, the ever-increasing threat of vector-borne diseases (VBDs) represents a great challenge to public and animal health managers. Complex life cycles, changing distribution ranges, a variety of potential vectors and hosts, and the possible role of reservoirs make surveillance for VBDs a grave concern in a changing environment with increasing economic constraints. Surveillance activities may have various specific objectives and may focus on clinical disease, pathogens, vectors, hosts and/or reservoirs, but ultimately such activities should improve our ability to predict, prevent and/or control the diseases concerned. This paper briefly reviews existing and newly developed tools for the surveillance of VBDs. A range of examples, by no means exhaustive, illustrates that VBD surveillance usually involves a combination of methods to achieve its aims, and is best accomplished when these techniques are adapted to the specific environment and constraints of the region. More so than any other diseases, VBDs respect no administrative boundaries; in addition, animal, human and commodity movements are increasing dramatically, with illegal or unknown movements difficult to quantify. Vector-borne disease surveillance therefore becomes a serious issue for local and national organisations and is being conducted more and more at the regional and international level through multidisciplinary networks. With economic and logistical constraints, tools for optimising and evaluating the performance of surveillance systems are essential and examples of recent developments in this area are included. The continuous development of mapping, analytical and modelling tools provides us with an enhanced ability to interpret, visualise and communicate surveillance results. This review also demonstrates the importance of the link between surveillance and research, with interactions and benefits in both directions.

Evaluation of meningitis surveillance before introduction of serogroup a meningococcal conjugate vaccine - Burkina Faso and Mali.

PubMed

2012-12-21

Each year, 450 million persons in a region of sub-Saharan Africa known as the "meningitis belt" are at risk for death and disability from epidemic meningitis caused by serogroup A Neisseria meningitidis. In 2009, the first serogroup A meningococcal conjugate vaccine (PsA-TT) developed solely for Africa (MenAfriVac, Serum Institute of India, Ltd.), was licensed for persons aged 1-29 years. During 2010-2011, the vaccine was introduced in the hyperendemic countries of Burkina Faso, Mali, and Niger through mass campaigns. Strong meningitis surveillance is critical for evaluating the impact of PsA-TT because it was licensed based on safety and immunogenicity data without field effectiveness trials. Case-based surveillance, which includes the collection of epidemiologic and laboratory data on individual cases year-round, is recommended for countries that aim to evaluate the vaccine's impact. A key component of case-based surveillance is expansion of laboratory confirmation to include every case of bacterial meningitis because multiple meningococcal serogroups and different pathogens such as Haemophilus influenzae type b and Streptococcus pneumoniae cause meningitis that is clinically indistinguishable from that caused by serogroup A Neisseria meningitidis. Before the introduction of PsA-TT, evaluations of the existing meningitis surveillance in Burkina Faso and Mali were conducted to assess the capacity for case-based surveillance. This report describes the results of those evaluations, which found that surveillance infrastructures were strong but opportunities existed for improving data management, handling of specimens shipped to reference laboratories, and laboratory capacity for confirming cases. These findings underscore the need to evaluate surveillance before vaccine introduction so that activities to strengthen surveillance are tailored to a country's needs and capacities.

Fostering International Collaboration in Birth Defects Research and Prevention: A Perspective From the International Clearinghouse for Birth Defects Surveillance and Research

PubMed Central

Botto, Lorenzo D.; Robert-Gnansia, Elisabeth; Siffel, Csaba; Harris, John; Borman, Barry; Mastroiacovo, Pierpaolo

2006-01-01

The International Clearing-house for Birth Defects Surveillance and Research, formerly known as International Clearinghouse of Birth Defects Monitoring Systems, consists of 40 registries worldwide that collaborate in monitoring 40 types of birth defects. Clearinghouse activities include the sharing and joint monitoring of birth defect data, epidemiologic and public health research, and capacity building, with the goal of reducing disease and promoting healthy birth outcomes through primary prevention. We discuss 3 of these activities: the collaborative assessment of the potential teratogenicity of first-trimester use of medications (the MADRE project), an example of the intersection of surveillance and research; the international databases of people with orofacial clefts, an example of the evolution from surveillance to outcome research; and the study of genetic polymorphisms, an example of collaboration in public health genetics. PMID:16571708

A simplified method of performance indicators development for epidemiological surveillance networks--application to the RESAPATH surveillance network.

PubMed

Sorbe, A; Chazel, M; Gay, E; Haenni, M; Madec, J-Y; Hendrikx, P

2011-06-01

Develop and calculate performance indicators allows to continuously follow the operation of an epidemiological surveillance network. This is an internal evaluation method, implemented by the coordinators in collaboration with all the actors of the network. Its purpose is to detect weak points in order to optimize management. A method for the development of performance indicators of epidemiological surveillance networks was developed in 2004 and was applied to several networks. Its implementation requires a thorough description of the network environment and all its activities to define priority indicators. Since this method is considered to be complex, our objective consisted in developing a simplified approach and applying it to an epidemiological surveillance network. We applied the initial method to a theoretical network model to obtain a list of generic indicators that can be adapted to any surveillance network. We obtained a list of 25 generic performance indicators, intended to be reformulated and described according to the specificities of each network. It was used to develop performance indicators for RESAPATH, an epidemiological surveillance network of antimicrobial resistance in pathogenic bacteria of animal origin in France. This application allowed us to validate the simplified method, its value in terms of practical implementation, and its level of user acceptance. Its ease of use and speed of application compared to the initial method argue in favor of its use on broader scale. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Tick Surveillance of Small Mammals Captured in Gyeonggi and Gangwon Provinces, Republic of Korea, 2004-2008

DTIC Science & Technology

2010-07-30

number of zoonotic pathogens: spotted fever group rickettsiae (Lee et al. 2003), Ehrlichia and Anaplasma spp. (Chae et al. 2003), Bartonella spp. (Kim...K.H. & Lee, S.H. (2003) Identification of the spotted fever group rickettsiae detected from Haemaphysalis longicornis in Korea. Microbiology and

Molecular characterization of Salmonella Paratyphi B dT+ and Salmonella Heidelberg from poultry and retail chicken meat in Colombia by pulsed-field gel electrophoresis

USDA-ARS?s Scientific Manuscript database

Salmonella Paratyphi B dT+ variant (also termed Salmonella Java) and Salmonella Heidelberg are human pathogens frequently isolated from poultry. As a step towards implementing the Colombian Integrated Program for Antimicrobial Resistant Surveillance (COIPARS), this study characterized molecular patt...

Hantavirus Pulmonary Syndrome Caused by Maripa Virus in French Guiana, 2008-2016.

PubMed

Matheus, Séverine; Kallel, Hatem; Mayence, Claire; Bremand, Laetitia; Houcke, Stéphanie; Rousset, Dominique; Lacoste, Vincent; de Thoisy, Benoit; Hommel, Didier; Lavergne, Anne

2017-10-01

We report 5 human cases of hantavirus pulmonary syndrome found during surveillance in French Guiana in 2008-2016; of the 5 patients, 4 died. This pathogen should continue to be monitored in humans and rodents in effort to reduce the occurrence of these lethal infections in humans stemming from ecosystem disturbances.

75 FR 26266 - Disease, Disability, and Injury Prevention and Control Special Emphasis Panel: Developing Novel...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-11

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Centers for Disease Control and Prevention Disease, Disability, and Injury Prevention and Control Special Emphasis Panel: Developing Novel Diagnostic Tests To Improve Surveillance for Antimicrobial Resistant Pathogens, Funding Opportunity Announcement CI10-002; Initial Review Correction: This notice was...

Infectious diseases of fishes in the Salish Sea

USGS Publications Warehouse

Hershberger, Paul; Rhodes, Linda; Kurath, Gael; Winton, James

2013-01-01

As in marine regions throughout other areas of the world, fishes in the Salish Sea serve as hosts for many pathogens, including nematodes, trematodes, protozoans, protists, bacteria, viruses, and crustaceans. Here, we review some of the better-documented infectious diseases that likely contribute to significant losses among free-ranging fishes in the Salish Sea and discuss the environmental and ecological factors that may affect the population-level impacts of disease. Demonstration of these diseases and their impacts to critical and endangered resources provides justification to expand pathogen surveillance efforts and to incorporate disease forecasting and mitigation tools into ecosystem restoration efforts.

Infectious hematopoietic necrosis virus virological and genetic surveillance 2000–2012

USGS Publications Warehouse

Breyta, Rachel; Brito, Ilana L.; Kurath, Gael; LaDeau, Shannon L.

2017-01-01

Surveillance records of the acute RNA pathogen of Pacific salmonid fish infectious hematopoietic necrosis virus are combined for the first time to enable landscape-level ecological analyses and modeling. The study area is the freshwater ecosystems of the large Columbia River watershed in the U.S. states of Washington, Oregon, and Idaho, as well as coastal rivers in Washington and Oregon. The study period is 2000–2012, and records were contributed by all five resource management agencies that operate conservation hatcheries in the study area. Additional records from wild fish were collected from the National Wild Fish Health Survey, operated by the U.S. Fish and Wildlife Survey. After curation and normalization, the data set consists of 6766 records, representing 1146 sample sites and 15 different fish hosts. The virus was found in an average of 12.4% of records, and of these 66.2% also have viral genetic analysis available. This data set is used to conduct univariate ecological and epidemiological analyses and develop a novel hierarchical landscape transmission model for an aquatic pathogen.

A BOX-SCAR fragment for the identification of Actinobacillus pleuropneumoniae.

PubMed

Rossi, Ciro C; Pereira, Monalessa F; Langford, Paul R; Bazzolli, Denise M S

2014-03-01

Bacterial respiratory diseases are responsible for considerable mortality, morbidity and economic losses in the swine industry. Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, is one of the most important disease agents, but its identification and surveillance can be impaired by the existence of many other related bacteria in normal swine microbiota. In this work, we have evaluated a BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) sequence characterised amplified region (SCAR) marker for the specific identification of A. pleuropneumoniae and its use in a multiplex PCR to detect additionally Haemophilus parasuis and Pasteurella multocida, two other major respiratory pathogens of pigs that are members of the family Pasteurellaceae. PCRs based on the BOX-SCAR fragment developed were rapid, sensitive and differentiated A. pleuropneumoniae from all swine-related members of the Pasteurellaceae family tested. Single and multiplex BOX-SCAR fragment-based PCRs can be used to identify A. pleuropneumoniae from other bacterial swine pathogens and will be useful in surveillance and epidemiological studies. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

A seventeen-year epidemiological surveillance study of Borrelia burgdorferi infections in two provinces of northern Spain.

PubMed

Lledó, Lourdes; Gegúndez, María Isabel; Giménez-Pardo, Consuelo; Álamo, Rufino; Fernández-Soto, Pedro; Nuncio, María Sofia; Saz, José Vicente

2014-01-30

This paper reports a 17-year seroepidemiological surveillance study of Borrelia burgdorferi infection, performed with the aim of improving our knowledge of the epidemiology of this pathogen. Serum samples (1,179) from patients (623, stratified with respect to age, sex, season, area of residence and occupation) bitten by ticks in two regions of northern Spain were IFA-tested for B. burgdorferi antibodies. Positive results were confirmed by western blotting. Antibodies specific for B. burgdorferi were found in 13.3% of the patients; 7.8% were IgM positive, 9.6% were IgG positive, and 4.33% were both IgM and IgG positive. Five species of ticks were identified in the seropositive patients: Dermacentor marginatus (41.17% of such patients) Dermacentor reticulatus (11.76%), Rhiphicephalus sanguineus (17.64%), Rhiphicephalus turanicus (5.88%) and Ixodes ricinus (23.52%). B. burgdorferi DNA was sought by PCR in ticks when available. One tick, a D. reticulatus male, was found carrying the pathogen. The seroprevalence found was similar to the previously demonstrated in similar studies in Spain and other European countries.

Early detection of emerging zoonotic diseases with animal morbidity and mortality monitoring.

PubMed

Bisson, Isabelle-Anne; Ssebide, Benard J; Marra, Peter P

2015-03-01

Diseases transmitted between animals and people have made up more than 50% of emerging infectious diseases in humans over the last 60 years and have continued to arise in recent months. Yet, public health and animal disease surveillance programs continue to operate independently. Here, we assessed whether recent emerging zoonotic pathogens (n = 143) are known to cause morbidity or mortality in their animal host and if so, whether they were first detected with an animal morbidity/mortality event. We show that although sick or dead animals are often associated with these pathogens (52%), only 9% were first detected from an animal morbidity or mortality event prior to or concurrent with signs of illness in humans. We propose that an animal morbidity and mortality reporting program will improve detection and should be an essential component of early warning systems for zoonotic diseases. With the use of widespread low-cost technology, such a program could engage both the public and professionals and be easily tested and further incorporated as part of surveillance efforts by public health officials.

Global antibiotic resistance in Streptococcus pneumoniae.

PubMed

Adam, Dieter

2002-07-01

The last two decades of the 20th century were marked by an increasing resistance rate among several bacteria. Threat of resistance is present in Staphylococcus spp., Enterococcus spp., Pseudomonas spp. and Enterobacteriaceae, which are the major pathogens in nosocomial infections. In the community, too, increasing resistance can be observed and is attributed mainly (but not exclusively) to Streptococcus pneumoniae and Haemophilus influenzae. To scrutinize this trend, resistance surveillance in the community was established about 10 years ago. One of the multinational, longitudinal surveillance programmes in place is the Alexander Project, which was established in 1992 to monitor the susceptibility of the major community-acquired lower respiratory tract pathogens to a range of antibacterial drugs. The Alexander Project has revealed a tendency towards increasing resistance of S. pneumoniae to penicillin and macrolide therapy. Within Europe, the prevalence of penicillin resistance among S. pneumoniae isolates is particularly high in France and Spain. Macrolide resistance in S. pneumoniae is also a growing problem in European countries such as France, Spain, Belgium and Italy, where the extent of macrolide resistance in S. pneumoniae now exceeds that of penicillin resistance.

Research Contributing to Improvements in Controlling Florida's Mosquitoes and Mosquito-borne Diseases.

PubMed

Tabachnick, Walter J

2016-09-28

Research on mosquitoes and mosquito-borne diseases has contributed to improvements in providing effective, efficient, and environmentally proper mosquito control. Florida has benefitted from several research accomplishments that have increased the state's mosquito control capabilities. Research with Florida's mosquitoes has resulted in the development of ecologically sound management of mosquito impoundments on Florida's east coast. This strategy, called Rotational Impoundment Management (RIM), has improved the ability to target the delivery of pesticides and has helped to reduce non-target effects and environmental damage. Research has led to the development of an arbovirus surveillance system which includes sentinel chicken surveillance, real time use of environmental contributing factors like meteorology and hydrology to target mosquito control, as well as public health efforts to mitigate disease outbreaks to areas with risk of disease. These research driven improvements have provided substantial benefits to all of Florida. More research is needed to meet the future challenges to reduce emerging pathogens like Zika virus and the consequences of environmental changes like global climate change that are likely to influence the effects of mosquito-borne pathogens on human health and well-being.

Record linkage for pharmacoepidemiological studies in cancer patients.

PubMed

Herk-Sukel, Myrthe P P van; Lemmens, Valery E P P; Poll-Franse, Lonneke V van de; Herings, Ron M C; Coebergh, Jan Willem W

2012-01-01

An increasing need has developed for the post-approval surveillance of (new) anti-cancer drugs by means of pharmacoepidemiology and outcomes research in the area of oncology. To create an overview that makes researchers aware of the available database linkages in Northern America and Europe which facilitate pharmacoepidemiology and outcomes research in cancer patients. In addition to our own database, i.e. the Eindhoven Cancer Registry (ECR) linked to the PHARMO Record Linkage System, we considered database linkages between a population-based cancer registry and an administrative healthcare database that at least contains information on drug use and offers a longitudinal perspective on healthcare utilization. Eligible database linkages were limited to those that had been used in multiple published articles in English language included in Pubmed. The HMO Cancer Research Network (CRN) in the US was excluded from this review, as an overview of the linked databases participating in the CRN is already provided elsewhere. Researchers who had worked with the data resources included in our review were contacted for additional information and verification of the data presented in the overview. The following database linkages were included: the Surveillance, Epidemiology, and End-Results-Medicare; cancer registry data linked to Medicaid; Canadian cancer registries linked to population-based drug databases; the Scottish cancer registry linked to the Tayside drug dispensing data; linked databases in the Nordic Countries of Europe: Norway, Sweden, Finland and Denmark; and the ECR-PHARMO linkage in the Netherlands. Descriptives of the included database linkages comprise population size, generalizability of the population, year of first data availability, contents of the cancer registry, contents of the administrative healthcare database, the possibility to select a cancer-free control cohort, and linkage to other healthcare databases. The linked databases offer a longitudinal perspective, allowing for observations of health care utilization before, during, and after cancer diagnosis. They create new powerful data resources for the monitoring of post-approval drug utilization, as well as a framework to explore the (cost-)effectiveness of new, often expensive, anti-cancer drugs as used in everyday practice. Copyright © 2011 John Wiley & Sons, Ltd.

The CSB Incident Screening Database: description, summary statistics and uses.

PubMed

Gomez, Manuel R; Casper, Susan; Smith, E Allen

2008-11-15

This paper briefly describes the Chemical Incident Screening Database currently used by the CSB to identify and evaluate chemical incidents for possible investigations, and summarizes descriptive statistics from this database that can potentially help to estimate the number, character, and consequences of chemical incidents in the US. The report compares some of the information in the CSB database to roughly similar information available from databases operated by EPA and the Agency for Toxic Substances and Disease Registry (ATSDR), and explores the possible implications of these comparisons with regard to the dimension of the chemical incident problem. Finally, the report explores in a preliminary way whether a system modeled after the existing CSB screening database could be developed to serve as a national surveillance tool for chemical incidents.

Injuries in the military: a review and commentary focused on prevention.

PubMed

Jones, B H; Perrotta, D M; Canham-Chervak, M L; Nee, M A; Brundage, J F

2000-04-01

In November 1996, the Armed Forces Epidemiological Board (AFEB) Injury Prevention and Control Work Group issued a report that cited injuries as the leading cause of morbidity and mortality among military service members. This article reviews the types and categories of military morbidity and mortality data examined by the AFEB work group and the companion Department of Defense (DoD) Injury Surveillance and Prevention Work Group. This article further uses the injury data reviewed to illustrate the role of surveillance and research in injury prevention. The review provides the context for discussion of the implications of the AFEB work group's findings for the prevention of injuries in the military. The AFEB work group consisted of 11 civilian injury epidemiologists, health professionals and scientists from academia, and other non-DoD government agencies, plus six military liaison officers. Injury data from medical databases were provided to the civilian experts on the AFEB work group by the all-military DoD Injury Surveillance and Prevention Work Group. The AFEB work group assessed the value of each database to the process of prevention and made recommendations for improvement and use of each data source. Both work groups found that injuries were the single leading cause of deaths, disabilities, hospitalizations, outpatient visits, and manpower losses among military service members. They also identified numerous data sources useful for determining the causes and risk factors for injuries. Those data sources indicate that training injuries, sports, falls, and motor vehicle crashes are among the most important causes of morbidity for military personnel. While the work group recommends ways to prevent injuries, they felt the top priority for injury prevention must be the formation of a comprehensive medical surveillance system. Data from this surveillance system must be used routinely to prioritize and monitor injury and disease prevention and research programs. The success of injury prevention will depend not just on use of surveillance but also partnerships among the medical, surveillance, and safety agencies of the military services as well as the military commanders, other decision makers, and service members whose direct actions can prevent injuries and disease.

Managing marine disease emergencies in an era of rapid change

PubMed Central

Maynard, Jeffrey; Breyta, Rachel; Carnegie, Ryan B.; Dobson, Andy; Friedman, Carolyn S.; Froelich, Brett; Garren, Melissa; Gulland, Frances M. D.; Heron, Scott F.; Noble, Rachel T.; Revie, Crawford W.; Shields, Jeffrey D.; Vanderstichel, Raphaël; Weil, Ernesto; Wyllie-Echeverria, Sandy; Harvell, C. Drew

2016-01-01

Infectious marine diseases can decimate populations and are increasing among some taxa due to global change and our increasing reliance on marine environments. Marine diseases become emergencies when significant ecological, economic or social impacts occur. We can prepare for and manage these emergencies through improved surveillance, and the development and iterative refinement of approaches to mitigate disease and its impacts. Improving surveillance requires fast, accurate diagnoses, forecasting disease risk and real-time monitoring of disease-promoting environmental conditions. Diversifying impact mitigation involves increasing host resilience to disease, reducing pathogen abundance and managing environmental factors that facilitate disease. Disease surveillance and mitigation can be adaptive if informed by research advances and catalysed by communication among observers, researchers and decision-makers using information-sharing platforms. Recent increases in the awareness of the threats posed by marine diseases may lead to policy frameworks that facilitate the responses and management that marine disease emergencies require. PMID:26880835

Diarrheal and Respiratory Illness Surveillance During US-RP Balikatan 2014.

PubMed

Velasco, John M; Valderamat, Maria T; Nogrado, Kathyleen; Wongstitwilairoong, Tippa; Swierczewski, Brett; Bodhidatta, Ladaporn; Lertsethtakarn, Paphavee; Klungthong, Chonticha; Fernandez, Stefan; Mason, Carl; Yoon, In-Kyu; Macareo, Louis

2015-06-01

Diarrheal and respiratory illness surveillance was conducted during the 2014 Republic of the Philippines-U.S. Exercise Balikatan in the Philippines. Seven stool and three respiratory specimens that met the inclusion criteria were collected. Diarrhea stool specimens were tested with commercial enzyme-linked immunosorbent assay kits and real-time polymerase chain reaction (PCR) for 12 viral, bacterial, and protozoan pathogens. Campylobacter, enterotoxigenic Escherichia coli (ETEC), and enteropathogenic Escherichia coli (EPEC) were detected in four of seven (57%), two of seven (29%), and four of seven (57%) specimens, respectively. There were co-infections of EPEC and ETEC in two cases and EPEC and Campylobacter spp. in one case. Respiratory samples were tested using RT-PCR. One of three samples was positive for influenza B. Laboratory-based surveillance is important in determining causative agents for illnesses experienced by military personnel during deployment. Development of vaccines for enteric diseases should be expedited to mitigate their impact on operational readiness.

Surveillance at the molecular level: Developing an integrated network for detecting variation in avian influenza viruses in Indonesia.

PubMed

Hartaningsih, Nining; Wibawa, Hendra; Pudjiatmoko; Rasa, Fadjar Sumping Tjatur; Irianingsih, Sri Handayani; Dharmawan, Rama; Azhar, Muhammad; Siregar, Elly Sawitri; McGrane, James; Wong, Frank; Selleck, Paul; Allen, John; Broz, Ivano; Torchetti, Mia Kim; Dauphin, Gwenaelle; Claes, Filip; Sastraningrat, Wiryadi; Durr, Peter A

2015-06-01

Since 2006, Indonesia has used vaccination as the principal means of control of H5N1-HPAI. During this time, the virus has undergone gradual antigenic drift, which has necessitated changes in seed strains for vaccine production and associated modifications to diagnostic antigens. In order to improve the system of monitoring such viral evolution, the Government of Indonesia, with the assistance of FAO/OFFLU, has developed an innovative network whereby H5N1 isolates are antigenically and genetically characterised. This molecular surveillance network ("Influenza Virus Monitoring" or "IVM") is based on the regional network of veterinary diagnostic laboratories, and is supported by a web-based data management system ("IVM Online"). The example of the Indonesian IVM network has relevance for other countries seeking to establish laboratory networks for the molecular surveillance of avian influenza and other pathogens. Copyright © 2015 Elsevier B.V. All rights reserved.

Managing marine disease emergencies in an era of rapid change.

PubMed

Groner, Maya L; Maynard, Jeffrey; Breyta, Rachel; Carnegie, Ryan B; Dobson, Andy; Friedman, Carolyn S; Froelich, Brett; Garren, Melissa; Gulland, Frances M D; Heron, Scott F; Noble, Rachel T; Revie, Crawford W; Shields, Jeffrey D; Vanderstichel, Raphaël; Weil, Ernesto; Wyllie-Echeverria, Sandy; Harvell, C Drew

2016-03-05

Infectious marine diseases can decimate populations and are increasing among some taxa due to global change and our increasing reliance on marine environments. Marine diseases become emergencies when significant ecological, economic or social impacts occur. We can prepare for and manage these emergencies through improved surveillance, and the development and iterative refinement of approaches to mitigate disease and its impacts. Improving surveillance requires fast, accurate diagnoses, forecasting disease risk and real-time monitoring of disease-promoting environmental conditions. Diversifying impact mitigation involves increasing host resilience to disease, reducing pathogen abundance and managing environmental factors that facilitate disease. Disease surveillance and mitigation can be adaptive if informed by research advances and catalysed by communication among observers, researchers and decision-makers using information-sharing platforms. Recent increases in the awareness of the threats posed by marine diseases may lead to policy frameworks that facilitate the responses and management that marine disease emergencies require. © 2016 The Author(s).

National surveillance and control costs for highly pathogenic avian influenza H5N1 in poultry: A benefit-cost assessment for a developing economy, Nigeria.

PubMed

Fasanmi, Olubunmi G; Kehinde, Olugbenga O; Laleye, Agnes T; Ekong, Bassey; Ahmed, Syed S U; Fasina, Folorunso O

2018-06-13

We conducted benefit-cost analysis of outbreak and surveillance costs for HPAI H5N1in poultry in Nigeria. Poultry's death directly cost US$ 939,734.0 due to outbreaks. The integrated disease surveillance and response originally created for comprehensive surveillance and laboratory investigation of human diseases was adapted for HPAI H5N1 in poultry. Input data were obtained from the field, government documents and repositories and peer-reviewed publications. Actual/forecasted bird numbers lost were integrated into a financial model and estimates of losses were calculated. Costs of surveillance as alternative intervention were determined based on previous outbreak control costs and outputs were generated in SurvCost® with sensitivity analyses for different scenarios. Uncontrolled outbreaks will lead to loss of over US$ 2.2 billion annually in Nigeria with 47.8% of the losses coming from eggs. The annual cost of all animal related health activities was

Molecular Identification and Databases in Fusarium

USDA-ARS?s Scientific Manuscript database

DNA sequence-based methods for identifying pathogenic and mycotoxigenic Fusarium isolates have become the gold standard worldwide. Moreover, fusarial DNA sequence data are increasing rapidly in several web-accessible databases for comparative purposes. Unfortunately, the use of Basic Alignment Sea...

Comparison of approaches to rheumatic fever surveillance across Organisation for Economic Co-operation and Development countries.

PubMed

Oliver, Jane; Baker, Michael G; Pierse, Nevil; Carapetis, Jonathan

2015-11-01

Rheumatic fever (RF) prevention, control and surveillance are increasingly important priorities in New Zealand (NZ) and Australia. We compared RF surveillance across Organisation for Economic Co-operation and Development (OECD) member countries to assist in benchmarking and identifying useful approaches. A structured literature review was completed using Medline and PubMed databases, investigating RF incidence rates. Surveillance methods were noted. Health department websites were searched to assess whether addressing RF was a Government priority. Of 32 OECD member countries, nine reported RF incidence rates after 1999. Highest rates were seen in indigenous Australians, and NZ Māori and Pacific peoples. NZ and Australian surveillance systems are highly developed, with notification and register data compiled regularly. Only these two Governments appeared to prioritise RF surveillance and control. Other countries relied mainly on hospitalisation data. There is a lack of standardisation across incidence rate calculations. Israel and Italy may have relatively high RF rates among developed countries. RF lingers in specific populations in OECD member countries. At a minimum, RF registers are needed in higher incidence countries. Countries with low RF incidences should periodically review surveillance information to ensure rates are not increasing. © 2015 The Authors. Journal of Paediatrics and Child Health © 2015 Paediatrics and Child Health Division (Royal Australasian College of Physicians).

Suitability of partial 16S ribosomal RNA gene sequence analysis for the identification of dangerous bacterial pathogens.

PubMed

Ruppitsch, W; Stöger, A; Indra, A; Grif, K; Schabereiter-Gurtner, C; Hirschl, A; Allerberger, F

2007-03-01

In a bioterrorism event a rapid tool is needed to identify relevant dangerous bacteria. The aim of the study was to assess the usefulness of partial 16S rRNA gene sequence analysis and the suitability of diverse databases for identifying dangerous bacterial pathogens. For rapid identification purposes a 500-bp fragment of the 16S rRNA gene of 28 isolates comprising Bacillus anthracis, Brucella melitensis, Burkholderia mallei, Burkholderia pseudomallei, Francisella tularensis, Yersinia pestis, and eight genus-related and unrelated control strains was amplified and sequenced. The obtained sequence data were submitted to three public and two commercial sequence databases for species identification. The most frequent reason for incorrect identification was the lack of the respective 16S rRNA gene sequences in the database. Sequence analysis of a 500-bp 16S rDNA fragment allows the rapid identification of dangerous bacterial species. However, for discrimination of closely related species sequencing of the entire 16S rRNA gene, additional sequencing of the 23S rRNA gene or sequencing of the 16S-23S rRNA intergenic spacer is essential. This work provides comprehensive information on the suitability of partial 16S rDNA analysis and diverse databases for rapid and accurate identification of dangerous bacterial pathogens.

Foodborne outbreak simulation to teach field epidemiology: the Moroccan Field Epidemiology Training Program.

PubMed

Jroundi, Imane; Belarbi, Abdellatif

2016-11-01

Morocco in 2010 launched a new field epidemiology training program to enhance the skills of health professionals in charge of epidemiological surveillance and to investigate outbreaks; including foodborne diseases that represent a very substantial burden of disease. To apply an active learning method to teach outbreak investigation within a controled environment for field epidemiology trainees program at the Moroccan National school of public Health. A scenario describing digestive symptoms evoking a restaurant-associated foodborne outbreak that would affect the school staff was designed for the residents to investigate, to assess their organizational capacity and application of all stages of epidemiological investigation. Nine Residents applied study design, database management and statistical analysis to investigate the foodborne outbreak, to estimate attack rates, classify cases and controls, to identify the contaminated foods and pathogens and to issue preventive recommendations for the control and the prevention of further transmission. The overall resident's satisfaction of the learning method was 67%. A simulation of an outbreak investigation within an academic setting is an active learning method to be used in the curriculum for introducing the residents on field epidemiology program to the principles and practices of outbreak investigation before their implication in a real situation.

[Mass gatherings: a systematic review of the literature on large events].

PubMed

Llorente Nieto, Pedro; González-Alcaide, Gregorio; Ramos, José M

2017-07-01

We reviewed the literature on mass gatherings published worldwide to determine event types and topics or epidemiologic aspects covered. Articles using the term mass gatherings indexed in the Scopus database between 2000 and 2015 were reviewed. Of the 518 returned, we selected 96 with relevant information. The main event types studied were related to sports (46%), music (25%) or religious/social content (23%), and the most commonly studied locations were the United States (n=21), the Kingdom of Saudi Arabia (n=17), Australia (n=11), and the United Kingdom (n=10). The four most often studied events were the Hajj (n=17), the Olympic games (n=13), World Youth Day (n=8), and the FIFA World Cup (n=6). The main topics studied were models of health care (n=55), health care evaluation by means of rates of patients presenting for care or transferred to hospitals (n=21), respiratory pathogens (n=18), syndromic surveillance (n=10), and the global spread of diseases (n=10). Mass gatherings are an emerging area of study addressed by various medical specialties that have focused on studying the health care models used at such events. Emergency medicine is particularly involved with this research topic.