Host persistence or extinction from emerging infectious disease: insights from white-nose syndrome in endemic and invading regions.

PubMed

Hoyt, Joseph R; Langwig, Kate E; Sun, Keping; Lu, Guanjun; Parise, Katy L; Jiang, Tinglei; Frick, Winifred F; Foster, Jeffrey T; Feng, Jiang; Kilpatrick, A Marm

2016-03-16

Predicting species' fates following the introduction of a novel pathogen is a significant and growing problem in conservation. Comparing disease dynamics between introduced and endemic regions can offer insight into which naive hosts will persist or go extinct, with disease acting as a filter on host communities. We examined four hypothesized mechanisms for host-pathogen persistence by comparing host infection patterns and environmental reservoirs for Pseudogymnoascus destructans (the causative agent of white-nose syndrome) in Asia, an endemic region, and North America, where the pathogen has recently invaded. Although colony sizes of bats and hibernacula temperatures were very similar, both infection prevalence and fungal loads were much lower on bats and in the environment in Asia than North America. These results indicate that transmission intensity and pathogen growth are lower in Asia, likely due to higher host resistance to pathogen growth in this endemic region, and not due to host tolerance, lower transmission due to smaller populations, or lower environmentally driven pathogen growth rate. Disease filtering also appears to be favouring initially resistant species in North America. More broadly, determining the mechanisms allowing species persistence in endemic regions can help identify species at greater risk of extinction in introduced regions, and determine the consequences for disease dynamics and host-pathogen coevolution. © 2016 The Author(s).

The effects of sudden oak death on foliar moisture content and crown fire potential in tanoak

Treesearch

H. Kuljian; J.M. Varner

2010-01-01

The introduction of non-native pathogens can have profound effects on forest ecosystems resulting in loss of species, changes in species composition, and altered fuel structure. The introduction of Phytophthora ramorum, the pathogen recognized as causing Sudden Oak Death (SOD), leads to rapid decline and mortality of tanoak (Lithocarpus densiflorus) in forests of...

Experimental introduction of a microsporidian into a wild population of Culex pipiens fatigans Wied

PubMed Central

Reynolds, D. G.

1972-01-01

Chemical control of C. p. fatigans frequently fails because the mosquito rapidly develops resistance to insecticides. A possible alternative or complementary method is biological control, including the introduction of pathogens. The microsporidian Plistophora culicis was known to infect readily and have an adverse effect on C. p. fatigans populations in the laboratory, so an attempt was made to introduce and establish this pathogen in a wild population of the mosquito on the Pacific island of Nauru. Two years after introduction the pathogen was still present in the wild population. However, the infection rate was similar to that found in naturally occurring infections in other mosquitos and is almost certainly not high enough to affect a natural population of C. p. fatigans adversely. PMID:4538542

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...

Modeling Mosquito-Borne Disease Spread in U.S. Urbanized Areas: The Case of Dengue in Miami

PubMed Central

Robert, Michael A.; Christofferson, Rebecca C.; Silva, Noah J. B.; Vasquez, Chalmers; Mores, Christopher N.; Wearing, Helen J.

2016-01-01

Expansion of mosquito-borne pathogens into more temperate regions of the world necessitates tools such as mathematical models for understanding the factors that contribute to the introduction and emergence of a disease in populations naïve to the disease. Often, these models are not developed and analyzed until after a pathogen is detected in a population. In this study, we develop a spatially explicit stochastic model parameterized with publicly available U.S. Census data for studying the potential for disease spread in Urbanized Areas of the United States. To illustrate the utility of the model, we specifically study the potential for introductions of dengue to lead to autochthonous transmission and outbreaks in a population representative of the Miami Urbanized Area, where introductions of dengue have occurred frequently in recent years. We describe seasonal fluctuations in mosquito populations by fitting a population model to trap data provided by the Miami-Dade Mosquito Control Division. We show that the timing and location of introduced cases could play an important role in determining both the probability that local transmission occurs as well as the total number of cases throughout the entire region following introduction. We show that at low rates of clinical presentation, small outbreaks of dengue could go completely undetected during a season, which may confound mitigation efforts that rely upon detection. We discuss the sensitivity of the model to several critical parameter values that are currently poorly characterized and motivate the collection of additional data to strengthen the predictive power of this and similar models. Finally, we emphasize the utility of the general structure of this model in studying mosquito-borne diseases such as chikungunya and Zika virus in other regions. PMID:27532496

The effect of seasonal birth pulses on pathogen persistence in wild mammal populations.

PubMed

Peel, A J; Pulliam, J R C; Luis, A D; Plowright, R K; O'Shea, T J; Hayman, D T S; Wood, J L N; Webb, C T; Restif, O

2014-07-07

The notion of a critical community size (CCS), or population size that is likely to result in long-term persistence of a communicable disease, has been developed based on the empirical observations of acute immunizing infections in human populations, and extended for use in wildlife populations. Seasonal birth pulses are frequently observed in wildlife and are expected to impact infection dynamics, yet their effect on pathogen persistence and CCS have not been considered. To investigate this issue theoretically, we use stochastic epidemiological models to ask how host life-history traits and infection parameters interact to determine pathogen persistence within a closed population. We fit seasonal birth pulse models to data from diverse mammalian species in order to identify realistic parameter ranges. When varying the synchrony of the birth pulse with all other parameters being constant, our model predicted that the CCS can vary by more than two orders of magnitude. Tighter birth pulses tended to drive pathogen extinction by creating large amplitude oscillations in prevalence, especially with high demographic turnover and short infectious periods. Parameters affecting the relative timing of the epidemic and birth pulse peaks determined the intensity and direction of the effect of pre-existing immunity in the population on the pathogen's ability to persist beyond the initial epidemic following its introduction.

The effect of seasonal birth pulses on pathogen persistence in wild mammal populations

PubMed Central

Peel, A. J.; Pulliam, J. R. C.; Luis, A. D.; Plowright, R. K.; O'Shea, T. J.; Hayman, D. T. S.; Wood, J. L. N.; Webb, C. T.; Restif, O.

2014-01-01

The notion of a critical community size (CCS), or population size that is likely to result in long-term persistence of a communicable disease, has been developed based on the empirical observations of acute immunizing infections in human populations, and extended for use in wildlife populations. Seasonal birth pulses are frequently observed in wildlife and are expected to impact infection dynamics, yet their effect on pathogen persistence and CCS have not been considered. To investigate this issue theoretically, we use stochastic epidemiological models to ask how host life-history traits and infection parameters interact to determine pathogen persistence within a closed population. We fit seasonal birth pulse models to data from diverse mammalian species in order to identify realistic parameter ranges. When varying the synchrony of the birth pulse with all other parameters being constant, our model predicted that the CCS can vary by more than two orders of magnitude. Tighter birth pulses tended to drive pathogen extinction by creating large amplitude oscillations in prevalence, especially with high demographic turnover and short infectious periods. Parameters affecting the relative timing of the epidemic and birth pulse peaks determined the intensity and direction of the effect of pre-existing immunity in the population on the pathogen's ability to persist beyond the initial epidemic following its introduction. PMID:24827436

Emerging foodborne pathogens

USDA-ARS?s Scientific Manuscript database

The emergence of new foodborne pathogens is due to a number of factors. An important factor is the globalization of the food supply with the possibility of the introduction of foodborne pathogens from other countries. Animal husbandry, food production, food processing, and food distribution system...

Host-Induced Gene Silencing of Rice Blast Fungus Magnaporthe oryzae Pathogenicity Genes Mediated by the Brome Mosaic Virus.

PubMed

Zhu, Lin; Zhu, Jian; Liu, Zhixue; Wang, Zhengyi; Zhou, Cheng; Wang, Hong

2017-09-26

Magnaporthe oryzae is a devastating plant pathogen, which has a detrimental impact on rice production worldwide. Despite its agronomical importance, some newly-emerging pathotypes often overcome race-specific disease resistance rapidly. It is thus desirable to develop a novel strategy for the long-lasting resistance of rice plants to ever-changing fungal pathogens. Brome mosaic virus (BMV)-induced RNA interference (RNAi) has emerged as a useful tool to study host-resistance genes for rice blast protection. Planta-generated silencing of targeted genes inside biotrophic pathogens can be achieved by expression of M. oryzae -derived gene fragments in the BMV-mediated gene silencing system, a technique termed host-induced gene silencing (HIGS). In this study, the effectiveness of BMV-mediated HIGS in M. oryzae was examined by targeting three predicted pathogenicity genes, MoABC1, MoMAC1 and MoPMK1 . Systemic generation of fungal gene-specific small interfering RNA (siRNA) molecules induced by inoculation of BMV viral vectors inhibited disease development and reduced the transcription of targeted fungal genes after subsequent M. oryzae inoculation. Combined introduction of fungal gene sequences in sense and antisense orientation mediated by the BMV silencing vectors significantly enhanced the efficiency of this host-generated trans-specific RNAi, implying that these fungal genes played crucial roles in pathogenicity. Collectively, our results indicated that BMV-HIGS system was a great strategy for protecting host plants against the invasion of pathogenic fungi.

A framework for optimizing phytosanitary thresholds in seed systems

USDA-ARS?s Scientific Manuscript database

Seedborne pathogens and pests limit production in many agricultural systems. Quarantine programs help prevent the introduction of exotic pathogens into a country, but few regulations directly apply to reducing the reintroduction and spread of endemic pathogens. Use of phytosanitary thresholds helps ...

Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen.

PubMed

Brar, Simren; Tsui, Clement K M; Dhillon, Braham; Bergeron, Marie-Josée; Joly, David L; Zambino, P J; El-Kassaby, Yousry A; Hamelin, Richard C

2015-01-01

White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C. ribicola. We characterized 1,292 samples of C. ribicola from 66 geographic locations in North America using single nucleotide polymorphisms (SNPs) and evaluated the effect of landscape features, host distribution, and colonization history on the structure of these pathogen populations. We identified eastern and western genetic populations in North America that are strongly differentiated. Genetic diversity is two to five times higher in eastern populations than in western ones, which can be explained by the repeated accidental introductions of the pathogen into northeastern North America compared with a single documented introduction into western North America. These distinct genetic populations are maintained by a barrier to gene flow that corresponds to a region where host connectivity is interrupted. Furthermore, additional cryptic spatial differentiation was identified in western populations. This differentiation corresponds to landscape features, such as mountain ranges, and also to host connectivity. We also detected genetic differentiation between the pathogen populations in natural stands and plantations, an indication that anthropogenic movement of this pathogen still takes place. These results highlight the importance of monitoring this invasive alien tree pathogen to prevent admixture of eastern and western populations where different pathogen races occur.

Drivers, dynamics, and control of emerging vector-borne zoonotic diseases

PubMed Central

Kilpatrick, A. Marm; Randolph, Sarah E.

2013-01-01

Emerging vector-borne diseases represent an important issue for global health. Many vector-borne pathogens have appeared in new regions in the past two decades, and many endemic diseases have increased in incidence. Although introductions and local emergence are frequently considered distinct processes, many emerging endemic pathogens are in fact invading at a local scale coincident with habitat change. We highlight key differences in the dynamics and disease burden that result from increased pathogen transmission following habitat change compared with the introduction of pathogens to new regions. Truly in situ emergence is commonly driven by changes in human factors as much as by enhanced enzootic cycles whereas pathogen invasion results from anthropogenic trade and travel and suitable conditions for a pathogen, including hosts, vectors, and climate. Once established, ecological factors related to vector characteristics shape the evolutionary selective pressure on pathogens that may result in increased use of humans as transmission hosts. We describe challenges inherent in the control of vector-borne zoonotic diseases and some emerging non-traditional strategies that may be more effective in the long term. PMID:23200503

Naturalization of host-dependent microbes after introduction into terrestrial ecosystems [Chapter 5

Treesearch

Geral I. McDonald; Paul J. Zambino; Ned B. Klopfenstein

2005-01-01

Introduction of plant pathogens, insects, parasites, and predators into terrestrial and marine ecosystems is second only to habitat loss among major threats to biodiversity (Torchin et. al. 2002), and the frequency of introductions continues to increase (Flather et al. 1998, Torchin et al. 2002, Wilcove et al. 1998). Despite their detrimental impacts, introductions can...

Developing hygiene protocols against mechanically transmitted pathogens in greenhouse tomato production systems

USDA-ARS?s Scientific Manuscript database

Greenhouse tomato propagation and production require intensive crop work that promotes the spread of mechanically transmitted pathogens (e.g. fungi, bacteria, viruses and viroids). Therefore, a clean seed program is very important to prevent any un-intentional introduction of seed-borne pathogens t...

Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici.

PubMed

Figueroa, Melania; Upadhyaya, Narayana M; Sperschneider, Jana; Park, Robert F; Szabo, Les J; Steffenson, Brian; Ellis, Jeff G; Dodds, Peter N

2016-01-01

The recent resurgence of wheat stem rust caused by new virulent races of Puccinia graminis f. sp. tritici (Pgt) poses a threat to food security. These concerns have catalyzed an extensive global effort toward controlling this disease. Substantial research and breeding programs target the identification and introduction of new stem rust resistance (Sr) genes in cultivars for genetic protection against the disease. Such resistance genes typically encode immune receptor proteins that recognize specific components of the pathogen, known as avirulence (Avr) proteins. A significant drawback to deploying cultivars with single Sr genes is that they are often overcome by evolution of the pathogen to escape recognition through alterations in Avr genes. Thus, a key element in achieving durable rust control is the deployment of multiple effective Sr genes in combination, either through conventional breeding or transgenic approaches, to minimize the risk of resistance breakdown. In this situation, evolution of pathogen virulence would require changes in multiple Avr genes in order to bypass recognition. However, choosing the optimal Sr gene combinations to deploy is a challenge that requires detailed knowledge of the pathogen Avr genes with which they interact and the virulence phenotypes of Pgt existing in nature. Identifying specific Avr genes from Pgt will provide screening tools to enhance pathogen virulence monitoring, assess heterozygosity and propensity for mutation in pathogen populations, and confirm individual Sr gene functions in crop varieties carrying multiple effective resistance genes. Toward this goal, much progress has been made in assembling a high quality reference genome sequence for Pgt, as well as a Pan-genome encompassing variation between multiple field isolates with diverse virulence spectra. In turn this has allowed prediction of Pgt effector gene candidates based on known features of Avr genes in other plant pathogens, including the related flax rust fungus. Upregulation of gene expression in haustoria and evidence for diversifying selection are two useful parameters to identify candidate Avr genes. Recently, we have also applied machine learning approaches to agnostically predict candidate effectors. Here, we review progress in stem rust pathogenomics and approaches currently underway to identify Avr genes recognized by wheat Sr genes.

A proactive approach to prevent invasive plant pathogens

Treesearch

Amy Rossman

2009-01-01

This paper describes proactive work by federal agencies to prevent new introductions of forest pathogens. Executive Order 13112 requires federal agencies to work together to enhance our abilities to prevent, eradicate, and control...

Biological Control of Aquatic Plants with Pathogenic Fungi

DTIC Science & Technology

1981-01-01

reverse side II necoosary and Ident•l•y by block number) Aquatic plant control Fungi Aquatic plants Pathogenic fungi Biological control Waterhyacinths...BACTERIA ............. ................. D1 2 1 BIOTIGICAL CONTROL OF AQUATIC PLANTS WITH PATHOGENIC FUNGI PART I: INTRODUCTION 1. Plant pathogens have...first noted in Florida. 13. In December of 1973, Dr. K. E. Ctnway isolated a Cercospora species, along with many other fungi , from declining

Bayesian data assimilation provides rapid decision support for vector-borne diseases

PubMed Central

Jewell, Chris P.; Brown, Richard G.

2015-01-01

Predicting the spread of vector-borne diseases in response to incursions requires knowledge of both host and vector demographics in advance of an outbreak. Although host population data are typically available, for novel disease introductions there is a high chance of the pathogen using a vector for which data are unavailable. This presents a barrier to estimating the parameters of dynamical models representing host–vector–pathogen interaction, and hence limits their ability to provide quantitative risk forecasts. The Theileria orientalis (Ikeda) outbreak in New Zealand cattle demonstrates this problem: even though the vector has received extensive laboratory study, a high degree of uncertainty persists over its national demographic distribution. Addressing this, we develop a Bayesian data assimilation approach whereby indirect observations of vector activity inform a seasonal spatio-temporal risk surface within a stochastic epidemic model. We provide quantitative predictions for the future spread of the epidemic, quantifying uncertainty in the model parameters, case infection times and the disease status of undetected infections. Importantly, we demonstrate how our model learns sequentially as the epidemic unfolds and provide evidence for changing epidemic dynamics through time. Our approach therefore provides a significant advance in rapid decision support for novel vector-borne disease outbreaks. PMID:26136225

Multiple introductions of divergent genetic lineages in an invasive fungal pathogen, Cryphonectria parasitica, in France.

PubMed

Dutech, C; Fabreguettes, O; Capdevielle, X; Robin, C

2010-08-01

The occurrence of multiple introductions may be a crucial factor in the successful establishment of invasive species, but few studies focus on the introduction of fungal pathogens, despite their significant effect on invaded habitats. Although Cryphonectria parasitica, the chestnut blight fungus introduced in North America and Europe from Asia during the 20th century, caused dramatic changes in its new range, the history of its introduction is not well retraced in Europe. Using 10 microsatellite loci, we investigated the genetic diversity of 583 isolates in France, where several introductions have been hypothesized. Our analyses showed that the seven most frequent multilocus genotypes belonged to three genetic lineages, which had a different and geographically limited distribution. These results suggest that different introduction events occurred in France. Genetic recombination was low among these lineages, despite the presence of the two mating types in each chestnut stand analysed. The spatial distribution of lineages suggests that the history of introductions in France associated with the slow expansion of the disease has contributed to the low observed rate of recombination among the divergent lineages. However, we discuss the possibility that environmental conditions or viral interactions could locally reduce recombination among genotypes.

Population Dynamics of a Salmonella Lytic Phage and Its Host: Implications of the Host Bacterial Growth Rate in Modelling

PubMed Central

Santos, Sílvio B.; Carvalho, Carla; Azeredo, Joana; Ferreira, Eugénio C.

2014-01-01

The prevalence and impact of bacteriophages in the ecology of bacterial communities coupled with their ability to control pathogens turn essential to understand and predict the dynamics between phage and bacteria populations. To achieve this knowledge it is essential to develop mathematical models able to explain and simulate the population dynamics of phage and bacteria. We have developed an unstructured mathematical model using delay-differential equations to predict the interactions between a broad-host-range Salmonella phage and its pathogenic host. The model takes into consideration the main biological parameters that rule phage-bacteria interactions likewise the adsorption rate, latent period, burst size, bacterial growth rate, and substrate uptake rate, among others. The experimental validation of the model was performed with data from phage-interaction studies in a 5 L bioreactor. The key and innovative aspect of the model was the introduction of variations in the latent period and adsorption rate values that are considered as constants in previous developed models. By modelling the latent period as a normal distribution of values and the adsorption rate as a function of the bacterial growth rate it was possible to accurately predict the behaviour of the phage-bacteria population. The model was shown to predict simulated data with a good agreement with the experimental observations and explains how a lytic phage and its host bacteria are able to coexist. PMID:25051248

A Simple Model to Rank Shellfish Farming Areas Based on the Risk of Disease Introduction and Spread.

PubMed

Thrush, M A; Pearce, F M; Gubbins, M J; Oidtmann, B C; Peeler, E J

2017-08-01

The European Union Council Directive 2006/88/EC requires that risk-based surveillance (RBS) for listed aquatic animal diseases is applied to all aquaculture production businesses. The principle behind this is the efficient use of resources directed towards high-risk farm categories, animal types and geographic areas. To achieve this requirement, fish and shellfish farms must be ranked according to their risk of disease introduction and spread. We present a method to risk rank shellfish farming areas based on the risk of disease introduction and spread and demonstrate how the approach was applied in 45 shellfish farming areas in England and Wales. Ten parameters were used to inform the risk model, which were grouped into four risk themes based on related pathways for transmission of pathogens: (i) live animal movement, (ii) transmission via water, (iii) short distance mechanical spread (birds) and (iv) long distance mechanical spread (vessels). Weights (informed by expert knowledge) were applied both to individual parameters and to risk themes for introduction and spread to reflect their relative importance. A spreadsheet model was developed to determine quantitative scores for the risk of pathogen introduction and risk of pathogen spread for each shellfish farming area. These scores were used to independently rank areas for risk of introduction and for risk of spread. Thresholds were set to establish risk categories (low, medium and high) for introduction and spread based on risk scores. Risk categories for introduction and spread for each area were combined to provide overall risk categories to inform a risk-based surveillance programme directed at the area level. Applying the combined risk category designation framework for risk of introduction and spread suggested by European Commission guidance for risk-based surveillance, 4, 10 and 31 areas were classified as high, medium and low risk, respectively. © 2016 Crown copyright.

Invasive forest pathogens: Summary of issues, critical needs, and future goals for Forest Service Research and Development

Treesearch

Ned B. Klopfenstein; Jennifer Juzwik; Michael E. Ostry; Mee-Sook Kim; Paul J. Zambino; Robert C. Venette; Bryce A. Richardson; John E. Lundquist; D. Jean Lodge; Jessie A. Glaeser; Susan J. Frankel; William J. Otrosina; Pauline Spaine; Brian W. Geils

2010-01-01

Invasive pathogens have caused immeasurable ecological and economic damage to forest ecosystems. Damage will undoubtedly increase over time due to increased introductions and evolution of invasive pathogens in concert with complex environmental disturbances, such as climate change. Forest Service Research and Development must fulfill critical roles and responsibilities...

A review of introductions of pathogens and nematodes for classical biological control of insects and mites

Treesearch

Ann E. Hajek; Michael L. McManus; Italo Delalibera Junior

2007-01-01

Compared with parasitoids and predators, classical biological control programs targeting arthropod pests have used pathogens and nematodes very little. However, some pathogens and nematodes that have been introduced have become established and provided excellent control and have been introduced in increasing numbers of areas over decades, often after distributions of...

Introduction: the goals of antimicrobial therapy.

PubMed

Song, Jae-Hoon

2003-03-01

Antimicrobial agents are generally evaluated in preclinical studies assessing in vitro activity, animal models demonstrating in vivo bacteriologic efficacy, and clinical trials primarily investigating safety and clinical efficacy. However, large sample sizes are required to detect any differences in outcomes between antimicrobials in clinical trials, and, generally, studies are powered to show only clinical equivalence. In addition, diagnosis is often based on clinical symptoms, rather than microbiological evidence of bacterial infection, and the patients most likely to have resistant pathogens are often excluded. Clinical efficacy can be achieved in some bacterial infections in which antimicrobials are suboptimal or even not prescribed. However, bacterial eradication maximizes clinical efficacy and may also reduce the development and spread of resistant organisms. The goal of antimicrobial therapy is, therefore, to eradicate bacteria at the site of infection. Bacterial eradication is not usually assessed as a primary endpoint within the limits of currently recommended clinical trial design. However, pharmacokinetic (PK) (serum concentration profiles, penetration to site of infection) and pharmacodynamic (PD) (susceptibility, concentration- versus time-dependent killing, post-antimicrobial effects) criteria can be used to predict bacteriologic efficacy. PK/PD predictions should be confirmed during all phases of antimicrobial development and throughout clinical use in response to changing patterns of resistance. A clear rationale for dose recommendations can be determined preclinically based on PK/PD parameters, and correlated with efficacy, safety and resistance endpoints in clinical trials. The duration of treatment and dose should be the shortest that will reliably eradicate the pathogen(s), and that is safe and well tolerated. Currently available agents vary significantly in their ability to achieve PK/PD parameters necessary for bacteriologic eradication. Recommendations for appropriate antimicrobial therapy should be based on PK/PD parameters, with the aim of achieving the maximum potential for eradication of both existing and emerging resistant pathogens.

Role of viral and bacterial pathogens in causing pneumonia among Western Australian children: a case–control study protocol

PubMed Central

Bhuiyan, Mejbah Uddin; Snelling, Thomas L; West, Rachel; Lang, Jurissa; Rahman, Tasmina; Borland, Meredith L; Thornton, Ruth; Kirkham, Lea-Ann; Sikazwe, Chisha; Martin, Andrew C; Richmond, Peter C; Smith, David W; Jaffe, Adam; Blyth, Christopher C

2018-01-01

Introduction Pneumonia is the leading cause of childhood morbidity and mortality globally. Introduction of the conjugate Haemophilus influenzae B and multivalent pneumococcal vaccines in developed countries including Australia has significantly reduced the overall burden of bacterial pneumonia. With the availability of molecular diagnostics, viruses are frequently detected in children with pneumonia either as primary pathogens or predispose to secondary bacterial infection. Many respiratory pathogens that are known to cause pneumonia are also identified in asymptomatic children, so the true contribution of these pathogens to childhood community-acquired pneumonia (CAP) remains unclear. Since the introduction of pneumococcal vaccines, very few comprehensive studies from developed countries have attempted to determine the bacterial and viral aetiology of pneumonia. We aim to determine the contribution of bacteria and viruses to childhood CAP to inform further development of effective diagnosis, treatment and preventive strategies. Methods and analysis We are conducting a prospective case–control study (PneumoWA) where cases are children with radiologically confirmed pneumonia admitted to Princess Margaret Hospital for Children (PMH) and controls are healthy children identified from PMH outpatient clinics and from local community immunisation clinics. The case–control ratio is 1:1 with 250 children to be recruited in each arm. Nasopharyngeal swabs are collected from both cases and controls to detect the presence of viruses and bacteria by PCR; pathogen load will be assessed by quantitative PCR. The prevalence of pathogens detected in cases and controls will be compared, the OR of detection and population attributable fraction to CAP for each pathogen will be determined; relationships between pathogen load and disease status and severity will be explored. Ethics and dissemination This study has been approved by the human research ethics committees of PMH, Perth, Australia (PMH HREC REF 2014117EP). Findings will be disseminated at research conferences and in peer-reviewed journals. PMID:29549211

Resistance in persisting bat populations after white-nose syndrome invasion.

PubMed

Langwig, Kate E; Hoyt, Joseph R; Parise, Katy L; Frick, Winifred F; Foster, Jeffrey T; Kilpatrick, A Marm

2017-01-19

Increases in anthropogenic movement have led to a rise in pathogen introductions and the emergence of infectious diseases in naive host communities worldwide. We combined empirical data and mathematical models to examine changes in disease dynamics in little brown bat (Myotis lucifugus) populations following the introduction of the emerging fungal pathogen Pseudogymnoascus destructans, which causes the disease white-nose syndrome. We found that infection intensity was much lower in persisting populations than in declining populations where the fungus has recently invaded. Fitted models indicate that this is most consistent with a reduction in the growth rate of the pathogen when fungal loads become high. The data are inconsistent with the evolution of tolerance or an overall reduced pathogen growth rate that might be caused by environmental factors. The existence of resistance in some persisting populations of little brown bats offers a glimmer of hope that a precipitously declining species will persist in the face of this deadly pathogen.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

Multiple introductions of highly pathogenic avian influenza H5N1 viruses into Bangladesh

PubMed Central

Marinova-Petkova, Atanaska; Feeroz, Mohammed M; Rabiul Alam, SM; Kamrul Hasan, M; Akhtar, Sharmin; Jones-Engel, Lisa; Walker, David; McClenaghan, Laura; Rubrum, Adam; Franks, John; Seiler, Patrick; Jeevan, Trushar; McKenzie, Pamela; Krauss, Scott; Webby, Richard J; Webster, Robert G

2014-01-01

Highly pathogenic H5N1 and low pathogenic H9N2 influenza viruses are endemic to poultry markets in Bangladesh and have cocirculated since 2008. H9N2 influenza viruses circulated constantly in the poultry markets, whereas highly pathogenic H5N1 viruses occurred sporadically, with peaks of activity in cooler months. Thirty highly pathogenic H5N1 influenza viruses isolated from poultry were characterized by antigenic, molecular, and phylogenetic analyses. Highly pathogenic H5N1 influenza viruses from clades 2.2.2 and 2.3.2.1 were isolated from live bird markets only. Phylogenetic analysis of the 30 H5N1 isolates revealed multiple introductions of H5N1 influenza viruses in Bangladesh. There was no reassortment between the local H9N2 influenza viruses and H5N1 genotype, despite their prolonged cocirculation. However, we detected two reassortant H5N1 viruses, carrying the M gene from the Chinese H9N2 lineage, which briefly circulated in the Bangladesh poultry markets and then disappeared. On the other hand, interclade reassortment occurred within H5N1 lineages and played a role in the genesis of the currently dominant H5N1 viruses in Bangladesh. Few ‘human-like' mutations in H5N1 may account for the limited number of human cases. Antigenically, clade 2.3.2.1 H5N1 viruses in Bangladesh have evolved since their introduction and are currently mainly homogenous, and show evidence of recent antigenic drift. Although reassortants containing H9N2 genes were detected in live poultry markets in Bangladesh, these reassortants failed to supplant the dominant H5N1 lineage. PMID:26038508

Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome.

PubMed

Drees, Kevin P; Lorch, Jeffrey M; Puechmaille, Sebastien J; Parise, Katy L; Wibbelt, Gudrun; Hoyt, Joseph R; Sun, Keping; Jargalsaikhan, Ariunbold; Dalannast, Munkhnast; Palmer, Jonathan M; Lindner, Daniel L; Marm Kilpatrick, A; Pearson, Talima; Keim, Paul S; Blehert, David S; Foster, Jeffrey T

2017-12-12

Globalization has facilitated the worldwide movement and introduction of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans , a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has exhibited few genetic polymorphisms in previous studies, presenting challenges for both epizoological tracking of the spread of this fungus and for determining its evolutionary history. We used single nucleotide polymorphisms (SNPs) from whole-genome sequencing and microsatellites to construct high-resolution phylogenies of P. destructans Shallow genetic diversity and the lack of geographic structuring among North American isolates support a recent introduction followed by expansion via clonal reproduction across the epizootic zone. Moreover, the genetic relationships of isolates within North America suggest widespread mixing and long-distance movement of the fungus. Genetic diversity among isolates of P. destructans from Europe was substantially higher than in those from North America. However, genetic distance between the North American isolates and any given European isolate was similar to the distance between the individual European isolates. In contrast, the isolates we examined from Asia were highly divergent from both European and North American isolates. Although the definitive source for introduction of the North American population has not been conclusively identified, our data support the origin of the North American invasion by P. destructans from Europe rather than Asia. IMPORTANCE This phylogenetic study of the bat white-nose syndrome agent, P. destructans , uses genomics to elucidate evolutionary relationships among populations of the fungal pathogen to understand the epizoology of this biological invasion. We analyze hypervariable and abundant genetic characters (microsatellites and genomic SNPs, respectively) to reveal previously uncharacterized diversity among populations of the pathogen from North America and Eurasia. We present new evidence supporting recent introduction of the fungus to North America from a diverse Eurasian population, with limited increase in genetic variation in North America since that introduction. Copyright © 2017 Drees et al.

Bayesian data assimilation provides rapid decision support for vector-borne diseases.

PubMed

Jewell, Chris P; Brown, Richard G

2015-07-06

Predicting the spread of vector-borne diseases in response to incursions requires knowledge of both host and vector demographics in advance of an outbreak. Although host population data are typically available, for novel disease introductions there is a high chance of the pathogen using a vector for which data are unavailable. This presents a barrier to estimating the parameters of dynamical models representing host-vector-pathogen interaction, and hence limits their ability to provide quantitative risk forecasts. The Theileria orientalis (Ikeda) outbreak in New Zealand cattle demonstrates this problem: even though the vector has received extensive laboratory study, a high degree of uncertainty persists over its national demographic distribution. Addressing this, we develop a Bayesian data assimilation approach whereby indirect observations of vector activity inform a seasonal spatio-temporal risk surface within a stochastic epidemic model. We provide quantitative predictions for the future spread of the epidemic, quantifying uncertainty in the model parameters, case infection times and the disease status of undetected infections. Importantly, we demonstrate how our model learns sequentially as the epidemic unfolds and provide evidence for changing epidemic dynamics through time. Our approach therefore provides a significant advance in rapid decision support for novel vector-borne disease outbreaks. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Rapidly expanding range of highly pathogenic avian influenza viruses

USDA-ARS?s Scientific Manuscript database

The recent introduction of highly pathogenic avian influenza virus (HPAIV) H5N8 into Europe and North America poses significant risks to poultry industries and wildlife populations and warrants continued and heightened vigilance. First discovered in South Korean poultry and wild birds in early 2014...

Modelling low pathogenic avian influenza introduction into the commercial poultry industry.

PubMed

Barnes, Belinda; Glass, Kathryn

2018-06-01

Outbreaks of highly pathogenic avian influenza (HPAI) in commercial poultry flocks are rare but highly disruptive to the industry. There is evidence that low pathogenic avian influenza (LPAI) can transfer from wild birds to domestic flocks, where it may mutate to HPAI, and the industry is concerned that an increasing demand for free-range produce may affect the risk of LPAI and HPAI outbreaks. In this paper we focus on LPAI introduction and establishment, and formulate a branching process model to compare risk between sectors and their contribution to overall industry-level risk. Our aim is to determine how heterogeneity in avian influenza viruses and the distinct population structures of each sector - caged, barn and free-range, meat and layer - interact with a continuous risk of virus introduction to affect outbreak probabilities. We show that free-range access is the most influential driver of LPAI outbreaks, with production cycle length having relatively little effect. We demonstrate that variation in virus transmission rates is particularly important when modelling avian influenza introduction to domestic poultry. Virus-free status is of interest for biosecurity and we distinguish how it differs from the usual probability of extinction, and discuss how production cycle length affects this difference. We also use the nonlinear relationship between shed size and risk to identify conditions for which shed size is most influential. Copyright © 2018 Elsevier Inc. All rights reserved.

Local dominance of exotic plants declines with residence time: a role for plant–soil feedback?

PubMed Central

Speek, Tanja A.A.; Schaminée, Joop H.J.; Stam, Jeltje M.; Lotz, Lambertus A.P.; Ozinga, Wim A.; van der Putten, Wim H.

2015-01-01

Recent studies have shown that introduced exotic plant species may be released from their native soil-borne pathogens, but that they become exposed to increased soil pathogen activity in the new range when time since introduction increases. Other studies have shown that introduced exotic plant species become less dominant when time since introduction increases, and that plant abundance may be controlled by soil-borne pathogens; however, no study yet has tested whether these soil effects might explain the decline in dominance of exotic plant species following their initial invasiveness. Here we determine plant–soil feedback of 20 plant species that have been introduced into The Netherlands. We tested the hypotheses that (i) exotic plant species with a longer residence time have a more negative soil feedback and (ii) greater local dominance of the introduced exotic plant species correlates with less negative, or more positive, plant–soil feedback. Although the local dominance of exotic plant species decreased with time since introduction, there was no relationship of local dominance with plant–soil feedback. Plant–soil feedback also did not become more negative with increasing time since introduction. We discuss why our results may deviate from some earlier published studies and why plant–soil feedback may not in all cases, or not in all comparisons, explain patterns of local dominance of introduced exotic plant species. PMID:25770013

Pathogenesis and transmission of highly pathogenic avian influenza H5Nx in swine

USDA-ARS?s Scientific Manuscript database

Introduction Influenza A viruses (IAV) periodically transmit between pigs, people, and birds. If two IAV strains infect the same host, genes can reassort to generate progeny virus with potential to be more infectious or avoid immunity. Pigs pose a risk for such reassortment. Highly pathogenic avian ...

Implementation of next generation sequencing for high-throughput pathogen detection in sugarcane introductions grown in quarantine

USDA-ARS?s Scientific Manuscript database

The USDA-APHIS Plant Germplasm Quarantine Program (PGQP) safeguards U.S. agriculture and natural resources against the entry, establishment, and spread of economically and environmentally significant pathogens, and facilitates the safe international movement of propagative plant parts. PGQP is the o...

Phylogenetics of a fungal invasion: origins and widespread dispersal of white-nose syndrome

Treesearch

Kevin P. Drees; Jeffrey M. Lorch; Sebastien J. Puechmaille; Katy L. Parise; Gudrun Wibbelt; Joseph R. Hoyt; Keping Sun; Ariunbold Jargalsaikhan; Munkhnast Dalannast; Jonathan M. Palmer; Daniel L. Lindner; A. Marm Kilpatrick; Talima Pearson; Paul S. Keim; David S. Blehert; Jeffrey T. Foster; Joseph Heitman

2017-01-01

Globalization has facilitated the worldwide movement and introduction of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans, a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has...

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...

Impacts of exotic forest pathogens on Mediterranean ecosystems: Four case studies

Treesearch

Matteo Garbelotto; Marco Pautasso

2011-01-01

Mediterranean ecosystems are hotspots of biodiversity. Because of a coincidence of high species richness and human presence, Mediterranean biodiversity is particularly threatened by processes such as habitat degradation, fragmentation and loss, pollution, climate change and introduction of invasive species. Invasive tree pathogens are among the problematic exotic...

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

PubMed

Zhou, Hufeng; Gao, Shangzhi; Nguyen, Nam Ninh; Fan, Mengyuan; Jin, Jingjing; Liu, Bing; Zhao, Liang; Xiong, Geng; Tan, Min; Li, Shijun; Wong, Limsoon

2014-04-08

H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homology-based prediction is frequently used in predicting both intra-species and inter-species PPIs. However, some limitations are not properly resolved in several published works that predict eukaryote-prokaryote inter-species PPIs using intra-species template PPIs. We develop a stringent homology-based prediction approach by taking into account (i) differences between eukaryotic and prokaryotic proteins and (ii) differences between inter-species and intra-species PPI interfaces. We compare our stringent homology-based approach to a conventional homology-based approach for predicting host-pathogen PPIs, based on cellular compartment distribution analysis, disease gene list enrichment analysis, pathway enrichment analysis and functional category enrichment analysis. These analyses support the validity of our prediction result, and clearly show that our approach has better performance in predicting H. sapiens-M. tuberculosis H37Rv PPIs. Using our stringent homology-based approach, we have predicted a set of highly plausible H. sapiens-M. tuberculosis H37Rv PPIs which might be useful for many of related studies. Based on our analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent homology-based approach, we have discovered several interesting properties which are reported here for the first time. We find that both host proteins and pathogen proteins involved in the host-pathogen PPIs tend to be hubs in their own intra-species PPI network. Also, both host and pathogen proteins involved in host-pathogen PPIs tend to have longer primary sequence, tend to have more domains, tend to be more hydrophilic, etc. And the protein domains from both host and pathogen proteins involved in host-pathogen PPIs tend to have lower charge, and tend to be more hydrophilic. Our stringent homology-based prediction approach provides a better strategy in predicting PPIs between eukaryotic hosts and prokaryotic pathogens than a conventional homology-based approach. The properties we have observed from the predicted H. sapiens-M. tuberculosis H37Rv PPI network are useful for understanding inter-species host-pathogen PPI networks and provide novel insights for host-pathogen interaction studies.

Comparing introduction to Europe of highly pathogenic avian influenza viruses A(H5N8) in 2014 and A(H5N1) in 2005.

PubMed

Adlhoch, C; Gossner, C; Koch, G; Brown, I; Bouwstra, R; Verdonck, F; Penttinen, P; Harder, T

2014-12-18

Since the beginning of November 2014, nine outbreaks of highly pathogenic avian influenza virus (HPAIV) A(H5N8) in poultry have been detected in four European countries. In this report, similarities and differences between the modes of introduction of HPAIV A(H5N1) and A(H5N8) into Europe are described. Experiences from outbreaks of A(H5N1) in Europe demonstrated that early detection to control HPAIV in poultry has proven pivotal to minimise the risk of zoonotic transmission and prevention of human cases.

A naturally occurring nucleotide polymorphism in the orf2/folc promoter is associated with Streptococcus suis virulence.

PubMed

de Greeff, Astrid; Buys, Herma; Wells, Jerry M; Smith, Hilde E

2014-11-12

Streptococcus suis is a major problem in the swine industry causing meningitis, arthritis and pericarditis in piglets. Pathogenesis of S. suis is poorly understood. We previously showed that introduction of a 3 kb genomic fragment from virulent serotype 2 strain 10 into a weakly virulent serotype 2 strain S735, generated a hypervirulent isolate. The 3 kb genomic fragment contained two complete open reading frames (ORF) in an operon-structure of which one ORF showed similarity to folylpolyglutamate synthetase, whereas the function of the second ORF could not be predicted based on database searches for protein similarity. In this study we demonstrate that introduction of orf2 from strain 10 into strain S735 is sufficient to dramatically increase the virulence of S735 in pigs. This increase in virulence could not be associated with changes in pro-inflammatory responses of porcine blood mononucleated cells in response to S. suis in vitro. Sequence analysis of the orf2-folC-operon of S. suis isolates 10 and S735 revealed an SNP in the -35 region of the putative promoter sequence of the operon, as well as several SNPs resulting in amino acid substitutions in the ORF2 protein. Transcript levels of orf2 and folC were significantly higher in the virulent strain 10 than in the weakly virulent strain S735 and in vitro mutagenesis of the orf2 promoter confirmed that this was due to a SNP in the predicted -35 region upstream of the orf2 promoter. In this study, we demonstrated that the stronger promoter was present in all virulent and highly virulent S. suis isolates included in our study. This highlights a correlation between high orf2 expression and virulence. Conversely, the weaker promoter was present in isolates known to be weakly pathogenic or non-pathogenic. In summary, we demonstrate the importance of orf2 in the virulence of S. suis.

Not in your usual Top 10: protists that infect plants and algae

PubMed Central

Badstöber, Julia; Bulman, Simon; Desoignies, Nicolas; Etemadi, Mohammad; Falloon, Richard E.; Gachon, Claire M. M.; Legreve, Anne; Lukeš, Julius; Merz, Ueli; Nenarokova, Anna; Strittmatter, Martina; Sullivan, Brooke K.; Neuhauser, Sigrid

2017-01-01

Summary Fungi, nematodes and oomycetes belong to the most prominent eukaryotic plant pathogenic organisms. Unicellular organisms from other eukaryotic lineages, commonly addressed as protists, also infect plants. This review provides an introduction to plant pathogenic protists, including algae infecting oomycetes, and their current state of research. PMID:29024322

Assessing peracetic acid as a means to control post-vaccination Saprolegniasis in Atlantic salmon Salmo salar parr in recirculation aquaculture systems

USDA-ARS?s Scientific Manuscript database

Land-based closed containment facilities, utilizing recirculation aquaculture system (RAS) technologies, can reduce or eliminate the introduction of obligate fish pathogens. Regardless, the presence of opportunistic pathogens must be assumed, and these agents can cause disease during unfavorable con...

Survival of generic E. coli and surrogate E. coli O157:H7 in manure-amended soils

USDA-ARS?s Scientific Manuscript database

Introduction: Recently released U.S. FDA standards state that untreated biological soil amendments must be applied to soil 9 months before produce crop harvest to reduce pathogen contamination risk on produce. Manure and soil type may impact survival of bacterial pathogens. Purpose: Determine survi...

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions

PubMed Central

2014-01-01

Background H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homology-based prediction is frequently used in predicting both intra-species and inter-species PPIs. However, some limitations are not properly resolved in several published works that predict eukaryote-prokaryote inter-species PPIs using intra-species template PPIs. Results We develop a stringent homology-based prediction approach by taking into account (i) differences between eukaryotic and prokaryotic proteins and (ii) differences between inter-species and intra-species PPI interfaces. We compare our stringent homology-based approach to a conventional homology-based approach for predicting host-pathogen PPIs, based on cellular compartment distribution analysis, disease gene list enrichment analysis, pathway enrichment analysis and functional category enrichment analysis. These analyses support the validity of our prediction result, and clearly show that our approach has better performance in predicting H. sapiens-M. tuberculosis H37Rv PPIs. Using our stringent homology-based approach, we have predicted a set of highly plausible H. sapiens-M. tuberculosis H37Rv PPIs which might be useful for many of related studies. Based on our analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent homology-based approach, we have discovered several interesting properties which are reported here for the first time. We find that both host proteins and pathogen proteins involved in the host-pathogen PPIs tend to be hubs in their own intra-species PPI network. Also, both host and pathogen proteins involved in host-pathogen PPIs tend to have longer primary sequence, tend to have more domains, tend to be more hydrophilic, etc. And the protein domains from both host and pathogen proteins involved in host-pathogen PPIs tend to have lower charge, and tend to be more hydrophilic. Conclusions Our stringent homology-based prediction approach provides a better strategy in predicting PPIs between eukaryotic hosts and prokaryotic pathogens than a conventional homology-based approach. The properties we have observed from the predicted H. sapiens-M. tuberculosis H37Rv PPI network are useful for understanding inter-species host-pathogen PPI networks and provide novel insights for host-pathogen interaction studies. Reviewers This article was reviewed by Michael Gromiha, Narayanaswamy Srinivasan and Thomas Dandekar. PMID:24708540

The importance of mRNA structure in determining the pathogenicity of synonymous and non-synonymous mutations in haemophilia

PubMed Central

Hamasaki-Katagiri, Nobuko; Lin, Brian C.; Simon, Jonathan; Hunt, Ryan C.; Schiller, Tal; Russek-Cohen, Estelle; Komar, Anton A.; Bar, Haim; Kimchi-Sarfaty, Chava

2016-01-01

Introduction Mutational analysis is commonly used to support the diagnosis and management of haemophilia. This has allowed for the generation of large mutation databases which provide unparalleled insight into genotype-phenotype relationships. Haemophilia is associated with inversions, deletions, insertions, nonsense and missense mutations. Both synonymous and non-synonymous mutations influence the base pairing of messenger RNA (mRNA), which can alter mRNA structure, cellular half-life and ribosome processivity/elongation. However, the role of mRNA structure in determining the pathogenicity of point mutations in haemophilia has not been evaluated. Aim To evaluate mRNA thermodynamic stability and associated RNA prediction software as a means to distinguish between neutral and disease-associated mutations in haemophilia. Methods Five mRNA structure prediction software programs were used to assess the thermodynamic stability of mRNA fragments carrying neutral vs. disease-associated and synonymous vs. non-synonymous point mutations in F8, F9 and a third X-linked gene, DMD (dystrophin). Results In F8 and DMD, disease-associated mutations tend to occur in more structurally stable mRNA regions, represented by lower MFE (minimum free energy) levels. In comparing multiple software packages for mRNA structure prediction, a 101–151 nucleotide fragment length appears to be a feasible range for structuring future studies. Conclusion mRNA thermodynamic stability is one predictive characteristic, which when combined with other RNA and protein features, may offer significant insight when screening sequencing data for novel disease-associated mutations. Our results also suggest potential utility in evaluating the mRNA thermodynamic stability profile of a gene when determining the viability of interchanging codons for biological and therapeutic applications. PMID:27933712

Surveillance of low pathogenic novel H7N9 avian influenza in commercial poultry barns: detection of outbreaks and estimation of virus introduction time.

PubMed

Pinsent, Amy; Blake, Isobel M; White, Michael T; Riley, Steven

2014-08-01

Both high and low pathogenic subtype A avian influenza remain ongoing threats to the commercial poultry industry globally. The emergence of a novel low pathogenic H7N9 lineage in China presents itself as a new concern to both human and animal health and may necessitate additional surveillance in commercial poultry operations in affected regions. Sampling data was simulated using a mechanistic model of H7N9 influenza transmission within commercial poultry barns together with a stochastic observation process. Parameters were estimated using maximum likelihood. We assessed the probability of detecting an outbreak at time of slaughter using both real-time polymerase chain reaction (rt-PCR) and a hemagglutinin inhibition assay (HI assay) before considering more intense sampling prior to slaughter. The day of virus introduction and R0 were estimated jointly from weekly flock sampling data. For scenarios where R0 was known, we estimated the day of virus introduction into a barn under different sampling frequencies. If birds were tested at time of slaughter, there was a higher probability of detecting evidence of an outbreak using an HI assay compared to rt-PCR, except when the virus was introduced <2 weeks before time of slaughter. Prior to the initial detection of infection N sample = 50 (1%) of birds were sampled on a weekly basis once, but after infection was detected, N sample = 2000 birds (40%) were sampled to estimate both parameters. We accurately estimated the day of virus introduction in isolation with weekly and 2-weekly sampling. A strong sampling effort would be required to infer both the day of virus introduction and R0. Such a sampling effort would not be required to estimate the day of virus introduction alone once R0 was known, and sampling N sample = 50 of birds in the flock on a weekly or 2 weekly basis would be sufficient.

Spatio-temporal patterns of distribution of West Nile virus vectors in eastern Piedmont Region, Italy

PubMed Central

2011-01-01

Background West Nile Virus (WNV) transmission in Italy was first reported in 1998 as an equine outbreak near the swamps of Padule di Fucecchio, Tuscany. No other cases were identified during the following decade until 2008, when horse and human outbreaks were reported in Emilia Romagna, North Italy. Since then, WNV outbreaks have occurred annually, spreading from their initial northern foci throughout the country. Following the outbreak in 1998 the Italian public health authority defined a surveillance plan to detect WNV circulation in birds, horses and mosquitoes. By applying spatial statistical analysis (spatial point pattern analysis) and models (Bayesian GLMM models) to a longitudinal dataset on the abundance of the three putative WNV vectors [Ochlerotatus caspius (Pallas 1771), Culex pipiens (Linnaeus 1758) and Culex modestus (Ficalbi 1890)] in eastern Piedmont, we quantified their abundance and distribution in space and time and generated prediction maps outlining the areas with the highest vector productivity and potential for WNV introduction and amplification. Results The highest abundance and significant spatial clusters of Oc. caspius and Cx. modestus were in proximity to rice fields, and for Cx. pipiens, in proximity to highly populated urban areas. The GLMM model showed the importance of weather conditions and environmental factors in predicting mosquito abundance. Distance from the preferential breeding sites and elevation were negatively associated with the number of collected mosquitoes. The Normalized Difference Vegetation Index (NDVI) was positively correlated with mosquito abundance in rice fields (Oc. caspius and Cx. modestus). Based on the best models, we developed prediction maps for the year 2010 outlining the areas where high abundance of vectors could favour the introduction and amplification of WNV. Conclusions Our findings provide useful information for surveillance activities aiming to identify locations where the potential for WNV introduction and local transmission are highest. Such information can be used by vector control offices to stratify control interventions in areas prone to the invasion of WNV and other mosquito-transmitted pathogens. PMID:22152822

Spatio-temporal patterns of distribution of West Nile virus vectors in eastern Piedmont Region, Italy.

PubMed

Bisanzio, Donal; Giacobini, Mario; Bertolotti, Luigi; Mosca, Andrea; Balbo, Luca; Kitron, Uriel; Vazquez-Prokopec, Gonzalo M

2011-12-09

West Nile Virus (WNV) transmission in Italy was first reported in 1998 as an equine outbreak near the swamps of Padule di Fucecchio, Tuscany. No other cases were identified during the following decade until 2008, when horse and human outbreaks were reported in Emilia Romagna, North Italy. Since then, WNV outbreaks have occurred annually, spreading from their initial northern foci throughout the country. Following the outbreak in 1998 the Italian public health authority defined a surveillance plan to detect WNV circulation in birds, horses and mosquitoes. By applying spatial statistical analysis (spatial point pattern analysis) and models (Bayesian GLMM models) to a longitudinal dataset on the abundance of the three putative WNV vectors [Ochlerotatus caspius (Pallas 1771), Culex pipiens (Linnaeus 1758) and Culex modestus (Ficalbi 1890)] in eastern Piedmont, we quantified their abundance and distribution in space and time and generated prediction maps outlining the areas with the highest vector productivity and potential for WNV introduction and amplification. The highest abundance and significant spatial clusters of Oc. caspius and Cx. modestus were in proximity to rice fields, and for Cx. pipiens, in proximity to highly populated urban areas. The GLMM model showed the importance of weather conditions and environmental factors in predicting mosquito abundance. Distance from the preferential breeding sites and elevation were negatively associated with the number of collected mosquitoes. The Normalized Difference Vegetation Index (NDVI) was positively correlated with mosquito abundance in rice fields (Oc. caspius and Cx. modestus). Based on the best models, we developed prediction maps for the year 2010 outlining the areas where high abundance of vectors could favour the introduction and amplification of WNV. Our findings provide useful information for surveillance activities aiming to identify locations where the potential for WNV introduction and local transmission are highest. Such information can be used by vector control offices to stratify control interventions in areas prone to the invasion of WNV and other mosquito-transmitted pathogens.

Defining the frontiers between antifungal resistance, tolerance and the concept of persistence.

PubMed

Delarze, Eric; Sanglard, Dominique

2015-11-01

A restricted number of antifungal agents are available for the therapy of fungal diseases. With the introduction of epidemiological cut-off values for each agent in important fungal pathogens based on the distribution of minimal inhibitory concentration (MIC), the distinction between wild type and drug-resistant populations has been facilitated. Antifungal resistance has been described for all currently available antifungal agents in several pathogens and most of the associated resistance mechanisms have been deciphered at the molecular level. Clinical breakpoints for some agents have been proposed and can have predictive value for the success or failure of therapy. Tolerance to antifungals has been a much more ignored area. By definition, tolerance operates at antifungal concentrations above individual intrinsic inhibitory values. Important is that tolerance to antifungal agents favours the emergence of persister cells, which are able to survive antifungal therapy and can cause relapses. Here we will review the current knowledge on antifungal tolerance, its potential mechanisms and also evaluate the role of antifungal tolerance in the efficacy of drug treatments. Copyright © 2015 Elsevier Ltd. All rights reserved.

Highly pathogenic avian influenza A(H5N8) viruses reintroduced into South Korea by migratory waterfowl, 2014–2015

USDA-ARS?s Scientific Manuscript database

Highly pathogenic avian influenza A(H5N8) viruses were isolated from migratory waterfowl in South Korea during all 2014–winter 2015, a recurrence after initial introduction in winter 2014. These reappeared viruses were phylogenetically distinct from isolates circulating in poultry farms in South Kor...

Investigating the effectiveness of peracetic acid to reduce post-vaccination Saprolegnia spp.-associated mortality in Atlantic salmon parr while assessing impact on nitrification in recirculation aquaculture systems

USDA-ARS?s Scientific Manuscript database

Closed containment operations utilizing recirculation aquaculture systems (RAS) can provide critical barriers to the introduction of obligate fish pathogens (Timmons and Ebeling, 2010); however, opportunistic pathogens will be present and can cause disease when conditions favor these agents. One par...

Subcontinental impacts of an invasive tree disease on forest structure and dynamics

Treesearch

Jeffrey R. Garnas; Matthew P. Ayres; Andrew M. Liebhold; Celia. Evans

2011-01-01

Introduced pests and pathogens are a major source of disturbance to ecosystems world-wide. The famous examples have produced dramatic reductions in host abundance, including virtual extirpation, but most introductions have more subtle impacts that are hard to quantify but are potentially at least as important due to the pathogens' effects on host reproduction,...

Highly Pathogenic Avian Influenza A(H5N8) Viruses Reintroduced into South Korea by Migratory Waterfowl, 2014-2015.

PubMed

Kwon, Jung-Hoon; Lee, Dong-Hun; Swayne, David E; Noh, Jin-Yong; Yuk, Seong-Su; Erdene-Ochir, Tseren-Ochir; Hong, Woo-Tack; Jeong, Jei-Hyun; Jeong, Sol; Gwon, Gyeong-Bin; Song, Chang-Seon

2016-03-01

Highly pathogenic avian influenza A(H5N8) viruses were isolated from migratory waterfowl in South Korea during fall 2014-winter 2015, a recurrence after initial introduction in winter 2014. These reappeared viruses were phylogenetically distinct from isolates circulating in poultry farms in South Korea.

Host specificity of microsporidia pathogenic to the gypsy moth, Lymantria dispar (L.): Field studies in Slovakia

Treesearch

Leellen F. Solter; Daniela K. Pilarska; Michael L. McManus; Milan Zubrik; Jan Patocka; Wei-Fone Huang; Julius Novotny

2010-01-01

Several species of microsporidia are important chronic pathogens of Lymantria dispar in Europe but have never been recovered from North American gypsy moth populations. The major issue for their introduction into North American L. dispar populations is concern about their safety to native non-target insects. In this study, we...

Diseases of Forest Trees: Consequences of Exotic Ecosystems?

Treesearch

William J. Otrosina

1998-01-01

Much attention is now given to risks and impacts of exotic pest introductions in forest ecosystems. This concern is for good reason because, once introduced, an exotic pathogen or insect encounters little resistance in the native plant population and can produce catastrophic losses in relatively short periods of time. Most native fungal pathogens of forest trees have...

Introduction and establishment of Entomophaga maimaiga, a fungal pathogen of gypsy moth (Lepidoptera: Lymantriidae) in Michigan

Treesearch

D. R. Smitley; L. S. Bauer; A. E. Hajek; F. J. Sapio; R. A. Humber

1995-01-01

In 1991, late instars of gypsy moth, Lymantria dispar (L.), were sampled and diagnosed for infections of the pathogenic fungus Entomophaga maimaiga Humber, Shimazu & Soper and for gypsy moth nuclear polyhedrosis virus (NPV) at 50 sites in Michigan. Approximately 1,500 larvae were collected and reared from these sites, and no...

Predicting pathogen growth during short-term temperature abuse of raw pork, beef, and poultry products: use of an isothermal-based predictive tool.

PubMed

Ingham, Steven C; Fanslau, Melody A; Burnham, Greg M; Ingham, Barbara H; Norback, John P; Schaffner, Donald W

2007-06-01

A computer-based tool (available at: www.wisc.edu/foodsafety/meatresearch) was developed for predicting pathogen growth in raw pork, beef, and poultry meat. The tool, THERM (temperature history evaluation for raw meats), predicts the growth of pathogens in pork and beef (Escherichia coli O157:H7, Salmonella serovars, and Staphylococcus aureus) and on poultry (Salmonella serovars and S. aureus) during short-term temperature abuse. The model was developed as follows: 25-g samples of raw ground pork, beef, and turkey were inoculated with a five-strain cocktail of the target pathogen(s) and held at isothermal temperatures from 10 to 43.3 degrees C. Log CFU per sample data were obtained for each pathogen and used to determine lag-phase duration (LPD) and growth rate (GR) by DMFit software. The LPD and GR were used to develop the THERM predictive tool, into which chronological time and temperature data for raw meat processing and storage are entered. The THERM tool then predicts a delta log CFU value for the desired pathogen-product combination. The accuracy of THERM was tested in 20 different inoculation experiments that involved multiple products (coarse-ground beef, skinless chicken breast meat, turkey scapula meat, and ground turkey) and temperature-abuse scenarios. With the time-temperature data from each experiment, THERM accurately predicted the pathogen growth and no growth (with growth defined as delta log CFU > 0.3) in 67, 85, and 95% of the experiments with E. coli 0157:H7, Salmonella serovars, and S. aureus, respectively, and yielded fail-safe predictions in the remaining experiments. We conclude that THERM is a useful tool for qualitatively predicting pathogen behavior (growth and no growth) in raw meats. Potential applications include evaluating process deviations and critical limits under the HACCP (hazard analysis critical control point) system.

Marine cargo imports and forest pest introductions

Treesearch

Frank H. Koch

2009-01-01

A major pathway for the introduction of nonindigenous forest pests is accidental transport on cargo imported from overseas. Diseases may be brought into the United States via commercial trade of nursery stock or other live plant material, as has been suggested for Phytophthora ramorum, the pathogen that causes sudden oak death (Ivors and others 2006). Insects may...

Introduction of Non-Native Pollinators Can Lead to Trans-Continental Movement of Bee-Associated Fungi.

PubMed

Hedtke, Shannon M; Blitzer, Eleanor J; Montgomery, Graham A; Danforth, Bryan N

2015-01-01

Bees are essential pollinators for many flowering plants, including agriculturally important crops such as apple. As geographic ranges of bees or their host plants change as a result of human activities, we need to identify pathogens that could be transmitted among newly sympatric species to evaluate and anticipate their effects on bee communities. We used PCR screening and DNA sequencing to evaluate exposure to potentially disease-causing microorganisms in a pollinator of apple, the horned mason bee (Osmia cornifrons). We did not detect microsporidia, Wolbachia, or trypanosomes, which are common pathogens of bees, in any of the hundreds of mason bees screened. We did detect both pathogenic and apathogenic (saprophytic) fungal species in the genus Ascosphaera (chalkbrood), an unidentified species of Aspergillus fungus, and a strain of bacteria in the genus Paenibacillus that is probably apathogenic. We detected pathogenic fungal strains in asymptomatic adult bees that therefore may be carriers of disease. We demonstrate that fungi from the genus Ascosphaera have been transported to North America along with the bee from its native range in Japan, and that O. cornifrons is exposed to fungi previously only identified from nests of other related bee species. Further study will be required to quantify pathogenicity and health effects of these different microbial species on O. cornifrons and on closely-related native North American mason bees that may now be exposed to novel pathogens. A global perspective is required for pathogen research as geographic ranges of insects and microorganisms shift due to intentional or accidental introductions.

Nowcasting the spread of chikungunya virus in the Americas.

PubMed

Johansson, Michael A; Powers, Ann M; Pesik, Nicki; Cohen, Nicole J; Staples, J Erin

2014-01-01

In December 2013, the first locally-acquired chikungunya virus (CHIKV) infections in the Americas were reported in the Caribbean. As of May 16, 55,992 cases had been reported and the outbreak was still spreading. Identification of newly affected locations is paramount to intervention activities, but challenging due to limitations of current data on the outbreak and on CHIKV transmission. We developed models to make probabilistic predictions of spread based on current data considering these limitations. Branching process models capturing travel patterns, local infection prevalence, climate dependent transmission factors, and associated uncertainty estimates were developed to predict probable locations for the arrival of CHIKV-infected travelers and for the initiation of local transmission. Many international cities and areas close to where transmission has already occurred were likely to have received infected travelers. Of the ten locations predicted to be the most likely locations for introduced CHIKV transmission in the first four months of the outbreak, eight had reported local cases by the end of April. Eight additional locations were likely to have had introduction leading to local transmission in April, but with substantial uncertainty. Branching process models can characterize the risk of CHIKV introduction and spread during the ongoing outbreak. Local transmission of CHIKV is currently likely in several Caribbean locations and possible, though uncertain, for other locations in the continental United States, Central America, and South America. This modeling framework may also be useful for other outbreaks where the risk of pathogen spread over heterogeneous transportation networks must be rapidly assessed on the basis of limited information.

Modeling the Spread of Methicillin-Resistant Staphylococcus aureus in Nursing Homes for Elderly

PubMed Central

Chamchod, Farida; Ruan, Shigui

2012-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) is endemic in many hospital settings, including nursing homes. It is an important nosocomial pathogen that causes mortality and an economic burden to patients, hospitals, and the community. The epidemiology of the bacteria in nursing homes is both hospital- and community-like. Transmission occurs via hands of health care workers (HCWs) and direct contacts among residents during social activities. In this work, mathematical modeling in both deterministic and stochastic frameworks is used to study dissemination of MRSA among residents and HCWs, persistence and prevalence of MRSA in a population, and possible means of controlling the spread of this pathogen in nursing homes. The model predicts that: without strict screening and decolonization of colonized individuals at admission, MRSA may persist; decolonization of colonized residents, improving hand hygiene in both residents and HCWs, reducing the duration of contamination of HCWs, and decreasing the resident∶staff ratio are possible control strategies; the mean time that a resident remains susceptible since admission may be prolonged by screening and decolonization treatment in colonized individuals; in the stochastic framework, the total number of colonized residents varies and may increase when the admission of colonized residents, the duration of colonization, the average number of contacts among residents, or the average number of contacts that each resident requires from HCWs increases; an introduction of a colonized individual into an MRSA-free nursing home has a much higher probability of leading to a major outbreak taking off than an introduction of a contaminated HCW. PMID:22238650

Prediction of pathogen growth on iceberg lettuce under real temperature history during distribution from farm to table.

PubMed

Koseki, Shigenobu; Isobe, Seiichiro

2005-10-25

The growth of pathogenic bacteria Escherichia coli O157:H7, Salmonella spp., and Listeria monocytogenes on iceberg lettuce under constant and fluctuating temperatures was modelled in order to estimate the microbial safety of this vegetable during distribution from the farm to the table. Firstly, we examined pathogen growth on lettuce at constant temperatures, ranging from 5 to 25 degrees C, and then we obtained the growth kinetic parameters (lag time, maximum growth rate (micro(max)), and maximum population density (MPD)) using the Baranyi primary growth model. The parameters were similar to those predicted by the pathogen modelling program (PMP), with the exception of MPD. The MPD of each pathogen on lettuce was 2-4 log(10) CFU/g lower than that predicted by PMP. Furthermore, the MPD of pathogens decreased with decreasing temperature. The relationship between mu(max) and temperature was linear in accordance with Ratkowsky secondary model as was the relationship between the MPD and temperature. Predictions of pathogen growth under fluctuating temperature used the Baranyi primary microbial growth model along with the Ratkowsky secondary model and MPD equation. The fluctuating temperature profile used in this study was the real temperature history measured during distribution from the field at harvesting to the retail store. Overall predictions for each pathogen agreed well with observed viable counts in most cases. The bias and root mean square error (RMSE) of the prediction were small. The prediction in which mu(max) was based on PMP showed a trend of overestimation relative to prediction based on lettuce. However, the prediction concerning E. coli O157:H7 and Salmonella spp. on lettuce greatly overestimated growth in the case of a temperature history starting relatively high, such as 25 degrees C for 5 h. In contrast, the overall prediction of L. monocytogenes under the same circumstances agreed with the observed data.

An improved method to simultaneously detect Salmonella enteritidis, Escherichia coli O157 and Listeria monocytogenes in ground black pepper using multiplex real-time PCR

USDA-ARS?s Scientific Manuscript database

Introduction: The three common foodborne pathogens implicated in foodborne outbreaks are Salmonella spp., Escherichia coli O157:H7 and Listeria monocytogenes. Hence, it is important to identify these pathogens in contaminated foods so that they can be eliminated from the marketplace. At present, the...

Resequencing of the Phytophthora ramorum genome to characterize genetic variation and population dynamics of the invasive pathogen

Treesearch

Jennifer Yuzon; David M. Rizzo; Mathu Malar C; Sucheta Tripathy; Takao Kasuga

2017-01-01

Phytophthora ramorum has spread and diversified throughout California’s northwestern coast since its introduction in the 1990s. Tracking the spread of P. ramorum and the functional response of the pathogen to the environment is of particular interest to managing the epidemic. Using genetic tools such as microsatellite...

Inactivation of Salmonella, Escherichia coli O157:H7 and non-O157 STEC by hypochlorite solutions with high organic loads

USDA-ARS?s Scientific Manuscript database

Introduction: Salmonella, E. coli O157:H7 and Non-O157 STEC have been recognized as foodborne pathogen concerns for fresh produce. Although chlorinated water (CW) is widely used in fresh produce processing to reduce pathogens and prevent cross-contamination, limited information is available on effic...

A quantitative assessment of the risk for highly pathogenic avian influenza introduction into Spain via legal trade of live poultry.

PubMed

Sánchez-Vizcaíno, Fernando; Perez, Andrés; Lainez, Manuel; Sánchez-Vizcaíno, José Manuel

2010-05-01

Highly pathogenic avian influenza (HPAI) is considered one of the most important diseases of poultry. During the last 9 years, HPAI epidemics have been reported in Asia, the Americas, Africa, and in 18 countries of the European Union (EU). For that reason, it is possible that the risk for HPAI virus (HPAIV) introduction into Spain may have recently increased. Because of the EU free-trade policy and because legal trade of live poultry was considered an important route for HPAI spread in certain regions of the world, there are fears that Spain may become HPAIV-infected as a consequence of the legal introduction of live poultry. However, no quantitative assessment of the risk for HPAIV introduction into Spain or into any other EU member state via the trade of poultry has been published in the peer-reviewed literature. This article presents the results of the first quantitative assessment of the risk for HPAIV introduction into a free country via legal trade of live poultry, along with estimates of the geographical variation of the risk and of the relative contribution of exporting countries and susceptible poultry species to the risk. The annual mean risk for HPAI introduction into Spain was estimated to be as low as 1.36 x 10(-3), suggesting that under prevailing conditions, introduction of HPAIV into Spain through the trade of live poultry is unlikely to occur. Moreover, these results support the hypothesis that legal trade of live poultry does not impose a significant risk for the spread of HPAI into EU member states.

Wildlife health implications of sewage disposal in wetlands

USGS Publications Warehouse

Friend, M.; Godfrey, P.J.; Kaynor, E.R.; Pelczarski, S.

1985-01-01

Wildlife health concerns associated with disposal of sewage effluent in wetlands are of three primary types: (1) introduction of pathogens, (2) introduction of pollutants that adversely impact on host body defense mechanisms, and (3) changes in the physical and chemical properties of wetlands that favor the development and maintenance of disease problems. Unlike the situation with human health concerns, introduction of pathogens is not the major concern regarding wildlife health. Instead, the focus of attention needs to be directed at environmental changes likely to take place as a result of effluent discharges into different types of wetlands. Unless these changes are adequately addressed from a disease perspective, marshes utilized for sewage disposal could become disease incubators and wildlife death traps. This result would be unfortunate because the backlash would likely negate the potentially beneficial aspects of the use of sewage wastewater for the creation of new wetlands and have a severe impact on progress being made towards evaluation of the compatibility of wildlife and sewage effluents.

Spread of the Tiger: Global Risk of Invasion by the Mosquito Aedes albopictus

PubMed Central

BENEDICT, MARK Q.; LEVINE, REBECCA S.; HAWLEY, WILLIAM A.; LOUNIBOS, L. PHILIP

2008-01-01

Aedes albopictus, commonly known as the Asian tiger mosquito, is currently the most invasive mosquito in the world. It is of medical importance due to its aggressive daytime human-biting behavior and ability to vector many viruses, including dengue, LaCrosse, and West Nile. Invasions into new areas of its potential range are often initiated through the transportation of eggs via the international trade in used tires. We use a genetic algorithm, Genetic Algorithm for Rule Set Production (GARP), to determine the ecological niche of Ae. albopictus and predict a global ecological risk map for the continued spread of the species. We combine this analysis with risk due to importation of tires from infested countries and their proximity to countries that have already been invaded to develop a list of countries most at risk for future introductions and establishments. Methods used here have potential for predicting risks of future invasions of vectors or pathogens. PMID:17417960

Computational prediction of host-pathogen protein-protein interactions.

PubMed

Dyer, Matthew D; Murali, T M; Sobral, Bruno W

2007-07-01

Infectious diseases such as malaria result in millions of deaths each year. An important aspect of any host-pathogen system is the mechanism by which a pathogen can infect its host. One method of infection is via protein-protein interactions (PPIs) where pathogen proteins target host proteins. Developing computational methods that identify which PPIs enable a pathogen to infect a host has great implications in identifying potential targets for therapeutics. We present a method that integrates known intra-species PPIs with protein-domain profiles to predict PPIs between host and pathogen proteins. Given a set of intra-species PPIs, we identify the functional domains in each of the interacting proteins. For every pair of functional domains, we use Bayesian statistics to assess the probability that two proteins with that pair of domains will interact. We apply our method to the Homo sapiens-Plasmodium falciparum host-pathogen system. Our system predicts 516 PPIs between proteins from these two organisms. We show that pairs of human proteins we predict to interact with the same Plasmodium protein are close to each other in the human PPI network and that Plasmodium pairs predicted to interact with same human protein are co-expressed in DNA microarray datasets measured during various stages of the Plasmodium life cycle. Finally, we identify functionally enriched sub-networks spanned by the predicted interactions and discuss the plausibility of our predictions. Supplementary data are available at http://staff.vbi.vt.edu/dyermd/publications/dyer2007a.html. Supplementary data are available at Bioinformatics online.

A really useful pathogen, Agrobacterium tumefaciens.

PubMed

Yuan, Ze-Chun; Williams, Mary

2012-10-01

Bacteria of the genus Agrobacterium are very useful and unusual plant pathogens. Through a rare inter-kingdom DNA transfer, the bacteria move some of their genes into their host's genome, thereby inducing the host cells to proliferate and produce opines, nutrients sources for the pathogen. Agrobacterium's ability to transfer DNA makes can be adapted to introduce other genes, such as those encoding useful traits, into plant genomes. The development of Agrobacterium as a tool to transform plants is a landmark event in modern plant biology. This lecture provides an introduction to Agrobacterium tumefaciens and related species, focusing on their modes of pathogenicity, their usefulness as tools for plant transformation, and their use as a model for the study of plant-pathogen interactions.

Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species

PubMed Central

Baroncelli, Riccardo; Zapparata, Antonio; Sarrocco, Sabrina; Sukno, Serenella A.; Lane, Charles R.; Thon, Michael R.; Vannacci, Giovanni; Holub, Eric; Sreenivasaprasad, Surapareddy

2015-01-01

Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production. PMID:26086351

Survey of Armillaria spp. in the Oregon East Cascades: Baseline data for predicting climatic influences on Armillaria root disease

Treesearch

J. W. Hanna; A. L. Smith; H. M. Maffei; M.-S. Kim; N. B. Klopfenstein

2008-01-01

Root disease pathogens, such as Armillaria solidipes Peck (recently recognized older name for A. ostoyae), will likely have increasing impacts to forest ecosystems as trees undergo stress due to climate change. Before we can predict future impacts of root disease pathogens, we must first develop an ability to predict current distributions of the pathogens (and their...

Evaluating the risk of pathogen transmission from wild animals to domestic pigs in Australia.

PubMed

Pearson, Hayley E; Toribio, Jenny-Ann L M L; Lapidge, Steven J; Hernández-Jover, Marta

2016-01-01

Wild animals contribute to endemic infection in livestock as well as the introduction, reintroduction and maintenance of pathogens. The source of introduction of endemic diseases to a piggery is often unknown and the extent of wildlife contribution to such local spread is largely unexplored. The aim of the current study was to quantitatively assess the probability of domestic pigs being exposed to different pathogens from wild animals commonly found around commercial piggeries in Australia. Specifically, this study aims to quantify the probability of exposure to the pathogens Escherichia coli, Salmonella spp. and Campylobacter spp. from European starlings (Sturnus vulgarus); Brachyspira hyodysenteriae, Lawsonia intracellularis and Salmonella spp. from rats (Rattus rattus and Rattus norvegicus); and Mycoplasma hyopneumoniae, Leptospira spp., Brucella suis and L. intracellularis from feral pigs (Sus scrofa). Exposure assessments, using scenario trees and Monte Carlo stochastic simulation modelling, were conducted to identify potential pathways of introduction and calculate the probabilities of these pathways occurring. Input parameters were estimated from a national postal survey of commercial pork producers and from disease detection studies conducted for European starlings, rats and feral pigs in close proximity to commercial piggeries in Australia. Based on the results of the exposure assessments, rats presented the highest probability of exposure of pathogens to domestic pigs at any point in time, and L. intracellularis (median 0.13, 5% and 95%, 0.05-0.23) and B. hyodysenteriae (median 0.10, 0.05-0.19) were the most likely pathogens to be transmitted. Regarding European starlings, the median probability of exposure of domestic pigs to pathogenic E. coli at any point in time was estimated to be 0.03 (0.02-0.04). The highest probability of domestic pig exposure to feral pig pathogens at any point in time was found to be for M. hyopneumoniae (median 0.013, 0.007-0.022) and L. intracellularis (median 0.006, 0.003-0.011) for pigs in free-range piggeries. The sensitivity analysis indicates that the presence and number of wild animals around piggeries, their access to piggeries and pig food and water, and, in the case of feral pigs, their proximity to piggeries, are the most influential parameters on the probability of exposure. Findings from this study support identification of mitigation strategies that could be implemented at on-farm and industry level to minimize the exposure risk from European starlings, rats and feral pigs. Copyright © 2015 Elsevier B.V. All rights reserved.

Not in your usual Top 10: protists that infect plants and algae.

PubMed

Schwelm, Arne; Badstöber, Julia; Bulman, Simon; Desoignies, Nicolas; Etemadi, Mohammad; Falloon, Richard E; Gachon, Claire M M; Legreve, Anne; Lukeš, Julius; Merz, Ueli; Nenarokova, Anna; Strittmatter, Martina; Sullivan, Brooke K; Neuhauser, Sigrid

2018-04-01

Fungi, nematodes and oomycetes belong to the most prominent eukaryotic plant pathogenic organisms. Unicellular organisms from other eukaryotic lineages, commonly addressed as protists, also infect plants. This review provides an introduction to plant pathogenic protists, including algae infecting oomycetes, and their current state of research. © 2017 THE AUTHORS. MOLECULAR PLANT PATHOLOGY PUBLISHED BY BRITISH SOCIETY FOR PLANT PATHOLOGY AND JOHN WILEY & SONS LTD.

Genetic Diversity of Highly Pathogenic Avian Influenza A(H5N8/H5N5) Viruses in Italy, 2016-17.

PubMed

Fusaro, Alice; Monne, Isabella; Mulatti, Paolo; Zecchin, Bianca; Bonfanti, Lebana; Ormelli, Silvia; Milani, Adelaide; Cecchettin, Krizia; Lemey, Philippe; Moreno, Ana; Massi, Paola; Dorotea, Tiziano; Marangon, Stefano; Terregino, Calogero

2017-09-01

In winter 2016-17, highly pathogenic avian influenza A(H5N8) and A(H5N5) viruses of clade 2.3.4.4 were identified in wild and domestic birds in Italy. We report the occurrence of multiple introductions and describe the identification in Europe of 2 novel genotypes, generated through multiple reassortment events.

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.

Gene Function Analysis in the Ubiquitous Human Commensal and Pathogen Malassezia Genus.

PubMed

Ianiri, Giuseppe; Averette, Anna F; Kingsbury, Joanne M; Heitman, Joseph; Idnurm, Alexander

2016-11-29

The genus Malassezia includes 14 species that are found on the skin of humans and animals and are associated with a number of diseases. Recent genome sequencing projects have defined the gene content of all 14 species; however, to date, genetic manipulation has not been possible for any species within this genus. Here, we develop and then optimize molecular tools for the transformation of Malassezia furfur and Malassezia sympodialis using Agrobacterium tumefaciens delivery of transfer DNA (T-DNA) molecules. These T-DNAs can insert randomly into the genome. In the case of M. furfur, targeted gene replacements were also achieved via homologous recombination, enabling deletion of the ADE2 gene for purine biosynthesis and of the LAC2 gene predicted to be involved in melanin biosynthesis. Hence, the introduction of exogenous DNA and direct gene manipulation are feasible in Malassezia species. Species in the genus Malassezia are a defining component of the microbiome of the surface of mammals. They are also associated with a wide range of skin disease symptoms. Many species are difficult to culture in vitro, and although genome sequences are available for the species in this genus, it has not been possible to assess gene function to date. In this study, we pursued a series of possible transformation methods and identified one that allows the introduction of DNA into two species of Malassezia, including the ability to make targeted integrations into the genome such that genes can be deleted. This research opens a new direction in terms of now being able to analyze gene functions in this little understood genus. These tools will contribute to define the mechanisms that lead to the commensalism and pathogenicity in this group of obligate fungi that are predominant on the skin of mammals. Copyright © 2016 Ianiri et al.

Evaluation of nanoparticles as endocytic tracers in cellular microbiology

NASA Astrophysics Data System (ADS)

Zhang, Yuying; Hensel, Michael

2013-09-01

The study of pathogen interactions with eukaryotic host cells requires the introduction of fluorescent probes to visualize processes such as endocytosis, intracellular transport or host cell manipulation by the pathogen. Here, three types of fluorescent nanoparticles (NPs), i.e. Rhodamine-labeled polymethacrylate (PMA) NPs, silica NPs and gold NPs, were employed to label the host cellular endolysosomal system and monitor manipulations by the pathogen Salmonella enterica. Using live cell imaging, we investigated the performance of NPs in cellular uptake, labeling of endocytic vesicles and lysosomes, as well as interaction with the pathogen. We show that fluorescent gold and silica, but not PMA NPs appropriately label host cell structures and efficiently track rearrangements of the host endosomal system by the activities of intracellular Salmonella. Silica NPs slightly aggregated and located in Salmonella-induced compartments as isolated dots, while gold NPs distributed uniformly inside such structures. Both silica and gold NPs exhibited no adverse impact on either host cells or pathogens, and are versatile tools for infection biology.The study of pathogen interactions with eukaryotic host cells requires the introduction of fluorescent probes to visualize processes such as endocytosis, intracellular transport or host cell manipulation by the pathogen. Here, three types of fluorescent nanoparticles (NPs), i.e. Rhodamine-labeled polymethacrylate (PMA) NPs, silica NPs and gold NPs, were employed to label the host cellular endolysosomal system and monitor manipulations by the pathogen Salmonella enterica. Using live cell imaging, we investigated the performance of NPs in cellular uptake, labeling of endocytic vesicles and lysosomes, as well as interaction with the pathogen. We show that fluorescent gold and silica, but not PMA NPs appropriately label host cell structures and efficiently track rearrangements of the host endosomal system by the activities of intracellular Salmonella. Silica NPs slightly aggregated and located in Salmonella-induced compartments as isolated dots, while gold NPs distributed uniformly inside such structures. Both silica and gold NPs exhibited no adverse impact on either host cells or pathogens, and are versatile tools for infection biology. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr01550e

PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data.

PubMed

Cosentino, Salvatore; Voldby Larsen, Mette; Møller Aarestrup, Frank; Lund, Ole

2013-01-01

Although the majority of bacteria are harmless or even beneficial to their host, others are highly virulent and can cause serious diseases, and even death. Due to the constantly decreasing cost of high-throughput sequencing there are now many completely sequenced genomes available from both human pathogenic and innocuous strains. The data can be used to identify gene families that correlate with pathogenicity and to develop tools to predict the pathogenicity of newly sequenced strains, investigations that previously were mainly done by means of more expensive and time consuming experimental approaches. We describe PathogenFinder (http://cge.cbs.dtu.dk/services/PathogenFinder/), a web-server for the prediction of bacterial pathogenicity by analysing the input proteome, genome, or raw reads provided by the user. The method relies on groups of proteins, created without regard to their annotated function or known involvement in pathogenicity. The method has been built to work with all taxonomic groups of bacteria and using the entire training-set, achieved an accuracy of 88.6% on an independent test-set, by correctly classifying 398 out of 449 completely sequenced bacteria. The approach here proposed is not biased on sets of genes known to be associated with pathogenicity, thus the approach could aid the discovery of novel pathogenicity factors. Furthermore the pathogenicity prediction web-server could be used to isolate the potential pathogenic features of both known and unknown strains.

Tropospheric ozone as a fungal elicitor.

PubMed

Zuccarini, Paolo

2009-03-01

Tropospheric ozone has been proven to trigger biochemical plant responses that are similar to the ones induced by an attack of fungal pathogens,i.e. it resembles fungal elicitors.This suggests that ozone can represent a valid tool for the study of stress responses and induction of resistance to pathogens. This review provides an overview of the implications of such a phenomenon for basic and applied research. After an introduction about the environmental implications of tropospheric ozone and plant responses to biotic stresses, the biochemistry of ozone stress is analysed, pointing out its similarities with plant responses to pathogens and its possible applications.

Risk factors for the introduction of high pathogenicity Avian Influenza virus into poultry farms during the epidemic in the Netherlands in 2003.

PubMed

Thomas, M E; Bouma, A; Ekker, H M; Fonken, A J M; Stegeman, J A; Nielen, M

2005-06-10

An epidemic of high pathogenicity Avian Influenza (HPAI) occurred in the Netherlands in 2003. A census survey of 173 infected and 401 uninfected commercial poultry farms was carried out to identify factors associated with the introduction of the HPAI virus into poultry farms. Data on farm size, production characteristics, type of housing, presence of cattle and pigs were gathered by the National Inspection Service for Livestock and Meat from all farms included in this study. For each risk factor (RF) available for analysis, the Mantel-Haenszel odds ratio was calculated (stratified on farm size and housing type). We found an increased risk of HPAI virus introduction in layer finisher type poultry: OR = 2.05 (95% confidence interval, CI = 1.29-3.27). An explanation for this increased risk is the high number of contacts between these farms, especially via cardboard egg trays used for removal of eggs during the epidemic. Our analysis did not indicate significant differences between the infected and uninfected farms with regard to housing type, presence of cattle or pigs. Since layer finisher type farms are assumed to be at higher risk for HPAI virus introduction, more specific control measures might be applied in future outbreaks.

A network approach to predict pathogenic genes for Fusarium graminearum.

PubMed

Liu, Xiaoping; Tang, Wei-Hua; Zhao, Xing-Ming; Chen, Luonan

2010-10-04

Fusarium graminearum is the pathogenic agent of Fusarium head blight (FHB), which is a destructive disease on wheat and barley, thereby causing huge economic loss and health problems to human by contaminating foods. Identifying pathogenic genes can shed light on pathogenesis underlying the interaction between F. graminearum and its plant host. However, it is difficult to detect pathogenic genes for this destructive pathogen by time-consuming and expensive molecular biological experiments in lab. On the other hand, computational methods provide an alternative way to solve this problem. Since pathogenesis is a complicated procedure that involves complex regulations and interactions, the molecular interaction network of F. graminearum can give clues to potential pathogenic genes. Furthermore, the gene expression data of F. graminearum before and after its invasion into plant host can also provide useful information. In this paper, a novel systems biology approach is presented to predict pathogenic genes of F. graminearum based on molecular interaction network and gene expression data. With a small number of known pathogenic genes as seed genes, a subnetwork that consists of potential pathogenic genes is identified from the protein-protein interaction network (PPIN) of F. graminearum, where the genes in the subnetwork are further required to be differentially expressed before and after the invasion of the pathogenic fungus. Therefore, the candidate genes in the subnetwork are expected to be involved in the same biological processes as seed genes, which imply that they are potential pathogenic genes. The prediction results show that most of the pathogenic genes of F. graminearum are enriched in two important signal transduction pathways, including G protein coupled receptor pathway and MAPK signaling pathway, which are known related to pathogenesis in other fungi. In addition, several pathogenic genes predicted by our method are verified in other pathogenic fungi, which demonstrate the effectiveness of the proposed method. The results presented in this paper not only can provide guidelines for future experimental verification, but also shed light on the pathogenesis of the destructive fungus F. graminearum.

Predicting factors for malaria re-introduction: an applied model in an elimination setting to prevent malaria outbreaks.

PubMed

Ranjbar, Mansour; Shoghli, Alireza; Kolifarhood, Goodarz; Tabatabaei, Seyed Mehdi; Amlashi, Morteza; Mohammadi, Mahdi

2016-03-02

Malaria re-introduction is a challenge in elimination settings. To prevent re-introduction, receptivity, vulnerability, and health system capacity of foci should be monitored using appropriate tools. This study aimed to design an applicable model to monitor predicting factors of re-introduction of malaria in highly prone areas. This exploratory, descriptive study was conducted in a pre-elimination setting with a high-risk of malaria transmission re-introduction. By using nominal group technique and literature review, a list of predicting indicators for malaria re-introduction and outbreak was defined. Accordingly, a checklist was developed and completed in the field for foci affected by re-introduction and for cleared-up foci as a control group, for a period of 12 weeks before re-introduction and for the same period in the previous year. Using field data and analytic hierarchical process (AHP), each variable and its sub-categories were weighted, and by calculating geometric means for each sub-category, score of corresponding cells of interaction matrices, lower and upper threshold of different risks strata, including low and mild risk of re-introduction and moderate and high risk of malaria outbreaks, were determined. The developed predictive model was calibrated through resampling with different sets of explanatory variables using R software. Sensitivity and specificity of the model were calculated based on new samples. Twenty explanatory predictive variables of malaria re-introduction were identified and a predictive model was developed. Unpermitted immigrants from endemic neighbouring countries were determined as a pivotal factor (AHP score: 0.181). Moreover, quality of population movement (0.114), following malaria transmission season (0.088), average daily minimum temperature in the previous 8 weeks (0.062), an outdoor resting shelter for vectors (0.045), and rainfall (0.042) were determined. Positive and negative predictive values of the model were 81.8 and 100 %, respectively. This study introduced a new, simple, yet reliable model to forecast malaria re-introduction and outbreaks eight weeks in advance in pre-elimination and elimination settings. The model incorporates comprehensive deterministic factors that can easily be measured in the field, thereby facilitating preventive measures.

Disease in marine aquaculture

NASA Astrophysics Data System (ADS)

Sindermann, C. J.

1984-03-01

It has become almost a truism that success in intensive production of animals must be based in part on development of methods for disease diagnosis and control. Excellent progress has been made in methods of diagnosis for major pathogens of cultivated fish, crustacean and molluscan species. In many instances these have proved to be facultative pathogens, able to exert severe effects in populations of animals under other stresses (marginal physical or chemical conditions; overcrowding). The concept of stress management as a critical prophylactic measure is not new, but its significance is being demonstrated repeatedly. The particular relationship of water quality and facultative pathogens such as Vibrio, Pseudomonas and Aeromonas species has been especially apparent. Virus diseases of marine vertebrates and invertebrates — little known two decades ago — are now recognized to be of significance to aquaculture. Virus infections of oysters, clams, shrimps and crabs have been described, and mortalities have been attributed to them. Several virus diseases of fish have also been recognized as potential or actual problems in culture. In some instances, the pathogens seem to be latent in natural populations, and may be provoked into patency by stresses of artificial environments. One of the most promising approaches to disease prophylaxis is through immunization. Fish respond well to various vaccination procedures, and new non-stressing methods have been developed. Vibriosis — probably the most severe disease of ocean-reared salmon — has been controlled to a great extent through use of a polyvalent bacterin, which can be modified as new pathogenic strains are isolated. Prophylactic immunization for other bacterial diseases of cultivated fish has been attempted, especially in Japan, with some success. There is also some evidence that the larger crustaceans may be immunologically responsive, and that at least short-term protection may be afforded to cultured populations. Some progress has been made in marine disease control through chemical treatment in intensive culture systems, principally through application and modification of methods developed for freshwater aquaculture. Major constraints to use of chemicals are restrictions due to public health concerns about food contamination, and the negative effects of some chemicals on biological filters and on algal food production. There is a continuing need, however, for development of specific treatments for acute disease episodes — such as the nitrofurans, developed in Japan, which are effective for some bacterial diseases. The history of aquaculture — freshwater as well as marine — has been characterized by transfers and introductions of species to waters beyond their present ranges. The process continues, and carries with it the possibility of transfers of pathogens to native species and to the recipient culture environments. International groups are attempting to define codes of practice to govern such mass movements, but examples of introductions of real or potential pathogens already exist. The most recent and the most dramatic is the world wide transfer of a virus pathogen of penaeid shrimps. Earlier examples include the introduction of a protozoan pathogen of salmonids to the western hemisphere, and the introduction of a parasitic copepod from the Far East to the west coast of North America and to France. The conclusion is inevitable — diseases are substantial deterrents to aquaculture production. Diagnostic and control procedures are and will be important components of emerging aquaculture technology.

Comparison of fecal indicators with pathogenic bacteria and rotavirus in groundwater.

PubMed

Ferguson, Andrew S; Layton, Alice C; Mailloux, Brian J; Culligan, Patricia J; Williams, Daniel E; Smartt, Abby E; Sayler, Gary S; Feighery, John; McKay, Larry D; Knappett, Peter S K; Alexandrova, Ekaterina; Arbit, Talia; Emch, Michael; Escamilla, Veronica; Ahmed, Kazi Matin; Alam, Md Jahangir; Streatfield, P Kim; Yunus, Mohammad; van Geen, Alexander

2012-08-01

Groundwater is routinely analyzed for fecal indicators but direct comparisons of fecal indicators to the presence of bacterial and viral pathogens are rare. This study was conducted in rural Bangladesh where the human population density is high, sanitation is poor, and groundwater pumped from shallow tubewells is often contaminated with fecal bacteria. Five indicator microorganisms (E. coli, total coliform, F+RNA coliphage, Bacteroides and human-associated Bacteroides) and various environmental parameters were compared to the direct detection of waterborne pathogens by quantitative PCR in groundwater pumped from 50 tubewells. Rotavirus was detected in groundwater filtrate from the largest proportion of tubewells (40%), followed by Shigella (10%), Vibrio (10%), and pathogenic E. coli (8%). Spearman rank correlations and sensitivity-specificity calculations indicate that some, but not all, combinations of indicators and environmental parameters can predict the presence of pathogens. Culture-dependent fecal indicator bacteria measured on a single date did not predict total bacterial pathogens, but annually averaged monthly measurements of culturable E. coli did improve prediction for total bacterial pathogens. A qPCR-based E. coli assay was the best indicator for the bacterial pathogens. F+RNA coliphage were neither correlated nor sufficiently sensitive towards rotavirus, but were predictive of bacterial pathogens. Since groundwater cannot be excluded as a significant source of diarrheal disease in Bangladesh and neighboring countries with similar characteristics, the need to develop more effective methods for screening tubewells with respect to microbial contamination is necessary. Copyright © 2012 Elsevier B.V. All rights reserved.

Comparison of fecal indicators with pathogenic bacteria and rotavirus in groundwater

PubMed Central

Ferguson, Andrew S.; Layton, Alice C.; Mailloux, Brian J; Culligan, Patricia J.; Williams, Daniel E.; Smartt, Abby E.; Sayler, Gary S.; Feighery, John; McKay, Larry; Knappett, Peter S.K.; Alexandrova, Ekaterina; Arbit, Talia; Emch, Michael; Escamilla, Veronica; Ahmed, Kazi Matin; Alam, Md. Jahangir; Streatfield, P. Kim; Yunus, Mohammad; van Geen, Alexander

2012-01-01

Groundwater is routinely analyzed for fecal indicators but direct comparisons of fecal indicators to the presence of bacterial and viral pathogens are rare. This study was conducted in rural Bangladesh where the human population density is high, sanitation is poor, and groundwater pumped from shallow tubewells is often contaminated with fecal bacteria. Five indicator microorganisms (E. coli, total coliform, F+RNA coliphage, Bacteroides and human-associated Bacteroides) and various environmental parameters were compared to the direct detection of waterborne pathogens by quantitative PCR in groundwater pumped from 50 tubewells. Rotavirus was detected in groundwater filtrate from the largest proportion of tubewells (40%), followed by Shigella (10%), Vibrio (10%), and pathogenic E. coli (8%). Spearman rank correlations and sensitivity-specificity calculations indicate that some, but not all, combinations of indicators and environmental parameters can predict the presence of pathogens. Culture-dependent fecal indicator bacteria measured on a single date did not predict total bacterial pathogens, but annually averaged monthly measurements of culturable E. coli did improve prediction for total bacterial pathogens. A qPCR-based E. coli assay was the best indicator for the bacterial pathogens. F+RNA coliphage were neither correlated nor sufficiently sensitive towards rotavirus, but were predictive of bacterial pathogens. Since groundwater cannot be excluded as a significant source of diarrheal disease in Bangladesh and neighboring countries with similar characteristics, the need to develop more effective methods for screening tubewells with respect to microbial contamination is necessary. PMID:22705866

Pathobiology of clade 2.3.4.4 H5Nx high pathogenicity avian influenza virus infections in minor gallinaceous poultry supports early backyard flock introductions in the Western United States in 2014-2015

USDA-ARS?s Scientific Manuscript database

In 2014 and 2015, the United States experienced an unprecedented outbreak of Eurasian clade 2.3.4.4 H5 highly pathogenic avian influenza (HPAI) virus. Initial cases affected mainly wild birds and mixed backyard poultry species, while later outbreaks affected mostly commercial chickens and turkeys. T...

Genetic Diversity of Highly Pathogenic Avian Influenza A(H5N8/H5N5) Viruses in Italy, 2016–17

PubMed Central

Monne, Isabella; Mulatti, Paolo; Zecchin, Bianca; Bonfanti, Lebana; Ormelli, Silvia; Milani, Adelaide; Cecchettin, Krizia; Lemey, Philippe; Moreno, Ana; Massi, Paola; Dorotea, Tiziano; Marangon, Stefano; Terregino, Calogero

2017-01-01

In winter 2016–17, highly pathogenic avian influenza A(H5N8) and A(H5N5) viruses of clade 2.3.4.4 were identified in wild and domestic birds in Italy. We report the occurrence of multiple introductions and describe the identification in Europe of 2 novel genotypes, generated through multiple reassortment events. PMID:28661831

Scaling up complexity in host-pathogens interaction models. Comment on "Coupled disease-behavior dynamics on complex networks: A review" by Z. Wang et al.

NASA Astrophysics Data System (ADS)

Aguiar, Maíra

2015-12-01

Caused by micro-organisms that are pathogenic to the host, infectious diseases have caused debilitation and premature death to large portions of the human population, leading to serious social-economic concerns. The persistence and increase in the occurrence of infectious diseases as well the emergence or resurgence of vector-borne diseases are closely related with demographic factors such as the uncontrolled urbanization and remarkable population growth, political, social and economical changes, deforestation, development of resistance to insecticides and drugs and increased human travel. In recent years, mathematical modeling became an important tool for the understanding of infectious disease epidemiology and dynamics, addressing ideas about the components of host-pathogen interactions. Acting as a possible tool to understand, predict the spread of infectious diseases these models are also used to evaluate the introduction of intervention strategies like vector control and vaccination. Many scientific papers have been published recently on these topics, and most of the models developed try to incorporate factors focusing on several different aspects of the disease (and eventually biological aspects of the vector), which can imply rich dynamic behavior even in the most basic dynamical models. As one example to be cited, there is a minimalistic dengue model that has shown rich dynamic structures, with bifurcations (Hopf, pitchfork, torus and tangent bifurcations) up to chaotic attractors in unexpected parameter regions [1,2], which was able to describe the large fluctuations observed in empirical outbreak data [3,4].

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.

Glycosylation on Hemagglutinin Affects the Virulence and Pathogenicity of Pandemic H1N1/2009 Influenza A Virus in Mice

PubMed Central

Li, Yongtao; Bradley, Konrad C.; Cao, Jiyue; Chen, Huanchun; Jin, Meilin; Zhou, Hongbo

2013-01-01

The two glycosylation sites (Asn142 and Asn177) were observed in the HA of most human seasonal influenza A/H1N1 viruses, while none in pandemic H1N1/2009 influenza A (pH1N1) viruses. We investigated the effect of the two glycosylation sites on viral virulence and pathogenicity in mice using recombinant pH1N1. The H1N1/144 and H1N1/177 mutants which gained potential glycosylation sites Asn142 and Asn177 on HA respectively were generated from A/Mexico/4486/2009(H1N1) by site-directed mutagenesis and reverse genetics, the same as the H1N1/144+177 gained both glycosylation sites Asn142 and Asn177. The biological characteristics and antigenicity of the mutants were compared with wild-type pH1N1. The virulence and pathogenicity of recombinants were also detected in mice. Our results showed that HA antigenicity and viral affinity for receptor may change with introduction of the glycosylation sites. Compared with wild-type pH1N1, the mutant H1N1/177 displayed an equivalent virus titer in chicken embryos and mice, and increased virulence and pathogenicity in mice. The H1N1/144 displayed the highest virus titer in mice lung. However, the H1N1/144+177 displayed the most serious alveolar inflammation and pathogenicity in infected mice. The introduction of the glycosylation sites Asn144 and Asn177 resulted in the enhancement on virulence and pathogenicity of pH1N1 in mice, and was also associated with the change of HA antigenicity and the viral affinity for receptor. PMID:23637827

Prediction of molecular mimicry candidates in human pathogenic bacteria.

PubMed

Doxey, Andrew C; McConkey, Brendan J

2013-08-15

Molecular mimicry of host proteins is a common strategy adopted by bacterial pathogens to interfere with and exploit host processes. Despite the availability of pathogen genomes, few studies have attempted to predict virulence-associated mimicry relationships directly from genomic sequences. Here, we analyzed the proteomes of 62 pathogenic and 66 non-pathogenic bacterial species, and screened for the top pathogen-specific or pathogen-enriched sequence similarities to human proteins. The screen identified approximately 100 potential mimicry relationships including well-characterized examples among the top-scoring hits (e.g., RalF, internalin, yopH, and others), with about 1/3 of predicted relationships supported by existing literature. Examination of homology to virulence factors, statistically enriched functions, and comparison with literature indicated that the detected mimics target key host structures (e.g., extracellular matrix, ECM) and pathways (e.g., cell adhesion, lipid metabolism, and immune signaling). The top-scoring and most widespread mimicry pattern detected among pathogens consisted of elevated sequence similarities to ECM proteins including collagens and leucine-rich repeat proteins. Unexpectedly, analysis of the pathogen counterparts of these proteins revealed that they have evolved independently in different species of bacterial pathogens from separate repeat amplifications. Thus, our analysis provides evidence for two classes of mimics: complex proteins such as enzymes that have been acquired by eukaryote-to-pathogen horizontal transfer, and simpler repeat proteins that have independently evolved to mimic the host ECM. Ultimately, computational detection of pathogen-specific and pathogen-enriched similarities to host proteins provides insights into potentially novel mimicry-mediated virulence mechanisms of pathogenic bacteria.

Prediction of molecular mimicry candidates in human pathogenic bacteria

PubMed Central

Doxey, Andrew C; McConkey, Brendan J

2013-01-01

Molecular mimicry of host proteins is a common strategy adopted by bacterial pathogens to interfere with and exploit host processes. Despite the availability of pathogen genomes, few studies have attempted to predict virulence-associated mimicry relationships directly from genomic sequences. Here, we analyzed the proteomes of 62 pathogenic and 66 non-pathogenic bacterial species, and screened for the top pathogen-specific or pathogen-enriched sequence similarities to human proteins. The screen identified approximately 100 potential mimicry relationships including well-characterized examples among the top-scoring hits (e.g., RalF, internalin, yopH, and others), with about 1/3 of predicted relationships supported by existing literature. Examination of homology to virulence factors, statistically enriched functions, and comparison with literature indicated that the detected mimics target key host structures (e.g., extracellular matrix, ECM) and pathways (e.g., cell adhesion, lipid metabolism, and immune signaling). The top-scoring and most widespread mimicry pattern detected among pathogens consisted of elevated sequence similarities to ECM proteins including collagens and leucine-rich repeat proteins. Unexpectedly, analysis of the pathogen counterparts of these proteins revealed that they have evolved independently in different species of bacterial pathogens from separate repeat amplifications. Thus, our analysis provides evidence for two classes of mimics: complex proteins such as enzymes that have been acquired by eukaryote-to-pathogen horizontal transfer, and simpler repeat proteins that have independently evolved to mimic the host ECM. Ultimately, computational detection of pathogen-specific and pathogen-enriched similarities to host proteins provides insights into potentially novel mimicry-mediated virulence mechanisms of pathogenic bacteria. PMID:23715053

Development of Convergence Nanoparticles (Phase II): Detection and Therapeutics of Pathogen Targets by Using Multi-Mode Hybrid Nanoparticle Probe

DTIC Science & Technology

2010-04-05

Chloride (Aldrich 45011, 5g) 1 -Ethyl- 3 -[ 3 - dimethylaminopropyl ]carbodiimide hydrochloride (Pierce 25952-53-8, 25g) Oleylamine (Aldrich O7805, 500g...email: jcheon@yonsei.ac.kr Table of Content 1 . Abstract 2. Introduction 3 . Approach 4. Results and discussions 5. Pay-off 6. Summary 7...highly accurate detection and therapeutics of biological pathogens. 3 . Approaches 1 ) Approach Our research was focused on the development of

Host specificity of microsporidia pathogenic to the gypsy moth, Lymantria dispar (L.): field studies in Slovakia.

PubMed

Solter, Leellen F; Pilarska, Daniela K; McManus, Michael L; Zúbrik, Milan; Patocka, Jan; Huang, Wei-Fone; Novotný, Julius

2010-09-01

Several species of microsporidia are important chronic pathogens of Lymantria dispar in Europe but have never been recovered from North American gypsy moth populations. The major issue for their introduction into North American L. dispar populations is concern about their safety to native non-target insects. In this study, we evaluated the susceptibility of sympatric non-target Lepidoptera to two species of microsporidia, Nosema lymantriae and Vairimorpha disparis, isolated from European populations of L. dispar and applied in field plots in Slovakia. Application of ultra low volume sprays of the microsporidia maximized coverage of infective spores in a complex natural environment and, thus, exposure of non-target species to the pathogens. Of 653 non-target larvae collected from plots treated with V. disparis in 2002, 18 individual larvae representing nine species in four families were infected. These plots were monitored for two subsequent seasons and V. disparis was not recovered from non-target species. Of 2571 non-target larvae collected in N. lymantriae-treated sites, one larva was found to be infected. Both species of microsporidia, particularly N. lymantriae, appear to have a very narrow host range in the field, even when an inundative technique is used for their introduction. V. disparis infections in L. dispar exceeded 40% of recovered larvae in the treated study sites; infection rates were lower in sites sprayed with N. lymantriae. Several naturally-occurring pathogens were recorded from the non-target species. The most common pathogen, isolated from 21 species in eight families, was a microsporidium in the genus Cystosporogenes. Copyright 2010 Elsevier Inc. All rights reserved.

Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9.

PubMed

Paquet, Dominik; Kwart, Dylan; Chen, Antonia; Sproul, Andrew; Jacob, Samson; Teo, Shaun; Olsen, Kimberly Moore; Gregg, Andrew; Noggle, Scott; Tessier-Lavigne, Marc

2016-05-05

The bacterial CRISPR/Cas9 system allows sequence-specific gene editing in many organisms and holds promise as a tool to generate models of human diseases, for example, in human pluripotent stem cells. CRISPR/Cas9 introduces targeted double-stranded breaks (DSBs) with high efficiency, which are typically repaired by non-homologous end-joining (NHEJ) resulting in nonspecific insertions, deletions or other mutations (indels). DSBs may also be repaired by homology-directed repair (HDR) using a DNA repair template, such as an introduced single-stranded oligo DNA nucleotide (ssODN), allowing knock-in of specific mutations. Although CRISPR/Cas9 is used extensively to engineer gene knockouts through NHEJ, editing by HDR remains inefficient and can be corrupted by additional indels, preventing its widespread use for modelling genetic disorders through introducing disease-associated mutations. Furthermore, targeted mutational knock-in at single alleles to model diseases caused by heterozygous mutations has not been reported. Here we describe a CRISPR/Cas9-based genome-editing framework that allows selective introduction of mono- and bi-allelic sequence changes with high efficiency and accuracy. We show that HDR accuracy is increased dramatically by incorporating silent CRISPR/Cas-blocking mutations along with pathogenic mutations, and establish a method termed 'CORRECT' for scarless genome editing. By characterizing and exploiting a stereotyped inverse relationship between a mutation's incorporation rate and its distance to the DSB, we achieve predictable control of zygosity. Homozygous introduction requires a guide RNA targeting close to the intended mutation, whereas heterozygous introduction can be accomplished by distance-dependent suboptimal mutation incorporation or by use of mixed repair templates. Using this approach, we generated human induced pluripotent stem cells with heterozygous and homozygous dominant early onset Alzheimer's disease-causing mutations in amyloid precursor protein (APP(Swe)) and presenilin 1 (PSEN1(M146V)) and derived cortical neurons, which displayed genotype-dependent disease-associated phenotypes. Our findings enable efficient introduction of specific sequence changes with CRISPR/Cas9, facilitating study of human disease.

Reassortment between swine H3N2 and 2009 pandemic H1N1 generated diverse genetic constellations in influenza A viruses currently circulating in pigs in the United States

USDA-ARS?s Scientific Manuscript database

Introduction Influenza A virus (IAV) is a significant pathogen to the swine industry. Since its introduction in 2009, the H1N1 pandemic virus (H1N1pdm09) has been repeatedly transmitted from humans to swine, but onward transmission in U.S. swine was mostly restricted to its internal genes. Reassortm...

Environmental controls, oceanography and population dynamics of pathogens and harmful algal blooms: connecting sources to human exposure.

PubMed

Dyble, Julianne; Bienfang, Paul; Dusek, Eva; Hitchcock, Gary; Holland, Fred; Laws, Ed; Lerczak, James; McGillicuddy, Dennis J; Minnett, Peter; Moore, Stephanie K; O'Kelly, Charles; Solo-Gabriele, Helena; Wang, John D

2008-11-07

Coupled physical-biological models are capable of linking the complex interactions between environmental factors and physical hydrodynamics to simulate the growth, toxicity and transport of infectious pathogens and harmful algal blooms (HABs). Such simulations can be used to assess and predict the impact of pathogens and HABs on human health. Given the widespread and increasing reliance of coastal communities on aquatic systems for drinking water, seafood and recreation, such predictions are critical for making informed resource management decisions. Here we identify three challenges to making this connection between pathogens/HABs and human health: predicting concentrations and toxicity; identifying the spatial and temporal scales of population and ecosystem interactions; and applying the understanding of population dynamics of pathogens/HABs to management strategies. We elaborate on the need to meet each of these challenges, describe how modeling approaches can be used and discuss strategies for moving forward in addressing these challenges.

Biosecurity and Vector Behaviour: Evaluating the Potential Threat Posed by Anglers and Canoeists as Pathways for the Spread of Invasive Non-Native Species and Pathogens

PubMed Central

Anderson, Lucy G.; White, Piran C. L.; Stebbing, Paul D.; Stentiford, Grant D.; Dunn, Alison M.

2014-01-01

Invasive non-native species (INNS) endanger native biodiversity and are a major economic problem. The management of pathways to prevent their introduction and establishment is a key target in the Convention on Biological Diversity's Aichi biodiversity targets for 2020. Freshwater environments are particularly susceptible to invasions as they are exposed to multiple introduction pathways, including non-native fish stocking and the release of boat ballast water. Since many freshwater INNS and aquatic pathogens can survive for several days in damp environments, there is potential for transport between water catchments on the equipment used by recreational anglers and canoeists. To quantify this biosecurity risk, we conducted an online questionnaire with 960 anglers and 599 canoeists to investigate their locations of activity, equipment used, and how frequently equipment was cleaned and/or dried after use. Anglers were also asked about their use and disposal of live bait. Our results indicate that 64% of anglers and 78.5% of canoeists use their equipment/boat in more than one catchment within a fortnight, the survival time of many of the INNS and pathogens considered in this study and that 12% of anglers and 50% of canoeists do so without either cleaning or drying their kit between uses. Furthermore, 8% of anglers and 28% of canoeists had used their equipment overseas without cleaning or drying it after each use which could facilitate both the introduction and secondary spread of INNS in the UK. Our results provide a baseline against which to evaluate the effectiveness of future biosecurity awareness campaigns, and identify groups to target with biosecurity awareness information. Our results also indicate that the biosecurity practices of these groups must improve to reduce the likelihood of inadvertently spreading INNS and pathogens through these activities. PMID:24717714

A model for multiseasonal spread of verticillium wilt of lettuce.

PubMed

Wu, B M; Subbarao, K V

2014-09-01

Verticillium wilt, caused by Verticillium dahliae, is a destructive disease in lettuce, and the pathogen is seedborne. Even though maximum seed infestation rates of <5% have been detected in commercial lettuce seed lots, it is necessary to establish acceptable contamination thresholds to prevent introduction and establishment of the pathogen in lettuce production fields. However, introduction of inoculum into lettuce fields for experimental purposes to determine its long term effects is undesirable. Therefore, we constructed a simulation model to study the spread of Verticillium wilt following pathogen introduction from seed. The model consists of four components: the first for simulating infection of host plants, the second for simulating reproduction of microsclerotia on diseased plants, the third for simulating the survival of microsclerotia, and the fourth for simulating the dispersal of microsclerotia. The simulation results demonstrated that the inoculum density-disease incidence curve parameters and the dispersal gradients affect disease spread in the field. Although a steep dispersal gradient facilitated the establishment of the disease in a new field with a low inoculum density, a long-tail gradient allowed microsclerotia to be dispersed over greater distances, promoting the disease spread in fields with high inoculum density. The simulation results also revealed the importance of avoiding successive lettuce crops in the same field, reducing survival rate of microsclerotia between crops, and the need for breeding resistance against V. dahliae in lettuce cultivars to lower the number of microsclerotia formed on each diseased plant. The simulation results, however, suggested that, even with a low seed infestation rate, the pathogen would eventually become established if susceptible lettuce cultivars were grown consecutively in the same field for many years. A threshold for seed infestation can be established only when two of the three drivers of the disease-(i) low microsclerotia production per diseased plant, (ii) long-tail dispersal gradient, and (iii) low microsclerotia survival between lettuce crops-are present.

Life histories of hosts and pathogens predict patterns in tropical fungal plant diseases.

PubMed

García-Guzmán, Graciela; Heil, Martin

2014-03-01

Plant pathogens affect the fitness of their hosts and maintain biodiversity. However, we lack theories to predict the type and intensity of infections in wild plants. Here we demonstrate using fungal pathogens of tropical plants that an examination of the life histories of hosts and pathogens can reveal general patterns in their interactions. Fungal infections were more commonly reported for light-demanding than for shade-tolerant species and for evergreen rather than for deciduous hosts. Both patterns are consistent with classical defence theory, which predicts lower resistance in fast-growing species and suggests that the deciduous habit can reduce enemy populations. In our literature survey, necrotrophs were found mainly to infect shade-tolerant woody species whereas biotrophs dominated in light-demanding herbaceous hosts. Far-red signalling and its inhibitory effects on jasmonic acid signalling are likely to explain this phenomenon. Multiple changes between the necrotrophic and the symptomless endophytic lifestyle at the ecological and evolutionary scale indicate that endophytes should be considered when trying to understand large-scale patterns in the fungal infections of plants. Combining knowledge about the molecular mechanisms of pathogen resistance with classical defence theory enables the formulation of testable predictions concerning general patterns in the infections of wild plants by fungal pathogens. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Semi-quantitative assessment of disease risks at the human, livestock, wildlife interface for the Republic of Korea using a nationwide survey of experts: A model for other countries

USGS Publications Warehouse

Hwang, Jusun; Lee, Kyunglee; Walsh, Daniel P.; Kim, SangWha; Sleeman, Jonathan M.; Lee, Hang

2018-01-01

Wildlife-associated diseases and pathogens have increased in importance; however, management of a large number of diseases and diversity of hosts is prohibitively expensive. Thus, the determination of priority wildlife pathogens and risk factors for disease emergence is warranted. We used an online questionnaire survey to assess release and exposure risks, and consequences of wildlife-associated diseases and pathogens in the Republic of Korea (ROK). We also surveyed opinions on pathways for disease exposure, and risk factors for disease emergence and spread. For the assessment of risk, we employed a two-tiered, statistical K-means clustering algorithm to group diseases into three levels (high, medium and low) of perceived risk based on release and exposure risks, societal consequences and the level of uncertainty of the experts’ opinions. To examine the experts’ perceived risk of routes of introduction of pathogens and disease amplification and spread, we used a Bayesian, multivariate normal order-statistics model. Six diseases or pathogens, including four livestock and two wildlife diseases, were identified as having high risk with low uncertainty. Similarly, 13 diseases were characterized as having high risk with medium uncertainty with three of these attributed to livestock, six associated with human disease, and the remainder having the potential to affect human, livestock and wildlife (i.e., One Health). Lastly, four diseases were described as high risk with high certainty, and were associated solely with fish diseases. Experts identified migration of wildlife, international human movement and illegal importation of wildlife as the three routes posing the greatest risk of pathogen introduction into ROK. Proximity of humans, livestock and wildlife was the most significant risk factor for promoting the spread of wildlife-associated diseases and pathogens, followed by high density of livestock populations, habitat loss and environmental degradation, and climate change. This study provides useful information to decision makers responsible for allocating resources to address disease risks. This approach provided a rapid, cost-effective method of risk assessment of wildlife-associated diseases and pathogens for which the published literature is sparse.

Impact of the implementation of rest days in live bird markets on the dynamics of H5N1 highly pathogenic avian influenza.

PubMed

Fournié, G; Guitian, F J; Mangtani, P; Ghani, A C

2011-08-07

Live bird markets (LBMs) act as a network 'hub' and potential reservoir of infection for domestic poultry. They may therefore be responsible for sustaining H5N1 highly pathogenic avian influenza (HPAI) virus circulation within the poultry sector, and thus a suitable target for implementing control strategies. We developed a stochastic transmission model to understand how market functioning impacts on the transmission dynamics. We then investigated the potential for rest days-periods during which markets are emptied and disinfected-to modulate the dynamics of H5N1 HPAI within the poultry sector using a stochastic meta-population model. Our results suggest that under plausible parameter scenarios, HPAI H5N1 could be sustained silently within LBMs with the time spent by poultry in markets and the frequency of introduction of new susceptible birds' dominant factors determining sustained silent spread. Compared with interventions applied in farms (i.e. stamping out, vaccination), our model shows that frequent rest days are an effective means to reduce HPAI transmission. Furthermore, our model predicts that full market closure would be only slightly more effective than rest days to reduce transmission. Strategies applied within markets could thus help to control transmission of the disease.

Impact of the implementation of rest days in live bird markets on the dynamics of H5N1 highly pathogenic avian influenza

PubMed Central

Fournié, G.; Guitian, F. J.; Mangtani, P.; Ghani, A. C.

2011-01-01

Live bird markets (LBMs) act as a network ‘hub’ and potential reservoir of infection for domestic poultry. They may therefore be responsible for sustaining H5N1 highly pathogenic avian influenza (HPAI) virus circulation within the poultry sector, and thus a suitable target for implementing control strategies. We developed a stochastic transmission model to understand how market functioning impacts on the transmission dynamics. We then investigated the potential for rest days—periods during which markets are emptied and disinfected—to modulate the dynamics of H5N1 HPAI within the poultry sector using a stochastic meta-population model. Our results suggest that under plausible parameter scenarios, HPAI H5N1 could be sustained silently within LBMs with the time spent by poultry in markets and the frequency of introduction of new susceptible birds' dominant factors determining sustained silent spread. Compared with interventions applied in farms (i.e. stamping out, vaccination), our model shows that frequent rest days are an effective means to reduce HPAI transmission. Furthermore, our model predicts that full market closure would be only slightly more effective than rest days to reduce transmission. Strategies applied within markets could thus help to control transmission of the disease. PMID:21131332

Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches.

PubMed

Guidugli, Lucia; Shimelis, Hermela; Masica, David L; Pankratz, Vernon S; Lipton, Gary B; Singh, Namit; Hu, Chunling; Monteiro, Alvaro N A; Lindor, Noralane M; Goldgar, David E; Karchin, Rachel; Iversen, Edwin S; Couch, Fergus J

2018-01-17

Many variants of uncertain significance (VUS) have been identified in BRCA2 through clinical genetic testing. VUS pose a significant clinical challenge because the contribution of these variants to cancer risk has not been determined. We conducted a comprehensive assessment of VUS in the BRCA2 C-terminal DNA binding domain (DBD) by using a validated functional assay of BRCA2 homologous recombination (HR) DNA-repair activity and defined a classifier of variant pathogenicity. Among 139 variants evaluated, 54 had ≥99% probability of pathogenicity, and 73 had ≥95% probability of neutrality. Functional assay results were compared with predictions of variant pathogenicity from the Align-GVGD protein-sequence-based prediction algorithm, which has been used for variant classification. Relative to the HR assay, Align-GVGD significantly (p < 0.05) over-predicted pathogenic variants. We subsequently combined functional and Align-GVGD prediction results in a Bayesian hierarchical model (VarCall) to estimate the overall probability of pathogenicity for each VUS. In addition, to predict the effects of all other BRCA2 DBD variants and to prioritize variants for functional studies, we used the endoPhenotype-Optimized Sequence Ensemble (ePOSE) algorithm to train classifiers for BRCA2 variants by using data from the HR functional assay. Together, the results show that systematic functional assays in combination with in silico predictors of pathogenicity provide robust tools for clinical annotation of BRCA2 VUS. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data

NASA Astrophysics Data System (ADS)

Deneke, Carlus; Rentzsch, Robert; Renard, Bernhard Y.

2017-01-01

The reliable detection of novel bacterial pathogens from next-generation sequencing data is a key challenge for microbial diagnostics. Current computational tools usually rely on sequence similarity and often fail to detect novel species when closely related genomes are unavailable or missing from the reference database. Here we present the machine learning based approach PaPrBaG (Pathogenicity Prediction for Bacterial Genomes). PaPrBaG overcomes genetic divergence by training on a wide range of species with known pathogenicity phenotype. To that end we compiled a comprehensive list of pathogenic and non-pathogenic bacteria with human host, using various genome metadata in conjunction with a rule-based protocol. A detailed comparative study reveals that PaPrBaG has several advantages over sequence similarity approaches. Most importantly, it always provides a prediction whereas other approaches discard a large number of sequencing reads with low similarity to currently known reference genomes. Furthermore, PaPrBaG remains reliable even at very low genomic coverages. CombiningPaPrBaG with existing approaches further improves prediction results.

Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

PubMed

Zhou, Hufeng; Rezaei, Javad; Hugo, Willy; Gao, Shangzhi; Jin, Jingjing; Fan, Mengyuan; Yong, Chern-Han; Wozniak, Michal; Wong, Limsoon

2013-01-01

H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are very important information to illuminate the infection mechanism of M. tuberculosis H37Rv. But current H. sapiens-M. tuberculosis H37Rv PPI data are very scarce. This seriously limits the study of the interaction between this important pathogen and its host H. sapiens. Computational prediction of H. sapiens-M. tuberculosis H37Rv PPIs is an important strategy to fill in the gap. Domain-domain interaction (DDI) based prediction is one of the frequently used computational approaches in predicting both intra-species and inter-species PPIs. However, the performance of DDI-based host-pathogen PPI prediction has been rather limited. We develop a stringent DDI-based prediction approach with emphasis on (i) differences between the specific domain sequences on annotated regions of proteins under the same domain ID and (ii) calculation of the interaction strength of predicted PPIs based on the interacting residues in their interaction interfaces. We compare our stringent DDI-based approach to a conventional DDI-based approach for predicting PPIs based on gold standard intra-species PPIs and coherent informative Gene Ontology terms assessment. The assessment results show that our stringent DDI-based approach achieves much better performance in predicting PPIs than the conventional approach. Using our stringent DDI-based approach, we have predicted a small set of reliable H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies. We also analyze the H. sapiens-M. tuberculosis H37Rv PPIs predicted by our stringent DDI-based approach using cellular compartment distribution analysis, functional category enrichment analysis and pathway enrichment analysis. The analyses support the validity of our prediction result. Also, based on an analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent DDI-based approach, we have discovered some important properties of domains involved in host-pathogen PPIs. We find that both host and pathogen proteins involved in host-pathogen PPIs tend to have more domains than proteins involved in intra-species PPIs, and these domains have more interaction partners than domains on proteins involved in intra-species PPI. The stringent DDI-based prediction approach reported in this work provides a stringent strategy for predicting host-pathogen PPIs. It also performs better than a conventional DDI-based approach in predicting PPIs. We have predicted a small set of accurate H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies.

Gene Function Analysis in the Ubiquitous Human Commensal and Pathogen Malassezia Genus

PubMed Central

Ianiri, Giuseppe; Averette, Anna F.; Kingsbury, Joanne M.; Heitman, Joseph

2016-01-01

ABSTRACT The genus Malassezia includes 14 species that are found on the skin of humans and animals and are associated with a number of diseases. Recent genome sequencing projects have defined the gene content of all 14 species; however, to date, genetic manipulation has not been possible for any species within this genus. Here, we develop and then optimize molecular tools for the transformation of Malassezia furfur and Malassezia sympodialis using Agrobacterium tumefaciens delivery of transfer DNA (T-DNA) molecules. These T-DNAs can insert randomly into the genome. In the case of M. furfur, targeted gene replacements were also achieved via homologous recombination, enabling deletion of the ADE2 gene for purine biosynthesis and of the LAC2 gene predicted to be involved in melanin biosynthesis. Hence, the introduction of exogenous DNA and direct gene manipulation are feasible in Malassezia species. PMID:27899504

Spatial and Temporal Analysis of Populations of the Sudden Oak Death Pathogen in Oregon Forests.

PubMed

Kamvar, Z N; Larsen, M M; Kanaskie, A M; Hansen, E M; Grünwald, N J

2015-07-01

Sudden oak death caused by the oomycete Phytophthora ramorum was first discovered in California toward the end of the 20th century and subsequently emerged on tanoak forests in Oregon before its first detection in 2001 by aerial surveys. The Oregon Department of Forestry has since monitored the epidemic and sampled symptomatic tanoak trees from 2001 to the present. Populations sampled over this period were genotyped using microsatellites and studied to infer the population genetic history. To date, only the NA1 clonal lineage is established in this region, although three lineages exist on the North American west coast. The original introduction into the Joe Hall area eventually spread to several regions: mostly north but also east and southwest. A new introduction into Hunter Creek appears to correspond to a second introduction not clustering with the early introduction. Our data are best explained by both introductions originating from nursery populations in California or Oregon and resulting from two distinct introduction events. Continued vigilance and eradication of nursery populations of P. ramorum are important to avoid further emergence and potential introduction of other clonal lineages.

Modelling pathogen log10 reduction values achieved by activated sludge treatment using naïve and semi naïve Bayes network models.

PubMed

Carvajal, Guido; Roser, David J; Sisson, Scott A; Keegan, Alexandra; Khan, Stuart J

2015-11-15

Risk management for wastewater treatment and reuse have led to growing interest in understanding and optimising pathogen reduction during biological treatment processes. However, modelling pathogen reduction is often limited by poor characterization of the relationships between variables and incomplete knowledge of removal mechanisms. The aim of this paper was to assess the applicability of Bayesian belief network models to represent associations between pathogen reduction, and operating conditions and monitoring parameters and predict AS performance. Naïve Bayes and semi-naïve Bayes networks were constructed from an activated sludge dataset including operating and monitoring parameters, and removal efficiencies for two pathogens (native Giardia lamblia and seeded Cryptosporidium parvum) and five native microbial indicators (F-RNA bacteriophage, Clostridium perfringens, Escherichia coli, coliforms and enterococci). First we defined the Bayesian network structures for the two pathogen log10 reduction values (LRVs) class nodes discretized into two states (< and ≥ 1 LRV) using two different learning algorithms. Eight metrics, such as Prediction Accuracy (PA) and Area Under the receiver operating Curve (AUC), provided a comparison of model prediction performance, certainty and goodness of fit. This comparison was used to select the optimum models. The optimum Tree Augmented naïve models predicted removal efficiency with high AUC when all system parameters were used simultaneously (AUCs for C. parvum and G. lamblia LRVs of 0.95 and 0.87 respectively). However, metrics for individual system parameters showed only the C. parvum model was reliable. By contrast individual parameters for G. lamblia LRV prediction typically obtained low AUC scores (AUC < 0.81). Useful predictors for C. parvum LRV included solids retention time, turbidity and total coliform LRV. The methodology developed appears applicable for predicting pathogen removal efficiency in water treatment systems generally. Copyright © 2015 Elsevier Ltd. All rights reserved.

Pathogens associated with native and exotic trout populations in Shenandoah National Park and the relationships to fish stocking practices

USGS Publications Warehouse

Panek, Frank M.; Atkinson, James; Coll, John

2008-01-01

Restrictive fish stocking policies in National Parks were developed as early as 1936 in order to preserve native fish assemblages and historic genetic diversity. Despite recent efforts to understand the effects of non-native or exotic fish introductions, park managers have limited information regarding the effects of these introductions on native fish communities. Shenandoah National Park was established in 1936 and brook trout (Salvelinus fontinalis) restoration within selected streams in the park began in 1937 in collaboration with the Virginia Department of Game and Inland Fisheries (VDGIF). An analysis of tissue samples from brook, brown (Salmo trutta), and rainbow trout (Oncorhynchus mykiss) from 29 streams within the park from 1998–2002 revealed the presence of Renibacterium salmoninarum, Yersinia ruckeri, and infectious pancreatic necrosis virus (IPNv). In order to investigate the relationships of the occurrence of fish pathogens with stocking histories we classified the streams into three categories: 1) streams with no record of stocking, 2) streams that are known to have been stocked historically, and 3) streams that were historically stocked within the park and continue to be stocked downstream of the park boundary. The occurrences of pathogens were summarized relative to this stocking history. Renibacterium salmoninarum, the causative agent of bacterial kidney disease, was the most prevalent pathogen found, occurring in all three species and stream stocking categories, and appears to be endemic to the park. Two other pathogens, Yersinia ruckeri and infectious pancreatic necrosis virus were also described from brook trout populations within the park. IPNv was only found in brook trout populations in streams with prior stocking histories. Yersinia ruckeri was only found in brook trout in steams that have never been stocked and like R. salmoninarum, is likely endemic.

Enteric virus and vibrio contamination of shellfish: intervention strategies

USDA-ARS?s Scientific Manuscript database

INTRODUCTION. Molluscan shellfish include oysters, clams, mussels, and cockles, which can cause illnesses from a variety of human pathogens. Enteric viruses, like norovirus and hepatitis A virus, are generally transmitted to shellfish through fecal contamination of shellfish harvesting areas, alth...

Environmental controls, oceanography and population dynamics of pathogens and harmful algal blooms: connecting sources to human exposure

PubMed Central

Dyble, Julianne; Bienfang, Paul; Dusek, Eva; Hitchcock, Gary; Holland, Fred; Laws, Ed; Lerczak, James; McGillicuddy, Dennis J; Minnett, Peter; Moore, Stephanie K; O'Kelly, Charles; Solo-Gabriele, Helena; Wang, John D

2008-01-01

Coupled physical-biological models are capable of linking the complex interactions between environmental factors and physical hydrodynamics to simulate the growth, toxicity and transport of infectious pathogens and harmful algal blooms (HABs). Such simulations can be used to assess and predict the impact of pathogens and HABs on human health. Given the widespread and increasing reliance of coastal communities on aquatic systems for drinking water, seafood and recreation, such predictions are critical for making informed resource management decisions. Here we identify three challenges to making this connection between pathogens/HABs and human health: predicting concentrations and toxicity; identifying the spatial and temporal scales of population and ecosystem interactions; and applying the understanding of population dynamics of pathogens/HABs to management strategies. We elaborate on the need to meet each of these challenges, describe how modeling approaches can be used and discuss strategies for moving forward in addressing these challenges. PMID:19025676

Effect of United States buckwheat honey on antibiotic-resistant hospital acquired pathogens

PubMed Central

Hammond, Eric Nee-Armah; Duster, Megan; Musuuza, Jackson Ssentalo; Safdar, Nasia

2016-01-01

Introduction Due to an upsurge in antibiotic-resistant infections and lack of therapeutic options, new approaches are needed for treatment. Honey may be one such potential therapeutic option. We investigated the susceptibility of hospital acquired pathogens to four honeys from Wisconsin, United States, and then determined if the antibacterial effect of each honey against these pathogens is primarily due to the high sugar content. Methods Thirteen pathogens including: four Clostridium difficile, two Methicillin-resistant Staphylococcus aureus, two Pseudomonas aeruginosa, one Methicillin-Susceptible Staphylococcus aureus, two Vancomycin-resistance Enterococcus, one Enterococcus faecalis and one Klebsiella pneumoniae were exposed to 1-50% (w/v) four Wisconsin honeys and Artificial honey to determine their minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) using the broth dilution method. Results Buckwheat honey predominantly exhibited a bactericidal mode of action against the tested pathogens, and this varied with each pathogen. C. difficile isolates were more sensitive to the Wisconsin buckwheat honey as compared to the other pathogens. Artificial honey at 50% (w/v) failed to kill any of the pathogens. The high sugar content of Wisconsin buckwheat honey is not the only factor responsible for its bactericidal activity. Conclusion Wisconsin buckwheat honey has the potential to be an important addition to therapeutic armamentarium against resistant pathogens and should be investigated further. PMID:28292167

MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH (Session introduction)

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

McDermott, Jason E.; Braun, Pascal; Bonneau, Richard A.

Pathogenic infections are a major cause of both human disease and loss of crop yields and animal stocks and thus cause immense damage to the worldwide economy. The significance of infectious diseases is expected to increase in an ever more connected warming world, in which new viral, bacterial and fungal pathogens can find novel hosts and ecologic niches. At the same time, the complex and sophisticated mechanisms by which diverse pathogenic agents evade defense mechanisms and subvert their hosts networks to suit their lifestyle needs is still very incompletely understood especially from a systems perspective [1]. Thus, understanding host-pathogen interactionsmore » is both an important and a scientifically fascinating topic. Recently, technology has offered the opportunity to investigate host-pathogen interactions on a level of detail and scope that offers immense computational and analytical possibilities. Genome sequencing was pioneered on some of these pathogens, and the number of strains and variants of pathogens sequenced to date vastly outnumbers the number of host genomes available. At the same time, for both plant and human hosts more and more data on population level genomic variation becomes available and offers a rich field for analysis into the genetic interactions between host and pathogen.« less

Complete genome sequence analysis of the fish pathogen Flavobacterium columnare provides insights into antibiotic resistance and pathogenicity related genes.

PubMed

Zhang, Yulei; Zhao, Lijuan; Chen, Wenjie; Huang, Yunmao; Yang, Ling; Sarathbabu, V; Wu, Zaohe; Li, Jun; Nie, Pin; Lin, Li

2017-10-01

We analyzed here the complete genome sequences of a highly virulent Flavobacterium columnare Pf1 strain isolated in our laboratory. The complete genome consists of a 3,171,081 bp circular DNA with 2784 predicted protein-coding genes. Among these, 286 genes were predicted as antibiotic resistance genes, including 32 RND-type efflux pump related genes which were associated with the export of aminoglycosides, indicating inducible aminoglycosides resistances in F. columnare. On the other hand, 328 genes were predicted as pathogenicity related genes which could be classified as virulence factors, gliding motility proteins, adhesins, and many putative secreted proteases. These genes were probably involved in the colonization, invasion and destruction of fish tissues during the infection of F. columnare. Apparently, our obtained complete genome sequences provide the basis for the explanation of the interactions between the F. columnare and the infected fish. The predicted antibiotic resistance and pathogenicity related genes will shed a new light on the development of more efficient preventional strategies against the infection of F. columnare, which is a major worldwide fish pathogen. Copyright © 2017 Elsevier Ltd. All rights reserved.

Climate warming and disease risks for terrestrial and marine biota

USGS Publications Warehouse

Harvell, C.D.; Mitchell, C.E.; Ward, J.R.; Altizer, S.; Dobson, A.P.; Ostfeld, R.S.; Samuel, M.D.

2002-01-01

Infectious diseases can cause rapid population declines or species extinctions. Many pathogens of terrestrial and marine taxa are sensitive to temperature, rainfall, and humidity, creating synergisms that could affect biodiversity. Climate warming can increase pathogen development and survival rates, disease transmission, and host susceptibility. Although most host-parasite systems are predicted to experience more frequent or severe disease impacts with warming, a subset of pathogens might decline with warming, releasing hosts from disease. Recently, changes in El Niño–Southern Oscillation events have had a detectable influence on marine and terrestrial pathogens, including coral diseases, oyster pathogens, crop pathogens, Rift Valley fever, and human cholera. To improve our ability to predict epidemics in wild populations, it will be necessary to separate the independent and interactive effects of multiple climate drivers on disease impact.

Climate Warming and Disease Risks for Terrestrial and Marine Biota

NASA Astrophysics Data System (ADS)

Harvell, C. Drew; Mitchell, Charles E.; Ward, Jessica R.; Altizer, Sonia; Dobson, Andrew P.; Ostfeld, Richard S.; Samuel, Michael D.

2002-06-01

Infectious diseases can cause rapid population declines or species extinctions. Many pathogens of terrestrial and marine taxa are sensitive to temperature, rainfall, and humidity, creating synergisms that could affect biodiversity. Climate warming can increase pathogen development and survival rates, disease transmission, and host susceptibility. Although most host-parasite systems are predicted to experience more frequent or severe disease impacts with warming, a subset of pathogens might decline with warming, releasing hosts from disease. Recently, changes in El Niño-Southern Oscillation events have had a detectable influence on marine and terrestrial pathogens, including coral diseases, oyster pathogens, crop pathogens, Rift Valley fever, and human cholera. To improve our ability to predict epidemics in wild populations, it will be necessary to separate the independent and interactive effects of multiple climate drivers on disease impact.

Machine learning for the meta-analyses of microbial pathogens' volatile signatures.

PubMed

Palma, Susana I C J; Traguedo, Ana P; Porteira, Ana R; Frias, Maria J; Gamboa, Hugo; Roque, Ana C A

2018-02-20

Non-invasive and fast diagnostic tools based on volatolomics hold great promise in the control of infectious diseases. However, the tools to identify microbial volatile organic compounds (VOCs) discriminating between human pathogens are still missing. Artificial intelligence is increasingly recognised as an essential tool in health sciences. Machine learning algorithms based in support vector machines and features selection tools were here applied to find sets of microbial VOCs with pathogen-discrimination power. Studies reporting VOCs emitted by human microbial pathogens published between 1977 and 2016 were used as source data. A set of 18 VOCs is sufficient to predict the identity of 11 microbial pathogens with high accuracy (77%), and precision (62-100%). There is one set of VOCs associated with each of the 11 pathogens which can predict the presence of that pathogen in a sample with high accuracy and precision (86-90%). The implemented pathogen classification methodology supports future database updates to include new pathogen-VOC data, which will enrich the classifiers. The sets of VOCs identified potentiate the improvement of the selectivity of non-invasive infection diagnostics using artificial olfaction devices.

Phenotypic interactions between tree hosts and invasive forest pathogens in the light of globalization and climate change

PubMed Central

2016-01-01

Invasive pathogens can cause considerable damage to forest ecosystems. Lack of coevolution is generally thought to enable invasive pathogens to bypass the defence and/or recognition systems in the host. Although mostly true, this argument fails to predict intermittent outcomes in space and time, underlining the need to include the roles of the environment and the phenotype in host–pathogen interactions when predicting disease impacts. We emphasize the need to consider host–tree imbalances from a phenotypic perspective, considering the lack of coevolutionary and evolutionary history with the pathogen and the environment, respectively. We describe how phenotypic plasticity and plastic responses to environmental shifts may become maladaptive when hosts are faced with novel pathogens. The lack of host–pathogen and environmental coevolution are aligned with two global processes currently driving forest damage: globalization and climate change, respectively. We suggest that globalization and climate change act synergistically, increasing the chances of both genotypic and phenotypic imbalances. Short moves on the same continent are more likely to be in balance than if the move is from another part of the world. We use Gremmeniella abietina outbreaks in Sweden to exemplify how host–pathogen phenotypic interactions can help to predict the impacts of specific invasive and emergent diseases. This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’. PMID:28080981

Phenotypic interactions between tree hosts and invasive forest pathogens in the light of globalization and climate change.

PubMed

Stenlid, Jan; Oliva, Jonàs

2016-12-05

Invasive pathogens can cause considerable damage to forest ecosystems. Lack of coevolution is generally thought to enable invasive pathogens to bypass the defence and/or recognition systems in the host. Although mostly true, this argument fails to predict intermittent outcomes in space and time, underlining the need to include the roles of the environment and the phenotype in host-pathogen interactions when predicting disease impacts. We emphasize the need to consider host-tree imbalances from a phenotypic perspective, considering the lack of coevolutionary and evolutionary history with the pathogen and the environment, respectively. We describe how phenotypic plasticity and plastic responses to environmental shifts may become maladaptive when hosts are faced with novel pathogens. The lack of host-pathogen and environmental coevolution are aligned with two global processes currently driving forest damage: globalization and climate change, respectively. We suggest that globalization and climate change act synergistically, increasing the chances of both genotypic and phenotypic imbalances. Short moves on the same continent are more likely to be in balance than if the move is from another part of the world. We use Gremmeniella abietina outbreaks in Sweden to exemplify how host-pathogen phenotypic interactions can help to predict the impacts of specific invasive and emergent diseases.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'. © 2016 The Author(s).

An ecosystem-scale model for the spread of a host-specific forest pathogen in the Greater Yellowstone Ecosystem

USGS Publications Warehouse

Hatala, J.A.; Dietze, M.C.; Crabtree, R.L.; Kendall, Katherine C.; Six, D.; Moorcroft, P.R.

2011-01-01

The introduction of nonnative pathogens is altering the scale, magnitude, and persistence of forest disturbance regimes in the western United States. In the high-altitude whitebark pine (Pinus albicaulis) forests of the Greater Yellowstone Ecosystem (GYE), white pine blister rust (Cronartium ribicola) is an introduced fungal pathogen that is now the principal cause of tree mortality in many locations. Although blister rust eradication has failed in the past, there is nonetheless substantial interest in monitoring the disease and its rate of progression in order to predict the future impact of forest disturbances within this critical ecosystem.This study integrates data from five different field-monitoring campaigns from 1968 to 2008 to create a blister rust infection model for sites located throughout the GYE. Our model parameterizes the past rates of blister rust spread in order to project its future impact on high-altitude whitebark pine forests. Because the process of blister rust infection and mortality of individuals occurs over the time frame of many years, the model in this paper operates on a yearly time step and defines a series of whitebark pine infection classes: susceptible, slightly infected, moderately infected, and dead. In our analysis, we evaluate four different infection models that compare local vs. global density dependence on the dynamics of blister rust infection. We compare models in which blister rust infection is: (1) independent of the density of infected trees, (2) locally density-dependent, (3) locally density-dependent with a static global infection rate among all sites, and (4) both locally and globally density-dependent. Model evaluation through the predictive loss criterion for Bayesian analysis supports the model that is both locally and globally density-dependent. Using this best-fit model, we predicted the average residence times for the four stages of blister rust infection in our model, and we found that, on average, whitebark pine trees within the GYE remain susceptible for 6.7 years, take 10.9 years to transition from slightly infected to moderately infected, and take 9.4 years to transition from moderately infected to dead. Using our best-fit model, we project the future levels of blister rust infestation in the GYE at critical sites over the next 20 years.

Disease Prediction Models and Operational Readiness

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

Corley, Courtney D.; Pullum, Laura L.; Hartley, David M.

2014-03-19

INTRODUCTION: The objective of this manuscript is to present a systematic review of biosurveillance models that operate on select agents and can forecast the occurrence of a disease event. One of the primary goals of this research was to characterize the viability of biosurveillance models to provide operationally relevant information for decision makers to identify areas for future research. Two critical characteristics differentiate this work from other infectious disease modeling reviews. First, we reviewed models that attempted to predict the disease event, not merely its transmission dynamics. Second, we considered models involving pathogens of concern as determined by the USmore » National Select Agent Registry (as of June 2011). Methods: We searched dozens of commercial and government databases and harvested Google search results for eligible models utilizing terms and phrases provided by public health analysts relating to biosurveillance, remote sensing, risk assessments, spatial epidemiology, and ecological niche-modeling, The publication date of search results returned are bound by the dates of coverage of each database and the date in which the search was performed, however all searching was completed by December 31, 2010. This returned 13,767 webpages and 12,152 citations. After de-duplication and removal of extraneous material, a core collection of 6,503 items was established and these publications along with their abstracts are presented in a semantic wiki at http://BioCat.pnnl.gov. Next, PNNL’s IN-SPIRE visual analytics software was used to cross-correlate these publications with the definition for a biosurveillance model resulting in the selection of 54 documents that matched the criteria resulting Ten of these documents, However, dealt purely with disease spread models, inactivation of bacteria, or the modeling of human immune system responses to pathogens rather than predicting disease events. As a result, we systematically reviewed 44 papers and the results are presented in this analysis.« less

Virtual Beach: Decision Support Tools for Beach Pathogen Prediction

EPA Science Inventory

The Virtual Beach Managers Tool (VB) is decision-making software developed to help local beach managers make decisions as to when beaches should be closed due to predicted high levels of water borne pathogens. The tool is being developed under the umbrella of EPA's Advanced Monit...

Reducing the risk of invasive forest pests and pathogens: Combining legislation, targeted management and public awareness.

PubMed

Klapwijk, Maartje J; Hopkins, Anna J M; Eriksson, Louise; Pettersson, Maria; Schroeder, Martin; Lindelöw, Åke; Rönnberg, Jonas; Keskitalo, E Carina H; Kenis, Marc

2016-02-01

Intensifying global trade will result in increased numbers of plant pest and pathogen species inadvertently being transported along with cargo. This paper examines current mechanisms for prevention and management of potential introductions of forest insect pests and pathogens in the European Union (EU). Current European legislation has not been found sufficient in preventing invasion, establishment and spread of pest and pathogen species within the EU. Costs associated with future invasions are difficult to estimate but past invasions have led to negative economic impacts in the invaded country. The challenge is combining free trade and free movement of products (within the EU) with protection against invasive pests and pathogens. Public awareness may mobilise the public for prevention and detection of potential invasions and, simultaneously, increase support for eradication and control measures. We recommend focus on commodities in addition to pathways, an approach within the EU using a centralised response unit and, critically, to engage the general public in the battle against establishment and spread of these harmful pests and pathogens.

Quarantine Regulations and the Impact of Modern Detection Methods.

PubMed

Martin, Robert R; Constable, Fiona; Tzanetakis, Ioannis E

2016-08-04

Producers worldwide need access to the best plant varieties and cultivars available to be competitive in global markets. This often means moving plants across international borders as soon as they are available. At the same time, quarantine agencies are tasked with minimizing the risk of introducing exotic pests and pathogens along with imported plant material, with the goal to protect domestic agriculture and native fauna and flora. These two drivers, the movement of more plant material and reduced risk of pathogen introduction, are at odds. Improvements in large-scale or next-generation sequencing (NGS) and bioinformatics for data analysis have resulted in improved speed and accuracy of pathogen detection that could facilitate plant trade with reduced risk of pathogen movement. There are concerns to be addressed before NGS can replace existing tools used for pathogen detection in plant quarantine and certification programs. Here, we discuss the advantages and possible pitfalls of this technology for meeting the needs of plant quarantine and certification.

Sentinel trees as a tool to forecast invasions of alien plant pathogens.

PubMed

Vettraino, AnnaMaria; Roques, Alain; Yart, Annie; Fan, Jian-ting; Sun, Jiang-hua; Vannini, Andrea

2015-01-01

Recent disease outbreaks caused by alien invasive pathogens into European forests posed a serious threat to forest sustainability with relevant environmental and economic effects. Many of the alien tree pathogens recently introduced into Europe were not previously included on any quarantine lists, thus they were not subject to phytosanitary inspections. The identification and description of alien fungi potentially pathogenic to native European flora before their introduction in Europe, is a paramount need in order to limit the risk of invasion and the impact to forest ecosystems. To determine the potential invasive fungi, a sentinel trees plot was established in Fuyang, China, using healthy seedlings of European tree species including Quercus petreae, Q. suber, and Q. ilex. The fungal assemblage associated with symptomatic specimens was studied using the tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS 1). Taxa with probable Asiatic origin were identified and included plant pathogenic genera. These results indicate that sentinel plants may be a strategic tool to improve the prevention of bioinvasions.

Introduction to Pathogenic Protozoa

DTIC Science & Technology

2011-06-01

hematoxylin suf- fers when the modified fixative, in which zinc or copper is substituted for mercury, is used. Specimens should be first grossly examined...specimens to detect light infections. The two most common procedures are zinc sulfate flotation and formalin-ethyl acetate sedi- mentation. Wet mount

Effects of simulated packing house operating conditions on pathogen internalization in tomatoes

USDA-ARS?s Scientific Manuscript database

Introduction: Food-borne illness outbreaks associated with Salmonella enterica have been traced back to tomatoes contaminated through bacterial attachment and possible internalization during post-harvest handling. However, no scientific information is available regarding the effect of current tomato...

Sensitivity of Mycobacterium bovis to common beef processing interventions

USDA-ARS?s Scientific Manuscript database

Introduction. Cattle infected with Mycobacterium bovis, the causative agent of bovine tuberculosis and a relevant zoonosis to humans, may be sent to slaughter before diagnosis of infection because of slow multiplication of the pathogen. Purpose. This study evaluates multiple processing interventi...

Distribution of triclosan-resistant genes in major pathogenic microorganisms revealed by metagenome and genome-wide analysis

PubMed Central

Khan, Raees; Roy, Nazish; Choi, Kihyuck

2018-01-01

The substantial use of triclosan (TCS) has been aimed to kill pathogenic bacteria, but TCS resistance seems to be prevalent in microbial species and limited knowledge exists about TCS resistance determinants in a majority of pathogenic bacteria. We aimed to evaluate the distribution of TCS resistance determinants in major pathogenic bacteria (N = 231) and to assess the enrichment of potentially pathogenic genera in TCS contaminated environments. A TCS-resistant gene (TRG) database was constructed and experimentally validated to predict TCS resistance in major pathogenic bacteria. Genome-wide in silico analysis was performed to define the distribution of TCS-resistant determinants in major pathogens. Microbiome analysis of TCS contaminated soil samples was also performed to investigate the abundance of TCS-resistant pathogens. We experimentally confirmed that TCS resistance could be accurately predicted using genome-wide in silico analysis against TRG database. Predicted TCS resistant phenotypes were observed in all of the tested bacterial strains (N = 17), and heterologous expression of selected TCS resistant genes from those strains conferred expected levels of TCS resistance in an alternative host Escherichia coli. Moreover, genome-wide analysis revealed that potential TCS resistance determinants were abundant among the majority of human-associated pathogens (79%) and soil-borne plant pathogenic bacteria (98%). These included a variety of enoyl-acyl carrier protein reductase (ENRs) homologues, AcrB efflux pumps, and ENR substitutions. FabI ENR, which is the only known effective target for TCS, was either co-localized with other TCS resistance determinants or had TCS resistance-associated substitutions. Furthermore, microbiome analysis revealed that pathogenic genera with intrinsic TCS-resistant determinants exist in TCS contaminated environments. We conclude that TCS may not be as effective against the majority of bacterial pathogens as previously presumed. Further, the excessive use of this biocide in natural environments may selectively enrich for not only TCS-resistant bacterial pathogens, but possibly for additional resistance to multiple antibiotics. PMID:29420585

A neighborhood statistics model for predicting stream pathogen indicator levels.

PubMed

Pandey, Pramod K; Pasternack, Gregory B; Majumder, Mahbubul; Soupir, Michelle L; Kaiser, Mark S

2015-03-01

Because elevated levels of water-borne Escherichia coli in streams are a leading cause of water quality impairments in the U.S., water-quality managers need tools for predicting aqueous E. coli levels. Presently, E. coli levels may be predicted using complex mechanistic models that have a high degree of unchecked uncertainty or simpler statistical models. To assess spatio-temporal patterns of instream E. coli levels, herein we measured E. coli, a pathogen indicator, at 16 sites (at four different times) within the Squaw Creek watershed, Iowa, and subsequently, the Markov Random Field model was exploited to develop a neighborhood statistics model for predicting instream E. coli levels. Two observed covariates, local water temperature (degrees Celsius) and mean cross-sectional depth (meters), were used as inputs to the model. Predictions of E. coli levels in the water column were compared with independent observational data collected from 16 in-stream locations. The results revealed that spatio-temporal averages of predicted and observed E. coli levels were extremely close. Approximately 66 % of individual predicted E. coli concentrations were within a factor of 2 of the observed values. In only one event, the difference between prediction and observation was beyond one order of magnitude. The mean of all predicted values at 16 locations was approximately 1 % higher than the mean of the observed values. The approach presented here will be useful while assessing instream contaminations such as pathogen/pathogen indicator levels at the watershed scale.

Assessing the probability of introduction and spread of avian influenza (AI) virus in commercial Australian poultry operations using an expert opinion elicitation

PubMed Central

Toribio, Jenny-Ann; Scott, Angela Bullanday; Groves, Peter; Barnes, Belinda; Glass, Kathryn; Moloney, Barbara; Black, Amanda; Hernandez-Jover, Marta

2018-01-01

The objective of this study was to elicit experts’ opinions and gather estimates on the perceived probability of introduction and spread of avian influenza (AI) virus in the Australian broiler and layer industry. Using a modified Delphi method and a 4-step elicitation process, 11 experts were asked to give initial individual estimates for the various pathways and practices in the presented scenarios using a questionnaire. Following this, a workshop was conducted to present group averages of estimates and discussion was facilitated to obtain final individual estimates. For each question, estimates for all experts were combined using a discrete distribution, with weights allocated representing the level of expertise. Indirect contact with wild birds either via a contaminated water source or fomites was considered the most likely pathway of introduction of low pathogenic avian influenza (LPAI) on poultry farms. Presence of a water body near the poultry farm was considered a potential pathway for introduction only when the operation type was free range and the water body was within 500m distance from the shed. The probability that LPAI will mutate to highly pathogenic avian influenza (HPAI) was considered to be higher in layer farms. Shared personnel, equipment and aerosol dispersion were the most likely pathways of shed to shed spread of the virus. For LPAI and HPAI spread from farm to farm, shared pick-up trucks for broiler and shared egg trays and egg pallets for layer farms were considered the most likely pathways. Findings from this study provide an insight on most influential practices on the introduction and spread of AI virus among commercial poultry farms in Australia, as elicited from opinions of experts. These findings will be used to support parameterization of a modelling study assessing the risk of AI introduction and spread among commercial poultry farms in Australia. PMID:29494696

Assessing the probability of introduction and spread of avian influenza (AI) virus in commercial Australian poultry operations using an expert opinion elicitation.

PubMed

Singh, Mini; Toribio, Jenny-Ann; Scott, Angela Bullanday; Groves, Peter; Barnes, Belinda; Glass, Kathryn; Moloney, Barbara; Black, Amanda; Hernandez-Jover, Marta

2018-01-01

The objective of this study was to elicit experts' opinions and gather estimates on the perceived probability of introduction and spread of avian influenza (AI) virus in the Australian broiler and layer industry. Using a modified Delphi method and a 4-step elicitation process, 11 experts were asked to give initial individual estimates for the various pathways and practices in the presented scenarios using a questionnaire. Following this, a workshop was conducted to present group averages of estimates and discussion was facilitated to obtain final individual estimates. For each question, estimates for all experts were combined using a discrete distribution, with weights allocated representing the level of expertise. Indirect contact with wild birds either via a contaminated water source or fomites was considered the most likely pathway of introduction of low pathogenic avian influenza (LPAI) on poultry farms. Presence of a water body near the poultry farm was considered a potential pathway for introduction only when the operation type was free range and the water body was within 500m distance from the shed. The probability that LPAI will mutate to highly pathogenic avian influenza (HPAI) was considered to be higher in layer farms. Shared personnel, equipment and aerosol dispersion were the most likely pathways of shed to shed spread of the virus. For LPAI and HPAI spread from farm to farm, shared pick-up trucks for broiler and shared egg trays and egg pallets for layer farms were considered the most likely pathways. Findings from this study provide an insight on most influential practices on the introduction and spread of AI virus among commercial poultry farms in Australia, as elicited from opinions of experts. These findings will be used to support parameterization of a modelling study assessing the risk of AI introduction and spread among commercial poultry farms in Australia.

Four different sublineages of highly pathogenic avian influenza H5N1 introduced in Hungary in 2006-2007.

PubMed

Szeleczky, Zsófia; Dán, Adám; Ursu, Krisztina; Ivanics, Eva; Kiss, István; Erdélyi, Károly; Belák, Sándor; Muller, Claude P; Brown, Ian H; Bálint, Adám

2009-10-20

Highly pathogenic avian influenza (HPAI) H5N1 viruses were introduced to Hungary during 2006-2007 in three separate waves. This study aimed at determining the full-length genomic coding regions of the index strains from these epizootics in order to: (i) understand the phylogenetic relationship to other European H5N1 isolates, (ii) elucidate the possible connection between the different outbreaks and (iii) determine the putative origin and way of introduction of the different virus variants. Molecular analysis of the HA gene of Hungarian HPAI isolates obtained from wild birds during the first introduction revealed two groups designated Hungarian1 (HUN1) and Hungarian2 (HUN2) within sublineage 2.2B and clade 2.2.1, respectively. Sequencing the whole coding region of the two index viruses A/mute swan/Hungary/3472/2006 and A/mute swan/4571/Hungary/2006 suggests the role of wild birds in the introduction of HUN1 and HUN2 viruses: the most similar isolates to HUN1 and HUN2 group were found in wild avian species in Croatia and Slovakia, respectively. The second introduction of HPAI H5N1 led to the largest epizootic in domestic waterfowl in Europe. The index strain of the epizootic A/goose/Hungary/14756/2006 clustered to sublineage 2.2.A1 forming the Hungarian3 (HUN3) group. A common ancestry of HUN3 isolates with Bavarian strains is suggested as the most likely scenario of origin. Hungarian4 (HUN4) viruses isolated from the third introduction clustered with isolate A/turkey/United Kingdom/750/2007 forming a sublineage 2.2.A2. The origin and way of introduction of HUN4 viruses is still obscure, thus further genetic, phylogenetic, ecological and epidemiological data are required in order to elucidate it.

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).

Modeling environmental contamination in hospital single- and four-bed rooms.

PubMed

King, M-F; Noakes, C J; Sleigh, P A

2015-12-01

Aerial dispersion of pathogens is recognized as a potential transmission route for hospital acquired infections; however, little is known about the link between healthcare worker (HCW) contacts' with contaminated surfaces, the transmission of infections and hospital room design. We combine computational fluid dynamics (CFD) simulations of bioaerosol deposition with a validated probabilistic HCW-surface contact model to estimate the relative quantity of pathogens accrued on hands during six types of care procedures in two room types. Results demonstrate that care type is most influential (P < 0.001), followed by the number of surface contacts (P < 0.001) and the distribution of surface pathogens (P = 0.05). Highest hand contamination was predicted during Personal care despite the highest levels of hand hygiene. Ventilation rates of 6 ac/h vs. 4 ac/h showed only minor reductions in predicted hand colonization. Pathogens accrued on hands decreased monotonically after patient care in single rooms due to the physical barrier of bioaerosol transmission between rooms and subsequent hand sanitation. Conversely, contamination was predicted to increase during contact with patients in four-bed rooms due to spatial spread of pathogens. Location of the infectious patient with respect to ventilation played a key role in determining pathogen loadings (P = 0.05). We present the first quantitative model predicting the surface contacts by HCW and the subsequent accretion of pathogenic material as they perform standard patient care. This model indicates that single rooms may significantly reduce the risk of cross-contamination due to indirect infection transmission. Not all care types pose the same risks to patients, and housekeeping performed by HCWs may be an important contribution in the transmission of pathogens between patients. Ventilation rates and positioning of infectious patients within four-bed rooms can mitigate the accretion of pathogens, whereby reducing the risk of missed hand hygiene opportunities. The model provides a tool to quantitatively evaluate the influence of hospital room design on infection risk. © 2015 The Authors. Indoor Air Published by John Wiley & Sons Ltd.

Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia.

PubMed

Sivley, R Michael; Sheehan, Jonathan H; Kropski, Jonathan A; Cogan, Joy; Blackwell, Timothy S; Phillips, John A; Bush, William S; Meiler, Jens; Capra, John A

2018-01-23

Next-generation sequencing of individuals with genetic diseases often detects candidate rare variants in numerous genes, but determining which are causal remains challenging. We hypothesized that the spatial distribution of missense variants in protein structures contains information about function and pathogenicity that can help prioritize variants of unknown significance (VUS) and elucidate the structural mechanisms leading to disease. To illustrate this approach in a clinical application, we analyzed 13 candidate missense variants in regulator of telomere elongation helicase 1 (RTEL1) identified in patients with Familial Interstitial Pneumonia (FIP). We curated pathogenic and neutral RTEL1 variants from the literature and public databases. We then used homology modeling to construct a 3D structural model of RTEL1 and mapped known variants into this structure. We next developed a pathogenicity prediction algorithm based on proximity to known disease causing and neutral variants and evaluated its performance with leave-one-out cross-validation. We further validated our predictions with segregation analyses, telomere lengths, and mutagenesis data from the homologous XPD protein. Our algorithm for classifying RTEL1 VUS based on spatial proximity to pathogenic and neutral variation accurately distinguished 7 known pathogenic from 29 neutral variants (ROC AUC = 0.85) in the N-terminal domains of RTEL1. Pathogenic proximity scores were also significantly correlated with effects on ATPase activity (Pearson r = -0.65, p = 0.0004) in XPD, a related helicase. Applying the algorithm to 13 VUS identified from sequencing of RTEL1 from patients predicted five out of six disease-segregating VUS to be pathogenic. We provide structural hypotheses regarding how these mutations may disrupt RTEL1 ATPase and helicase function. Spatial analysis of missense variation accurately classified candidate VUS in RTEL1 and suggests how such variants cause disease. Incorporating spatial proximity analyses into other pathogenicity prediction tools may improve accuracy for other genes and genetic diseases.

Stringent DDI-based Prediction of H. sapiens-M. tuberculosis H37Rv Protein-Protein Interactions

PubMed Central

2013-01-01

Background H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are very important information to illuminate the infection mechanism of M. tuberculosis H37Rv. But current H. sapiens-M. tuberculosis H37Rv PPI data are very scarce. This seriously limits the study of the interaction between this important pathogen and its host H. sapiens. Computational prediction of H. sapiens-M. tuberculosis H37Rv PPIs is an important strategy to fill in the gap. Domain-domain interaction (DDI) based prediction is one of the frequently used computational approaches in predicting both intra-species and inter-species PPIs. However, the performance of DDI-based host-pathogen PPI prediction has been rather limited. Results We develop a stringent DDI-based prediction approach with emphasis on (i) differences between the specific domain sequences on annotated regions of proteins under the same domain ID and (ii) calculation of the interaction strength of predicted PPIs based on the interacting residues in their interaction interfaces. We compare our stringent DDI-based approach to a conventional DDI-based approach for predicting PPIs based on gold standard intra-species PPIs and coherent informative Gene Ontology terms assessment. The assessment results show that our stringent DDI-based approach achieves much better performance in predicting PPIs than the conventional approach. Using our stringent DDI-based approach, we have predicted a small set of reliable H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies. We also analyze the H. sapiens-M. tuberculosis H37Rv PPIs predicted by our stringent DDI-based approach using cellular compartment distribution analysis, functional category enrichment analysis and pathway enrichment analysis. The analyses support the validity of our prediction result. Also, based on an analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent DDI-based approach, we have discovered some important properties of domains involved in host-pathogen PPIs. We find that both host and pathogen proteins involved in host-pathogen PPIs tend to have more domains than proteins involved in intra-species PPIs, and these domains have more interaction partners than domains on proteins involved in intra-species PPI. Conclusions The stringent DDI-based prediction approach reported in this work provides a stringent strategy for predicting host-pathogen PPIs. It also performs better than a conventional DDI-based approach in predicting PPIs. We have predicted a small set of accurate H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies. PMID:24564941

A historical overview of bacteriophage therapy as an alternative to antibiotics for the treatment of bacterial pathogens

PubMed Central

Wittebole, Xavier; De Roock, Sophie; Opal, Steven M

2014-01-01

The seemingly inexorable spread of antibiotic resistance genes among microbial pathogens now threatens the long-term viability of our current antimicrobial therapy to treat severe bacterial infections such as sepsis. Antibiotic resistance is reaching a crisis situation in some bacterial pathogens where few therapeutic alternatives remain and pan-resistant strains are becoming more prevalent. Non-antibiotic therapies to treat bacterial infections are now under serious consideration and one possible option is the therapeutic use of specific phage particles that target bacterial pathogens. Bacteriophage therapy has essentially been re-discovered by modern medicine after widespread use of phage therapy in the pre-antibiotic era lost favor, at least in Western countries, after the introduction of antibiotics. We review the current therapeutic rationale and clinical experience with phage therapy as a treatment for invasive bacterial infection as novel alternative to antimicrobial chemotherapy. PMID:23973944

Drug-resistant human Staphylococcus aureus in sanctuary apes pose a threat to endangered wild ape populations.

PubMed

Schaumburg, Frieder; Mugisha, Lawrence; Peck, Bruce; Becker, Karsten; Gillespie, Thomas R; Peters, Georg; Leendertz, Fabian H

2012-12-01

Reintroduction of sanctuary apes to natural habitat is considered an important tool for conservation; however, reintroduction has the potential to endanger resident wild apes through the introduction of human pathogens. We found a high prevalence of drug-resistant, human-associated lineages of Staphylococcus aureus in sanctuary chimpanzees (Pan troglodytes) from Zambia and Uganda. This pathogen is associated with skin and soft tissue diseases and severe invasive infections (i.e. pneumonia and septicemia). Colonization by this bacterium is difficult to clear due to frequent recolonization. In addition to its pathogenic potential, human-related S. aureus can serve as an indicator organism for the transmission of other potential pathogens like pneumococci or mycobacteria. Plans to reintroduce sanctuary apes should be reevaluated in light of the high risk of introducing human-adapted S. aureus into wild ape populations where treatment is impossible. © 2012 Wiley Periodicals, Inc.

Cage size, movement in and out of housing during daily care, and other environmental and population health risk factors for feline upper respiratory disease in nine North American animal shelters.

PubMed

Wagner, Denae C; Kass, Philip H; Hurley, Kate F

2018-01-01

Upper respiratory infection (URI) is not an inevitable consequence of sheltering homeless cats. This study documents variation in risk of URI between nine North American shelters; determines whether this reflects variation in pathogen frequency on intake or differences in transmission and expression of disease; and identifies modifiable environmental and group health factors linked to risk for URI. This study demonstrated that although periodic introduction of pathogens into shelter populations may be inevitable, disease resulting from those pathogens is not. Housing and care of cats, particularly during their first week of stay in an animal shelter environment, significantly affects the rate of upper respiratory infection.

Disease introduction is associated with a phase transition in bighorn sheep demographics

PubMed Central

Manlove, Kezia; Cassirer, E. Frances; Cross, Paul Chafee; Plowright, Raina K.; Hudson, Peter J.

2016-01-01

Ecological theory suggests that pathogens are capable of regulating or limiting host population dynamics, and this relationship has been empirically established in several settings. However, although studies of childhood diseases were integral to the development of disease ecology, few studies show population limitation by a disease affecting juveniles. Here, we present empirical evidence that disease in lambs constrains population growth in bighorn sheep (Ovis canadensis) based on 45 years of population-level and 18 years of individual-level monitoring across 12 populations. While populations generally increased (lambda =1.11) prior to disease introduction, most of these same populations experienced an abrupt change in trajectory at the time of disease invasion, usually followed by stagnant-to-declining growth rates (lambda = 0.98) over the next twenty years. Disease-induced juvenile mortality imposed strong constraints on population growth that were not observed prior to disease introduction, even as adult survival returned to pre-invasion levels. Simulations suggested that models including persistent disease-induced mortality in juveniles qualitatively matched observed population trajectories, whereas models that only incorporated all-age disease events did not. We use these results to argue that pathogen persistence may pose a lasting, but under-recognized, threat to host populations, particularly in cases where clinical disease manifests primarily in juveniles. PMID:27859120

Disease introduction is associated with a phase transition in bighorn sheep demographics

USGS Publications Warehouse

Manlove, Kezia; Cassirer, E. Frances; Cross, Paul C.; Plowright, Raina K.; Hudson, Peter J.

2016-01-01

Ecological theory suggests that pathogens are capable of regulating or limiting host population dynamics, and this relationship has been empirically established in several settings. However, although studies of childhood diseases were integral to the development of disease ecology, few studies show population limitation by a disease affecting juveniles. Here, we present empirical evidence that disease in lambs constrains population growth in bighorn sheep (Ovis canadensis) based on 45 years of population-level and 18 years of individual-level monitoring across 12 populations. While populations generally increased (λ = 1.11) prior to disease introduction, most of these same populations experienced an abrupt change in trajectory at the time of disease invasion, usually followed by stagnant-to-declining growth rates (λ = 0.98) over the next 20 years. Disease-induced juvenile mortality imposed strong constraints on population growth that were not observed prior to disease introduction, even as adult survival returned to pre-invasion levels. Simulations suggested that models including persistent disease-induced mortality in juveniles qualitatively matched observed population trajectories, whereas models that only incorporated all-age disease events did not. We use these results to argue that pathogen persistence may pose a lasting, but under-recognized, threat to host populations, particularly in cases where clinical disease manifests primarily in juveniles.

Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors

PubMed Central

Sperschneider, Jana; Ying, Hua; Dodds, Peter N.; Gardiner, Donald M.; Upadhyaya, Narayana M.; Singh, Karam B.; Manners, John M.; Taylor, Jennifer M.

2014-01-01

Plant pathogens cause severe losses to crop plants and threaten global food production. One striking example is the wheat stem rust fungus, Puccinia graminis f. sp. tritici, which can rapidly evolve new virulent pathotypes in response to resistant host lines. Like several other filamentous fungal and oomycete plant pathogens, its genome features expanded gene families that have been implicated in host-pathogen interactions, possibly encoding effector proteins that interact directly with target host defense proteins. Previous efforts to understand virulence largely relied on the prediction of secreted, small and cysteine-rich proteins as candidate effectors and thus delivered an overwhelming number of candidates. Here, we implement an alternative analysis strategy that uses the signal of adaptive evolution as a line of evidence for effector function, combined with comparative information and expression data. We demonstrate that in planta up-regulated genes that are rapidly evolving are found almost exclusively in pathogen-associated gene families, affirming the impact of host-pathogen co-evolution on genome structure and the adaptive diversification of specialized gene families. In particular, we predict 42 effector candidates that are conserved only across pathogens, induced during infection and rapidly evolving. One of our top candidates has recently been shown to induce genotype-specific hypersensitive cell death in wheat. This shows that comparative genomics incorporating the evolutionary signal of adaptation is powerful for predicting effector candidates for laboratory verification. Our system can be applied to a wide range of pathogens and will give insight into host-pathogen dynamics, ultimately leading to progress in strategies for disease control. PMID:25225496

Adaptive potential of maritime pine (Pinus pinaster) populations to the emerging pitch canker pathogen, Fusarium circinatum.

PubMed

Elvira-Recuenco, Margarita; Iturritxa, Eugenia; Majada, Juan; Alia, Ricardo; Raposo, Rosa

2014-01-01

There is a concern on how emerging pests and diseases will affect the distribution range and adaptability of their host species, especially due to different conditions derived from climate change and growing globalization. Fusarium circinatum, which causes pitch canker disease in Pinus species, is an exotic pathogen of recent introduction in Spain that threatens its maritime pine (P. pinaster) stands. To predict the impact this disease will have on the species, we examine host resistance traits and their genetic architecture. Resistance phenotyping was done in a clonal provenance/progeny trial, using three-year-old cuttings artificially inoculated with the pathogen and maintained under controlled environmental conditions. A total number of 670 ramets were assessed, distributed in 10 populations, with a total of 47 families, 2 to 5 half-sibs per family, and 3-7 ramets per clone. High genetic variation was found at the three hierarchical levels studied: population, family and clone, being both additive and non-additive effects important. Narrow-sense and broad-sense heritability estimates were relatively high, with respective values of 0.43-0.58 and 0.51-0.8, depending on the resistance traits measured (lesion length, lesion length rate, time to wilting, and survival). These values suggest the species' high capacity of evolutionary response to the F. circinatum pathogen. A population originated in Northern Spain was the most resistant, while another from Morocco was the most susceptible. The total number of plants that did not show lesion development or presented a small lesion (length<30 mm) was 224 out of 670, indicating a high proportion of resistant trees in the offspring within the analyzed populations. We found large differences among populations and considerable genetic variation within populations, which should allow, through natural or artificial selection, the successful adaptation of maritime pine to pitch canker disease.

Adaptive Potential of Maritime Pine (Pinus pinaster) Populations to the Emerging Pitch Canker Pathogen, Fusarium circinatum

PubMed Central

Elvira-Recuenco, Margarita; Iturritxa, Eugenia; Majada, Juan; Alia, Ricardo; Raposo, Rosa

2014-01-01

There is a concern on how emerging pests and diseases will affect the distribution range and adaptability of their host species, especially due to different conditions derived from climate change and growing globalization. Fusarium circinatum, which causes pitch canker disease in Pinus species, is an exotic pathogen of recent introduction in Spain that threatens its maritime pine (P. pinaster) stands. To predict the impact this disease will have on the species, we examine host resistance traits and their genetic architecture. Resistance phenotyping was done in a clonal provenance/progeny trial, using three-year-old cuttings artificially inoculated with the pathogen and maintained under controlled environmental conditions. A total number of 670 ramets were assessed, distributed in 10 populations, with a total of 47 families, 2 to 5 half-sibs per family, and 3–7 ramets per clone. High genetic variation was found at the three hierarchical levels studied: population, family and clone, being both additive and non-additive effects important. Narrow-sense and broad-sense heritability estimates were relatively high, with respective values of 0.43–0.58 and 0.51–0.8, depending on the resistance traits measured (lesion length, lesion length rate, time to wilting, and survival). These values suggest the species' high capacity of evolutionary response to the F. circinatum pathogen. A population originated in Northern Spain was the most resistant, while another from Morocco was the most susceptible. The total number of plants that did not show lesion development or presented a small lesion (length<30 mm) was 224 out of 670, indicating a high proportion of resistant trees in the offspring within the analyzed populations. We found large differences among populations and considerable genetic variation within populations, which should allow, through natural or artificial selection, the successful adaptation of maritime pine to pitch canker disease. PMID:25500822

Can biosecurity and local network properties predict pathogen species richness in the salmonid industry?

PubMed

Yatabe, Tadaishi; More, Simon J; Geoghegan, Fiona; McManus, Catherine; Hill, Ashley E; Martínez-López, Beatriz

2018-01-01

Salmonid farming in Ireland is mostly organic, which implies limited disease treatment options. This highlights the importance of biosecurity for preventing the introduction and spread of infectious agents. Similarly, the effect of local network properties on infection spread processes has rarely been evaluated. In this paper, we characterized the biosecurity of salmonid farms in Ireland using a survey, and then developed a score for benchmarking the disease risk of salmonid farms. The usefulness and validity of this score, together with farm indegree (dichotomized as ≤ 1 or > 1), were assessed through generalized Poisson regression models, in which the modeled outcome was pathogen richness, defined here as the number of different diseases affecting a farm during a year. Seawater salmon (SW salmon) farms had the highest biosecurity scores with a median (interquartile range) of 82.3 (5.4), followed by freshwater salmon (FW salmon) with 75.2 (8.2), and freshwater trout (FW trout) farms with 74.8 (4.5). For FW salmon and trout farms, the top ranked model (in terms of leave-one-out information criteria, looic) was the null model (looic = 46.1). For SW salmon farms, the best ranking model was the full model with both predictors and their interaction (looic = 33.3). Farms with a higher biosecurity score were associated with lower pathogen richness, and farms with indegree > 1 (i.e. more than one fish supplier) were associated with increased pathogen richness. The effect of the interaction between these variables was also important, showing an antagonistic effect. This would indicate that biosecurity effectiveness is achieved through a broader perspective on the subject, which includes a minimization in the number of suppliers and hence in the possibilities for infection to enter a farm. The work presented here could be used to elaborate indicators of a farm's disease risk based on its biosecurity score and indegree, to inform risk-based disease surveillance and control strategies for private and public stakeholders.

Can biosecurity and local network properties predict pathogen species richness in the salmonid industry?

PubMed Central

More, Simon J.; Geoghegan, Fiona; McManus, Catherine; Hill, Ashley E.; Martínez-López, Beatriz

2018-01-01

Salmonid farming in Ireland is mostly organic, which implies limited disease treatment options. This highlights the importance of biosecurity for preventing the introduction and spread of infectious agents. Similarly, the effect of local network properties on infection spread processes has rarely been evaluated. In this paper, we characterized the biosecurity of salmonid farms in Ireland using a survey, and then developed a score for benchmarking the disease risk of salmonid farms. The usefulness and validity of this score, together with farm indegree (dichotomized as ≤ 1 or > 1), were assessed through generalized Poisson regression models, in which the modeled outcome was pathogen richness, defined here as the number of different diseases affecting a farm during a year. Seawater salmon (SW salmon) farms had the highest biosecurity scores with a median (interquartile range) of 82.3 (5.4), followed by freshwater salmon (FW salmon) with 75.2 (8.2), and freshwater trout (FW trout) farms with 74.8 (4.5). For FW salmon and trout farms, the top ranked model (in terms of leave-one-out information criteria, looic) was the null model (looic = 46.1). For SW salmon farms, the best ranking model was the full model with both predictors and their interaction (looic = 33.3). Farms with a higher biosecurity score were associated with lower pathogen richness, and farms with indegree > 1 (i.e. more than one fish supplier) were associated with increased pathogen richness. The effect of the interaction between these variables was also important, showing an antagonistic effect. This would indicate that biosecurity effectiveness is achieved through a broader perspective on the subject, which includes a minimization in the number of suppliers and hence in the possibilities for infection to enter a farm. The work presented here could be used to elaborate indicators of a farm’s disease risk based on its biosecurity score and indegree, to inform risk-based disease surveillance and control strategies for private and public stakeholders. PMID:29381760

Dermatosis due to plants (phytodermatosis).

PubMed

dos Reis, Vitor Manoel Silva

2010-01-01

Dermatosis caused by plants is relatively common and may occur by various pathogenic mechanisms. Dermatitis due to physical trauma, pharmacological action, irritation, sensitization, mediated by IgE and induced by light are described. Pseudophytodermatosis caused by plant-delivered elements is also described in the introduction to this work.

Development of a loop-mediated isothermal amplification method for rapid campylobacter jejuni detection

USDA-ARS?s Scientific Manuscript database

Introduction: Campylobacter jejuni is the leading foodborne pathogen that causes human bacterial gastroenteritis worldwide. Poultry products are regarded as a major source for human infection. Early, rapid detection of this microorganism in poultry products is necessary for contamination control ...

Introduction to Oomycetes

USDA-ARS?s Scientific Manuscript database

The oomycetes, also known as “water molds”, are a group of several hundred organisms that include some of the most devastating plant pathogens. The diseases they cause include seedling blights, damping-off, root rots, foliar blights and downy mildews. Some notable diseases are the late blight of po...

Tolerance to Phytophthora Fruit Rot in Watermelon Plant Introductions

USDA-ARS?s Scientific Manuscript database

Phytophthora capsici is distributed worldwide, and is an aggressive pathogen with a broad host range infecting solanaceous, leguminaceous, and cucurbitaceous crops. Fruit rot, caused by P. capsici is an emerging disease in most watermelon producing regions of Southeast US. Resistance to fruit rot o...

Isolation, characterization and immunological reaction of proteus mirabilis isolates from broilers

USDA-ARS?s Scientific Manuscript database

Introduction: Proteus mirabilis, which is ubiquitous in the environment, is an opportunistic human pathogen that causes urinary tract infections. Recently, this bacterium has been isolated from many food producing animals, including poultry and its products. Moreover, reports have shown P. mirabi...

A golden jackal (Canis aureus) from Austria bearing Hepatozoon canis--import due to immigration into a non-endemic area?

PubMed

Duscher, Georg Gerhard; Kübber-Heiss, Anna; Richter, Barbara; Suchentrunk, Franz

2013-02-01

The protozoan Hepatozoon canis, which is transmitted via ingestion of infected ticks by canine hosts, is not endemic to mid-latitude regions in Europe. Its distribution is supposed to be linked to the occurrence of its primary tick vector Rhipicephalus sanguineus. A young male golden jackal (Canis aureus) found as road kill close to Vienna, Austria, was infected by this pathogen. Cloning and sequencing of the PCR product revealed 6 different haplotypes of H. canis. Based on the sequences, no clear relationship to the origin of infection could be traced. This is the first report of H. canis for Austria, and wild canines such as the currently found jackal may provide a source of natural spread of this parasite into non-endemic areas. This natural immigration of wild animals represents a way of pathogen introduction, which has to be considered in disease prevention in addition to human-made introduction due to animal import and export. Copyright © 2012 Elsevier GmbH. All rights reserved.

Wild birds and urban ecology of ticks and tick-borne pathogens, Chicago, Illinois, USA, 2005-2010.

PubMed

Hamer, Sarah A; Goldberg, Tony L; Kitron, Uriel D; Brawn, Jeffrey D; Anderson, Tavis K; Loss, Scott R; Walker, Edward D; Hamer, Gabriel L

2012-10-01

Bird-facilitated introduction of ticks and associated pathogens is postulated to promote invasion of tick-borne zoonotic diseases into urban areas. Results of a longitudinal study conducted in suburban Chicago, Illinois, USA, during 2005-2010 show that 1.6% of 6,180 wild birds captured in mist nets harbored ticks. Tick species in order of abundance were Haemaphysalis leporispalustris, Ixodes dentatus, and I. scapularis, but 2 neotropical tick species of the genus Amblyomma were sampled during the spring migration. I. scapularis ticks were absent at the beginning of the study but constituted the majority of ticks by study end and were found predominantly on birds captured in areas designated as urban green spaces. Of 120 ticks, 5 were infected with Borrelia burgdorferi, spanning 3 ribotypes, but none were infected with Anaplasma phagocytophilum. Results allow inferences about propagule pressure for introduction of tick-borne diseases and emphasize the large sample sizes required to estimate this pressure.

Wild Birds and Urban Ecology of Ticks and Tick-borne Pathogens, Chicago, Illinois, USA, 2005–2010

PubMed Central

Goldberg, Tony L.; Kitron, Uriel D.; Brawn, Jeffrey D.; Anderson, Tavis K.; Loss, Scott R.; Walker, Edward D.; Hamer, Gabriel L.

2012-01-01

Bird-facilitated introduction of ticks and associated pathogens is postulated to promote invasion of tick-borne zoonotic diseases into urban areas. Results of a longitudinal study conducted in suburban Chicago, Illinois, USA, during 2005–2010 show that 1.6% of 6,180 wild birds captured in mist nets harbored ticks. Tick species in order of abundance were Haemaphysalis leporispalustris, Ixodes dentatus, and I. scapularis, but 2 neotropical tick species of the genus Amblyomma were sampled during the spring migration. I. scapularis ticks were absent at the beginning of the study but constituted the majority of ticks by study end and were found predominantly on birds captured in areas designated as urban green spaces. Of 120 ticks, 5 were infected with Borrelia burgdorferi, spanning 3 ribotypes, but none were infected with Anaplasma phagocytophilum. Results allow inferences about propagule pressure for introduction of tick-borne diseases and emphasize the large sample sizes required to estimate this pressure. PMID:23017244

Characterization of Microsatellites in Pseudogymnoascus destructans for White-nose Syndrome Genetic Analysis.

PubMed

Drees, Kevin P; Parise, Katy L; Rivas, Stephanie M; Felton, Lindsey L; Puechmaille, Sébastien J; Keim, Paul; Foster, Jeffrey T

2017-10-01

Despite only emerging in the past decade, white-nose syndrome has become among the most devastating wildlife diseases known. The pathogenic fungus Pseudogymnoascus destructans infects hibernating bats and typically leads to high rates of mortality at hibernacula during winter in North America. We developed a set of genetic markers to better differentiate P. destructans isolates. We designed and successfully characterized these 23 microsatellite markers of P. destructans for use in disease ecology and epidemiology research. We validated these loci with DNA extracted from a collection of P. destructans isolates from the US and Canada, as well as from Europe (the likely introduction source based on currently available data). Genetic diversity calculated for each locus and for the multilocus panel as a whole indicates sufficient allelic diversity to differentiate among and between samples from both Europe and North America. Indices of genetic diversity indicate a loss of allelic diversity that is consistent with the recent introduction and rapid spread of an emerging pathogen.

Risk for Low Pathogenicity Avian Influenza Virus on Poultry Farms, the Netherlands, 2007-2013.

PubMed

Bouwstra, Ruth; Gonzales, Jose L; de Wit, Sjaak; Stahl, Julia; Fouchier, Ron A M; Elbers, Armin R W

2017-09-01

Using annual serologic surveillance data from all poultry farms in the Netherlands during 2007-2013, we quantified the risk for the introduction of low pathogenicity avian influenza virus (LPAIV) in different types of poultry production farms and putative spatial-environmental risk factors: distance from poultry farms to clay soil, waterways, and wild waterfowl areas. Outdoor-layer, turkey (meat and breeder), and duck (meat and breeder) farms had a significantly higher risk for LPAIV introduction than did indoor-layer farms. Except for outdoor-layer, all poultry types (i.e., broilers, chicken breeders, ducks, and turkeys) are kept indoors. For all production types, LPAIV risk decreased significantly with increasing distance to medium-sized waterways and with increasing distance to areas with defined wild waterfowl, but only for outdoor-layer and turkey farms. Future research should focus not only on production types but also on distance to waterways and wild bird areas. In addition, settlement of new poultry farms in high-risk areas should be discouraged.

How to keep punishment to maintain cooperation: Introducing social vaccine

NASA Astrophysics Data System (ADS)

Yamamoto, Hitoshi; Okada, Isamu

2016-02-01

Although there is much support for the punishment system as a sophisticated approach to resolving social dilemmas, more than a few researchers have also pointed out the limitations of such an approach. Second-order free riding is a serious issue facing the punishment system. Various pioneering works have suggested that an anti-social behavior or noise stemming from a mutation may, surprisingly, be helpful for avoiding second-order freeloaders. In this work, we show through mathematical analysis and an agent-based simulation of a model extending the meta-norms game that the coercive introduction of a small number of non-cooperators can maintain a cooperative regime robustly. This paradoxical idea was inspired by the effect of a vaccine, which is a weakened pathogen injected into a human body to create antibodies and ward off infection by that pathogen. Our expectation is that the coercive introduction of a few defectors, i.e., a social vaccine, will help maintain a highly cooperative regime because it will ensure that the punishment system works.

Risk for Low Pathogenicity Avian Influenza Virus on Poultry Farms, the Netherlands, 2007–2013

PubMed Central

Bouwstra, Ruth; Gonzales, Jose L.; de Wit, Sjaak; Stahl, Julia; Fouchier, Ron A.M.

2017-01-01

Using annual serologic surveillance data from all poultry farms in the Netherlands during 2007–2013, we quantified the risk for the introduction of low pathogenicity avian influenza virus (LPAIV) in different types of poultry production farms and putative spatial-environmental risk factors: distance from poultry farms to clay soil, waterways, and wild waterfowl areas. Outdoor-layer, turkey (meat and breeder), and duck (meat and breeder) farms had a significantly higher risk for LPAIV introduction than did indoor-layer farms. Except for outdoor-layer, all poultry types (i.e., broilers, chicken breeders, ducks, and turkeys) are kept indoors. For all production types, LPAIV risk decreased significantly with increasing distance to medium-sized waterways and with increasing distance to areas with defined wild waterfowl, but only for outdoor-layer and turkey farms. Future research should focus not only on production types but also on distance to waterways and wild bird areas. In addition, settlement of new poultry farms in high-risk areas should be discouraged. PMID:28820139

Semi-quantitative assessment of disease risks at the human, livestock, wildlife interface for the Republic of Korea using a nationwide survey of experts: A model for other countries.

PubMed

Hwang, J; Lee, K; Walsh, D; Kim, S W; Sleeman, J M; Lee, H

2018-02-01

Wildlife-associated diseases and pathogens have increased in importance; however, management of a large number of diseases and diversity of hosts is prohibitively expensive. Thus, the determination of priority wildlife pathogens and risk factors for disease emergence is warranted. We used an online questionnaire survey to assess release and exposure risks, and consequences of wildlife-associated diseases and pathogens in the Republic of Korea (ROK). We also surveyed opinions on pathways for disease exposure, and risk factors for disease emergence and spread. For the assessment of risk, we employed a two-tiered, statistical K-means clustering algorithm to group diseases into three levels (high, medium and low) of perceived risk based on release and exposure risks, societal consequences and the level of uncertainty of the experts' opinions. To examine the experts' perceived risk of routes of introduction of pathogens and disease amplification and spread, we used a Bayesian, multivariate normal order-statistics model. Six diseases or pathogens, including four livestock and two wildlife diseases, were identified as having high risk with low uncertainty. Similarly, 13 diseases were characterized as having high risk with medium uncertainty with three of these attributed to livestock, six associated with human disease, and the remainder having the potential to affect human, livestock and wildlife (i.e., One Health). Lastly, four diseases were described as high risk with high certainty, and were associated solely with fish diseases. Experts identified migration of wildlife, international human movement and illegal importation of wildlife as the three routes posing the greatest risk of pathogen introduction into ROK. Proximity of humans, livestock and wildlife was the most significant risk factor for promoting the spread of wildlife-associated diseases and pathogens, followed by high density of livestock populations, habitat loss and environmental degradation, and climate change. This study provides useful information to decision makers responsible for allocating resources to address disease risks. This approach provided a rapid, cost-effective method of risk assessment of wildlife-associated diseases and pathogens for which the published literature is sparse. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions

PubMed Central

2013-01-01

Background Subunit vaccines based on recombinant proteins have been effective in preventing infectious diseases and are expected to meet the demands of future vaccine development. Computational approach, especially reverse vaccinology (RV) method has enormous potential for identification of protein vaccine candidates (PVCs) from a proteome. The existing protective antigen prediction software and web servers have low prediction accuracy leading to limited applications for vaccine development. Besides machine learning techniques, those software and web servers have considered only protein’s adhesin-likeliness as criterion for identification of PVCs. Several non-adhesin functional classes of proteins involved in host-pathogen interactions and pathogenesis are known to provide protection against bacterial infections. Therefore, knowledge of bacterial pathogenesis has potential to identify PVCs. Results A web server, Jenner-Predict, has been developed for prediction of PVCs from proteomes of bacterial pathogens. The web server targets host-pathogen interactions and pathogenesis by considering known functional domains from protein classes such as adhesin, virulence, invasin, porin, flagellin, colonization, toxin, choline-binding, penicillin-binding, transferring-binding, fibronectin-binding and solute-binding. It predicts non-cytosolic proteins containing above domains as PVCs. It also provides vaccine potential of PVCs in terms of their possible immunogenicity by comparing with experimentally known IEDB epitopes, absence of autoimmunity and conservation in different strains. Predicted PVCs are prioritized so that only few prospective PVCs could be validated experimentally. The performance of web server was evaluated against known protective antigens from diverse classes of bacteria reported in Protegen database and datasets used for VaxiJen server development. The web server efficiently predicted known vaccine candidates reported from Streptococcus pneumoniae and Escherichia coli proteomes. The Jenner-Predict server outperformed NERVE, Vaxign and VaxiJen methods. It has sensitivity of 0.774 and 0.711 for Protegen and VaxiJen dataset, respectively while specificity of 0.940 has been obtained for the latter dataset. Conclusions Better prediction accuracy of Jenner-Predict web server signifies that domains involved in host-pathogen interactions and pathogenesis are better criteria for prediction of PVCs. The web server has successfully predicted maximum known PVCs belonging to different functional classes. Jenner-Predict server is freely accessible at http://117.211.115.67/vaccine/home.html PMID:23815072

Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors

USDA-ARS?s Scientific Manuscript database

Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the...

Pathogens and diseases of freshwater mussels in the United States: Studies on bacterial transmission and depuration

USGS Publications Warehouse

Starliper, Clifford E.; Cipriano, R.C.; Bruckner, A.W.; Shchelkunov, I.S.

2011-01-01

Unionid mussels are recognized as important contributors to healthy aquatic ecosystems, as well as bioindicators of environmental perturbations. Because they are sedentary, filter feeding animals and require hosts (i.e., fishes) to transform embryonic glochidia, mussels are susceptible to direct adverse environmental parameters, and indirect parameters that restrict the timely presence of the host(s). Their numbers have declined in recent decades to a point that this fauna is regarded as one of the most imperiled in North America. The most significant threat to populations of native unionids in recent years has been the introduction and spread of zebra mussels Dreissena polymorpha. Many federal and state agencies, and private interests are now engaged in mussel conservation efforts, including collecting selected imperiled species from impacted rivers and lakes and propagating them at refuges for future population augmentations. One essential consideration with mussel propagation and their intensive culture at refugia is the prevention of pathogen introductions and control of diseases. Currently, there are few reports of etiological agents causing diseases among freshwater mussels; however, because of increased observations of mussel die-offs in conjunction with transfers of live animals between natural waters and refugia, disease problems can be anticipated to emerge. This review summarizes research to develop bacterial isolation techniques, study pathogen transmission between fish and mussels, identify causes of seasonal mussel die-offs, and develop non-destructive methods for pathogen detection. These efforts were done to develop disease preventative techniques for use by resource managers to avoid potential large-scale disease problems in restoration and population augmentation efforts among imperiled populations.

Unlocking the proteomic information encoded in MALDI-TOF-MS data used for microbial identification and characterization

USDA-ARS?s Scientific Manuscript database

Introduction: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS)is increasingly utilized as a rapid technique to identify microorganisms including pathogenic bacteria. However, little attention has been paid to the significant proteomic information encoded in ...

Influence of amendment type on persistence of Salmonella Newport in soil

USDA-ARS?s Scientific Manuscript database

Introduction: Salmonella Newport is a foodborne pathogen isolated from several environmental reservoirs on the DelMarVa Peninsula and has been associated with several produce-related outbreaks.Little is known about interactions between S. Newport and soil amendments used as fertilizers. Purpose: Th...

Introduction to 2009 Symposium on Alternative Methods of Controlling Pests and Diseases

USDA-ARS?s Scientific Manuscript database

Numerous pests and diseases limit potato productivity, and control of weeds, insects and pathogens remains a costly part of potato production. Although conventional agrichemical pest control is amazingly effective, interest in non-synthetic chemical and integrated methods of pest management is drive...

Mutual benefits through formalized international collaboration on biological control of weeds with plant pathogens

USDA-ARS?s Scientific Manuscript database

In the U.S., introduced invasive weeds have catastrophic effects on agricultural, aquatic, rangeland, riparian, and natural ecosystems. Often the only economically feasible means for controlling these weeds is classical biological control through the introduction of natural enemies, including plant ...

Improving Pathogen Reduction by Chlorine Wash Prior to Cutting in Fresh-Cut Processing

USDA-ARS?s Scientific Manuscript database

Introduction: Currently, most fresh-cut processing facilities in the United States use chlorinated water or other sanitizer solutions for microbial reduction after lettuce is cut. Freshly cut lettuce releases significant amounts of organic matter that negatively impacts the effectiveness of chlorine...

Host resistance to phytophthora fruit rot in U.S. watermelon plant introductions

USDA-ARS?s Scientific Manuscript database

Phytophthora capsici, distributed worldwide, is an aggressive pathogen with a broad host range, infecting solanaceous, leguminaceous, and cucurbitaceous crops. Phytophthora fruit rot of watermelon (Citrullus lanatus) caused by P. capsici was first reported in the U.S. in 1940. Since then, the dise...

Reactions of broiler sera to salmonella FlgK and FliD flagellar proteins

USDA-ARS?s Scientific Manuscript database

Introduction: Salmonella, a Gram-negative bacterium, is the leading foodborne pathogen. It causes human acute bacterial gastroenteritis worldwide. Poultry products are considered as one of major reservoirs of this bacterium. Because the bacterial flagellum is involved in motility, adhesion and o...

On the Origin and Spread of the Scab Disease of Apple: Out of Central Asia

PubMed Central

Gladieux, Pierre; Zhang, Xiu-Guo; Afoufa-Bastien, Damien; Valdebenito Sanhueza, Rosa-Maria; Sbaghi, Mohamed; Le Cam, Bruno

2008-01-01

Background Venturia inaequalis is an ascomycete fungus responsible for apple scab, a disease that has invaded almost all apple growing regions worldwide, with the corresponding adverse effects on apple production. Monitoring and predicting the effectiveness of intervention strategies require knowledge of the origin, introduction pathways, and population biology of pathogen populations. Analysis of the variation of genetic markers using the inferential framework of population genetics offers the potential to retrieve this information. Methodology/Principal Findings Here, we present a population genetic analysis of microsatellite variation in 1,273 strains of V. inaequalis representing 28 orchard samples from seven regions in five continents. Analysis of molecular variance revealed that most of the variation (88%) was distributed within localities, which is consistent with extensive historical migrations of the fungus among and within regions. Despite this shallow population structure, clustering analyses partitioned the data set into separate groups corresponding roughly to geography, indicating that each region hosts a distinct population of the fungus. Comparison of the levels of variability among populations, along with coalescent analyses of migration models and estimates of genetic distances, was consistent with a scenario in which the fungus emerged in Central Asia, where apple was domesticated, before its introduction into Europe and, more recently, into other continents with the expansion of apple growing. Across the novel range, levels of variability pointed to multiple introductions and all populations displayed signatures of significant post-introduction increases in population size. Most populations exhibited high genotypic diversity and random association of alleles across loci, indicating recombination both in native and introduced areas. Conclusions/Significance Venturia inaequalis is a model of invasive phytopathogenic fungus that has now reached the ultimate stage of the invasion process with a broad geographic distribution and well-established populations displaying high genetic variability, regular sexual reproduction, and demographic expansion. PMID:18197265

Predicting the Pathogenicity of Aminoacyl-tRNA Synthetase Mutations

PubMed Central

Oprescu, Stephanie N.; Griffin, Laurie B.; Beg, Asim A.; Antonellis, Anthony

2016-01-01

Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed, essential enzymes responsible for charging tRNA with cognate amino acids—the first step in protein synthesis. ARSs are required for protein translation in the cytoplasm and mitochondria of all cells. Surprisingly, mutations in 28 of the 37 nuclear-encoded human ARS genes have been linked to a variety of recessive and dominant tissue-specific disorders. Current data sustains that impaired enzyme function is a robust predictor of the pathogenicity of ARS mutations. However, experimental model systems that distinguish between pathogenic and non-pathogenic ARS variants are required for implicating newly identified ARS mutations in disease. Here, we outline strategies to assist in predicting the pathogenicity of ARS variants and urge cautious evaluation of genetic and functional data prior to linking an ARS mutation to a human disease phenotype. PMID:27876679

Individualizing Risk of Multidrug-Resistant Pathogens in Community-Onset Pneumonia

PubMed Central

Falcone, Marco; Russo, Alessandro; Giannella, Maddalena; Cangemi, Roberto; Scarpellini, Maria Gabriella; Bertazzoni, Giuliano; Alarcón, José Martínez; Taliani, Gloria; Palange, Paolo; Farcomeni, Alessio; Vestri, Annarita; Bouza, Emilio; Violi, Francesco; Venditti, Mario

2015-01-01

Introduction The diffusion of multidrug-resistant (MDR) bacteria has created the need to identify risk factors for acquiring resistant pathogens in patients living in the community. Objective To analyze clinical features of patients with community-onset pneumonia due to MDR pathogens, to evaluate performance of existing scoring tools and to develop a bedside risk score for an early identification of these patients in the Emergency Department. Patients and Methods This was an open, observational, prospective study of consecutive patients with pneumonia, coming from the community, from January 2011 to January 2013. The new score was validated on an external cohort of 929 patients with pneumonia admitted in internal medicine departments participating at a multicenter prospective study in Spain. Results A total of 900 patients were included in the study. The final logistic regression model consisted of four variables: 1) one risk factor for HCAP, 2) bilateral pulmonary infiltration, 3) the presence of pleural effusion, and 4) the severity of respiratory impairment calculated by use of PaO2/FiO2 ratio. A new risk score, the ARUC score, was developed; compared to Aliberti, Shorr, and Shindo scores, this point score system has a good discrimination performance (AUC 0.76, 95% CI 0.71-0.82) and calibration (Hosmer-Lemeshow, χ2 = 7.64; p = 0.469). The new score outperformed HCAP definition in predicting etiology due to MDR organism. The performance of this bedside score was confirmed in the validation cohort (AUC 0.68, 95% CI 0.60-0.77). Conclusion Physicians working in ED should adopt simple risk scores, like ARUC score, to select the most appropriate antibiotic regimens. This individualized approach may help clinicians to identify those patients who need an empirical broad-spectrum antibiotic therapy. PMID:25860142

The Complex Biogeography of the Plant Pathogen Xylella fastidiosa: Genetic Evidence of Introductions and Subspecific Introgression in Central America

PubMed Central

Nunney, Leonard; Ortiz, Beatriz; Russell, Stephanie A.; Ruiz Sánchez, Rebeca; Stouthamer, Richard

2014-01-01

The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST) of isolates from Costa Rica. Six (five from oleander, one from coffee) defined a new sequence type (ST53) that carried alleles at six of the eight loci sequenced (five of the seven MLST loci) diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee) showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa. PMID:25379725

The complex biogeography of the plant pathogen Xylella fastidiosa: genetic evidence of introductions and Subspecific introgression in Central America.

PubMed

Nunney, Leonard; Ortiz, Beatriz; Russell, Stephanie A; Ruiz Sánchez, Rebeca; Stouthamer, Richard

2014-01-01

The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST) of isolates from Costa Rica. Six (five from oleander, one from coffee) defined a new sequence type (ST53) that carried alleles at six of the eight loci sequenced (five of the seven MLST loci) diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee) showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa.

Transport of ixodid ticks and tick-borne pathogens by migratory birds.

PubMed

Hasle, Gunnar

2013-01-01

Birds, particularly passerines, can be parasitized by Ixodid ticks, which may be infected with tick-borne pathogens, like Borrelia spp., Babesia spp., Anaplasma, Rickettsia/Coxiella, and tick-borne encephalitis virus. The prevalence of ticks on birds varies over years, season, locality and different bird species. The prevalence of ticks on different species depends mainly on the degree of feeding on the ground. In Europe, the Turdus spp., especially the blackbird, Turdus merula, appears to be most important for harboring ticks. Birds can easily cross barriers, like fences, mountains, glaciers, desserts and oceans, which would stop mammals, and they can move much faster than the wingless hosts. Birds can potentially transport tick-borne pathogens by transporting infected ticks, by being infected with tick-borne pathogens and transmit the pathogens to the ticks, and possibly act as hosts for transfer of pathogens between ticks through co-feeding. Knowledge of the bird migration routes and of the spatial distribution of tick species and tick-borne pathogens is crucial for understanding the possible impact of birds as spreaders of ticks and tick-borne pathogens. Successful colonization of new tick species or introduction of new tick-borne pathogens will depend on suitable climate, vegetation and hosts. Although it has never been demonstrated that a new tick species, or a new tick pathogen, actually has been established in a new locality after being seeded there by birds, evidence strongly suggests that this could occur.

Transport of ixodid ticks and tick-borne pathogens by migratory birds

PubMed Central

Hasle, Gunnar

2013-01-01

Birds, particularly passerines, can be parasitized by Ixodid ticks, which may be infected with tick-borne pathogens, like Borrelia spp., Babesia spp., Anaplasma, Rickettsia/Coxiella, and tick-borne encephalitis virus. The prevalence of ticks on birds varies over years, season, locality and different bird species. The prevalence of ticks on different species depends mainly on the degree of feeding on the ground. In Europe, the Turdus spp., especially the blackbird, Turdus merula, appears to be most important for harboring ticks. Birds can easily cross barriers, like fences, mountains, glaciers, desserts and oceans, which would stop mammals, and they can move much faster than the wingless hosts. Birds can potentially transport tick-borne pathogens by transporting infected ticks, by being infected with tick-borne pathogens and transmit the pathogens to the ticks, and possibly act as hosts for transfer of pathogens between ticks through co-feeding. Knowledge of the bird migration routes and of the spatial distribution of tick species and tick-borne pathogens is crucial for understanding the possible impact of birds as spreaders of ticks and tick-borne pathogens. Successful colonization of new tick species or introduction of new tick-borne pathogens will depend on suitable climate, vegetation and hosts. Although it has never been demonstrated that a new tick species, or a new tick pathogen, actually has been established in a new locality after being seeded there by birds, evidence strongly suggests that this could occur. PMID:24058903

Institute for Genomics and Systems Biology

Science.gov Websites

Institute for Genomics and Systems Biology Discover. Predict. Improve. Advancing Human and , 2015 See all Research Papers Featured Video Introduction to Systems Biology Video: Introduction to Systems Biology News Jack Gilbert Heading UChicago Startup that Aims to Predict Behavior of Trillions of

Comparing Data Input Requirements of Statistical vs. Process-based Watershed Models Applied for Prediction of Fecal Indicator and Pathogen Levels in Recreational Beaches

EPA Science Inventory

Same day prediction of fecal indicator bacteria (FIB) concentrations and bather protection from the risk of exposure to pathogens are two important goals of implementing a modeling program at recreational beaches. Sampling efforts for modelling applications can be expensive and t...

Modeling of pathogen survival during simulated gastric digestion.

PubMed

Koseki, Shige; Mizuno, Yasuko; Sotome, Itaru

2011-02-01

The objective of the present study was to develop a mathematical model of pathogenic bacterial inactivation kinetics in a gastric environment in order to further understand a part of the infectious dose-response mechanism. The major bacterial pathogens Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella spp. were examined by using simulated gastric fluid adjusted to various pH values. To correspond to the various pHs in a stomach during digestion, a modified logistic differential equation model and the Weibull differential equation model were examined. The specific inactivation rate for each pathogen was successfully described by a square-root model as a function of pH. The square-root models were combined with the modified logistic differential equation to obtain a complete inactivation curve. Both the modified logistic and Weibull models provided a highly accurate fitting of the static pH conditions for every pathogen. However, while the residuals plots of the modified logistic model indicated no systematic bias and/or regional prediction problems, the residuals plots of the Weibull model showed a systematic bias. The modified logistic model appropriately predicted the pathogen behavior in the simulated gastric digestion process with actual food, including cut lettuce, minced tuna, hamburger, and scrambled egg. Although the developed model enabled us to predict pathogen inactivation during gastric digestion, its results also suggested that the ingested bacteria in the stomach would barely be inactivated in the real digestion process. The results of this study will provide important information on a part of the dose-response mechanism of bacterial pathogens.

Modeling of Pathogen Survival during Simulated Gastric Digestion ▿

PubMed Central

Koseki, Shige; Mizuno, Yasuko; Sotome, Itaru

2011-01-01

The objective of the present study was to develop a mathematical model of pathogenic bacterial inactivation kinetics in a gastric environment in order to further understand a part of the infectious dose-response mechanism. The major bacterial pathogens Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella spp. were examined by using simulated gastric fluid adjusted to various pH values. To correspond to the various pHs in a stomach during digestion, a modified logistic differential equation model and the Weibull differential equation model were examined. The specific inactivation rate for each pathogen was successfully described by a square-root model as a function of pH. The square-root models were combined with the modified logistic differential equation to obtain a complete inactivation curve. Both the modified logistic and Weibull models provided a highly accurate fitting of the static pH conditions for every pathogen. However, while the residuals plots of the modified logistic model indicated no systematic bias and/or regional prediction problems, the residuals plots of the Weibull model showed a systematic bias. The modified logistic model appropriately predicted the pathogen behavior in the simulated gastric digestion process with actual food, including cut lettuce, minced tuna, hamburger, and scrambled egg. Although the developed model enabled us to predict pathogen inactivation during gastric digestion, its results also suggested that the ingested bacteria in the stomach would barely be inactivated in the real digestion process. The results of this study will provide important information on a part of the dose-response mechanism of bacterial pathogens. PMID:21131530

Recent introduction of a chytrid fungus endangers Western Palearctic salamanders

PubMed Central

Martel, A.; Beukema, W.; Fisher, M. C.; Farrer, R. A.; Schmidt, B. R.; Tobler, U.; Goka, K.; Lips, K. R.; Muletz, C.; Zamudio, K. R.; Bosch, J.; Lötters, S.; Wombwell, E.; Garner, T.W. J.; Cunningham, A. A.; Spitzen-van der Sluijs, A.; Salvidio, S.; Ducatelle, R.; Nishikawa, K.; Nguyen, T. T.; Kolby, J. E.; Van Bocxlaer, I.; Bossuyt, F.; Pasmans, F.

2018-01-01

Emerging infectious diseases are reducing biodiversity on a global scale. Recently, the emergence of the chytrid fungus Batrachochytrium salamandrivorans resulted in rapid declines in populations of European fire salamanders. Here, we screened more than 5000 amphibians from across four continents and combined experimental assessment of pathogenicity with phylogenetic methods to estimate the threat that this infection poses to amphibian diversity. Results show that B. salamandrivorans is restricted to, but highly pathogenic for, salamanders and newts (Urodela). The pathogen likely originated and remained in coexistence with a clade of salamander hosts for millions of years in Asia. As a result of globalization and lack of biosecurity, it has recently been introduced into naïve European amphibian populations, where it is currently causing biodiversity loss. PMID:25359973

Biosecurity and Health Monitoring at the Zebrafish International Resource Center

PubMed Central

Varga, Zoltán M.; Kent, Michael L.

2016-01-01

Abstract The Zebrafish International Resource Center (ZIRC) is a repository and distribution center for mutant, transgenic, and wild-type zebrafish. In recent years annual imports of new zebrafish lines to ZIRC have increased tremendously. In addition, after 15 years of research, we have identified some of the most virulent pathogens affecting zebrafish that should be avoided in large production facilities, such as ZIRC. Therefore, while importing a high volume of new lines we prioritize safeguarding the health of our in-house fish colony. Here, we describe the biosecurity and health-monitoring program implemented at ZIRC. This strategy was designed to prevent introduction of new zebrafish pathogens, minimize pathogens already present in the facility, and ensure a healthy zebrafish colony for in-house uses and shipment to customers. PMID:27031282

Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens

PubMed Central

Pamer, Eric G.

2016-01-01

The intestinal microbiota, which is composed of diverse populations of commensal bacterial species, provides resistance against colonization and invasion by pathogens. Antibiotic treatment can damage the intestinal microbiota and, paradoxically, increase susceptibility to infections. Reestablishing microbiota-mediated colonization resistance after antibiotic treatment could markedly reduce infections, particularly those caused by antibiotic-resistant bacteria. Ongoing studies are identifying commensal bacterial species that can be developed into next-generation probiotics to reestablish or enhance colonization resistance. These live medicines are at various stages of discovery, testing, and production and are being subjected to existing regulatory gauntlets for eventual introduction into clinical practice. The development of next-generation probiotics to reestablish colonization resistance and eliminate potential pathogens from the gut is warranted and will reduce health care–associated infections caused by highly antibiotic-resistant bacteria. PMID:27126035

Highly Pathogenic Avian Influenza H5N8 in Germany: Outbreak Investigations.

PubMed

Conraths, F J; Sauter-Louis, C; Globig, A; Dietze, K; Pannwitz, G; Albrecht, K; Höreth-Böntgen, D; Beer, M; Staubach, C; Homeier-Bachmann, T

2016-02-01

Epidemiological outbreak investigations were conducted in highly pathogenic avian influenza virus of the subtype H5N8 (HPAIV H5N8)-affected poultry holdings and a zoo to identify potential routes of entry of the pathogen via water, feedstuffs, animals, people, bedding material, other fomites (equipment, vehicles etc.) and the presence of wild birds near affected holdings. Indirect introduction of HPAIV H5N8 via material contaminated by infected wild bird seems the most reasonable explanation for the observed outbreak series in three commercial holdings in Mecklenburg-Western Pomerania and Lower Saxony, while direct contact to infected wild birds may have led to outbreaks in a zoo in Rostock and in two small free-range holdings in Anklam, Mecklenburg-Western Pomerania. © 2015 Blackwell Verlag GmbH.

Thermal inactivation of enzymes and pathogens in biosamples for MS analysis.

PubMed

Ahnoff, Martin; Cazares, Lisa H; Sköld, Karl

2015-01-01

Protein denaturation is the common basis for enzyme inactivation and inactivation of pathogens, necessary for preservation and safe handling of biosamples for downstream analysis. While heat-stabilization technology has been used in proteomic and peptidomic research since its introduction in 2009, the advantages of using the technique for simultaneous pathogen inactivation have only recently been addressed. The time required for enzyme inactivation by heat (≈1 min) is short compared with chemical treatments, and inactivation is irreversible in contrast to freezing. Heat stabilization thus facilitates mass spectrometric studies of biomolecules with a fast conversion rate, and expands the chemical space of potential biomarkers to include more short-lived entities, such as phosphorylated proteins, in tissue samples as well as whole-blood (dried blood sample) samples.

Pathogen Screening of Naturally Produced Yakima River Spring Chinook Smolts; Yakima/Klickitat Fisheries Project Monitoring and Evaluation Report 6 of 7, 2003-2004 Annual Report.

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

Thomas, Joan B.

2004-05-01

In 1999 the Cle Elum Hatchery began releasing spring chinook salmon smolts into the upper Yakima River to increase natural production. Part of the evaluation of this program is to monitor whether introduction of hatchery produced smolts would impact the prevalence of specific pathogens in the naturally produced spring chinook smolts. Increases in prevalence of any of these pathogens could negatively impact the survival of these fish. In 1998 and 2000 through 2003 naturally produced smolts were collected for monitoring at the Chandler smolt collection facility on the lower Yakima River. Smolts were collected from mid to late outmigration, withmore » a target of 200 fish each year. The pathogens monitored were infectious hematopoeitic necrosis virus, infectious pancreatic necrosis virus, viral hemorrhagic septicemia virus, Flavobacterium psychrophilum, Flavobacterium columnare, Aeromonas salmonicida, Yersinia ruckeri, Edwardsiella ictaluri, Renibacterium salmoninarum and Myxobolus cerebralis. To date, only the bacterial pathogens have been detected and prevalences have been low. Prevalences have varied each year and these changes are attributed to normal fluctuation of prevalence. All of the pathogens detected are widely distributed in Washington State.« less

Pathogen Screening of Naturally Produced Yakima River Spring Chinook Smolts; Yakima/Klickitat Fisheries Project Monitoring and Evaluation, 2002 Annual Report.

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

Thomas, Joan B.

2003-05-01

In 1999 the Cle Elem Hatchery began releasing spring chinook smolts into the upper Yakima River for restoration and supplementation. This project was designed to evaluate whether introduction of intensively reared hatchery produced smolts would impact the prevalence of specific pathogens in the naturally produced spring chinook smolts. Increases in prevalence of any of these pathogens could negatively impact the survival of these fish. Approximately 200 smolts were collected at the Chandler smolt collection facility on the lower Yakima River during 1998, 2000 and 2001 and 130 smolts were collected in 2002 for monitoring for specific pathogens. The pathogens monitoredmore » were infectious hematopoeitic necrosis virus, infectious pancreatic necrosis virus, viral hemorrhagic septicemia, Flavobacterium psychrophilum, Flavobacterium columnare, Aeromonas salmonicida, Yersinia ruckeri, Edwardsiella ictaluri, Renibacterium salmoninarum and Myxobolus cerebralis. In addition the fish were tested for Ceratomyxa shasta spores in 2000 and 2001 (a correction from the 2001 report). To date, the only changes have been in the levels the bacterial pathogens in the naturally produced smolts and they have been minimal. These changes are attributed to normal fluctuation of prevalence.« less

Experimental evidence of a pathogen invasion threshold

PubMed Central

Krkošek, Martin

2018-01-01

Host density thresholds to pathogen invasion separate regions of parameter space corresponding to endemic and disease-free states. The host density threshold is a central concept in theoretical epidemiology and a common target of human and wildlife disease control programmes, but there is mixed evidence supporting the existence of thresholds, especially in wildlife populations or for pathogens with complex transmission modes (e.g. environmental transmission). Here, we demonstrate the existence of a host density threshold for an environmentally transmitted pathogen by combining an epidemiological model with a microcosm experiment. Experimental epidemics consisted of replicate populations of naive crustacean zooplankton (Daphnia dentifera) hosts across a range of host densities (20–640 hosts l−1) that were exposed to an environmentally transmitted fungal pathogen (Metschnikowia bicuspidata). Epidemiological model simulations, parametrized independently of the experiment, qualitatively predicted experimental pathogen invasion thresholds. Variability in parameter estimates did not strongly influence outcomes, though systematic changes to key parameters have the potential to shift pathogen invasion thresholds. In summary, we provide one of the first clear experimental demonstrations of pathogen invasion thresholds in a replicated experimental system, and provide evidence that such thresholds may be predictable using independently constructed epidemiological models. PMID:29410876

Genetic diversity predicts pathogen resistance and cell-mediated immunocompetence in house finches

PubMed Central

Hawley, Dana M; Sydenstricker, Keila V; Kollias, George V; Dhondt, André A

2005-01-01

Evidence is accumulating that genetic variation within individual hosts can influence their susceptibility to pathogens. However, there have been few opportunities to experimentally test this relationship, particularly within outbred populations of non-domestic vertebrates. We performed a standardized pathogen challenge in house finches (Carpodacus mexicanus) to test whether multilocus heterozygosity across 12 microsatellite loci predicts resistance to a recently emerged strain of the bacterial pathogen, Mycoplasma gallisepticum (MG). We simultaneously tested whether the relationship between heterozygosity and pathogen susceptibility is mediated by differences in cell-mediated or humoral immunocompetence. We inoculated 40 house finches with MG under identical conditions and assayed both humoral and cell-mediated components of the immune response. Heterozygous house finches developed less severe disease when infected with MG, and they mounted stronger cell-mediated immune responses to phytohaemagglutinin. Differences in cell-mediated immunocompetence may, therefore, partly explain why more heterozygous house finches show greater resistance to MG. Overall, our results underscore the importance of multilocus heterozygosity for individual pathogen resistance and immunity. PMID:17148199

Antimicrobial efficacy of radiant catalytic ionization against shiga toxin-producing Escherichia coli on inoculated beef

USDA-ARS?s Scientific Manuscript database

Introduction: Shiga Toxin-producing Escherichia coli (STEC), as a common foodborne pathogen, may cause severe human hemorrhagic colitis infection. The radiant catalytic ionization (RCI) technology utilizes a combination of UV light and low-level oxidizers such as ozone, hydroxyl radicals, and hydrog...

Process Requirements for Achieving Full-Flow Disinfection of Recirculating Water Using Ozonation and UV Irradiation

USDA-ARS?s Scientific Manuscript database

A continuous water disinfection process can be used to prevent the introduction and accumulation of obligate and opportunistic fish pathogens in recirculating aquaculture systems (RAS), especially during a disease outbreak when the causative agent would otherwise proliferate within the system. To p...

Overnight incubation of entire broiler carcass for increased detection of Salmonella

USDA-ARS?s Scientific Manuscript database

Introduction Broiler carcasses are generally sampled for presence of human pathogens such as Salmonella by whole carcass rinse and enrichment of a portion of the rinse. This may leave firmly attached cells out of the analysis potentially leading to false negative results. Purpose The objective of ...

Comparison of microbial methods to detect fecal coliforms, E. coli and Salmonella spp. in finished compost

USDA-ARS?s Scientific Manuscript database

Introduction: Compost provides nutrients for produce crops. Improperly composted feedstocks can harbor pathogens which can be transferred to produce crops. The US Environmental Protection Agency (EPA) and US Composting Council (USCC) provide methods to test biosolids and compost, respectively, fo...

An immunologist's perspective on nutrition, immunity and infectious diseases: Introduction and overview

USDA-ARS?s Scientific Manuscript database

The immune system is a multifaceted arrangement of membranes (skin, epithelial, mucus), cells, and molecules whose function is to eradicate invading pathogens or cancer cells from a host. Working together, the various components of the immune system perform a balancing act of being lethal enough to...

The genetic diversity of contemporary swine influenza A viruses in the United States

USDA-ARS?s Scientific Manuscript database

Introduction: Influenza A virus (IAV) is one of the most important respiratory pathogens of swine. It impacts mortality and causes significant financial losses through decreased production and the costs associated with vaccination and treatment. Further, due to the susceptibility of swine to transie...

Rapid and potentially portable detection and quantification technologies for foodborne pathogens

USDA-ARS?s Scientific Manuscript database

Introduction Traditional microbial culture methods are able to detect and identify a single specific bacterium, but may require days or weeks and typically do not produce quantitative data. The quest for faster, quantitative results has spurred development of “rapid methods” which usually employ bio...

Efficacy of current lures for detection of redbay ambrosia beetle, Xyleborus glabratus (Coleoptera: Curculionidae: Scolytinae)

USDA-ARS?s Scientific Manuscript database

Since its introduction into the USA in 2002, the exotic redbay ambrosia beetle, Xyleborus glabratus Eichhoff, has become a serious invasive pest, currently established in eight southeastern states. Females are the primary vectors of a pathogenic fungus, Raffaelea lauricola, that causes laurel wilt....

Dynamics of House Sparrows (Passer domesticus) in Newcastle disease virus transmission within the avifaunal-poultry interface: an epidemiological modeling approach

USDA-ARS?s Scientific Manuscript database

As emerging and persistent pathogens increase in prevalence, the agriculture-wildlife interface has been identified as a field requiring further research. Acceleration of wildlife urbanization, exotic species introductions, and habitat encroachment are disrupting barriers that once separated microb...

Identification of novel bacteriophage peptides using a combination of gene sequence LC-MS-MS analysis and BLASTP

USDA-ARS?s Scientific Manuscript database

Introduction: In an effort to characterize novel bacteriophage with lytic activity against pathogenic E.coli associated with foodborne illness, gene sequencing and mass spectrometry have been used to identify expressed peptides which differentiate isolated bacteriophage from other known phage. Here,...

Assessment of indicator bacteria and Aeromonas spp. in surface and nontraditional irrigation water: a conserve study

USDA-ARS?s Scientific Manuscript database

Introduction: The use of surface and nontraditional irrigation water (SNIW) (pond, tidal and non-tidal river water, reclaimed wastewater) is one way to conserve groundwater. However, SNIW may serve as reservoirs and vehicles for under-recognized enteric pathogens, spreading localized contamination d...

Gamma irradiation reduces the survival and regrowth of inoculated antibiotic-resistant bacteria and antibiotic resistant genes on romaine lettuce

USDA-ARS?s Scientific Manuscript database

Introduction: Gamma irradiation effectively reduces foodborne pathogens and spoilage microorganisms on fresh produce. However, limited research is available regarding the effect of gamma irradiation on the survival and regrowth of antibiotic-resistant bacteria (ARB) or the persistence of antibiotic ...

School Occupational Exposure to Bloodborne Pathogens. A Report To Provide Information.

ERIC Educational Resources Information Center

Iowa State Dept. of Education, Des Moines. Bureau of Special Education.

This report discusses a federally mandated standard concerning establishment of a program to reduce exposure to blood and other potentially infectious materials (OPIM) in Iowa schools and education agencies. The standard includes the following components: introduction, scope and application, definitions, exposure control, methods of compliance,…

Pathogen Screening of Naturally Produced Yakima River Spring Chinook Smolts; Yakima/Klickitat Fisheries Project Monitoring and Evaluation, 2001 Annual Report.

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

Pearsons, Todd N.; Thomas, Joan B.

2003-01-01

The change in pathogens prevalence to wild fish is probably the least studied ecological interaction associated with hatchery operations. In 1999, the Cle Elum Hatchery began releasing spring chinook smolts into the upper Yakima River to increase natural production. Part of the evaluation of this program is to evaluate whether introduction of hatchery produced smolts would impact the prevalence of specific pathogens in the naturally produced spring chinook smolts. Increases in prevalence of any of these pathogens could negatively impact the survival of these fish. Approximately 200 smolts were collected at the Chandler smolt collection facility on the lower Yakimamore » River during 1998, 2000 and 2001 and monitored for specific pathogens. The pathogens monitored were infectious hematopoeitic necrosis virus, infectious pancreatic necrosis virus, viral hemorrhagic septicemia, Flavobacterium psychrophilum, Flavobacterium columnare, Aeromonas salmonicida, Yersinia ruckeri, Edwardsiella ictaluri, Renibacterium salmoninarum and Myxobolus cerebralis. In addition, the fish were tested for Ceratomyxa shasta spores in 2001. Not all testing has been completed for every year, but to date, there have only been minimal changes in levels of the bacterial pathogens in the naturally produced smolts. At this point, due to the limited testing so far, these changes are attributed to normal fluctuation of prevalence.« less

Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues.

PubMed

Schaad, Norman W; Frederick, Reid D; Shaw, Joe; Schneider, William L; Hickson, Robert; Petrillo, Michael D; Luster, Douglas G

2003-01-01

Awareness of crop biosecurity and phytosanitation has been heightened since 9/11 and the unresolved anthrax releases in October 2001. Crops are highly vulnerable to accidental or deliberate introductions of crop pathogens from outside U.S. borders. Strategic thinking about protection against deliberate or accidental release of a plant pathogen is an urgent priority. Rapid detection will be the key to success. This review summarizes recent progress in the development of rapid real-time PCR protocols and evaluates their effectiveness in a proposed nationwide network of diagnostic laboratories that will facilitate rapid diagnostics and improved communication.

Highly pathogenic avian influenza A(H5N8) outbreaks: protection and management of exposed people in Europe, 2014/15 and 2016

PubMed Central

Adlhoch, Cornelia; Brown, Ian H.; Angelova, Svetla G.; Bálint, Ádám; Bouwstra, Ruth; Buda, Silke; Castrucci, Maria R.; Dabrera, Gavin; Dán, Ádám; Grund, Christian; Harder, Timm; van der Hoek, Wim; Krisztalovics, Katalin; Parry-Ford, Frances; Popescu, Rodica; Wallensten, Anders; Zdravkova, Anna; Zohari, Siamak; Tsolova, Svetla; Penttinen, Pasi

2016-01-01

Introduction of highly pathogenic avian influenza (HPAI) virus A(H5N8) into Europe prompted animal and human health experts to implement protective measures to prevent transmission to humans. We describe the situation in 2016 and list public health measures and recommendations in place. We summarise critical interfaces identified during the A(H5N1) and A(H5N8) outbreaks in 2014/15. Rapid exchange of information between the animal and human health sectors is critical for a timely, effective and efficient response. PMID:27983512

The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.

PubMed

Azarian, Taj; Grant, Lindsay R; Arnold, Brian J; Hammitt, Laura L; Reid, Raymond; Santosham, Mathuram; Weatherholtz, Robert; Goklish, Novalene; Thompson, Claudette M; Bentley, Stephen D; O'Brien, Katherine L; Hanage, William P; Lipsitch, Marc

2018-04-01

In the United States, the introduction of the heptavalent pneumococcal conjugate vaccine (PCV) largely eliminated vaccine serotypes (VT); non-vaccine serotypes (NVT) subsequently increased in carriage and disease. Vaccination also disrupts the composition of the pneumococcal pangenome, which includes mobile genetic elements and polymorphic non-capsular antigens important for virulence, transmission, and pneumococcal ecology. Antigenic proteins are of interest for future vaccines; yet, little is known about how the they are affected by PCV use. To investigate the evolutionary impact of vaccination, we assessed recombination, evolution, and pathogen demographic history of 937 pneumococci collected from 1998-2012 among Navajo and White Mountain Apache Native American communities. We analyzed changes in the pneumococcal pangenome, focusing on metabolic loci and 19 polymorphic protein antigens. We found the impact of PCV on the pneumococcal population could be observed in reduced diversity, a smaller pangenome, and changing frequencies of accessory clusters of orthologous groups (COGs). Post-PCV7, diversity rebounded through clonal expansion of NVT lineages and inferred in-migration of two previously unobserved lineages. Accessory COGs frequencies trended toward pre-PCV7 values with increasing time since vaccine introduction. Contemporary frequencies of protein antigen variants are better predicted by pre-PCV7 values (1998-2000) than the preceding period (2006-2008), suggesting balancing selection may have acted in maintaining variant frequencies in this population. Overall, we present the largest genomic analysis of pneumococcal carriage in the United States to date, which includes a snapshot of a true vaccine-naïve community prior to the introduction of PCV7. These data improve our understanding of pneumococcal evolution and emphasize the need to consider pangenome composition when inferring the impact of vaccination and developing future protein-based pneumococcal vaccines.

Risk of Introduction in Northern Vietnam of HPAI Viruses from China: Description, Patterns and Drivers of Illegal Poultry Trade.

PubMed

Desvaux, S; Nguyen, C O; Vu, D T; Henriquez, C; Ky, V D; Roger, F; Fenwick, S; Goutard, F

2016-08-01

Poultry movement is known to contribute to the dissemination of highly pathogenic avian influenza (HPAI) viruses. In Northern Vietnam, the illegal trade of poultry from China is a source of concern and is considered as responsible for the regular introduction of new H5N1 viruses. The general objective of this study was to get a better understanding of this illegal trade (organization, volume, actors involved and drivers) to propose adequate preventive and control options. The information was also used to qualitatively evaluate the risk of exposure of susceptible poultry to HPAI H5N1 virus introduced from China by illegally traded poultry. We found that the main products imported from China are spent hens, day-old chicks (DOCs) and ducklings; spent hens being introduced in very large number. The drivers of this trade are multiple: economic (especially for spent hens) but also technical (demand for improved genetic potential for DOC and ducklings). Furthermore, these introductions also meet a high consumer demand at certain periods of the year. We also found that spatial dispersion of a batch of poultry illegally introduced from China is extensive and rapid, making any prediction of possible new outbreaks very hazardous. Finally, a risk mitigation plan should include measures to tackle the drivers of this trade or to legally organize it, to limit the threat to the local poultry sector. It is also essential for traders to be progressively better organized and biosecure and for hygienic practices to be enforced, as our study confirmed that at-risk behaviours are still very common among this profession. © 2014 Blackwell Verlag GmbH.

The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome

PubMed Central

Hammitt, Laura L.; Santosham, Mathuram; Goklish, Novalene; Thompson, Claudette M.; Bentley, Stephen D.; O’Brien, Katherine L.

2018-01-01

In the United States, the introduction of the heptavalent pneumococcal conjugate vaccine (PCV) largely eliminated vaccine serotypes (VT); non-vaccine serotypes (NVT) subsequently increased in carriage and disease. Vaccination also disrupts the composition of the pneumococcal pangenome, which includes mobile genetic elements and polymorphic non-capsular antigens important for virulence, transmission, and pneumococcal ecology. Antigenic proteins are of interest for future vaccines; yet, little is known about how the they are affected by PCV use. To investigate the evolutionary impact of vaccination, we assessed recombination, evolution, and pathogen demographic history of 937 pneumococci collected from 1998–2012 among Navajo and White Mountain Apache Native American communities. We analyzed changes in the pneumococcal pangenome, focusing on metabolic loci and 19 polymorphic protein antigens. We found the impact of PCV on the pneumococcal population could be observed in reduced diversity, a smaller pangenome, and changing frequencies of accessory clusters of orthologous groups (COGs). Post-PCV7, diversity rebounded through clonal expansion of NVT lineages and inferred in-migration of two previously unobserved lineages. Accessory COGs frequencies trended toward pre-PCV7 values with increasing time since vaccine introduction. Contemporary frequencies of protein antigen variants are better predicted by pre-PCV7 values (1998–2000) than the preceding period (2006–2008), suggesting balancing selection may have acted in maintaining variant frequencies in this population. Overall, we present the largest genomic analysis of pneumococcal carriage in the United States to date, which includes a snapshot of a true vaccine-naïve community prior to the introduction of PCV7. These data improve our understanding of pneumococcal evolution and emphasize the need to consider pangenome composition when inferring the impact of vaccination and developing future protein-based pneumococcal vaccines. PMID:29617440

Mixed infections reveal virulence differences between host-specific bee pathogens.

PubMed

Klinger, Ellen G; Vojvodic, Svjetlana; DeGrandi-Hoffman, Gloria; Welker, Dennis L; James, Rosalind R

2015-07-01

Dynamics of host-pathogen interactions are complex, often influencing the ecology, evolution and behavior of both the host and pathogen. In the natural world, infections with multiple pathogens are common, yet due to their complexity, interactions can be difficult to predict and study. Mathematical models help facilitate our understanding of these evolutionary processes, but empirical data are needed to test model assumptions and predictions. We used two common theoretical models regarding mixed infections (superinfection and co-infection) to determine which model assumptions best described a group of fungal pathogens closely associated with bees. We tested three fungal species, Ascosphaera apis, Ascosphaera aggregata and Ascosphaera larvis, in two bee hosts (Apis mellifera and Megachile rotundata). Bee survival was not significantly different in mixed infections vs. solo infections with the most virulent pathogen for either host, but fungal growth within the host was significantly altered by mixed infections. In the host A. mellifera, only the most virulent pathogen was present in the host post-infection (indicating superinfective properties). In M. rotundata, the most virulent pathogen co-existed with the lesser-virulent one (indicating co-infective properties). We demonstrated that the competitive outcomes of mixed infections were host-specific, indicating strong host specificity among these fungal bee pathogens. Published by Elsevier Inc.

Sentinel Trees as a Tool to Forecast Invasions of Alien Plant Pathogens

PubMed Central

Vettraino, AnnaMaria; Roques, Alain; Yart, Annie; Fan, Jian-ting; Sun, Jiang-hua; Vannini, Andrea

2015-01-01

Recent disease outbreaks caused by alien invasive pathogens into European forests posed a serious threat to forest sustainability with relevant environmental and economic effects. Many of the alien tree pathogens recently introduced into Europe were not previously included on any quarantine lists, thus they were not subject to phytosanitary inspections. The identification and description of alien fungi potentially pathogenic to native European flora before their introduction in Europe, is a paramount need in order to limit the risk of invasion and the impact to forest ecosystems. To determine the potential invasive fungi, a sentinel trees plot was established in Fuyang, China, using healthy seedlings of European tree species including Quercus petreae, Q. suber, and Q. ilex. The fungal assemblage associated with symptomatic specimens was studied using the tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS 1). Taxa with probable Asiatic origin were identified and included plant pathogenic genera. These results indicate that sentinel plants may be a strategic tool to improve the prevention of bioinvasions. PMID:25826684

Pathogen Screening of Naturally Produced Yakima River Spring Chinook Smolts; Yakima/Klickitat Fisheries Project Monitoring and Evaluation, 2004-2005 Annual Report.

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

Thomas, Joan B.

2005-05-01

In the spring of 2004 naturally produced smolts outmigrating from the Yakima River Basin were collected for the sixth year of pathogen screening. This component of the evaluation is to monitor whether introduction of hatchery produced smolts would impact the prevalence of specific pathogens in the naturally produced spring chinook smolts. Increases in prevalence of any of these pathogens could negatively impact the survival of these fish. Since 1999 the Cle Elum Hatchery has been releasing spring chinook salmon smolts into the upper Yakima River to increase natural production. In 1998 and 2000 through 2004 naturally produced smolts were collectedmore » for monitoring at the Chandler smolt collection facility on the lower Yakima River. Smolts were collected from mid to late outmigration, with a target of 200 fish each year. The pathogens monitored were infectious hematopoeitic necrosis virus, infectious pancreatic necrosis virus, viral hemorrhagic septicemia virus, Flavobacterium psychrophilum, Flavobacterium columnare, Aeromonas salmonicida, Yersinia ruckeri, Edwardsiella ictaluri, Renibacterium salmoninarum and Myxobolus cerebralis. Of these pathogens, only R. salmoninarum was detected in very low levels in the naturally produced smolts outmigrating in 2004. To date, only bacterial pathogens have been detected and prevalences have been low. There have been small variations each year and these changes are attributed to normal fluctuations in prevalence. All of the pathogens detected are widely distributed in Washington State.« less

An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome

PubMed Central

Ferlaino, Michael; Rogers, Mark F.; Shihab, Hashem A.; Mort, Matthew; Cooper, David N.; Gaunt, Tom R.; Campbell, Colin

2018-01-01

Background Small insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of mutations associated with complex traits are located outside the exome, it is crucial to investigate the potential pathogenic impact of indels in non-coding regions of the human genome. Results We present FATHMM-indel, an integrative approach to predict the functional effect, pathogenic or neutral, of indels in non-coding regions of the human genome. Our method exploits various genomic annotations in addition to sequence data. When validated on benchmark data, FATHMM-indel significantly outperforms CADD and GAVIN, state of the art models in assessing the pathogenic impact of non-coding variants. FATHMM-indel is available via a web server at indels.biocompute.org.uk. Conclusions FATHMM-indel can accurately predict the functional impact and prioritise small indels throughout the whole non-coding genome. PMID:28985712

An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome.

PubMed

Ferlaino, Michael; Rogers, Mark F; Shihab, Hashem A; Mort, Matthew; Cooper, David N; Gaunt, Tom R; Campbell, Colin

2017-10-06

Small insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of mutations associated with complex traits are located outside the exome, it is crucial to investigate the potential pathogenic impact of indels in non-coding regions of the human genome. We present FATHMM-indel, an integrative approach to predict the functional effect, pathogenic or neutral, of indels in non-coding regions of the human genome. Our method exploits various genomic annotations in addition to sequence data. When validated on benchmark data, FATHMM-indel significantly outperforms CADD and GAVIN, state of the art models in assessing the pathogenic impact of non-coding variants. FATHMM-indel is available via a web server at indels.biocompute.org.uk. FATHMM-indel can accurately predict the functional impact and prioritise small indels throughout the whole non-coding genome.

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

PubMed Central

Jombart, Thibaut; Cori, Anne; Didelot, Xavier; Cauchemez, Simon; Fraser, Christophe; Ferguson, Neil

2014-01-01

Recent years have seen progress in the development of statistically rigorous frameworks to infer outbreak transmission trees (“who infected whom”) from epidemiological and genetic data. Making use of pathogen genome sequences in such analyses remains a challenge, however, with a variety of heuristic approaches having been explored to date. We introduce a statistical method exploiting both pathogen sequences and collection dates to unravel the dynamics of densely sampled outbreaks. Our approach identifies likely transmission events and infers dates of infections, unobserved cases and separate introductions of the disease. It also proves useful for inferring numbers of secondary infections and identifying heterogeneous infectivity and super-spreaders. After testing our approach using simulations, we illustrate the method with the analysis of the beginning of the 2003 Singaporean outbreak of Severe Acute Respiratory Syndrome (SARS), providing new insights into the early stage of this epidemic. Our approach is the first tool for disease outbreak reconstruction from genetic data widely available as free software, the R package outbreaker. It is applicable to various densely sampled epidemics, and improves previous approaches by detecting unobserved and imported cases, as well as allowing multiple introductions of the pathogen. Because of its generality, we believe this method will become a tool of choice for the analysis of densely sampled disease outbreaks, and will form a rigorous framework for subsequent methodological developments. PMID:24465202

The challenges and promises of genetic approaches for ballast water management

NASA Astrophysics Data System (ADS)

Rey, Anaïs; Basurko, Oihane C.; Rodríguez-Ezpeleta, Naiara

2018-03-01

Ballast water is a main vector of introduction of Harmful Aquatic Organisms and Pathogens, which includes Non-Indigenous Species. Numerous and diversified organisms are transferred daily from a donor to a recipient port. Developed to prevent these introduction events, the International Convention for the Control and Management of Ships' Ballast Water and Sediments will enter into force in 2017. This international convention is asking for the monitoring of Harmful Aquatic Organisms and Pathogens. In this review, we highlight the urgent need to develop cost-effective methods to: (1) perform the biological analyses required by the convention; and (2) assess the effectiveness of two main ballast water management strategies, i.e. the ballast water exchange and the use of ballast water treatment systems. We have compiled the biological analyses required by the convention, and performed a comprehensive evaluation of the potential and challenges of the use of genetic tools in this context. Following an overview of the studies applying genetic tools to ballast water related research, we present metabarcoding as a relevant approach for early detection of Harmful Aquatic Organisms and Pathogens in general and for ballast water monitoring and port risk assessment in particular. Nonetheless, before implementation of genetic tools in the context of the ballast water management convention, benchmarked tests against traditional methods should be performed, and standard, reproducible and easy to apply protocols should be developed.

Feeder use predicts both acquisition and transmission of a contagious pathogen in a North American songbird.

PubMed

Adelman, James S; Moyers, Sahnzi C; Farine, Damien R; Hawley, Dana M

2015-09-22

Individual heterogeneity can influence the dynamics of infectious diseases in wildlife and humans alike. Thus, recent work has sought to identify behavioural characteristics that contribute disproportionately to individual variation in pathogen acquisition (super-receiving) or transmission (super-spreading). However, it remains unknown whether the same behaviours enhance both acquisition and transmission, a scenario likely to result in explosive epidemics. Here, we examined this possibility in an ecologically relevant host-pathogen system: house finches and their bacterial pathogen, Mycoplasma gallisepticum, which causes severe conjunctivitis. We examined behaviours likely to influence disease acquisition (feeder use, aggression, social network affiliations) in an observational field study, finding that the time an individual spends on bird feeders best predicted the risk of conjunctivitis. To test whether this behaviour also influences the likelihood of transmitting M. gallisepticum, we experimentally inoculated individuals based on feeding behaviour and tracked epidemics within captive flocks. As predicted, transmission was fastest when birds that spent the most time on feeders initiated the epidemic. Our results suggest that the same behaviour underlies both pathogen acquisition and transmission in this system and potentially others. Identifying individuals that exhibit such behaviours is critical for disease management. © 2015 The Author(s).

Disease introduction is associated with a phase transition in bighorn sheep demographics.

PubMed

Manlove, Kezia; Cassirer, E Frances; Cross, Paul C; Plowright, Raina K; Hudson, Peter J

2016-10-01

Ecological theory suggests that pathogens are capable of regulating or limiting host population dynamics, and this relationship has been empirically established in several settings. However, although studies of childhood diseases were integral to the development of disease ecology, few studies show population limitation by a disease affecting juveniles. Here, we present empirical evidence that disease in lambs constrains population growth in bighorn sheep (Ovis canadensis) based on 45 years of population-level and 18 years of individual-level monitoring across 12 populations. While populations generally increased (λ = 1.11) prior to disease introduction, most of these same populations experienced an abrupt change in trajectory at the time of disease invasion, usually followed by stagnant-to-declining growth rates (λ = 0.98) over the next 20 years. Disease-induced juvenile mortality imposed strong constraints on population growth that were not observed prior to disease introduction, even as adult survival returned to pre-invasion levels. Simulations suggested that models including persistent disease-induced mortality in juveniles qualitatively matched observed population trajectories, whereas models that only incorporated all-age disease events did not. We use these results to argue that pathogen persistence may pose a lasting, but under-recognized, threat to host populations, particularly in cases where clinical disease manifests primarily in juveniles. © 2016 by the Ecological Society of America.

Predicting the potential distribution of the amphibian pathogen Batrachochytrium dendrobatidis in East and Southeast Asia.

PubMed

Moriguchi, Sachiko; Tominaga, Atsushi; Irwin, Kelly J; Freake, Michael J; Suzuki, Kazutaka; Goka, Koichi

2015-04-08

Batrachochytrium dendrobatidis (Bd) is the pathogen responsible for chytridiomycosis, a disease that is associated with a worldwide amphibian population decline. In this study, we predicted the potential distribution of Bd in East and Southeast Asia based on limited occurrence data. Our goal was to design an effective survey area where efforts to detect the pathogen can be focused. We generated ecological niche models using the maximum-entropy approach, with alleviation of multicollinearity and spatial autocorrelation. We applied eigenvector-based spatial filters as independent variables, in addition to environmental variables, to resolve spatial autocorrelation, and compared the model's accuracy and the degree of spatial autocorrelation with those of a model estimated using only environmental variables. We were able to identify areas of high suitability for Bd with accuracy. Among the environmental variables, factors related to temperature and precipitation were more effective in predicting the potential distribution of Bd than factors related to land use and cover type. Our study successfully predicted the potential distribution of Bd in East and Southeast Asia. This information should now be used to prioritize survey areas and generate a surveillance program to detect the pathogen.

Impact of Vector Dispersal and Host-Plant Fidelity on the Dissemination of an Emerging Plant Pathogen

PubMed Central

Johannesen, Jes; Foissac, Xavier; Kehrli, Patrik; Maixner, Michael

2012-01-01

Dissemination of vector-transmitted pathogens depend on the survival and dispersal of the vector and the vector's ability to transmit the pathogen, while the host range of vector and pathogen determine the breath of transmission possibilities. In this study, we address how the interaction between dispersal and plant fidelities of a pathogen (stolbur phytoplasma tuf-a) and its vector (Hyalesthes obsoletus: Cixiidae) affect the emergence of the pathogen. Using genetic markers, we analysed the geographic origin and range expansion of both organisms in Western Europe and, specifically, whether the pathogen's dissemination in the northern range is caused by resident vectors widening their host-plant use from field bindweed to stinging nettle, and subsequent host specialisation. We found evidence for common origins of pathogen and vector south of the European Alps. Genetic patterns in vector populations show signals of secondary range expansion in Western Europe leading to dissemination of tuf-a pathogens, which might be newly acquired and of hybrid origin. Hence, the emergence of stolbur tuf-a in the northern range was explained by secondary immigration of vectors carrying stinging nettle-specialised tuf-a, not by widening the host-plant spectrum of resident vectors with pathogen transmission from field bindweed to stinging nettle nor by primary co-migration from the resident vector's historical area of origin. The introduction of tuf-a to stinging nettle in the northern range was therefore independent of vector's host-plant specialisation but the rapid pathogen dissemination depended on the vector's host shift, whereas the general dissemination elsewhere was linked to plant specialisation of the pathogen but not of the vector. PMID:23284774

Impact of vector dispersal and host-plant fidelity on the dissemination of an emerging plant pathogen.

PubMed

Johannesen, Jes; Foissac, Xavier; Kehrli, Patrik; Maixner, Michael

2012-01-01

Dissemination of vector-transmitted pathogens depend on the survival and dispersal of the vector and the vector's ability to transmit the pathogen, while the host range of vector and pathogen determine the breath of transmission possibilities. In this study, we address how the interaction between dispersal and plant fidelities of a pathogen (stolbur phytoplasma tuf-a) and its vector (Hyalesthes obsoletus: Cixiidae) affect the emergence of the pathogen. Using genetic markers, we analysed the geographic origin and range expansion of both organisms in Western Europe and, specifically, whether the pathogen's dissemination in the northern range is caused by resident vectors widening their host-plant use from field bindweed to stinging nettle, and subsequent host specialisation. We found evidence for common origins of pathogen and vector south of the European Alps. Genetic patterns in vector populations show signals of secondary range expansion in Western Europe leading to dissemination of tuf-a pathogens, which might be newly acquired and of hybrid origin. Hence, the emergence of stolbur tuf-a in the northern range was explained by secondary immigration of vectors carrying stinging nettle-specialised tuf-a, not by widening the host-plant spectrum of resident vectors with pathogen transmission from field bindweed to stinging nettle nor by primary co-migration from the resident vector's historical area of origin. The introduction of tuf-a to stinging nettle in the northern range was therefore independent of vector's host-plant specialisation but the rapid pathogen dissemination depended on the vector's host shift, whereas the general dissemination elsewhere was linked to plant specialisation of the pathogen but not of the vector.

Infant and maternal predictors of early life feeding decisions: The timing of solid food introduction

PubMed Central

Doub, Allison E.; Moding, Kameron J.; Stifter, Cynthia A.

2015-01-01

There is limited research on the maternal and infant characteristics associated with the timing of solid food introduction. The current study examined how maternal feeding style and infant temperament independently and interactively predicted the age at which infants were introduced to solid food. Data from 115 predominately white, middle-class mothers were collected when infants were 4 and 6 months of age. The timing of solid food introduction was positively correlated with mothers' age, education, breastfeeding at 4 months, self-reported responsiveness to infants' hunger and satiety cues, and negatively correlated with mothers' pre-pregnancy body mass index (BMI), beliefs about feeding infants solid food prior to 6 months of age, and infants' temperamental motor reactivity. When controlling for maternal age, education, pre-pregnancy BMI, and milk feeding method at 4 months, the timing of solid food introduction was negatively predicted by mothers' beliefs about feeding solid food prior to 6 months of age. Exploratory interaction analyses suggested that infant temperament marginally moderated maternal feeding style in predicting the timing of solid food introduction. PMID:26025089

Infant and maternal predictors of early life feeding decisions. The timing of solid food introduction.

PubMed

Doub, Allison E; Moding, Kameron J; Stifter, Cynthia A

2015-09-01

There is limited research on the maternal and infant characteristics associated with the timing of solid food introduction. The current study examined how maternal feeding style and infant temperament independently and interactively predicted the age at which infants were introduced to solid food. Data from 115 predominately white, middle-class mothers were collected when infants were 4 and 6 months of age. The timing of solid food introduction was positively correlated with mothers' age, education, breastfeeding at 4 months, self-reported responsiveness to infants' hunger and satiety cues, and negatively correlated with mothers' pre-pregnancy body mass index (BMI), beliefs about feeding infants solid food prior to 6 months of age, and infants' temperamental motor reactivity. When controlling for maternal age, education, pre-pregnancy BMI, and milk feeding method at 4 months, the timing of solid food introduction was negatively predicted by mothers' beliefs about feeding solid food prior to 6 months of age. Exploratory interaction analyses suggested that infant temperament marginally moderated maternal feeding style in predicting the timing of solid food introduction. Copyright © 2015 Elsevier Ltd. All rights reserved.

Thermally-actuated, phase change flow control for microfluidic systems.

PubMed

Chen, Zongyuan; Wang, Jing; Qian, Shizhi; Bau, Haim H

2005-11-01

An easy to implement, thermally-actuated, noninvasive method for flow control in microfluidic devices is described. This technique takes advantage of the phase change of the working liquid itself-the freezing and melting of a portion of a liquid slug-to noninvasively close and open flow passages (referred to as a phase change valve). The valve was designed for use in a miniature diagnostic system for detecting pathogens in oral fluids at the point of care. The paper describes the modeling, construction, and characteristics of the valve. The experimental results favorably agree with theoretical predictions. In addition, the paper demonstrates the use of the phase change valves for flow control, sample metering and distribution into multiple analysis paths, sealing of a polymerase chain reaction (PCR) chamber, and sample introduction into and withdrawal from a closed loop. The phase change valve is electronically addressable, does not require any moving parts, introduces only minimal dead volume, is leakage and contamination free, and is biocompatible.

The interplay of extracellular matrix and microbiome in urothelial bladder cancer.

PubMed

Alfano, Massimo; Canducci, Filippo; Nebuloni, Manuela; Clementi, Massimo; Montorsi, Francesco; Salonia, Andrea

2016-02-01

Many pathological changes in solid tumours are caused by the accumulation of genetic mutations and epigenetic molecular alterations. In addition, tumour progression is profoundly influenced by the environment surrounding the transformed cells. The interplay between tumour cells and their microenvironment has been recognized as one of the key determinants of cancer development and is being extensively investigated. Data suggest that both the extracellular matrix and the microbiota represent microenvironments that contribute to the onset and progression of tumours. Through the introduction of omics technologies and pyrosequencing analyses, a detailed investigation of these two microenvironments is now possible. In urological research, assessment of their dysregulation has become increasingly important to provide diagnostic, prognostic and predictive biomarkers for urothelial bladder cancer. Understanding the roles of the extracellular matrix and microbiota, two key components of the urothelial mucosa, in the sequelae of pathogenic events that occur in the development and progression of urothelial carcinomas will be important to overcome the shortcomings in current bladder cancer treatment strategies.

Genomic Analysis of Salmonella enterica Serovar Typhimurium DT160 Associated with a 14-Year Outbreak, New Zealand, 1998–2012

PubMed Central

Benschop, Jackie; Biggs, Patrick J.; Marshall, Jonathan C.; Hayman, David T.S.; Carter, Philip E.; Midwinter, Anne C.; Mather, Alison E.; French, Nigel P.

2017-01-01

During 1998–2012, an extended outbreak of Salmonella enterica serovar Typhimurium definitive type 160 (DT160) affected >3,000 humans and killed wild birds in New Zealand. However, the relationship between DT160 within these 2 host groups and the origin of the outbreak are unknown. Whole-genome sequencing was used to compare 109 Salmonella Typhimurium DT160 isolates from sources throughout New Zealand. We provide evidence that DT160 was introduced into New Zealand around 1997 and rapidly propagated throughout the country, becoming more genetically diverse over time. The genetic heterogeneity was evenly distributed across multiple predicted functional protein groups, and we found no evidence of host group differentiation between isolates collected from human, poultry, bovid, and wild bird sources, indicating ongoing transmission between these host groups. Our findings demonstrate how a comparative genomic approach can be used to gain insight into outbreaks, disease transmission, and the evolution of a multihost pathogen after a probable point-source introduction. PMID:28516864

Introduction to the Symposium: Parasites and Pests in Motion: Biology, Biodiversity and Climate Change.

PubMed

Williams, Jason D; Boyko, Christopher B

2016-10-01

Although climate change can cause extreme alterations to ecosystems, only limited research has investigated how altered physical conditions (e.g., warming, extreme temperature events, sea level rise, ocean acidification, and altered precipitation) influence species interactions. In particular, the interplay between host and parasites in such a changing world is in need of study. Our objective in organizing this symposium was to bring together researchers working on a wide variety of natural enemies (parasites, pathogens, and pests), to exchange knowledge on how aspects of global climate change may alter the distribution and ecology of these organisms and their hosts. It is our intention that the symposium and the resulting articles will foster more accurate modeling of and predictions about the impacts of climate change on the biology and ecology of natural enemies and their hosts. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Weeds, as ancillary hosts, pose disproportionate risk for virulent pathogen transfer to crops.

PubMed

Linde, Celeste C; Smith, Leon M; Peakall, Rod

2016-05-12

The outcome of the arms race between hosts and pathogens depends heavily on the interactions between their genetic diversity, population size and transmission ability. Theory predicts that genetically diverse hosts will select for higher virulence and more diverse pathogens than hosts with low genetic diversity. Cultivated hosts typically have lower genetic diversity and thus small effective population sizes, but can potentially harbour large pathogen population sizes. On the other hand, hosts, such as weeds, which are genetically more diverse and thus have larger effective population sizes, usually harbour smaller pathogen population sizes. Large pathogen population sizes may lead to more opportunities for mutation and hence more diverse pathogens. Here we test the predictions that pathogen neutral genetic diversity will increase with large pathogen population sizes and host diversity, whereas diversity under selection will increase with host diversity. We assessed and compared the diversity of a fungal pathogen, Rhynchosporium commune, on weedy barley grass (which have a large effective population size) and cultivated barley (low genetic diversity) using microsatellites, effector locus nip1 diversity and pathogen aggressiveness in order to assess the importance of weeds in the evolution of the neutral and selected diversity of pathogens. The findings indicated that the large barley acreage and low host diversity maintains higher pathogen neutral genetic diversity and lower linkage disequilibrium, while the weed maintains more pathotypes and higher virulence diversity at nip1. Strong evidence for more pathogen migration from barley grass to barley suggests transmission of virulence from barley grass to barley is common. Pathogen census population size is a better predictor for neutral genetic diversity than host diversity. Despite maintaining a smaller pathogen census population size, barley grass acts as an important ancillary host to R. commune, harbouring highly virulent pathogen types capable of transmission to barley. Management of disease on crops must therefore include management of weedy ancillary hosts, which may harbour disproportionate supplies of virulent pathogen strains.

How direct competition shapes coexistence and vaccine effects in multi-strain pathogen systems.

PubMed

Gjini, Erida; Valente, Carina; Sá-Leão, Raquel; Gomes, M Gabriela M

2016-01-07

We describe an integrated modeling framework for understanding strain coexistence in polymorphic pathogen systems. Previous studies have debated the utility of neutral formulations and focused on cross-immunity between strains as a major stabilizing mechanism. Here we convey that direct competition for colonization mediates stable coexistence only when competitive abilities amongst pathogen clones satisfy certain pairwise asymmetries. We illustrate our ideas with nested SIS models of single and dual colonization, applied to polymorphic pneumococcal bacteria. By fitting the models to cross-sectional prevalence data from Portugal (before and after the introduction of a seven-valent pneumococcal conjugate vaccine), we are able to not only statistically compare neutral and non-neutral epidemiological formulations, but also estimate vaccine efficacy, transmission and competition parameters simultaneously. Our study highlights that the response of polymorphic pathogen populations to interventions holds crucial information about strain interactions, which can be extracted by suitable nested modeling. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bonamia parasites: a rapidly changing perspective on a genus of important mollusc pathogens.

PubMed

Engelsma, Marc Y; Culloty, Sarah C; Lynch, Sharon A; Arzul, Isabelle; Carnegie, Ryan B

2014-07-24

Organisms of the genus Bonamia are intracellular protistan parasites of oysters. To date, 4 species have been described (B. ostreae, B. exitiosa, B. perspora and B. roughleyi), although the status of B. roughleyi is controversial. Introduction especially of B. ostreae and B. exitiosa to naïve host populations has been shown to cause mass mortalities in the past and has had a dramatic impact on oyster production. Both B. ostreae and B. exitiosa are pathogens notifiable to the World Organisation for Animal Health (OIE) and the European Union. Effective management of the disease caused by these pathogens is complicated by the extensive nature of the oyster production process and limited options for disease control of the cultured stocks in open water. This review focuses on the recent advances in research on genetic relationships between Bonamia isolates, geographical distribution, susceptible host species, diagnostics, epizootiology, host-parasite interactions, and disease resistance and control of this globally important genus of oyster pathogens.

Oomycete Interactions with Plants: Infection Strategies and Resistance Principles

PubMed Central

Doumane, Mehdi

2015-01-01

SUMMARY The Oomycota include many economically significant microbial pathogens of crop species. Understanding the mechanisms by which oomycetes infect plants and identifying methods to provide durable resistance are major research goals. Over the last few years, many elicitors that trigger plant immunity have been identified, as well as host genes that mediate susceptibility to oomycete pathogens. The mechanisms behind these processes have subsequently been investigated and many new discoveries made, marking a period of exciting research in the oomycete pathology field. This review provides an introduction to our current knowledge of the pathogenic mechanisms used by oomycetes, including elicitors and effectors, plus an overview of the major principles of host resistance: the established R gene hypothesis and the more recently defined susceptibility (S) gene model. Future directions for development of oomycete-resistant plants are discussed, along with ways that recent discoveries in the field of oomycete-plant interactions are generating novel means of studying how pathogen and symbiont colonizations overlap. PMID:26041933

Tomorrow's vector vaccines for small ruminants.

PubMed

Kyriakis, C S

2015-12-14

Inactivated and attenuated vaccines have contributed to the control or even the eradication of significant animal pathogens. However, these traditional vaccine technologies have limitations and disadvantages. Inactivated vaccines lack efficacy against certain pathogens, while attenuated vaccines are not always as safe. New technology vaccines, namely DNA and recombinant viral vector vaccines, are being developed and tested against pathogens of small ruminants. These vaccines induce both humoral and cellular immune responses, are safe to manufacture and use and can be utilized in strategies for differentiation of infected from vaccinated animals. Although there are more strict regulatory requirements for the safety standards of these vaccines, once a vaccine platform is evaluated and established, effective vaccines can be rapidly produced and deployed in the field to prevent spread of emerging pathogens. The present article offers an introduction to these next generation technologies and examples of vaccines that have been tested against important diseases of sheep and goats. Copyright © 2015 Elsevier B.V. All rights reserved.

Real-world clinical applicability of pathogenicity predictors assessed on SERPINA1 mutations in alpha-1-antitrypsin deficiency.

PubMed

Giacopuzzi, Edoardo; Laffranchi, Mattia; Berardelli, Romina; Ravasio, Viola; Ferrarotti, Ilaria; Gooptu, Bibek; Borsani, Giuseppe; Fra, Annamaria

2018-06-07

The growth of publicly available data informing upon genetic variations, mechanisms of disease and disease sub-phenotypes offers great potential for personalised medicine. Computational approaches are likely required to assess large numbers of novel genetic variants. However, the integration of genetic, structural and pathophysiological data still represents a challenge for computational predictions and their clinical use. We addressed these issues for alpha-1-antitrypsin deficiency, a disease mediated by mutations in the SERPINA1 gene encoding alpha-1-antitrypsin. We compiled a comprehensive database of SERPINA1 coding mutations and assigned them apparent pathological relevance based upon available data. 'Benign' and 'Pathogenic' mutations were used to assess performance of 31 pathogenicity predictors. Well-performing algorithms clustered the subset of variants known to be severely pathogenic with high scores. Eight new mutations identified in the ExAC database and achieving high scores were selected for characterisation in cell models and showed secretory deficiency and polymer formation, supporting the predictive power of our computational approach. The behaviour of the pathogenic new variants and consistent outliers were rationalised by considering the protein structural context and residue conservation. These findings highlight the potential of computational methods to provide meaningful predictions of the pathogenic significance of novel mutations and identify areas for further investigation. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Plasmodesmal regulation during plant-pathogen interactions.

PubMed

Cheval, Cecilia; Faulkner, Christine

2018-01-01

Contents Summary 62 I. Introduction 62 II. Plasmodesmal regulation is an innate defence response 63 III. Reactive oxygen species regulate plasmodesmal function 63 IV. Plasmodesmal regulation by and of defence-associated small molecules 64 V. Plasmodesmata facilitate systemic defence signalling 64 VI. Virulent pathogens exploit plasmodesmata 66 VII. Outlook 66 Acknowledgements 66 References 66 SUMMARY: Plasmodesmata (PD) are plasma membrane-lined pores that connect neighbouring plant cells, bridging the cell wall and establishing cytoplasmic and membrane continuity between cells. PD are dynamic structures regulated by callose deposition in a variety of stress and developmental contexts. This process crudely controls the aperture of the pore and thus the flux of molecules between cells. During pathogen infection, plant cells initiate a range of immune responses and it was recently identified that, following perception of fungal and bacterial pathogens, plant cells initially close their PD. Systemic defence responses depend on the spread of signals between cells, raising questions about whether PD are in different functional states during different immune responses. It is well established that viral pathogens exploit PD to spread between cells, but it has more recently been identified that protein effectors secreted by fungal pathogens can spread between host cells via PD. It is possible that many classes of pathogens specifically target PD to aid infection, which would infer antagonistic regulation of PD by host and pathogen. How PD regulation benefits both host immune responses and pathogen infection is an important question and demands that we examine the multicellular nature of plant-pathogen interactions. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Reducing Listeria spp. and Escherichia coli O157:H12 on cantaloupes at pre-harvest level by octenidine hydrochloride

USDA-ARS?s Scientific Manuscript database

Introduction: Cantaloupes have been increasingly implicated in outbreaks of human illnesses in recent years. The cantaloupe industry has traditionally relied on various chemical wash treatments to reduce pathogens at post-harvest level. Effective interventions applied at the pre-harvest level could ...

Ten-year performance of the United States national elm trial

Treesearch

Jason J. Griffin; William R. Jacobi; E. Gregory McPherson; Clifford S. Sadof; James R. McKenna; Mark L. Gleason; Nicole Ward Gauthier; Daniel A. Potter; David R. Smitley; Gerard C. Adams; Ann Brooks Gould; Christian R. Cash; James A. Walla; Mark C. Starrett; Gary Chastagner; Jeff L. Sibley; Vera A. Krischik; Adam F. Newby

2017-01-01

Ulmus americana (American elm) was an important urban tree in North America prior to the introduction of the Dutch elm disease pathogen in 1930. Subsequently, urban and community forests were devastated by the loss of large canopies. Tree improvement programs produced disease tolerant American and Eurasian elm cultivars and introduced them into the...

Title: Efficacy of chlorine dioxide gas to decontaminate fresh produce used for in-store and vendor juicing operations

USDA-ARS?s Scientific Manuscript database

Introduction: Unpasteurized juices are increasingly popular as consumers aim to find convenient, healthy options. Contamination of produce with pathogens such as Salmonella, Escherichia coli O157:H7, and Listeria monocytogenes poses a risk. In-store treatment of small batches of mixed types of fresh...

Complete genome sequence of the thermotolerant foodborne pathogen Salmonella enterica serovar Senftenberg ATCC 43845 and phylogenetic analysis of loci encoding thermotolerance

USDA-ARS?s Scientific Manuscript database

Introduction: Previous studies in Cronobacter sakazakii, Klebsiella spp., and Escherichia coli have identified a genomic island that confers thermotolerance to its hosts. This island has recently been identified in Salmonella enterica serovar Senfentenberg ATCC 43845, a historically important, heat ...

Peracetic acid: the long road to introduction of this disinfectant into U.S. aquaculture

USDA-ARS?s Scientific Manuscript database

Peracetic acid (PAA) is a promising disinfectant for biosecurity in the US aquaculture industry to prevent disease outbreaks from fish pathogens. PAA is a stabilized mixture of acetic acid, hydrogen peroxide and water that breaks down quickly to water and vinegar. It has replaced chlorine in some ...

The introduction of peracetic acid as a new disinfectant for U.S. aquaculture

USDA-ARS?s Scientific Manuscript database

Peracetic acid (PAA) is a promising disinfectant for biosecurity in the US aquaculture industry to prevent disease outbreaks from fish pathogens. PAA is a stabilized mixture of acetic acid, hydrogen peroxide and water that breaks down quickly to water and vinegar. It has replaced chlorine in some ...

Sequence variation and recognition specificity of the avirulence gene AvrPiz-t in Magnaporthe oryzae field populations

USDA-ARS?s Scientific Manuscript database

Magnaporthe oryzae, the rice blast pathogen, causes significant annual yield loss of rice worldwide. Currently, the most effective disease control approach is deployment of host resistance through introduction of resistance (R) genes into elite cultivars. The function of each R gene relies on the sp...

Effect of spinach cultivar and strain variation on survival of Escherichia coli O157:H7 on spinach leaves

USDA-ARS?s Scientific Manuscript database

Introduction: Escherichia coli O157:H7 outbreaks of infections associated with the consumption of fresh produce have increased in recent years. Bacterial cell surface appendages such as curli and the spinach leaf structure topography influence pathogen attachment and subsequent survival on spinach ...

Funding needed for assessments of weed biological control

Treesearch

John L. Maron; Dean E. Pearson; Stephen M. Hovick; Walter P. Carson

2010-01-01

Invasive non-native plants are a serious economic and ecological problem worldwide, and major efforts are therefore devoted to reducing weed abundance in agricultural and natural settings. Effective options for reducing invasive abundance and spread are few, although one common approach is biological control - the introduction of specialist herbivores or pathogens from...

Evaluation of an Alcohol-Based Sanitizer Spray's Bactericidal Effects on Salmonella Inoculated onto Stainless Steel and Shell Egg Processing Equipment

USDA-ARS?s Scientific Manuscript database

Introduction: Safety regulations are being drafted for the shell egg industry. Sanitation standard operating procedures are an important precursor to HACCP regulations. Salmonella is the pathogen was most often associated with egg-borne outbreaks. Developing effective sanitation procedures that wil...

Safe Procurement and Production Manual: A systems approach for the production of healthy nursery stock

USDA-ARS?s Scientific Manuscript database

The introduction and spread of plant pests and pathogens threatens the long-term health and profitability of the nursery and greenhouse industry. As the global economy has boomed, there has been a dramatic increase in goods moved between countries and continents. These goods can include live plants ...

The introduction of peracetic acid as a new disinfectant for U.S. aquaculture

USDA-ARS?s Scientific Manuscript database

Peracetic acid (PAA) is a promising disinfectant for biosecurity in the US aquaculture industry to prevent disease outbreaks from fish pathogens. PAA is a stabilized mixture of acetic acid, hydrogen peroxide and water that breaks down quickly to water and vinegar. It is being increasingly used to ...

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...

Operational program to develop Phytophthora lateralis-resistant populations of Port-Orford-cedar (Chamaecyparis lawsoniana)

Treesearch

R.A. Sniezko; J. Hamlin; E.M. Hansen

2012-01-01

Port-Orford-cedar (Chamaecyparis lawsoniana (A. Murr.) Parl.) (POC) is a long-lived conifer native to northwestern California and southwestern Oregon. It has been widely used in horticulture in both western North America and elsewhere. The accidental introduction of the non-native pathogen Phytophthora lateralis into North...

An introduction to joint research by the USEPA and USGS on contaminants of emerging concern in source and treated drinking waters of the United States

EPA Science Inventory

Improvements in analytical methodology have allowed low-level detection of an ever increasing number of pharmaceuticals, personal care products, hormones, pathogens and other contaminants of emerging concern (CECs). The use of these improved analytical tools has allowed researche...

Persistence of fecal shedding of Salmonella Enteritidis by experimentally infected laying hens housed in conventional or enriched cages

USDA-ARS?s Scientific Manuscript database

: Because Salmonella Enteritidis can be deposited inside eggs laid by infected hens, the prevalence of this pathogen in commercial egg-producing flocks is an important risk factor for human illness. Opportunities for the introduction, transmission, and persistence of salmonellae in poultry are poten...

Persistence of fecal shedding of Salmonella Enteritidis by experimentally infected laying hens housed in conventional or enriched cages.

USDA-ARS?s Scientific Manuscript database

Because Salmonella Enteritidis can be deposited inside eggs laid by infected hens, the prevalence of this pathogen in commercial egg-producing flocks is an important risk factor for human illness. Opportunities for the introduction, transmission, and persistence of salmonellae in poultry are potenti...

Antibiotic resistance patterns in E. coli and Salmonella isolates recovered from commercially vailable compost

USDA-ARS?s Scientific Manuscript database

Introduction: Compost is used by both conventional and organic farming practices as an eco-friendly means to enhance soil properties and to reduce fertilizer inputs. Inadequate composting may lead to residual human pathogens (e.g. Escherichia coli O157:H7 and Salmonella spp.) in the final compost ...

Antibiotic resistance patterns in E. coli and Salmonella isolates recovered from commercially available compost

USDA-ARS?s Scientific Manuscript database

Introduction: Compost is used by both conventional and organic farming practices as an eco-friendly means to enhance soil properties and to reduce fertilizer inputs. Inadequate composting may lead to residual human pathogens (e.g. Escherichia coli O157:H7 and Salmonella spp.) in the final compost ...

An introduction to on-farm strategies to control foodborne pathogens

USDA-ARS?s Scientific Manuscript database

Foodborne illnesses affect more than 48 million Americans each year. The economic impact of these foodborne illnesses caused by bacteria associated with food animals ranges from $10 to 40 billion (USD) per year, and effects across the EU are similar in scale. Because of the large drain on the GDP,...

The Mississippi River Campaign 1862-1863: The Impact of Climate and Pathogens on Operational Art at the Port Hudson Siege

DTIC Science & Technology

2017-04-13

48 1 Introduction Sun Tzu , for one, advised commanders to, “camp on hard ground, the army...51 Bibliography ...Society Papers Volume XIII January to December 1885 (Richmond, VA: The Society, 1891), 329; Bell, 31. 248 Bell, 30. 52 Bibliography Army Doctrine

Procurement and persistence of GFP-expressing Escherichia coli and Salmonella Typhimurium in male and female house flies exposed to cattle manure

USDA-ARS?s Scientific Manuscript database

Introduction: Adult house flies, Musca domestica L., are associated with animal manure and other microbe-rich substrates. Consequently, both sexes can acquire and potentially disseminate pathogenic bacteria to surrounding environments, including residential areas, via contaminated body parts and/or ...

Development of a process-based model to predict pathogen budgets for the Sydney drinking water catchment.

PubMed

Ferguson, Christobel M; Croke, Barry F W; Beatson, Peter J; Ashbolt, Nicholas J; Deere, Daniel A

2007-06-01

In drinking water catchments, reduction of pathogen loads delivered to reservoirs is an important priority for the management of raw source water quality. To assist with the evaluation of management options, a process-based mathematical model (pathogen catchment budgets - PCB) is developed to predict Cryptosporidium, Giardia and E. coli loads generated within and exported from drinking water catchments. The model quantifies the key processes affecting the generation and transport of microorganisms from humans and animals using land use and flow data, and catchment specific information including point sources such as sewage treatment plants and on-site systems. The resultant pathogen catchment budgets (PCB) can be used to prioritize the implementation of control measures for the reduction of pathogen risks to drinking water. The model is applied in the Wingecarribee catchment and used to rank those sub-catchments that would contribute the highest pathogen loads in dry weather, and in intermediate and large wet weather events. A sensitivity analysis of the model identifies that pathogen excretion rates from animals and humans, and manure mobilization rates are significant factors determining the output of the model and thus warrant further investigation.

Equine disease events resulting from international horse movements: Systematic review and lessons learned.

PubMed

Dominguez, M; Münstermann, S; de Guindos, I; Timoney, P

2016-09-01

An analysis of the factors leading to equine disease events was used to support the development of international recommendations for mitigating the risk of disease dissemination through sport horse movements (high health, high performance - 'HHP' horses). A review was undertaken to identify the factors resulting in equine disease events following international movement of horses to draw lessons in support of the development of international recommendations for the safe movements of a specific subpopulation of horses: the HHP sport horses. Systematic review carried out in accordance with the PRISMA statement. The review covered disease events that occurred from 1995 to 2014, identified from the databases of the World Organisation for Animal Health (OIE) and international surveillance reports. Overall, 54 disease events were identified, of which 7 were contained in post arrival quarantine and the others resulted in the introduction of pathogens into importing countries. For 81% of the introductions, the OIE recommendations applicable to the diseases involved had not been complied with. Subclinical infections are a challenge for international trade: 88% of the regulated movements that resulted in introductions involved infected horses that showed no clinical signs at the time of import. Biosecurity and management practices in resident equine populations were identified as important mitigating factors in preventing disease spread to the local horse population. The global increase in international horse movements, if not appropriately regulated and supervised by competent veterinary authorities and respective equine industry partners, could potentially lead to increased global spread of infectious equine diseases. Appropriate mitigation measures and compliance with OIE import recommendations for specific diseases can significantly reduce this risk. The recommendations proposed under the HHP approach take into account the mitigation measures identified by this review as important factors in preventing pathogen introduction and spread. © 2015 EVJ Ltd.

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

Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs.

PubMed

Huo, Tong; Liu, Wei; Guo, Yu; Yang, Cheng; Lin, Jianping; Rao, Zihe

2015-03-26

Emergence of multiple drug resistant strains of M. tuberculosis (MDR-TB) threatens to derail global efforts aimed at reigning in the pathogen. Co-infections of M. tuberculosis with HIV are difficult to treat. To counter these new challenges, it is essential to study the interactions between M. tuberculosis and the host to learn how these bacteria cause disease. We report a systematic flow to predict the host pathogen interactions (HPIs) between M. tuberculosis and Homo sapiens based on sequence motifs. First, protein sequences were used as initial input for identifying the HPIs by 'interolog' method. HPIs were further filtered by prediction of domain-domain interactions (DDIs). Functional annotations of protein and publicly available experimental results were applied to filter the remaining HPIs. Using such a strategy, 118 pairs of HPIs were identified, which involve 43 proteins from M. tuberculosis and 48 proteins from Homo sapiens. A biological interaction network between M. tuberculosis and Homo sapiens was then constructed using the predicted inter- and intra-species interactions based on the 118 pairs of HPIs. Finally, a web accessible database named PATH (Protein interactions of M. tuberculosis and Human) was constructed to store these predicted interactions and proteins. This interaction network will facilitate the research on host-pathogen protein-protein interactions, and may throw light on how M. tuberculosis interacts with its host.

Reduced Set of Virulence Genes Allows High Accuracy Prediction of Bacterial Pathogenicity in Humans

PubMed Central

Iraola, Gregorio; Vazquez, Gustavo; Spangenberg, Lucía; Naya, Hugo

2012-01-01

Although there have been great advances in understanding bacterial pathogenesis, there is still a lack of integrative information about what makes a bacterium a human pathogen. The advent of high-throughput sequencing technologies has dramatically increased the amount of completed bacterial genomes, for both known human pathogenic and non-pathogenic strains; this information is now available to investigate genetic features that determine pathogenic phenotypes in bacteria. In this work we determined presence/absence patterns of different virulence-related genes among more than finished bacterial genomes from both human pathogenic and non-pathogenic strains, belonging to different taxonomic groups (i.e: Actinobacteria, Gammaproteobacteria, Firmicutes, etc.). An accuracy of 95% using a cross-fold validation scheme with in-fold feature selection is obtained when classifying human pathogens and non-pathogens. A reduced subset of highly informative genes () is presented and applied to an external validation set. The statistical model was implemented in the BacFier v1.0 software (freely available at ), that displays not only the prediction (pathogen/non-pathogen) and an associated probability for pathogenicity, but also the presence/absence vector for the analyzed genes, so it is possible to decipher the subset of virulence genes responsible for the classification on the analyzed genome. Furthermore, we discuss the biological relevance for bacterial pathogenesis of the core set of genes, corresponding to eight functional categories, all with evident and documented association with the phenotypes of interest. Also, we analyze which functional categories of virulence genes were more distinctive for pathogenicity in each taxonomic group, which seems to be a completely new kind of information and could lead to important evolutionary conclusions. PMID:22916122

Biogeography of Human Infectious Diseases: A Global Historical Analysis

PubMed Central

Cashdan, Elizabeth

2014-01-01

Objectives Human pathogen richness and prevalence vary widely across the globe, yet we know little about whether global patterns found in other taxa also predict diversity in this important group of organisms. This study (a) assesses the relative importance of temperature, precipitation, habitat diversity, and population density on the global distributions of human pathogens and (b) evaluates the species-area predictions of island biogeography for human pathogen distributions on oceanic islands. Methods Historical data were used in order to minimize the influence of differential access to modern health care on pathogen prevalence. The database includes coded data (pathogen, environmental and cultural) for a worldwide sample of 186 non-industrial cultures, including 37 on islands. Prevalence levels for 10 pathogens were combined into a pathogen prevalence index, and OLS regression was used to model the environmental determinants of the prevalence index and number of pathogens. Results Pathogens (number and prevalence index) showed the expected latitudinal gradient, but predictors varied by latitude. Pathogens increased with temperature in high-latitude zones, while mean annual precipitation was a more important predictor in low-latitude zones. Other environmental factors associated with more pathogens included seasonal dry extremes, frost-free climates, and human population density outside the tropics. Islands showed the expected species-area relationship for all but the smallest islands, and the relationship was not mediated by habitat diversity. Although geographic distributions of free-living and parasitic taxa typically have different determinants, these data show that variables that influence the distribution of free-living organisms also shape the global distribution of human pathogens. Understanding the cause of these distributions is potentially important, since geographical variation in human pathogens has an important influence on global disparities in human welfare. PMID:25271730

Biogeography of human infectious diseases: a global historical analysis.

PubMed

Cashdan, Elizabeth

2014-01-01

Human pathogen richness and prevalence vary widely across the globe, yet we know little about whether global patterns found in other taxa also predict diversity in this important group of organisms. This study (a) assesses the relative importance of temperature, precipitation, habitat diversity, and population density on the global distributions of human pathogens and (b) evaluates the species-area predictions of island biogeography for human pathogen distributions on oceanic islands. Historical data were used in order to minimize the influence of differential access to modern health care on pathogen prevalence. The database includes coded data (pathogen, environmental and cultural) for a worldwide sample of 186 non-industrial cultures, including 37 on islands. Prevalence levels for 10 pathogens were combined into a pathogen prevalence index, and OLS regression was used to model the environmental determinants of the prevalence index and number of pathogens. Pathogens (number and prevalence index) showed the expected latitudinal gradient, but predictors varied by latitude. Pathogens increased with temperature in high-latitude zones, while mean annual precipitation was a more important predictor in low-latitude zones. Other environmental factors associated with more pathogens included seasonal dry extremes, frost-free climates, and human population density outside the tropics. Islands showed the expected species-area relationship for all but the smallest islands, and the relationship was not mediated by habitat diversity. Although geographic distributions of free-living and parasitic taxa typically have different determinants, these data show that variables that influence the distribution of free-living organisms also shape the global distribution of human pathogens. Understanding the cause of these distributions is potentially important, since geographical variation in human pathogens has an important influence on global disparities in human welfare.

Pathogen exposure varies widely among sympatric populations of wild and domestic felids across the United States

USGS Publications Warehouse

Carver, Scott; Bevins, Sarah N.; Lappin, Michael R.; Boydston, Erin E.; Lyren, Lisa M.; Alldredge, Mathew W.; Logan, Kenneth A.; Sweanor, Linda L.; Riley, Seth P.D.; Serieys, Laurel E.K.; Fisher, Robert N.; Vickers, T. Winston; Boyce, Walter M.; McBride, Roy; Cunnigham, Mark C.; Jennings, Megan; Lewis, Jesse S.; Lunn, Tamika; Crooks, Kevin R.; VandeWoude, Sue

2016-01-01

Understanding how landscape, host, and pathogen traits contribute to disease exposure requires systematic evaluations of pathogens within and among host species and geographic regions. The relative importance of these attributes is critical for management of wildlife and mitigating domestic animal and human disease, particularly given rapid ecological changes, such as urbanization. We screened >1,000 samples from sympatric populations of puma (Puma concolor), bobcat (Lynx rufus) and domestic cat (Felis catus) across urban gradients in six sites, representing three regions, in North America for exposure to a representative suite of bacterial, protozoal and viral pathogens (Bartonella sp., Toxoplasma gondii, feline herpesvirus-1, feline panleukopenea virus, feline calicivirus, feline immunodeficiency virus). We evaluated prevalence within each species, and examined host trait and land cover determinants of exposure-providing an unprecedented analysis of factors relating to potential for infections in domesticated and wild felids. Prevalence differed among host species (highest for puma and lowest for domestic cat) and was greater for indirectly transmitted pathogens. Sex was inconsistently predictive of exposure to directly transmitted pathogens only, and age infrequently predictive of both direct and indirectly transmitted pathogens. Determinants of pathogen exposure were widely divergent between the wild felid species. For puma, suburban landuse predicted increased exposure to Bartonella sp. in southern California, and FHV-1 exposure increased near urban edges in Florida. This may suggest inter-specific transmission with domestic cats via flea vectors (California) and direct contact (Florida) around urban boundaries. Bobcats captured near urban areas had increased exposure to T. gondii in Florida, suggesting an urban source of prey. Bobcats captured near urban areas in Colorado and Florida had higher FIV exposure, possibly suggesting increased intra-specific interactions through pile-up of home ranges. Beyond these regional and pathogen specific relationships, proximity to the wildland urban interface did not generally increase the probability of disease exposure in wild or domestic felids, emphasizing the importance of local ecological determinants. Indeed, pathogen exposure was often negatively associated with the wildland urban interface for all felids. Our analyses suggest cross-species pathogen transmission events around this interface may be infrequent, but followed by self-sustaining propagation within the new host species.

QPCR Analysis of Total and Viable Enterococci in Waste Water Treatment: Comparison with Culture in Predicting Pathogen Reductions

EPA Science Inventory

BEACH Act amendment to Clean Water Act requires EPA to establish more expeditious methods for the timely detection of pathogens and pathogen indicators in coastal waters New methods should demonstrate utility for and be compatible with all CWA 304(a) criteria needs including:...

Apparent competition in canopy trees determined by pathogen transmission rather than susceptibility.

Treesearch

Richard Cobb; Ross Meentemeyer; David Rizzo

2010-01-01

Epidemiological theory predicts that asymmetric transmission, susceptibility, and mortality within a community will drive pathogen and disease dynamics. These epidemiological asymmetries can result in apparent competition, where a highly infectious host reduces the abundance of less infectious or more susceptible members in a community via a shared pathogen. We show...

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

Free-living pathogens: life-history constraints and strain competition.

PubMed

Caraco, Thomas; Wang, Ing-Nang

2008-02-07

Many pathogen life histories include a free-living stage, often with anatomical and physiological adaptations promoting persistence outside of host tissues. More durable particles presumably require that the pathogen metabolize more resources per particle. Therefore, we hypothesize functional dependencies, pleiotropic constraints, between the rate at which free-living particles decay outside of host tissues and other pathogen traits, including virulence, the probability of infecting a host upon contact, and pathogen reproduction within host tissues. Assuming that pathogen strains compete for hosts preemptively, we find patterns in trait dependencies predicting whether or not strain competition favors a highly persistent free-living stage.

Probability of introducing foot and mouth disease into the United States via live animal importation.

PubMed

Miller, G Y; Ming, J; Williams, I; Gorvett, R

2012-12-01

Foot and mouth disease (FMD) continues to be a disease of major concern for the United States Department of Agriculture (USDA) and livestock industries. Foot and mouth disease virus is a high-consequence pathogen for the United States (USA). Live animal trade is a major risk factor for introduction of FMD into a country. This research estimates the probability of FMD being introduced into the USA via the legal importation of livestock. This probability is calculated by considering the potential introduction of FMD from each country from which the USA imports live animals. The total probability of introduction into the USA of FMD from imported livestock is estimated to be 0.415% per year, which is equivalent to one introduction every 241 years. In addition, to provide a basis for evaluating the significance of risk management techniques and expenditures, the sensitivity of the above result to changes in various risk parameter assumptions is determined.

The sentinel tree nursery as an early warning system for pathway risk assessment: Fungal pathogens associated with Chinese woody plants commonly shipped to Europe

PubMed Central

Vettraino, Anna Maria; Li, Hong-Mei; Eschen, Rene; Morales-Rodriguez, Carmen

2017-01-01

Introduction of and invasion by alien plant pathogens represents the main cause of emerging infectious diseases affecting domesticated and wild plant species worldwide. The trade in living plants is the most common pathway of introduction. Many of the alien tree pathogens recently introduced into Europe were not previously included on any quarantine lists. To help determine the potential risk of pest introduction through trading of ornamental plants, a sentinel nursery was established in Beijing, China in 2008. The sentinel nursery planting included four of the most common ornamental woody species shipped to Europe including Ilex cornuta var. fortunae, Zelkova schneideriana, Fraxinus chinensis and Buxus microphylla. Symptoms developing on these species within the sentinel nursery were detected in 2013 and consisted of necrotic spots on leaves, canker and stem necrosis, shoot blight and shoot necrosis. Fungi associated with the trees and their symptoms included Alternaria alternata detected from all hosts; Diaporthe liquidambaris and Diaporthe capsici from bark and leaf necrosis of Zelkova schneideriana; Botryosphaeria dothidea and Nothophoma quercina from stem cankers on Fraxinus chinensis and leaf necrosis on Ilex cornuta; and Pseudonectria foliicola from leaf necrosis on Buxus microphylla. Next generation sequencing analysis from asymptomatic tissues detected eighteen OTU’s at species level among which some taxa had not been previously recorded in Europe. These results clearly demonstrate that looking at trees of internationally traded species in the region of origin can reveal the presence of potentially harmful organisms of major forestry, landscape or crop trees. Results of this study also provide an indication as to how some disease agents can be introduced using pathways other than the co-generic hosts. Hence, sentinel nurseries represent one potential mechanism to address the current lack of knowledge about pests in the countries from where live plants are shipped and the threats they represent to native flora and crops in importing countries. PMID:29186190

The sentinel tree nursery as an early warning system for pathway risk assessment: Fungal pathogens associated with Chinese woody plants commonly shipped to Europe.

PubMed

Vettraino, Anna Maria; Li, Hong-Mei; Eschen, Rene; Morales-Rodriguez, Carmen; Vannini, Andrea

2017-01-01

Introduction of and invasion by alien plant pathogens represents the main cause of emerging infectious diseases affecting domesticated and wild plant species worldwide. The trade in living plants is the most common pathway of introduction. Many of the alien tree pathogens recently introduced into Europe were not previously included on any quarantine lists. To help determine the potential risk of pest introduction through trading of ornamental plants, a sentinel nursery was established in Beijing, China in 2008. The sentinel nursery planting included four of the most common ornamental woody species shipped to Europe including Ilex cornuta var. fortunae, Zelkova schneideriana, Fraxinus chinensis and Buxus microphylla. Symptoms developing on these species within the sentinel nursery were detected in 2013 and consisted of necrotic spots on leaves, canker and stem necrosis, shoot blight and shoot necrosis. Fungi associated with the trees and their symptoms included Alternaria alternata detected from all hosts; Diaporthe liquidambaris and Diaporthe capsici from bark and leaf necrosis of Zelkova schneideriana; Botryosphaeria dothidea and Nothophoma quercina from stem cankers on Fraxinus chinensis and leaf necrosis on Ilex cornuta; and Pseudonectria foliicola from leaf necrosis on Buxus microphylla. Next generation sequencing analysis from asymptomatic tissues detected eighteen OTU's at species level among which some taxa had not been previously recorded in Europe. These results clearly demonstrate that looking at trees of internationally traded species in the region of origin can reveal the presence of potentially harmful organisms of major forestry, landscape or crop trees. Results of this study also provide an indication as to how some disease agents can be introduced using pathways other than the co-generic hosts. Hence, sentinel nurseries represent one potential mechanism to address the current lack of knowledge about pests in the countries from where live plants are shipped and the threats they represent to native flora and crops in importing countries.

Apoplastic effectors secreted by two unrelated eukaryotic plant pathogens target the tomato defense protease Rcr3.

PubMed

Song, Jing; Win, Joe; Tian, Miaoying; Schornack, Sebastian; Kaschani, Farnusch; Ilyas, Muhammad; van der Hoorn, Renier A L; Kamoun, Sophien

2009-02-03

Current models of plant-pathogen interactions stipulate that pathogens secrete effector proteins that disable plant defense components known as virulence targets. Occasionally, the perturbations caused by these effectors trigger innate immunity via plant disease resistance proteins as described by the "guard hypothesis." This model is nicely illustrated by the interaction between the fungal plant pathogen Cladosporium fulvum and tomato. C. fulvum secretes a protease inhibitor Avr2 that targets the tomato cysteine protease Rcr3(pim). In plants that carry the resistance protein Cf2, Rcr3(pim) is required for resistance to C. fulvum strains expressing Avr2, thus fulfilling one of the predictions of the guard hypothesis. Another prediction of the guard hypothesis has not yet been tested. Considering that virulence targets are important components of defense, different effectors from unrelated pathogens are expected to evolve to disable the same host target. In this study we confirm this prediction using a different pathogen of tomato, the oomycete Phytophthora infestans that is distantly related to fungi such as C. fulvum. This pathogen secretes an array of protease inhibitors including EPIC1 and EPIC2B that inhibit tomato cysteine proteases. Here we show that, similar to Avr2, EPIC1 and EPIC2B bind and inhibit Rcr3(pim). However, unlike Avr2, EPIC1 and EPIC2B do not trigger hypersensitive cell death or defenses on Cf-2/Rcr3(pim) tomato. We also found that the rcr3-3 mutant of tomato that carries a premature stop codon in the Rcr3 gene exhibits enhanced susceptibility to P. infestans, suggesting a role for Rcr3(pim) in defense. In conclusion, our findings fulfill a key prediction of the guard hypothesis and suggest that the effectors Avr2, EPIC1, and EPIC2B secreted by two unrelated pathogens of tomato target the same defense protease Rcr3(pim). In contrast to C. fulvum, P. infestans appears to have evolved stealthy effectors that carry inhibitory activity without triggering plant innate immunity.

Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif

PubMed Central

2010-01-01

Background Effector secretion is a common strategy of pathogen in mediating host-pathogen interaction. Eight EPIYA-motif containing effectors have recently been discovered in six pathogens. Once these effectors enter host cells through type III/IV secretion systems (T3SS/T4SS), tyrosine in the EPIYA motif is phosphorylated, which triggers effectors binding other proteins to manipulate host-cell functions. The objectives of this study are to evaluate the distribution pattern of EPIYA motif in broad biological species, to predict potential effectors with EPIYA motif, and to suggest roles and biological functions of potential effectors in host-pathogen interactions. Results A hidden Markov model (HMM) of five amino acids was built for the EPIYA-motif based on the eight known effectors. Using this HMM to search the non-redundant protein database containing 9,216,047 sequences, we obtained 107,231 sequences with at least one EPIYA motif occurrence and 3115 sequences with multiple repeats of the EPIYA motif. Although the EPIYA motif exists among broad species, it is significantly over-represented in some particular groups of species. For those proteins containing at least four copies of EPIYA motif, most of them are from intracellular bacteria, extracellular bacteria with T3SS or T4SS or intracellular protozoan parasites. By combining the EPIYA motif and the adjacent SH2 binding motifs (KK, R4, Tarp and Tir), we built HMMs of nine amino acids and predicted many potential effectors in bacteria and protista by the HMMs. Some potential effectors for pathogens (such as Lawsonia intracellularis, Plasmodium falciparum and Leishmania major) are suggested. Conclusions Our study indicates that the EPIYA motif may be a ubiquitous functional site for effectors that play an important pathogenicity role in mediating host-pathogen interactions. We suggest that some intracellular protozoan parasites could secrete EPIYA-motif containing effectors through secretion systems similar to the T3SS/T4SS in bacteria. Our predicted effectors provide useful hypotheses for further studies. PMID:21143776

Computational prediction and biochemical characterization of novel RNA aptamers to Rift Valley fever virus nucleocapsid protein.

PubMed

Ellenbecker, Mary; St Goddard, Jeremy; Sundet, Alec; Lanchy, Jean-Marc; Raiford, Douglas; Lodmell, J Stephen

2015-10-01

Rift Valley fever virus (RVFV) is a potent human and livestock pathogen endemic to sub-Saharan Africa and the Arabian Peninsula that has potential to spread to other parts of the world. Although there is no proven effective and safe treatment for RVFV infections, a potential therapeutic target is the virally encoded nucleocapsid protein (N). During the course of infection, N binds to viral RNA, and perturbation of this interaction can inhibit viral replication. To gain insight into how N recognizes viral RNA specifically, we designed an algorithm that uses a distance matrix and multidimensional scaling to compare the predicted secondary structures of known N-binding RNAs, or aptamers, that were isolated and characterized in previous in vitro evolution experiment. These aptamers did not exhibit overt sequence or predicted structure similarity, so we employed bioinformatic methods to propose novel aptamers based on analysis and clustering of secondary structures. We screened and scored the predicted secondary structures of novel randomly generated RNA sequences in silico and selected several of these putative N-binding RNAs whose secondary structures were similar to those of known N-binding RNAs. We found that overall the in silico generated RNA sequences bound well to N in vitro. Furthermore, introduction of these RNAs into cells prior to infection with RVFV inhibited viral replication in cell culture. This proof of concept study demonstrates how the predictive power of bioinformatics and the empirical power of biochemistry can be jointly harnessed to discover, synthesize, and test new RNA sequences that bind tightly to RVFV N protein. The approach would be easily generalizable to other applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phytophthora Species, New Threats to the Plant Health in Korea

PubMed Central

Hyun, Ik-Hwa; Choi, Woobong

2014-01-01

Given the lack of a resistant genetic pool in host plants, the introduction of exotic invasive pathogens can result in epidemics that affect a specific ecosystem and economy. Plant quarantine, which is designed to protect endemic plant resources, is a highly invaluable safeguard that should keep biosecurity with increasing international trade and global transportation. A total of 34 species of plant pathogens including Phytophthora infestans were documented as introduced from other countries into Korea from 1900 to 2010. The genus Phytophthora, classified in oomycetes, includes more than 120 species that are mostly recognized worldwide as highly invasive plant pathogens. After 2000, over 50 new species of Phytophthora were identified internationally as plant pathogens occurring in crops and forest trees. In Korea, Phytophthora is also one of the most serious plant pathogens. To date, 22 species (about one-fifth of known species) of the genus have been identified and reported as plant pathogens in the country. The likelihood of new exotic Phytophthora species being introduced into Korea continues to increase, thus necessitating intensive plant quarantine inspections. As new potential threats to plant health in Korea, six Phytophthora species, namely, P. alni, P. inundata, P. kernoviae, P. pinifolia, P. quercina, and P. ramorum, are discussed in this review with focus on history, disease, biology, management, and plant quarantine issues. PMID:25506298

Global food and fibre security threatened by current inefficiencies in fungal identification.

PubMed

Crous, Pedro W; Groenewald, Johannes Z; Slippers, Bernard; Wingfield, Michael J

2016-12-05

Fungal pathogens severely impact global food and fibre crop security. Fungal species that cause plant diseases have mostly been recognized based on their morphology. In general, morphological descriptions remain disconnected from crucially important knowledge such as mating types, host specificity, life cycle stages and population structures. The majority of current fungal species descriptions lack even the most basic genetic data that could address at least some of these issues. Such information is essential for accurate fungal identifications, to link critical metadata and to understand the real and potential impact of fungal pathogens on production and natural ecosystems. Because international trade in plant products and introduction of pathogens to new areas is likely to continue, the manner in which fungal pathogens are identified should urgently be reconsidered. The technologies that would provide appropriate information for biosecurity and quarantine already exist, yet the scientific community and the regulatory authorities are slow to embrace them. International agreements are urgently needed to enforce new guidelines for describing plant pathogenic fungi (including key DNA information), to ensure availability of relevant data and to modernize the phytosanitary systems that must deal with the risks relating to trade-associated plant pathogens.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'. © 2016 The Author(s).

Case-Control Pilot Study on Acute Diarrheal Disease in a Geographically Defined Pediatric Population in a Middle Income Country

PubMed Central

Farfán-García, Ana E.; Zhang, Chengxian; Imdad, Aamer; Arias-Guerrero, Monica Y.; Sánchez-Alvarez, Nayibe T.; Shah, Rikhil; Iqbal, Junaid; Tamborski, Maria E.

2017-01-01

Introduction Acute diarrheal disease (ADD) is a common cause of morbidity and mortality in children under 5 years of age. Understanding of the etiology of ADD is lacking in most low and middle income countries because reference laboratories detect limited number of pathogens. The objective of this study was to determine the feasibility to conduct a comprehensive case-control study to survey diarrheal pathogens among children with and without moderate-to-severe ADD. Materials and Methods Microbiology and molecular-based techniques were used to detect viral, bacterial, and parasitic enteropathogens. The study was conducted in Bucaramanga, Colombia, after Institutional Review Board approval was obtained. Results Ninety children less than 5 years of age were recruited after a written informed consent was obtained from parents or guardians. Forty-five subjects served as cases with ADD and 45 as controls. Thirty-six subjects out of 90 (40.0%) were positive for at least one enteropathogen, that is, 20 (44.4%) cases and 16 (35.5%) controls. Conclusions The three most common enteric pathogens were enteroaggregative E. coli (10.0%), Norovirus (6.7%), and Salmonella spp. (5.6%). The E. coli pathogens were 18.8% of all infections making them the most frequent pathogens. Half of ADD cases were negative for any pathogens. PMID:28855919

Highly pathogenic avian influenza A(H5N8) outbreaks: protection and management of exposed people in Europe, 2014/15 and 2016.

PubMed

Adlhoch, Cornelia; Brown, Ian H; Angelova, Svetla G; Bálint, Ádám; Bouwstra, Ruth; Buda, Silke; Castrucci, Maria R; Dabrera, Gavin; Dán, Ádám; Grund, Christian; Harder, Timm; van der Hoek, Wim; Krisztalovics, Katalin; Parry-Ford, Frances; Popescu, Rodica; Wallensten, Anders; Zdravkova, Anna; Zohari, Siamak; Tsolova, Svetla; Penttinen, Pasi

2016-12-08

Introduction of highly pathogenic avian influenza (HPAI) virus A(H5N8) into Europe prompted animal and human health experts to implement protective measures to prevent transmission to humans. We describe the situation in 2016 and list public health measures and recommendations in place. We summarise critical interfaces identified during the A(H5N1) and A(H5N8) outbreaks in 2014/15. Rapid exchange of information between the animal and human health sectors is critical for a timely, effective and efficient response. This article is copyright of ECDC, 2016.

The next target of bioterrorism: your food.

PubMed Central

Pellerin, C

2000-01-01

One of the many forms that biological warfare may take is the targeting of major food crops. In a poor country where millions of citizens depend on staple crops such as rice, an act of bioterrorism that destroys the crop would create a famine, resulting not only in malnutrition and starvation but also in reduced immune resistance to a range of common illnesses. To reduce the potential of deliberate introductions of crop pathogens as acts of terrorism, researchers must be able to "fingerprint" pathogens at the molecular level and discriminate between naturally occurring and deliberately introduced outbreaks. Several domestic and international surveillance, tracking, and reporting efforts are under way. PMID:10706540

[Etiological analysis and establishment of a discriminant model for lower respiratory tract infections in hospitalized patients].

PubMed

Chen, Y S; Lin, X H; Li, H R; Hua, Z D; Lin, M Q; Huang, W S; Yu, T; Lyu, H Y; Mao, W P; Liang, Y Q; Peng, X R; Chen, S J; Zheng, H; Lian, S Q; Hu, X L; Yao, X Q

2017-12-12

Objective: To analyze the pathogens of lower respiratory tract infection(LRTI) including bacterial, viral and mixed infection, and to establish a discriminant model based on clinical features in order to predict the pathogens. Methods: A total of 243 hospitalized patients with lower respiratory tract infections were enrolled in Fujian Provincial Hospital from April 2012 to September 2015. The clinical data and airway (sputum and/or bronchoalveolar lavage) samples were collected. Microbes were identified by traditional culture (for bacteria), loop-mediated isothermal amplification(LAMP) and gene sequencing (for bacteria and atypical pathogen), or Real-time quantitative polymerase chain reaction (Real-time PCR)for viruses. Finally, a discriminant model was established by using the discriminant analysis methods to help to predict bacterial, viral and mixed infections. Results: Pathogens were detected in 53.9% (131/243) of the 243 cases.Bacteria accounted for 23.5%(57/243, of which 17 cases with the virus, 1 case with Mycoplasma pneumoniae and virus), mainly Pseudomonas Aeruginosa and Klebsiella Pneumonia. Atypical pathogens for 4.9% (12/243, of which 3 cases with the virus, 1 case of bacteria and viruses), all were mycoplasma pneumonia. Viruses for 34.6% (84/243, of which 17 cases of bacteria, 3 cases with Mycoplasma pneumoniae, 1 case with Mycoplasma pneumoniae and bacteria) of the cases, mainly Influenza A virus and Human Cytomegalovirus, and other virus like adenovirus, human parainfluenza virus, respiratory syncytial virus, human metapneumovirus, human boca virus were also detected fewly. Seven parameters including mental status, using antibiotics prior to admission, complications, abnormal breath sounds, neutrophil alkaline phosphatase (NAP) score, pneumonia severity index (PSI) score and CRUB-65 score were enrolled after univariate analysis, and discriminant analysis was used to establish the discriminant model by applying the identified pathogens as the dependent variable. The total positive predictive value was 64.7%(77/119), with 66.7% for bacterial infection, 78.0% for viral infection and 33.3% for the mixed infection. Conclusions: The mostly detected pathogens were Pseudomonas aeruginosa, atypitcal pathogens, Klebsiella pneumoniae, influenza A virus and human cytomegalovirus in hospitalized patients with LRTI in this hospital. The discriminant diagnostic model established by clinical features may contribute to predict the pathogens of LRTI.

EffectorP: predicting fungal effector proteins from secretomes using machine learning.

PubMed

Sperschneider, Jana; Gardiner, Donald M; Dodds, Peter N; Tini, Francesco; Covarelli, Lorenzo; Singh, Karam B; Manners, John M; Taylor, Jennifer M

2016-04-01

Eukaryotic filamentous plant pathogens secrete effector proteins that modulate the host cell to facilitate infection. Computational effector candidate identification and subsequent functional characterization delivers valuable insights into plant-pathogen interactions. However, effector prediction in fungi has been challenging due to a lack of unifying sequence features such as conserved N-terminal sequence motifs. Fungal effectors are commonly predicted from secretomes based on criteria such as small size and cysteine-rich, which suffers from poor accuracy. We present EffectorP which pioneers the application of machine learning to fungal effector prediction. EffectorP improves fungal effector prediction from secretomes based on a robust signal of sequence-derived properties, achieving sensitivity and specificity of over 80%. Features that discriminate fungal effectors from secreted noneffectors are predominantly sequence length, molecular weight and protein net charge, as well as cysteine, serine and tryptophan content. We demonstrate that EffectorP is powerful when combined with in planta expression data for predicting high-priority effector candidates. EffectorP is the first prediction program for fungal effectors based on machine learning. Our findings will facilitate functional fungal effector studies and improve our understanding of effectors in plant-pathogen interactions. EffectorP is available at http://effectorp.csiro.au. © 2015 CSIRO New Phytologist © 2015 New Phytologist Trust.

The RpfCG two-component system negatively regulates the colonization of sugar cane stalks by Xanthomonas albilineans.

PubMed

Rott, Philippe; Fleites, Laura A; Mensi, Imène; Sheppard, Lauren; Daugrois, Jean-Heinrich; Dow, J Maxwell; Gabriel, Dean W

2013-06-01

The genome of Xanthomonas albilineans, the causal agent of sugar cane leaf scald, carries a gene cluster encoding a predicted quorum sensing system that is highly related to the diffusible signalling factor (DSF) systems of the plant pathogens Xylella fastidiosa and Xanthomonas campestris. In these latter pathogens, a cluster of regulation of pathogenicity factors (rpf) genes encodes the DSF system and is involved in control of various cellular processes. Mutation of Xanthomonas albilineans rpfF, encoding a predicted DSF synthase, in Florida strain XaFL07-1 resulted in a small reduction of disease severity (DS). Single-knockout mutations of rpfC and rpfG (encoding a predicted DSF sensor and regulator, respectively) had no effect on DS or swimming motility of the pathogen. However, capacity of the pathogen to cause disease was slightly reduced and swimming motility was severely affected when rpfG and rpfC were both deleted. Similar results were obtained when the entire rpfGCF region was deleted. Surprisingly, when the pathogen was mutated in rpfG or rpfC (single or double mutations) it was able to colonize sugar cane spatially more efficiently than the wild-type. Mutation in rpfF alone did not affect the degree of spatial invasion. We conclude that the DSF signal contributes to symptom expression but not to invasion of sugar cane stalks by Xanthomonas albilineans strain XaFL07-1, which is mainly controlled by the RpfCG two-component system.

Modeling the impact of the indigenous microbial population on the maximum population density of Salmonella on alfalfa.

PubMed

Rijgersberg, Hajo; Franz, Eelco; Nierop Groot, Masja; Tromp, Seth-Oscar

2013-07-01

Within a microbial risk assessment framework, modeling the maximum population density (MPD) of a pathogenic microorganism is important but often not considered. This paper describes a model predicting the MPD of Salmonella on alfalfa as a function of the initial contamination level, the total count of the indigenous microbial population, the maximum pathogen growth rate and the maximum population density of the indigenous microbial population. The model is parameterized by experimental data describing growth of Salmonella on sprouting alfalfa seeds at inoculum size, native microbial load and Pseudomonas fluorescens 2-79. The obtained model fits well to the experimental data, with standard errors less than ten percent of the fitted average values. The results show that the MPD of Salmonella is not only dictated by performance characteristics of Salmonella but depends on the characteristics of the indigenous microbial population like total number of cells and its growth rate. The model can improve the predictions of microbiological growth in quantitative microbial risk assessments. Using this model, the effects of preventive measures to reduce pathogenic load and a concurrent effect on the background population can be better evaluated. If competing microorganisms are more sensitive to a particular decontamination method, a pathogenic microorganism may grow faster and reach a higher level. More knowledge regarding the effect of the indigenous microbial population (size, diversity, composition) of food products on pathogen dynamics is needed in order to make adequate predictions of pathogen dynamics on various food products.

Livestock abundance predicts vampire bat demography, immune profiles and bacterial infection risk

PubMed Central

Czirják, Gábor Á.; Volokhov, Dmitriy V.; Carrera, Jorge E.; Camus, Melinda S.; Navara, Kristen J.; Chizhikov, Vladimir E.; Fenton, M. Brock; Simmons, Nancy B.; Recuenco, Sergio E.; Gilbert, Amy T.

2018-01-01

Human activities create novel food resources that can alter wildlife–pathogen interactions. If resources amplify or dampen, pathogen transmission probably depends on both host ecology and pathogen biology, but studies that measure responses to provisioning across both scales are rare. We tested these relationships with a 4-year study of 369 common vampire bats across 10 sites in Peru and Belize that differ in the abundance of livestock, an important anthropogenic food source. We quantified innate and adaptive immunity from bats and assessed infection with two common bacteria. We predicted that abundant livestock could reduce starvation and foraging effort, allowing for greater investments in immunity. Bats from high-livestock sites had higher microbicidal activity and proportions of neutrophils but lower immunoglobulin G and proportions of lymphocytes, suggesting more investment in innate relative to adaptive immunity and either greater chronic stress or pathogen exposure. This relationship was most pronounced in reproductive bats, which were also more common in high-livestock sites, suggesting feedbacks between demographic correlates of provisioning and immunity. Infection with both Bartonella and haemoplasmas were correlated with similar immune profiles, and both pathogens tended to be less prevalent in high-livestock sites, although effects were weaker for haemoplasmas. These differing responses to provisioning might therefore reflect distinct transmission processes. Predicting how provisioning alters host–pathogen interactions requires considering how both within-host processes and transmission modes respond to resource shifts. This article is part of the theme issue ‘Anthropogenic resource subsidies and host–parasite dynamics in wildlife’. PMID:29531144

A Framework for Optimizing Phytosanitary Thresholds in Seed Systems.

PubMed

Choudhury, Robin Alan; Garrett, Karen A; Klosterman, Steven J; Subbarao, Krishna V; McRoberts, Neil

2017-10-01

Seedborne pathogens and pests limit production in many agricultural systems. Quarantine programs help prevent the introduction of exotic pathogens into a country, but few regulations directly apply to reducing the reintroduction and spread of endemic pathogens. Use of phytosanitary thresholds helps limit the movement of pathogen inoculum through seed, but the costs associated with rejected seed lots can be prohibitive for voluntary implementation of phytosanitary thresholds. In this paper, we outline a framework to optimize thresholds for seedborne pathogens, balancing the cost of rejected seed lots and benefit of reduced inoculum levels. The method requires relatively small amounts of data, and the accuracy and robustness of the analysis improves over time as data accumulate from seed testing. We demonstrate the method first and illustrate it with a case study of seedborne oospores of Peronospora effusa, the causal agent of spinach downy mildew. A seed lot threshold of 0.23 oospores per seed could reduce the overall number of oospores entering the production system by 90% while removing 8% of seed lots destined for distribution. Alternative mitigation strategies may result in lower economic losses to seed producers, but have uncertain efficacy. We discuss future challenges and prospects for implementing this approach.

Substitutions near the hemagglutinin receptor-binding site determine the antigenic evolution of influenza A H3N2 viruses in U.S. swine.

PubMed

Lewis, Nicola S; Anderson, Tavis K; Kitikoon, Pravina; Skepner, Eugene; Burke, David F; Vincent, Amy L

2014-05-01

Swine influenza A virus is an endemic and economically important pathogen in pigs, with the potential to infect other host species. The hemagglutinin (HA) protein is the primary target of protective immune responses and the major component in swine influenza A vaccines. However, as a result of antigenic drift, vaccine strains must be regularly updated to reflect currently circulating strains. Characterizing the cross-reactivity between strains in pigs and seasonal influenza virus strains in humans is also important in assessing the relative risk of interspecies transmission of viruses from one host population to the other. Hemagglutination inhibition (HI) assay data for swine and human H3N2 viruses were used with antigenic cartography to quantify the antigenic differences among H3N2 viruses isolated from pigs in the United States from 1998 to 2013 and the relative cross-reactivity between these viruses and current human seasonal influenza A virus strains. Two primary antigenic clusters were found circulating in the pig population, but with enough diversity within and between the clusters to suggest updates in vaccine strains are needed. We identified single amino acid substitutions that are likely responsible for antigenic differences between the two primary antigenic clusters and between each antigenic cluster and outliers. The antigenic distance between current seasonal influenza virus H3 strains in humans and those endemic in swine suggests that population immunity may not prevent the introduction of human viruses into pigs, and possibly vice versa, reinforcing the need to monitor and prepare for potential incursions. Influenza A virus (IAV) is an important pathogen in pigs and humans. The hemagglutinin (HA) protein is the primary target of protective immune responses and the major target of vaccines. However, vaccine strains must be updated to reflect current strains. Characterizing the differences between seasonal IAV in humans and swine IAV is important in assessing the relative risk of interspecies transmission of viruses. We found two primary antigenic clusters of H3N2 in the U.S. pig population, with enough diversity to suggest updates in swine vaccine strains are needed. We identified changes in the HA protein that are likely responsible for these differences and that may be useful in predicting when vaccines need to be updated. The difference between human H3N2 viruses and those in swine is enough that population immunity is unlikely to prevent new introductions of human IAV into pigs or vice versa, reinforcing the need to monitor and prepare for potential introductions.

GESPA: classifying nsSNPs to predict disease association.

PubMed

Khurana, Jay K; Reeder, Jay E; Shrimpton, Antony E; Thakar, Juilee

2015-07-25

Non-synonymous single nucleotide polymorphisms (nsSNPs) are the most common DNA sequence variation associated with disease in humans. Thus determining the clinical significance of each nsSNP is of great importance. Potential detrimental nsSNPs may be identified by genetic association studies or by functional analysis in the laboratory, both of which are expensive and time consuming. Existing computational methods lack accuracy and features to facilitate nsSNP classification for clinical use. We developed the GESPA (GEnomic Single nucleotide Polymorphism Analyzer) program to predict the pathogenicity and disease phenotype of nsSNPs. GESPA is a user-friendly software package for classifying disease association of nsSNPs. It allows flexibility in acceptable input formats and predicts the pathogenicity of a given nsSNP by assessing the conservation of amino acids in orthologs and paralogs and supplementing this information with data from medical literature. The development and testing of GESPA was performed using the humsavar, ClinVar and humvar datasets. Additionally, GESPA also predicts the disease phenotype associated with a nsSNP with high accuracy, a feature unavailable in existing software. GESPA's overall accuracy exceeds existing computational methods for predicting nsSNP pathogenicity. The usability of GESPA is enhanced by fast SQL-based cloud storage and retrieval of data. GESPA is a novel bioinformatics tool to determine the pathogenicity and phenotypes of nsSNPs. We anticipate that GESPA will become a useful clinical framework for predicting the disease association of nsSNPs. The program, executable jar file, source code, GPL 3.0 license, user guide, and test data with instructions are available at http://sourceforge.net/projects/gespa.

The utility and limitations of current web-available algorithms to predict peptides recognized by CD4 T cells in response to pathogen infection #

PubMed Central

Chaves, Francisco A.; Lee, Alvin H.; Nayak, Jennifer; Richards, Katherine A.; Sant, Andrea J.

2012-01-01

The ability to track CD4 T cells elicited in response to pathogen infection or vaccination is critical because of the role these cells play in protective immunity. Coupled with advances in genome sequencing of pathogenic organisms, there is considerable appeal for implementation of computer-based algorithms to predict peptides that bind to the class II molecules, forming the complex recognized by CD4 T cells. Despite recent progress in this area, there is a paucity of data regarding their success in identifying actual pathogen-derived epitopes. In this study, we sought to rigorously evaluate the performance of multiple web-available algorithms by comparing their predictions and our results using purely empirical methods for epitope discovery in influenza that utilized overlapping peptides and cytokine Elispots, for three independent class II molecules. We analyzed the data in different ways, trying to anticipate how an investigator might use these computational tools for epitope discovery. We come to the conclusion that currently available algorithms can indeed facilitate epitope discovery, but all shared a high degree of false positive and false negative predictions. Therefore, efficiencies were low. We also found dramatic disparities among algorithms and between predicted IC50 values and true dissociation rates of peptide:MHC class II complexes. We suggest that improved success of predictive algorithms will depend less on changes in computational methods or increased data sets and more on changes in parameters used to “train” the algorithms that factor in elements of T cell repertoire and peptide acquisition by class II molecules. PMID:22467652

The structural effects of mutations can aid in differential phenotype prediction of beta-myosin heavy chain (Myosin-7) missense variants.

PubMed

Al-Numair, Nouf S; Lopes, Luis; Syrris, Petros; Monserrat, Lorenzo; Elliott, Perry; Martin, Andrew C R

2016-10-01

High-throughput sequencing platforms are increasingly used to screen patients with genetic disease for pathogenic mutations, but prediction of the effects of mutations remains challenging. Previously we developed SAAPdap (Single Amino Acid Polymorphism Data Analysis Pipeline) and SAAPpred (Single Amino Acid Polymorphism Predictor) that use a combination of rule-based structural measures to predict whether a missense genetic variant is pathogenic. Here we investigate whether the same methodology can be used to develop a differential phenotype predictor, which, once a mutation has been predicted as pathogenic, is able to distinguish between phenotypes-in this case the two major clinical phenotypes (hypertrophic cardiomyopathy, HCM and dilated cardiomyopathy, DCM) associated with mutations in the beta-myosin heavy chain (MYH7) gene product (Myosin-7). A random forest predictor trained on rule-based structural analyses together with structural clustering data gave a Matthews' correlation coefficient (MCC) of 0.53 (accuracy, 75%). A post hoc removal of machine learning models that performed particularly badly, increased the performance (MCC = 0.61, Acc = 79%). This proof of concept suggests that methods used for pathogenicity prediction can be extended for use in differential phenotype prediction. Analyses were implemented in Perl and C and used the Java-based Weka machine learning environment. Please contact the authors for availability. andrew@bioinf.org.uk or andrew.martin@ucl.ac.uk Supplementary data are available at Bioinformatics online. © The Authors 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Field application of a combined pig and poultry market chain and risk pathway analysis within the Pacific Islands region as a tool for targeted disease surveillance and biosecurity.

PubMed

Brioudes, Aurélie; Gummow, Bruce

2016-07-01

Limited resources are one of the major constraints in effective disease monitoring and control in developing countries. This paper examines the pig and poultry market chains of four targeted Pacific Island countries and territories (PICTs): Fiji, Papua New Guinea, Solomon Islands and Vanuatu and combines them with a risk pathway analysis to identify the highest risk areas (risk hotspots) and risky practices and behaviours (risk factors) of animal disease introduction and/or spread, using highly pathogenic avian influenza (HPAI) and foot-and-mouth disease (FMD) as model diseases because of their importance in the region. The results show that combining a market chain analysis with risk pathways is a practical way of communicating risk to animal health officials and improving biosecurity. It provides a participatory approach that helps officials to better understand the trading regulations in place in their country and to better evaluate their role as part of the control system. Common risk patterns were found to play a role in all four PICTs. Legal trade pathways rely essentially on preventive measures put in place in the exporting countries while no or only limited control measures are undertaken by the importing countries. Legal importations of animals and animal products are done mainly by commercial farms which then supply local smallholders. Targeting surveillance on these potential hotspots would limit the risk of introduction and spread of animal diseases within the pig and poultry industry and better rationalize use of skilled manpower. Swill feeding is identified as a common practice in the region that represents a recognized risk factor for dissemination of pathogens to susceptible species. Illegal introduction of animals and animal products is suspected, but appears restricted to small holder farms in remote areas, limiting the risk of spread of transboundary animal diseases along the market chain. Introduction of undeclared goods hidden within a legal trade activity was identified as a major risk pathway. Activities such as awareness campaigns for pig and poultry farmers regarding disease reporting, biosecurity measures or danger of swill feeding and training of biosecurity officers in basic animal health and import-associated risks are recommended to prevent and limit the spread of pathogens within the PICTs. Copyright © 2016 Elsevier B.V. All rights reserved.

Potential applications of nonthermal plasmas against biofilm-associated micro-organisms in vitro.

PubMed

Puligundla, P; Mok, C

2017-05-01

Biofilms as complex microbial communities attached to surfaces pose several challenges in different sectors, ranging from food and healthcare to desalination and power generation. The biofilm mode of growth allows microorganisms to survive in hostile environments and biofilm cells exhibit distinct physiology and behaviour in comparison with their planktonic counterparts. They are ubiquitous, resilient and difficult to eradicate due to their resistant phenotype. Several chemical-based cleaning and disinfection regimens are conventionally used against biofilm-dwelling micro-organisms in vitro. Although such approaches are generally considered to be effective, they may contribute to the dissemination of antimicrobial resistance and environmental pollution. Consequently, advanced green technologies for biofilm control are constantly emerging. Disinfection using nonthermal plasmas (NTPs) is one of the novel strategies having a great potential for control of biofilms of a broad spectrum of micro-organisms. This review discusses several aspects related to the inactivation of biofilm-associated bacteria and fungi by different types of NTPs under in vitro conditions. A brief introduction summarizes prevailing methods in biofilm inactivation, followed by introduction to gas discharge plasmas, active plasma species and their inactivating mechanism. Subsequently, significance and aspects of NTP inactivation of biofilm-associated bacteria, especially those of medical importance, including opportunistic pathogens, oral pathogenic bacteria, foodborne pathogens and implant bacteria, are discussed. The remainder of the review discusses majorly about the synergistic effect of NTPs and their activity against biofilm-associated fungi, especially Candida species. © 2017 The Society for Applied Microbiology.

Recent introduction and recombination in Colletotrichum acutatum populations associated with citrus postbloom fruit drop epidemics in São Paulo, Brazil.

PubMed

Ciampi-Guillardi, Maisa; Baldauf, Cristina; Souza, Anete Pereira; Silva-Junior, Geraldo José; Amorim, Lilian

2014-07-01

Citrus crops in São Paulo State, Brazil, have been severely affected by postbloom fruit drop disease (PFD), which is caused by Colletotrichum acutatum. This disease leads to the drop of up to 100% of young fruits. Previous studies have assumed that this pathogen exhibits a clonal reproductive mode, although no population genetic studies have been conducted so far. Thus, the genetic structure of six C. acutatum populations from sweet orange orchards showing PFD symptoms was determined using nine microsatellite markers, enabling inference on predominant mode of reproduction. C. acutatum populations exhibit a nearly panmictic genetic structure and a high degree of admixture, indicating either ongoing contemporary gene flow at a regional scale or a recent introduction from a common source, since this pathogen was introduced in Brazil only very recently. Sharing haplotypes among orchards separated by 400 km suggests the natural dispersal of fungal propagules, with the possible involvement of pollinators. A significant population expansion was detected, which was consistent with an increase in host density associated with crop expansion toward new areas across the state. Findings of moderate to high levels of haplotypic diversity and gametic equilibrium suggest that recombination might play an important role in these pathogen populations, possibly via parasexual reproduction or a cryptic sexual cycle. This study provides additional tools for epidemiological studies of C. acutatum to improve prevention and management strategies for this disease.

Effect of temperature and colonization of Legionella pneumophila and Vermamoeba vermiformis on bacterial community composition of copper drinking water biofilms.

PubMed

Buse, Helen Y; Ji, Pan; Gomez-Alvarez, Vicente; Pruden, Amy; Edwards, Marc A; Ashbolt, Nicholas J

2017-07-01

It is unclear how the water-based pathogen, Legionella pneumophila (Lp), and associated free-living amoeba (FLA) hosts change or are changed by the microbial composition of drinking water (DW) biofilm communities. Thus, this study characterized the bacterial community structure over a 7-month period within mature (> 600-day-old) copper DW biofilms in reactors simulating premise plumbing and assessed the impact of temperature and introduction of Lp and its FLA host, Vermamoeba vermiformis (Vv), co-cultures (LpVv). Sequence and quantitative PCR (qPCR) analyses indicated a correlation between LpVv introduction and increases in Legionella spp. levels at room temperature (RT), while at 37°C, Lp became the dominant Legionella spp. qPCR analysis suggested Vv presence may not be directly associated with Lp biofilm growth at RT and 37°C, but may contribute to or be associated with non-Lp legionellae persistence at RT. Two-way PERMANOVA and PCoA revealed that temperature was a major driver of microbiome diversity. Biofilm community composition also changed over the seven-month period and could be associated with significant shifts in dissolved oxygen, alkalinity and various metals in the influent DW. Hence, temperature, biofilm age, DW quality and transient intrusions/amplification of pathogens and FLA hosts may significantly impact biofilm microbiomes and modulate pathogen levels over extended periods. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Status of Phytophthora ramorum and P. kernoviae in Europe

Treesearch

Joan F. Webber

2008-01-01

Following the recognition that Phytophthora ramorum (the cause of sudden oak death in the U.S.) was present in Europe as well as America, emergency European Community (EC) phytosanitary measures were put in place in September 2002 to prevent spread of P. ramorum, and also to stop introductions of the pathogen from elsewhere. A 3...

Evaluation of enterohemorrhagic Escherichia coli (EHEC) growth media against six EHEC strains

USDA-ARS?s Scientific Manuscript database

Introduction: Food safety specialists continue to be challenged by the need to determine the presence of pathogenic bacteria in foods. This is especially true for E. coli O157:H7 and emerging EHEC strains. Such EHECs survive well in meat and poultry, and although stressed, can remain viable in dry o...

Zero-valent iron-biosand filtration is capable of reducing antimicrobials and generic E. coli concentrations in unbuffered conventionally-treated reclaimed water: a CONSERVE project

USDA-ARS?s Scientific Manuscript database

Introduction: If conventionally treated reclaimed water (RW) is to be adopted as analternative to freshwater irrigation, it is necessary to investigate reuse site-based mitigation options that can further reduce contaminantssuch as foodborne pathogens andpharmaceuticals and personal care products (P...

Utilization of evolutionary model, bioinformatics and heuristics for development of a multiplex Escherichia coli O157:H7 PCR assay

USDA-ARS?s Scientific Manuscript database

Introduction: Escherichia coli O157:H7 is a devastating foodborne pathogen causing many foodborne outbreaks worldwide with significant morbidity and mortality. The plasticity of the E. coli O157:H7 genome, inconsistent expression of surface antigens, and sharing of genetic elements with other non-...

Recovery of Escherichia coli O157:H7 by immunomagnetic separation techniques and potential for regrowth in finished composts

USDA-ARS?s Scientific Manuscript database

Introduction: Mature, finished compost made from various feedstocks should undergo testing for the presence of Escherichia coli O157:H7 to ensure thermal destruction of the pathogen during composting. Immunomagnetic separation (IMS) –based methods may provide an assay which can be conducted within...

Phytophthora ramorum: update On the impact and wider consequences of the epidemic in Britain

Treesearch

J.F. Webber

2017-01-01

Many new Phytophthora pathogens have arrived in the UK via the plant trade in recent decades, but arguably Phytophthora ramorum has been one of the most significant introductions to affect trees. From 2002 onwards during the early stages of the epidemic, the first impacts of P. ramorum were seen in...

Loss of foundation species: consequences for the structure and dynamics of forested ecosystems

Treesearch

Aaron M. Ellison; Michael S. Bank; Barton D. Clinton; Elizabeth A. Colburn; Katherine Elliott; Chelcy Rae Ford; David R. Foster; Brian D. Kloeppel; Jennifer D. Knoepp; Gary M. Lovett; Jacqueline Mohan; David A. Orwig; Nicholas L. Rodenhouse; William V. Sobczak; Kristina A. Stinson; Jeffrey K. Stone; Christopher M. Swan; Jill Thompson; Betsy Von Holle; Jackson R. Webster

2005-01-01

In many forested ecosystems, the architecture and functional ecology of certain tree species define forest structure and their species-specific traits control ecosystem dynamics. Such foundation tree species are declining throughout the world due to introductions and outbreaks of pests and pathogens, selective removal of individual taxa, and over-harvesting. Through a...

Analysis of transporter responsible for the secretion of fusaric acid from the plant pathogen Fusarium oxysporum f. sp. vasinfectum

USDA-ARS?s Scientific Manuscript database

Fusaric acid (FA), a phytotoxic polyketide produced by Fusarium oxysporum f. sp. vasinfectum (Fov), has been suggested to be associated with disease symptoms on cotton. In response to a potential threat on cotton production by the introduction of high FA producing strains from Australia, new sources...

Prevalence of E. coli, Salmonella spp. and L. monocytogenes in non-traditional irrigation waters in the Mid-Atlantic U.S.: a conserve project

USDA-ARS?s Scientific Manuscript database

Introduction: Surface and non-traditional irrigation water (SNIW) sources can increase the irrigation water supplies without consuming potable water. However, these sources must be evaluated for enteric pathogens that could adulterate crops intended for human consumption and comply with Food Safety ...

Combining field observations and genetic data to reconstruct the invasion of Phytophthora ramorum in California

Treesearch

Peter J.P. Croucher; Silvia Mascheretti; Matteo Garbelotto

2013-01-01

Although it has been convincingly shown that forest populations of the pathogen Phytophthora ramorum have undergone a significant bottleneck and reproduce exclusively asexually (Ivors et al. 2004, 2006; Mascheretti et al. 2008), objective results showing that nurseries were the original source of the introduction remain elusive (Mascheretti et al....

Inactivation of E. coli O157:H7 and nonpathogenic E. coli in strawberry juice by pulsed electric field, sodium benzoate, potassium sorbate, and citric acid

USDA-ARS?s Scientific Manuscript database

Introduction: Current regulations require that juice processors effect a 5 log CFU/ml reduction of a target pathogen prior to distributing products. Whereas thermal pasteurization reduces the sensory characteristics of juice by altering flavor components, pulsed electric field (PEF) treatment may ...

Translational errors in expression of Shiga toxin from pathogenic Escherichia coli as measured by MALDI-TOF-TOF and Orbitrap mass spectrometry

USDA-ARS?s Scientific Manuscript database

Introduction: Shiga toxin (Stx) is an AB5 toxin expressed by Shiga toxin-producing E. coli (STEC) and Shigella dysenteriae. The Stx holotoxin attaches to surface receptors of eukaryotic cells. After cellular envelopment, the toxin disrupts ribosomal protein synthesis causing cell death. Variations i...

Antimicrobial synergy of apple skin polyphenol and thyme essential oil in Açaí edible films and their effects on film properties (abstract)

USDA-ARS?s Scientific Manuscript database

Introduction: Diseases caused by food borne pathogens are of great concern to the food industry. The consumption of foods with chemical preservatives has led to increased consumer concern and demand for natural and minimally processed foods. In addition, environmental concerns are generated from cur...

Informing pest prevention efforts through Sentinel Plant Monitoring

Treesearch

2010-01-01

Botanic gardens with international collections provide a unique opportunity to help detect potential invasive threats to forest health. Nursery stock is well-recognized as a major pathway for the introduction of invasive insects and pathogens to native ecosystems. Plant health regulators need help knowing what pests attack host plants abroad so they can develop ways to...

Effectiveness of Sanitizer D7(TM) against Escherichia coli O157:H7 and Salmonella biofilms

USDA-ARS?s Scientific Manuscript database

Introduction: Biofilm formation by E. coli O157:H7 and Salmonella enterica at meat processing plants poses a serious risk of meat product contamination. Available studies have shown that many common sanitizers were unable to completely eradicate biofilms by these foodborne pathogens due to the 3-dim...

Spatial estimation of the density and carbon content of host populations for Phytophthora ramorum in California and Oregon

Treesearch

Sanjay Lamsal; Richard C. Cobb; J. Hall Cushman; Qingmin Meng; David M. Rizzo; Ross K. Meentemeyer.

2011-01-01

Outbreak of the emerging infectious disease sudden oak death continues to threaten California and Oregon forests following introduction of the exotic plant pathogen Phytophthora ramorum. Identifying areas at risk and forecasting changes in forest carbon following disease outbreak requires an understanding of the geographical distribution of host...

Microbial population analysis of broilers in different flock and embryonic ages from GI, yolk and egg wash via Illumina MiSeq and QIIME pipeline (abstract)

USDA-ARS?s Scientific Manuscript database

There are several food-safety issues related to broiler egg production, including the introduction/proliferation of zoonotic pathogens during embryonic gastrointestinal (GI) tract development. Little is known about the overall GI bacterial communities, how they change over time, or how their composi...

Invasive forest pests: trends and impacts

Treesearch

Deborah G. McCullough

2011-01-01

Non-native forest insects and pathogens affect a variety of forest and urban settings across the U.S., and introductions are likely to continue as global trade and travel expand. Past efforts to assess economic impacts of invasive forest pests have been useful for bringing attention to the issue, but a broad, rigorous cost analysis is critically needed by policymakers...

Modeling Fate and Transport of Rotavirus in Surface Flow by Integrating WEPP and a Pathogen Transport Model

NASA Astrophysics Data System (ADS)

Bhattarai, R.; Kalita, P. K.; Davidson, P. C.; Kuhlenschmidt, M. S.

2012-12-01

More than 3.5 million people die each year from a water related diseases in this world. Every 20 seconds, a child dies from a water-related illness. Even in a developed country like the United States, there have been at least 1870 outbreaks associated with drinking water during the period of 1920 to 2002, causing 883,806 illnesses. Most of these outbreaks are resulted due to the presence of microbial pathogens in drinking water. Rotavirus infection has been recognized as the most common cause of diarrhea in young children throughout the world. Laboratory experiments conducted at the University of Illinois have demonstrated that recovery of rotavirus has been significantly affected by climatic and soil-surface conditions like slope, soil types, and ground cover. The objective of this study is to simulate the fate and transport of Rotavirus in overland and near-surface flow using a process-based model. In order to capture the dynamics of sediment-bound pathogens, the Water Erosion Prediction Project (WEPP) is coupled with the pathogen transport model. Transport of pathogens in overland flow can be simulated mathematically by including terms for the concentration of the pathogens in the liquid phase (in suspension or free-floating) and the solid phase (adsorbed to the fine solid particles like clay and silt). Advection, adsorption, and decay processes are considered. The mass balance equations are solved using numerical technique to predict spatial and temporal changes in pathogen concentrations in two phases. Outputs from WEPP simulations (flow velocity, depth, saturated conductivity and the soil particle fraction exiting in flow) are transferred as input for the pathogen transport model. Three soil types and three different surface cover conditions have been used in the experimental investigations. Results from these conditions have been used in calibrating and validating the simulation results. Bare surface conditions have produced very good agreement between observed and predicted results; however, transport of pathogens from vegetated surface has been challenging. This paper will provide concepts of the pathogen transport model, integration with WEPP, and results obtained from the modeling framework.

Free-living pathogens: life-history constraints and strain competition

PubMed Central

Caraco, Thomas; Wang, Ing-Nang

2008-01-01

Many pathogen life histories include a free-living stage, often with anatomical and physiological adaptations promoting persistence outside of host tissues. More durable particles presumably require that the pathogen metabolize more resources per particle. Therefore, we hypothesize functional dependencies, pleiotropic constraints, between the rate at which free-living particles decay outside of host tissues and other pathogen traits, including virulence, the probability of infecting a host upon contact, and pathogen reproduction within host tissues. Assuming that pathogen strains compete for hosts preemptively, we find patterns in trait dependencies predicting whether or not strain competition favors a highly persistent free-living stage. PMID:18062992

First detection of bat white-nose syndrome in western North America

USGS Publications Warehouse

Lorch, Jeffrey M.; Palmer, Jonathan M.; Lindner, Daniel L.; Ballmann, Anne; George, Kyle; Griffin, Kathryn M.; Knowles, Susan N.; Huckabee, John R.; Haman, Katherine H.; Anderson, Christopher D.; Becker, Penny A.; Buchanan, Joseph B.; Foster, Jeffrey T.; Blehert, David

2016-01-01

White-nose syndrome (WNS) is an emerging fungal disease of bats caused by Pseudogymnoascus destructans. Since it was first detected near Albany, NY, in 2006, the fungus has spread across eastern North America, killing unprecedented numbers of hibernating bats. The devastating impacts of WNS on Nearctic bat species are attributed to the likely introduction of P. destructans from Eurasia to naive host populations in eastern North America. Since 2006, the disease has spread in a gradual wavelike pattern consistent with introduction of the pathogen at a single location. Here, we describe the first detection of P. destructans in western North America in a little brown bat (Myotis lucifugus) from near Seattle, WA, far from the previously recognized geographic distribution of the fungus. Whole-genome sequencing and phylogenetic analyses indicated that the isolate of P. destructans from Washington grouped with other isolates of a presumed clonal lineage from the eastern United States. Thus, the occurrence of P. destructans in Washington does not likely represent a novel introduction of the fungus from Eurasia, and the lack of intensive surveillance in the western United States makes it difficult to interpret whether the occurrence of P. destructans in the Pacific Northwest is disjunct from that in eastern North America. Although there is uncertainty surrounding the impacts of WNS in the Pacific Northwest, the presence of the pathogen in western North America could have major consequences for bat conservation.

Phylogenetics of a fungal invasion: Origins and widespread dispersal of white-nose syndrome

USGS Publications Warehouse

Drees, Kevin P.; Lorch, Jeffrey M.; Puechmaille, Sebastein J.; Parise, Katy L.; Wibbelt, Gudrun; Hoyt, Joseph R.; Sun, Keping; Jargalsaikhan, Ariunbold; Dalannast, Munkhnast; Palmer, Jonathan M.; Linder, Daniel L.; Kilpatrick, Marm; Pearson, Talima; Keim, Paul S.; Blehert, David; Foster, Jeffrey T.

2017-01-01

Globalization has facilitated the worldwide movement and introduction of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans, a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has exhibited few genetic polymorphisms in previous studies, presenting challenges for both epizoological tracking of the spread of this fungus and for determining its evolutionary history. We used single nucleotide polymorphisms (SNPs) from whole-genome sequencing and microsatellites to construct high-resolution phylogenies of P. destructans. Shallow genetic diversity and the lack of geographic structuring among North American isolates support a recent introduction followed by expansion via clonal reproduction across the epizootic zone. Moreover, the genetic relationships of isolates within North America suggest widespread mixing and long-distance movement of the fungus. Genetic diversity among isolates of P. destructans from Europe was substantially higher than in those from North America. However, genetic distance between the North American isolates and any given European isolate was similar to the distance between the individual European isolates. In contrast, the isolates we examined from Asia were highly divergent from both European and North American isolates. Although the definitive source for introduction of the North American population has not been conclusively identified, our data support the origin of the North American invasion by P. destructans from Europe rather than Asia.

Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome

PubMed Central

Drees, Kevin P.; Lorch, Jeffrey M.; Puechmaille, Sebastien J.; Parise, Katy L.; Wibbelt, Gudrun; Hoyt, Joseph R.; Sun, Keping; Jargalsaikhan, Ariunbold; Dalannast, Munkhnast; Lindner, Daniel L.; Marm Kilpatrick, A.; Pearson, Talima; Blehert, David S.

2017-01-01

ABSTRACT Globalization has facilitated the worldwide movement and introduction of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans, a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has exhibited few genetic polymorphisms in previous studies, presenting challenges for both epizoological tracking of the spread of this fungus and for determining its evolutionary history. We used single nucleotide polymorphisms (SNPs) from whole-genome sequencing and microsatellites to construct high-resolution phylogenies of P. destructans. Shallow genetic diversity and the lack of geographic structuring among North American isolates support a recent introduction followed by expansion via clonal reproduction across the epizootic zone. Moreover, the genetic relationships of isolates within North America suggest widespread mixing and long-distance movement of the fungus. Genetic diversity among isolates of P. destructans from Europe was substantially higher than in those from North America. However, genetic distance between the North American isolates and any given European isolate was similar to the distance between the individual European isolates. In contrast, the isolates we examined from Asia were highly divergent from both European and North American isolates. Although the definitive source for introduction of the North American population has not been conclusively identified, our data support the origin of the North American invasion by P. destructans from Europe rather than Asia. PMID:29233897

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.

PubMed

Ioannidis, Nilah M; Rothstein, Joseph H; Pejaver, Vikas; Middha, Sumit; McDonnell, Shannon K; Baheti, Saurabh; Musolf, Anthony; Li, Qing; Holzinger, Emily; Karyadi, Danielle; Cannon-Albright, Lisa A; Teerlink, Craig C; Stanford, Janet L; Isaacs, William B; Xu, Jianfeng; Cooney, Kathleen A; Lange, Ethan M; Schleutker, Johanna; Carpten, John D; Powell, Isaac J; Cussenot, Olivier; Cancel-Tassin, Geraldine; Giles, Graham G; MacInnis, Robert J; Maier, Christiane; Hsieh, Chih-Lin; Wiklund, Fredrik; Catalona, William J; Foulkes, William D; Mandal, Diptasri; Eeles, Rosalind A; Kote-Jarai, Zsofia; Bustamante, Carlos D; Schaid, Daniel J; Hastie, Trevor; Ostrander, Elaine A; Bailey-Wilson, Joan E; Radivojac, Predrag; Thibodeau, Stephen N; Whittemore, Alice S; Sieh, Weiva

2016-10-06

The vast majority of coding variants are rare, and assessment of the contribution of rare variants to complex traits is hampered by low statistical power and limited functional data. Improved methods for predicting the pathogenicity of rare coding variants are needed to facilitate the discovery of disease variants from exome sequencing studies. We developed REVEL (rare exome variant ensemble learner), an ensemble method for predicting the pathogenicity of missense variants on the basis of individual tools: MutPred, FATHMM, VEST, PolyPhen, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP, SiPhy, phyloP, and phastCons. REVEL was trained with recently discovered pathogenic and rare neutral missense variants, excluding those previously used to train its constituent tools. When applied to two independent test sets, REVEL had the best overall performance (p < 10 -12 ) as compared to any individual tool and seven ensemble methods: MetaSVM, MetaLR, KGGSeq, Condel, CADD, DANN, and Eigen. Importantly, REVEL also had the best performance for distinguishing pathogenic from rare neutral variants with allele frequencies <0.5%. The area under the receiver operating characteristic curve (AUC) for REVEL was 0.046-0.182 higher in an independent test set of 935 recent SwissVar disease variants and 123,935 putatively neutral exome sequencing variants and 0.027-0.143 higher in an independent test set of 1,953 pathogenic and 2,406 benign variants recently reported in ClinVar than the AUCs for other ensemble methods. We provide pre-computed REVEL scores for all possible human missense variants to facilitate the identification of pathogenic variants in the sea of rare variants discovered as sequencing studies expand in scale. Copyright © 2016 American Society of Human Genetics. All rights reserved.

Meta-analysis diagnostic accuracy of SNP-based pathogenicity detection tools: a case of UTG1A1 gene mutations.

PubMed

Galehdari, Hamid; Saki, Najmaldin; Mohammadi-Asl, Javad; Rahim, Fakher

2013-01-01

Crigler-Najjar syndrome (CNS) type I and type II are usually inherited as autosomal recessive conditions that result from mutations in the UGT1A1 gene. The main objective of the present review is to summarize results of all available evidence on the accuracy of SNP-based pathogenicity detection tools compared to published clinical result for the prediction of in nsSNPs that leads to disease using prediction performance method. A comprehensive search was performed to find all mutations related to CNS. Database searches included dbSNP, SNPdbe, HGMD, Swissvar, ensemble, and OMIM. All the mutation related to CNS was extracted. The pathogenicity prediction was done using SNP-based pathogenicity detection tools include SIFT, PHD-SNP, PolyPhen2, fathmm, Provean, and Mutpred. Overall, 59 different SNPs related to missense mutations in the UGT1A1 gene, were reviewed. Comparing the diagnostic OR, PolyPhen2 and Mutpred have the highest detection 4.983 (95% CI: 1.24 - 20.02) in both, following by SIFT (diagnostic OR: 3.25, 95% CI: 1.07 - 9.83). The highest MCC of SNP-based pathogenicity detection tools, was belong to SIFT (34.19%) followed by Provean, PolyPhen2, and Mutpred (29.99%, 29.89%, and 29.89%, respectively). Hence the highest SNP-based pathogenicity detection tools ACC, was fit to SIFT (62.71%) followed by PolyPhen2, and Mutpred (61.02%, in both). Our results suggest that some of the well-established SNP-based pathogenicity detection tools can appropriately reflect the role of a disease-associated SNP in both local and global structures.

Validity of the Indicator Organism Paradigm for Pathogen Reduction in Reclaimed Water and Public Health Protection†

PubMed Central

Harwood, Valerie J.; Levine, Audrey D.; Scott, Troy M.; Chivukula, Vasanta; Lukasik, Jerzy; Farrah, Samuel R.; Rose, Joan B.

2005-01-01

The validity of using indicator organisms (total and fecal coliforms, enterococci, Clostridium perfringens, and F-specific coliphages) to predict the presence or absence of pathogens (infectious enteric viruses, Cryptosporidium, and Giardia) was tested at six wastewater reclamation facilities. Multiple samplings conducted at each facility over a 1-year period. Larger sample volumes for indicators (0.2 to 0.4 liters) and pathogens (30 to 100 liters) resulted in more sensitive detection limits than are typical of routine monitoring. Microorganisms were detected in disinfected effluent samples at the following frequencies: total coliforms, 63%; fecal coliforms, 27%; enterococci, 27%; C. perfringens, 61%; F-specific coliphages, ∼40%; and enteric viruses, 31%. Cryptosporidium oocysts and Giardia cysts were detected in 70% and 80%, respectively, of reclaimed water samples. Viable Cryptosporidium, based on cell culture infectivity assays, was detected in 20% of the reclaimed water samples. No strong correlation was found for any indicator-pathogen combination. When data for all indicators were tested using discriminant analysis, the presence/absence patterns for Giardia cysts, Cryptosporidium oocysts, infectious Cryptosporidium, and infectious enteric viruses were predicted for over 71% of disinfected effluents. The failure of measurements of single indicator organism to correlate with pathogens suggests that public health is not adequately protected by simple monitoring schemes based on detection of a single indicator, particularly at the detection limits routinely employed. Monitoring a suite of indicator organisms in reclaimed effluent is more likely to be predictive of the presence of certain pathogens, and a need for additional pathogen monitoring in reclaimed water in order to protect public health is suggested by this study. PMID:15933017

Report of two paediatric cases of central line infections caused by species of the genus Kocuria

PubMed Central

Hamula, Camille L.; Dingle, Tanis C.

2016-01-01

Introduction: Species of the genus Kocuria are Gram-positive cocci of the family Micrococcacceae that are ubiquitous in the environment and part of the normal skin and oral flora in humans. A paucity of cases have been reported of Kocuria as human pathogens and there are currently no evidence-based guidelines for managing these uncommon infections. Case presentation: We present two paediatric cases of central line infections with species of the genus Kocuria that required line removal despite antimicrobial therapy. Conclusion: Species of the genus Kocuria are uncommon human pathogens that have rarely been reported to cause opportunistic infections in both adult and paediatric populations. The cases presented here add to the growing body of literature documenting the pathogenicity of these organisms and the possible need for line removal to achieve clinical cure in central line-associated bacteraemia caused by species of the genus Kocuria. PMID:28348760

Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management

PubMed Central

Thomas, William J; Gordon, Michael I; Stevens, Danielle M; Creason, Allison L; Belcher, Michael S; Serdani, Maryna; Wiseman, Michele S; Grünwald, Niklaus J; Putnam, Melodie L

2017-01-01

Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses. PMID:29231813

Nasal, oral and rectal microbiota of Black lion tamarins (Leontopithecus chrysopygus)

PubMed Central

Carvalho, Vania M.; Vanstreels, Ralph E.T.; Paula, Cátia D.; Kolesnikovas, Cristiane K.M.; Ramos, Maria Christina C.; Coutinho, Selene D.; Martins, Cristiana S.; Pissinatti, Alcides; Catão-Dias, José L.

2014-01-01

Black lion tamarins (Leontopithecus chrysopygus) are endangered callithrichids. Their conservation may require future translocations or reintroductions; however these approaches involve risks of pathogen introduction in the environment and stress-related opportunistic infections in these animals. In order to screen for opportunistic and potential pathogenic bacterial and fungal microbiota, ten free-ranging and ten captive Black lion tamarins were studied and the results compared. Nasal, oral and rectal swabs were collected and cultured for aerobic and facultative anaerobic bacteria and fungi, and a total 203 bacterial and 84 fungal isolates were obtained. Overall, the most frequent organisms were Staphylococcus spp., Bacillus spp., Candida spp. and Aspergillus spp. Microbiota of free-ranging and captive animals were similar in composition. A number of potentially pathogenic organisms were identified, emphasizing the importance of microbiological screening in future translocation or reintroduction conservation management programs. PMID:25763064

Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management.

PubMed

Savory, Elizabeth A; Fuller, Skylar L; Weisberg, Alexandra J; Thomas, William J; Gordon, Michael I; Stevens, Danielle M; Creason, Allison L; Belcher, Michael S; Serdani, Maryna; Wiseman, Michele S; Grünwald, Niklaus J; Putnam, Melodie L; Chang, Jeff H

2017-12-12

Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus , and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses.

[Usefulness of the molecular techniques for detecting and/or identifing of parasites and fungi in humans and animals or pathogens transmitted by ticks (Part I)].

PubMed

Myjak, P; Majewska, A C; Bajer, A; Siński, E; Wedrychowicz, H; Gołab, E; Budak, A; Stańczak, J

2001-01-01

After a long period of using basic microscopic, immunological and biochemical methods for diagnosis, rapid development of nucleic acids investigation enabled introduction of specific and sensitive methods of detection of pathogenic agents on the molecular level. Among others, polymerase chain reaction (PCR), discovered in mid of 80'ies and then automatized, offered an attractive alternative to conventional testing systems. In this paper we describe reliable diagnostic tests widely used in the world, including Poland, and capable of detecting different disease agents as parasites and fungi in clinical specimens and pathogens of emerging zoonotic diseases in ticks. The possibilities of using molecular methods for determination of Plasmodium falciparum drug resistance is also discussed. Moreover, the report offers information concerning kinds of molecular tests and institutions in which there are executed.

Challenges in predicting climate and environmental effects on vector-borne disease episystems in a changing world.

PubMed

Tabachnick, W J

2010-03-15

Vector-borne pathogens cause enormous suffering to humans and animals. Many are expanding their range into new areas. Dengue, West Nile and Chikungunya have recently caused substantial human epidemics. Arthropod-borne animal diseases like Bluetongue, Rift Valley fever and African horse sickness pose substantial threats to livestock economies around the world. Climate change can impact the vector-borne disease epidemiology. Changes in climate will influence arthropod vectors, their life cycles and life histories, resulting in changes in both vector and pathogen distribution and changes in the ability of arthropods to transmit pathogens. Climate can affect the way pathogens interact with both the arthropod vector and the human or animal host. Predicting and mitigating the effects of future changes in the environment like climate change on the complex arthropod-pathogen-host epidemiological cycle requires understanding of a variety of complex mechanisms from the molecular to the population level. Although there has been substantial progress on many fronts the challenges to effectively understand and mitigate the impact of potential changes in the environment on vector-borne pathogens are formidable and at an early stage of development. The challenges will be explored using several arthropod-borne pathogen systems as illustration, and potential avenues to meet the challenges will be presented.

Assessing Seasonal Risks for the Introduction and Mosquito-borne Spread of Zika Virus in Europe.

PubMed

Rocklöv, Joacim; Quam, Mikkel Brandon; Sudre, Bertrand; German, Matthew; Kraemer, Moritz U G; Brady, Oliver; Bogoch, Isaac I; Liu-Helmersson, Jing; Wilder-Smith, Annelies; Semenza, Jan C; Ong, Mark; Aaslav, Kaja Kaasik; Khan, Kamran

2016-07-01

The explosive Zika virus epidemic in the Americas is amplifying spread of this emerging pathogen into previously unaffected regions of the world, including Europe (Gulland, 2016), where local populations are immunologically naïve. As summertime approaches in the northern hemisphere, Aedes mosquitoes in Europe may find suitable climatic conditions to acquire and subsequently transmit Zika virus from viremic travellers to local populations. While Aedes albopictus has proven to be a vector for the transmission of dengue and chikungunya viruses in Europe (Delisle et al., 2015; ECDC, n.d.) there is growing experimental and ecological evidence to suggest that it may also be competent for Zika virus(Chouin-Carneiro et al., 2016; Grard et al., 2014; Li et al., 2012; Wong et al., 2013). Here we analyze and overlay the monthly flows of airline travellers arriving into European cities from Zika affected areas across the Americas, the predicted monthly estimates of the basic reproduction number of Zika virus in areas where Aedes mosquito populations reside in Europe (Aedes aegypti in Madeira, Portugal and Ae. albopictus in continental Europe), and human populations living within areas where mosquito-borne transmission of Zika virus may be possible. We highlight specific geographic areas and timing of risk for Zika virus introduction and possible spread within Europe to inform the efficient use of human disease surveillance, vector surveillance and control, and public education resources. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Host identity matters in the amphibian-Batrachochytrium dendrobatidis system: fine-scale patterns of variation in responses to a multi-host pathogen

Treesearch

Stephanie Gervasi; Carmen Gondhalekar; Deanna H. Olson; Andrew R. Blaustein

2013-01-01

Species composition within ecological assemblages can drive disease dynamics including pathogen invasion, spread, and persistence. In multi-host pathogen systems, interspecific variation in responses to infection creates important context dependency when predicting the outcome of disease. Here, we examine the responses of three sympatric host species to a single fungal...

X-ray requesting patterns before and after introduction of the Ottawa Knee Rules in a UK emergency department.

PubMed

Atkinson, Paul; Boyle, Adrian; Chisholm, Edward

2004-08-01

To compare knee radiology requesting rates among junior doctors before and after the formal introduction of the Ottawa Knee Rules (OKR) in a UK emergency department (ED), and to test the validity of the OKR for decisions on the use of radiography for acute, isolated knee injuries. All junior doctors in a district general hospital ED seeing adult patients with isolated knee injuries completed a questionnaire before and after the introduction of the OKR. All patients were followed up to obtain a final diagnosis. The outcome measures were: adherence to the OKR, the presence of a fracture and whether a radiograph had been requested. The results were analysed to determine the sensitivity, specificity, positive and negative predictive values of the OKR. Comparisons between the request rate for knee radiography before and after the introduction of the OKR were made. A total of 130 patients were enrolled and followed up over a 3-month period; 58 before and 72 after OKR introduction. The OKR had a sensitivity of 100% (71.8-100%), a specificity of 55.1% (46.1-64.1%), a positive predictive value of 18.5% (9.03-27.9%) and a negative predictive value of 100% (87.8-100%) for the detection of bony injury. The introduction of the OKR did not result in a significant reduction in the number of radiographs performed (58.6-55.6%; P= 0.726). This study shows the OKR to be a highly sensitive clinical guide with a high negative predictive value in the setting of a UK ED. It suggests that the reduction in radiograph requests seen elsewhere may not be as apparent in this setting.

Comprehensive splicing functional analysis of DNA variants of the BRCA2 gene by hybrid minigenes

PubMed Central

2012-01-01

Introduction The underlying pathogenic mechanism of a large fraction of DNA variants of disease-causing genes is the disruption of the splicing process. We aimed to investigate the effect on splicing of the BRCA2 variants c.8488-1G > A (exon 20) and c.9026_9030del (exon 23), as well as 41 BRCA2 variants reported in the Breast Cancer Information Core (BIC) mutation database. Methods DNA variants were analyzed with the splicing prediction programs NNSPLICE and Human Splicing Finder. Functional analyses of candidate variants were performed by lymphocyte RT-PCR and/or hybrid minigene assays. Forty-one BIC variants of exons 19, 20, 23 and 24 were bioinformatically selected and generated by PCR-mutagenesis of the wild type minigenes. Results Lymphocyte RT-PCR of c.8488-1G > A showed intron 19 retention and a 12-nucleotide deletion in exon 20, whereas c.9026_9030del did not show any splicing anomaly. Minigene analysis of c.8488-1G > A displayed the aforementioned aberrant isoforms but also exon 20 skipping. We further evaluated the splicing outcomes of 41 variants of four BRCA2 exons by minigene analysis. Eighteen variants presented splicing aberrations. Most variants (78.9%) disrupted the natural splice sites, whereas four altered putative enhancers/silencers and had a weak effect. Fluorescent RT-PCR of minigenes accurately detected 14 RNA isoforms generated by cryptic site usage, exon skipping and intron retention events. Fourteen variants showed total splicing disruptions and were predicted to truncate or eliminate essential domains of BRCA2. Conclusions A relevant proportion of BRCA2 variants are correlated with splicing disruptions, indicating that RNA analysis is a valuable tool to assess the pathogenicity of a particular DNA change. The minigene system is a straightforward and robust approach to detect variants with an impact on splicing and contributes to a better knowledge of this gene expression step. PMID:22632462

Marital infidelity and its effect on pathogen diversity

NASA Astrophysics Data System (ADS)

Berryman, Matthew J.

2007-01-01

Marital infidelity is usually examined solely in terms of strategies of men and women, with an emphasis on the enhanced payoff for male infidelity (provided he can get away with it). What are not clear are the strategies used, in terms of how often to engage in extra-marital affairs. It has been proposed that female strategies are governed by a "decision" to maximize the genetic diversity of her offspring, in order to better guarantee that at least some will survive against a common pathogen. This strategy would then impact on the strategies and diversity of pathogens. I make a number of predictions about both strategies and the genetic diversity of humans and pathogens, couched in game-theoretic terms. These predictions are then compared with the existing evidence on the strategies used by women and also in terms of the genetic diversity of human populations.

Comprehensive analysis of microRNA-Seq and target mRNAs of rice sheath blight pathogen provides new insights into pathogenic regulatory mechanisms.

PubMed

Lin, Runmao; He, Liye; He, Jiayu; Qin, Peigang; Wang, Yanran; Deng, Qiming; Yang, Xiaoting; Li, Shuangcheng; Wang, Shiquan; Wang, Wenming; Liu, Huainian; Li, Ping; Zheng, Aiping

2016-07-03

MicroRNAs (miRNAs) are ∼22 nucleotide non-coding RNAs that regulate gene expression by targeting mRNAs for degradation or inhibiting protein translation. To investigate whether miRNAs regulate the pathogenesis in necrotrophic fungus Rhizoctonia solani AG1 IA, which causes significant yield loss in main economically important crops, and to determine the regulatory mechanism occurring during pathogenesis, we constructed hyphal small RNA libraries from six different infection periods of the rice leaf. Through sequencing and analysis, 177 miRNA-like small RNAs (milRNAs) were identified, including 15 candidate pathogenic novel milRNAs predicted by functional annotations of their target mRNAs and expression patterns of milRNAs and mRNAs during infection. Reverse transcription-quantitative polymerase chain reaction results for randomly selected milRNAs demonstrated that our novel comprehensive predictions had a high level of accuracy. In our predicted pathogenic protein-protein interaction network of R. solani, we added the related regulatory milRNAs of these core coding genes into the network, and could understand the relationships among these regulatory factors more clearly at the systems level. Furthermore, the putative pathogenic Rhi-milR-16, which negatively regulates target gene expression, was experimentally validated to have regulatory functions by a dual-luciferase reporter assay. Additionally, 23 candidate rice miRNAs that may involve in plant immunity against R. solani were discovered. This first study on novel pathogenic milRNAs of R. solani AG1 IA and the recognition of target genes involved in pathogenicity, as well as rice miRNAs, participated in defence against R. solani could provide new insights into revealing the pathogenic mechanisms of the severe rice sheath blight disease. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Antimicrobial activity of fresh garlic juice: An in vitro study

PubMed Central

Yadav, Seema; Trivedi, Niyati A.; Bhatt, Jagat D.

2015-01-01

Introduction: Antimicrobial resistance has been a global concern. Currently, interest has been focused on exploring antimicrobial properties of plants and herbs. One such botanical is Allium sativum (garlic). Aim: To evaluate the antimicrobial activity of fresh juice of garlic. Materials and Methods: Varying concentrations of fresh garlic juice (FGJ) were tested for their antimicrobial activity against common pathogenic organisms isolated at SSG Hospital, Vadodara, using well diffusion method. Moreover, minimum inhibitory concentration (MIC) and minimum lethal concentration (MLC) of FGJ were tested using broth dilution method. Sensitivity pattern of the conventional antimicrobials against common pathogenic bacteria was tested using disc diffusion method. Results: FGJ produced dose-dependent increase in the zone of inhibition at a concentration of 10% and higher. MIC of FGJ against the pathogens ranged from 4% to 16% v/v whereas MLC value ranged from 4% to 32% v/v with Escherichia coli and Staphylococcus aureus spp. showed highest sensitivity. Conclusion: FGJ has definite antimicrobial activity against common pathogenic organisms isolated at SSG Hospital, Vadodara. Further studies are needed to find out the efficacy, safety, and kinetic data of its active ingredients. PMID:27011724

[A METHOD FOR DIFFERENTIATION OF BACILLUS ANTHRACIS STRAINS AND PHYLOGENETICALLY RELATED SPECIES BASED ON DETERMINATION OF THE STRUCTURAL DIFFERENCESBETWEEN CHROMOSOMAL GENES FOR BIOSYNTHESIS OF FLAGELLIN AND METHIONINE].

PubMed

Mikshis, N I; Kashtanova, T N; Kutyrev, V V

2015-01-01

Nucleotide sequence analysis of several genes responsible for the anthrax pathogen definitive properties--motility and penicillinase activity--determined a chromosomal locus promising for interspecies differentiation. We demonstrated that the gene fliC encoding flagellin synthesis contains extended region, distinguishing B. anthracis strains from the majority of non-pathogenic and opportunistic bacilli. A novel method for the anthrax pathogen indication and identification based on determination of the differences in the chromosomal genes fliC and hom2 structure was suggested. A total of 60 strains of different Bacillus spp. (B. anthracis, B. cereus, B. thuringiensis, B. mycoides, B. megaterium, B. subtilis, etc.) were tested using two chromosomal DNA targets. The algorithm developed in this work permits to detect the pathogenic microorganism and reliably differentiate it from other Bacillus spp. representatives. The introduction of primers complementary to specific sequences of pXO1 and pXQ2 plasmids into the multiplex PCR makes it possible to receive additional information on proposed virulence of the isolate.

Assessment of bacterial diversity in Hyalomma aegyptium, H. marginatum and H. excavatum ticks through tag-encoded pyrosequencing.

PubMed

Keskin, Adem; Bursali, Ahmet; Snow, David E; Dowd, Scot E; Tekin, Saban

2017-12-01

Ticks are among the most significant human-biting ectoparasites and they play a major role in transmission of many pathogenic agents to humans. In the present study, three species of Hyalomma ticks, Hyalomma aegyptium, H. marginatum and H. excavatum, were examined for the presence of zoonotic bacteria, both male and female ticks alike. Examination of microbial diversity with tag-encoded pyrosequencing indicates that H. marginatum and H. excavatum were more diversity rich than H. aegyptium. Although numerous pathogenic and non-pathogenic bacterial genera were detected, including Acidovorax, Bacillus, Bacteroides, Bdellovibrio, Clostridium, Curvibacter, Escherichia, Flavobacterium, Limnohabitans, Paenibacillus, Ralstonia, Sarcina, Sediminibacterium, Segetibacter Stenotrophomonas and Variovorax, the predominant zoonotic bacteria represented in these ticks were genera Borrelia, Francisella, and Rickettsia. To the authors' knowledge, this work represents the first detection of Yersinia enterocolitica in the tick H. excavatum, raising questions regarding the vector competency of this tick, as well as associations of different disease representations perhaps through previously unforeseen routes of pathogen introduction. Likewise, similar questions are related to the presence of Legionella pneumophila in one H. excavatum sample.

Modeling the intracellular pathogen-immune interaction with cure rate

NASA Astrophysics Data System (ADS)

Dubey, Balram; Dubey, Preeti; Dubey, Uma S.

2016-09-01

Many common and emergent infectious diseases like Influenza, SARS, Hepatitis, Ebola etc. are caused by viral pathogens. These infections can be controlled or prevented by understanding the dynamics of pathogen-immune interaction in vivo. In this paper, interaction of pathogens with uninfected and infected cells in presence or absence of immune response are considered in four different cases. In the first case, the model considers the saturated nonlinear infection rate and linear cure rate without absorption of pathogens into uninfected cells and without immune response. The next model considers the effect of absorption of pathogens into uninfected cells while all other terms are same as in the first case. The third model incorporates innate immune response, humoral immune response and Cytotoxic T lymphocytes (CTL) mediated immune response with cure rate and without absorption of pathogens into uninfected cells. The last model is an extension of the third model in which the effect of absorption of pathogens into uninfected cells has been considered. Positivity and boundedness of solutions are established to ensure the well-posedness of the problem. It has been found that all the four models have two equilibria, namely, pathogen-free equilibrium point and pathogen-present equilibrium point. In each case, stability analysis of each equilibrium point is investigated. Pathogen-free equilibrium is globally asymptotically stable when basic reproduction number is less or equal to unity. This implies that control or prevention of infection is independent of initial concentration of uninfected cells, infected cells, pathogens and immune responses in the body. The proposed models show that introduction of immune response and cure rate strongly affects the stability behavior of the system. Further, on computing basic reproduction number, it has been found to be minimum for the fourth model vis-a-vis other models. The analytical findings of each model have been exemplified by numerical simulations.

Pneumonia in bighorn sheep: Risk and resilience

USGS Publications Warehouse

Cassirer, E. Frances; Manlove, Kezia R.; Almberg, Emily S.; Kamath, Pauline; Cox, Mike; Wolff, Peregrine L.; Roug, Annette; Shannon, Justin M.; Robinson, Rusty; Harris, Richard B.; Gonzales, Ben J.; Plowright, Raina K.; Hudson, Peter J.; Cross, Paul C.; Dobson, Andrew; Besser, Thomas E.

2018-01-01

Infectious disease was an important driver of historic declines and extirpations of bighorn sheep (Ovis canadensis) in North America and continues to impede population restoration and management. Domestic sheep have long been linked to pneumonia outbreaks in bighorn sheep and this association has now been confirmed in 13 captive commingling experiments. However, ecological and etiological complexities still hinder our understanding and control of the disease. We provide an overview of the current state of knowledge about the biology and management of respiratory disease in bighorn sheep and propose strategies for moving forward. Epizootic pneumonia in bighorn sheep is polymicrobial. Mycoplasma ovipneumoniae, a bacterium host-specific to Caprinae and commonly carried by healthy domestic sheep and goats appears to be a necessary primary agent. All-age epizootics following introduction of M. ovipneumoniae along with other pathogens into bighorn sheep populations are usually severe (median mortality 47%) but fatality rates vary widely, from 15 – 100%. Disease severity may be influenced by the strain of M. ovipneumoniae, by secondary bacterial and viral pathogens, and by factors affecting transmission and host immunity. Once introduced, M. ovipneumoniae can persist in bighorn sheep populations for decades. Carrier dams transmit the pathogen to their susceptible lambs, triggering fatal pneumonia outbreaks in nursery groups, which limits recruitment and slows or prevents population recovery. The result is that demographic costs of pathogen persistence often outweigh the impacts of the initial invasion and die-off. There is currently no effective vaccine or antibiotic for domestic or wild sheep and to date, no management actions have been successful in reducing morbidity, mortality, or disease spread once pathogen invasion has occurred. Molecular-based strain typing suggests that spillover of M. ovipneumoniae into bighorn sheep populations from domestic small ruminants is ongoing, and that consequences of pathogen invasion are amplified by movements of infected bighorn sheep. Therefore, current disease management strategies focus on reducing risk of spillover from reservoir populations of domestic small ruminants and on limiting transmission among bighorn sheep. A broad array of approaches has been tried and more are needed to prevent pathogen introduction, induce disease fadeout in persistently infected populations, and promote population resilience across the diverse landscapes bighorn sheep inhabit. A comprehensive examination of disease dynamics across populations could help elucidate how disease fades out naturally and if population resilience can be increased in the face of infection. Cross-jurisdictional adaptive management experiments and transdisciplinary collaboration, including partnerships with members of the domestic sheep and goat community, are needed to facilitate innovation and speed progress towards sustainable solutions for managing pneumonia to protect and restore bighorn sheep populations.

Prediction of BRCA1 and BRCA2 mutation status using post-irradiation assays of lymphoblastoid cell lines is compromised by inter-cell-line phenotypic variability.

PubMed

Lovelock, Paul K; Wong, Ee Ming; Sprung, Carl N; Marsh, Anna; Hobson, Karen; French, Juliet D; Southey, Melissa; Sculley, Tom; Pandeya, Nirmala; Brown, Melissa A; Chenevix-Trench, Georgia; Spurdle, Amanda B; McKay, Michael J

2007-09-01

Assays to determine the pathogenicity of unclassified sequence variants in disease-associated genes include the analysis of lymphoblastoid cell lines (LCLs). We assessed the ability of several assays of LCLs to distinguish carriers of germline BRCA1 and BRCA2 gene mutations from mutation-negative controls to determine their utility for use in a diagnostic setting. Post-ionising radiation cell viability and micronucleus formation, and telomere length were assayed in LCLs carrying BRCA1 or BRCA2 mutations, and in unaffected mutation-negative controls. Post-irradiation cell viability and micronucleus induction assays of LCLs from individuals carrying pathogenic BRCA1 mutations, unclassified BRCA1 sequence variants or wildtype BRCA1 sequence showed significant phenotypic heterogeneity within each group. Responses were not consistent with predicted functional consequences of known pathogenic or normal sequences. Telomere length was also highly heterogeneous within groups of LCLs carrying pathogenic BRCA1 or BRCA2 mutations, and normal BRCA1 sequences, and was not predictive of mutation status. Given the significant degree of phenotypic heterogeneity of LCLs after gamma-irradiation, and the lack of association with BRCA1 or BRCA2 mutation status, we conclude that the assays evaluated in this study should not be used as a means of differentiating pathogenic and non-pathogenic sequence variants for clinical application. We suggest that a range of normal controls must be included in any functional assays of LCLs to ensure that any observed differences between samples reflect the genotype under investigation rather than generic inter-individual variation.

General introduction into the Ebola virus biology and disease.

PubMed

Zawilińska, Barbara; Kosz-Vnenchak, Magdalena

2014-01-01

Epidemic of Ebola hemorrhagic fever which appeared in the countries of West Africa in 2014, is the largest outbreak which occurred so far. The virus causing this epidemic, Zaire Ebolavirus (ZEBOV), along with four other species of Ebolaviruses is classified to the genus Ebolavirus in the family Filoviridae. ZEBOV is one of the most virulent pathogens among the viral haemorrhagic fevers, and case fatality rates up to 90% have been reported. Mortality is the result of multi-organ failure and severe bleeding complications. The aim of this review is to present the general characteristics of the virus and its biological properties, pathogenicity and epidemiology, with a focus on laboratory methods used in the diagnosis of these infections.

Ebolavirus: An Overview of Molecular and Clinical Pathogenesis.

PubMed

Vine, Veronica; Scott, Dana P; Feldmann, Heinz

2017-01-01

Ebolaviruses cause severe, often fatal hemorrhagic fever in Central, East, and West Africa. Until recently, they have been viewed as rare but highly pathogenic infections with regional, but limited, global public health impact. This view has changed with the emergence of the first epidemic of Ebola hemorrhagic fever in West Africa. In this chapter we provide an introduction of the pathogenesis of ebolaviruses as well as a description of clinical disease features. We also describe the current animal models used in ebolavirus research, detailing each model's unique strengths and weaknesses. We focus on Ebola virus representing the type species Zaire ebolavirus of the genus Ebolavirus, as most work relates to this pathogen.

MP3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data.

PubMed

Gupta, Ankit; Kapil, Rohan; Dhakan, Darshan B; Sharma, Vineet K

2014-01-01

The identification of virulent proteins in any de-novo sequenced genome is useful in estimating its pathogenic ability and understanding the mechanism of pathogenesis. Similarly, the identification of such proteins could be valuable in comparing the metagenome of healthy and diseased individuals and estimating the proportion of pathogenic species. However, the common challenge in both the above tasks is the identification of virulent proteins since a significant proportion of genomic and metagenomic proteins are novel and yet unannotated. The currently available tools which carry out the identification of virulent proteins provide limited accuracy and cannot be used on large datasets. Therefore, we have developed an MP3 standalone tool and web server for the prediction of pathogenic proteins in both genomic and metagenomic datasets. MP3 is developed using an integrated Support Vector Machine (SVM) and Hidden Markov Model (HMM) approach to carry out highly fast, sensitive and accurate prediction of pathogenic proteins. It displayed Sensitivity, Specificity, MCC and accuracy values of 92%, 100%, 0.92 and 96%, respectively, on blind dataset constructed using complete proteins. On the two metagenomic blind datasets (Blind A: 51-100 amino acids and Blind B: 30-50 amino acids), it displayed Sensitivity, Specificity, MCC and accuracy values of 82.39%, 97.86%, 0.80 and 89.32% for Blind A and 71.60%, 94.48%, 0.67 and 81.86% for Blind B, respectively. In addition, the performance of MP3 was validated on selected bacterial genomic and real metagenomic datasets. To our knowledge, MP3 is the only program that specializes in fast and accurate identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs exceptionally well on complete protein sequences. MP3 is publicly available at http://metagenomics.iiserb.ac.in/mp3/index.php.

MP3: A Software Tool for the Prediction of Pathogenic Proteins in Genomic and Metagenomic Data

PubMed Central

Gupta, Ankit; Kapil, Rohan; Dhakan, Darshan B.; Sharma, Vineet K.

2014-01-01

The identification of virulent proteins in any de-novo sequenced genome is useful in estimating its pathogenic ability and understanding the mechanism of pathogenesis. Similarly, the identification of such proteins could be valuable in comparing the metagenome of healthy and diseased individuals and estimating the proportion of pathogenic species. However, the common challenge in both the above tasks is the identification of virulent proteins since a significant proportion of genomic and metagenomic proteins are novel and yet unannotated. The currently available tools which carry out the identification of virulent proteins provide limited accuracy and cannot be used on large datasets. Therefore, we have developed an MP3 standalone tool and web server for the prediction of pathogenic proteins in both genomic and metagenomic datasets. MP3 is developed using an integrated Support Vector Machine (SVM) and Hidden Markov Model (HMM) approach to carry out highly fast, sensitive and accurate prediction of pathogenic proteins. It displayed Sensitivity, Specificity, MCC and accuracy values of 92%, 100%, 0.92 and 96%, respectively, on blind dataset constructed using complete proteins. On the two metagenomic blind datasets (Blind A: 51–100 amino acids and Blind B: 30–50 amino acids), it displayed Sensitivity, Specificity, MCC and accuracy values of 82.39%, 97.86%, 0.80 and 89.32% for Blind A and 71.60%, 94.48%, 0.67 and 81.86% for Blind B, respectively. In addition, the performance of MP3 was validated on selected bacterial genomic and real metagenomic datasets. To our knowledge, MP3 is the only program that specializes in fast and accurate identification of partial pathogenic proteins predicted from short (100–150 bp) metagenomic reads and also performs exceptionally well on complete protein sequences. MP3 is publicly available at http://metagenomics.iiserb.ac.in/mp3/index.php. PMID:24736651

ANTIMICROBIAL SENSITIVITY PATTERNS OF MAJOR ZOONOTIC PATHOGENS FROM A SEASON-LONG “FARM-TO-FORK” STUDY OF ALL NATURAL, ANTIBIOTIC-FREE, PASTURE-RAISED BROILER FLOCKS IN THE SOUTHEASTERN UNITED STATES

USDA-ARS?s Scientific Manuscript database

Introduction: The prevalence of antibiotic resistance microorganisms has significant implications for environmental, animal, and human health. One focus is the use of antibiotics in animal agriculture and its effects on antibiotic resistant bacterial populations within those systems, but before thi...

Summary results of the 2014-2015 DARPA Chikungunya challenge

DOE PAGES

Del Valle, Sara Y.; McMahon, Benjamin Hamilton; Asher, Jason; ...

2018-05-30

Here, emerging pathogens such as Zika, chikungunya, Ebola, and dengue viruses are serious threats to national and global health security. Accurate forecasts of emerging epidemics and their severity are critical to minimizing subsequent mortality, morbidity, and economic loss. The recent introduction of chikungunya and Zika virus to the Americas underscores the need for better methods for disease surveillance and forecasting.

Effect of volumetric water content and clover (Trifolium incarnatum) on the survival of Escherichia coli O157:H7 in a soil matrix

USDA-ARS?s Scientific Manuscript database

Due to the inevitable introduction of zoonotic manure-born human pathogens, such as Escherichia coli O157:H7, into minimally processed, ready-to-eat and organic vegetable production systems via animal manure-based organic fertilizer, studies aimed at understanding the survival dynamics of these path...

Synoptic climatology of the long-distance dispersal of white pine blister rust II. Combination of surface and upper level conditions

Treesearch

K. L. Frank; B. W. Geils; L. S. Kalkstein; H. W. Thistle

2008-01-01

An invasive forest pathogen, Cronartium ribicola, white pine blister rust (WPBR), is believed to have arrived in the Sacramento Mountains of south-central New Mexico about 1970. Epidemiological and genetic evidence supports the hypothesis that introduction was the result of long-distance dispersal (LDD) by atmospheric transport from California. This...

The Italian elm breeding program for Dutch elm disease resistance

Treesearch

Alberto Santini; Francesco Pecori; Luisa Ghelardini

2012-01-01

In the 20th century, elms across Europe and North America were devastated by two pandemics of Dutch elm disease (DED), caused by the introduction of two fungal pathogens: Ophiostoma ulmi, followed by O. novo-ulmi. At the end of 1920s, research into a resistance to DED began in Europe and then in the United States. No...

Tracking contamination through ground beef production and identifying points of recontamination using a novel green fluorescent protein (GFP) expressing, E. coli O103, non-pathogenic surrogate

USDA-ARS?s Scientific Manuscript database

Introduction: Commonly, ground beef processors conduct studies to model contaminant flow through their production systems using surrogate organisms. Typical surrogate organisms may not behave as Escherichia coli O157:H7 during grinding and are not easy to detect at very low levels. Purpose: Develop...

‘Carolina Broadleaf’ mustard green (Brassica juncea L.) resistant to the bacterial leaf blight pathogen Pseudomonas cannabina pv. alisalensis

USDA-ARS?s Scientific Manuscript database

A leafy-green mustard (Brassica juncea L.) cultivar designated ‘Carolina Broadleaf’ has been released by the Agricultural Research Service of the U.S. Dept. of Agriculture in 2015. This released cultivar is a narrow-based population of leafy-green mustard derived from a U.S. plant introduction (PI)...

75 FR 15672 - Notice of Revision and Request for Extension of Approval of an Information Collection; Highly...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-30

... Avian Influenza; Subtype H5N1 AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION: Revision... introduction of the H5N1 subtype of highly pathogenic avian influenza through imported birds, poultry, and... influenza, subtype H5N1, contact Dr. Bettina Cooper, Staff Veterinarian, Technical Trade Services Team...

Vaccine efficacy of live-attenuated virus, whole inactivated virus and alphavirus vectored subunit vaccines against antigenically distinct H3N2 swine influenza A viruses

USDA-ARS?s Scientific Manuscript database

Introduction Influenza A virus (IAV) is an important pathogen in swine, and the main intervention strategy is vaccination to induce neutralizing antibodies against the hemagglutinin (HA). Three major antigenic clusters, cyan, red, and green, were identified among H3N2 viruses circulating in pigs in ...

Effect of proximity to a cattle feedlot on the occurrence of Escherichia coli 0157:H7-positive pest flies in a leafy green crop

USDA-ARS?s Scientific Manuscript database

Introduction: Escherichia coli O157:H7 outbreaks linked to produce have focused attention on cattle as contamination sources. Cattle pest flies can harbor this pathogen, and may disseminate it to produce. The Leafy Greens Marketing Agreement proposes an interim guidance distance of 400 feet betwee...

Summary results of the 2014-2015 DARPA Chikungunya challenge

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

Del Valle, Sara Y.; McMahon, Benjamin Hamilton; Asher, Jason

Here, emerging pathogens such as Zika, chikungunya, Ebola, and dengue viruses are serious threats to national and global health security. Accurate forecasts of emerging epidemics and their severity are critical to minimizing subsequent mortality, morbidity, and economic loss. The recent introduction of chikungunya and Zika virus to the Americas underscores the need for better methods for disease surveillance and forecasting.

Role of curli and contamination level on Escherichia coli O157:H7 internalization into organic spinach plants grown on hydroponics and in soil

USDA-ARS?s Scientific Manuscript database

Introduction: E. coli O157:H7 may be internalized into organic leafy greens via root uptake. Understanding the mechanisms of E. coli O157:H7 internalization into organic leafy greens is important as produce wash treatment may not remove internalized pathogens. Purpose: The internalization potential...

Disaggregating Tropical Disease Prevalence by Climatic and Vegetative Zones within Tropical West Africa.

PubMed

Beckley, Carl S; Shaban, Salisu; Palmer, Guy H; Hudak, Andrew T; Noh, Susan M; Futse, James E

2016-01-01

Tropical infectious disease prevalence is dependent on many socio-cultural determinants. However, rainfall and temperature frequently underlie overall prevalence, particularly for vector-borne diseases. As a result these diseases have increased prevalence in tropical as compared to temperate regions. Specific to tropical Africa, the tendency to incorrectly infer that tropical diseases are uniformly prevalent has been partially overcome with solid epidemiologic data. This finer resolution data is important in multiple contexts, including understanding risk, predictive value in disease diagnosis, and population immunity. We hypothesized that within the context of a tropical climate, vector-borne pathogen prevalence would significantly differ according to zonal differences in rainfall, temperature, relative humidity and vegetation condition. We then determined if these environmental data were predictive of pathogen prevalence. First we determined the prevalence of three major pathogens of cattle, Anaplasma marginale, Babesia bigemina and Theileria spp, in the three vegetation zones where cattle are predominantly raised in Ghana: Guinea savannah, semi-deciduous forest, and coastal savannah. The prevalence of A. marginale was 63%, 26% for Theileria spp and 2% for B. bigemina. A. marginale and Theileria spp. were significantly more prevalent in the coastal savannah as compared to either the Guinea savanna or the semi-deciduous forest, supporting acceptance of the first hypothesis. To test the predictive power of environmental variables, the data over a three year period were considered in best subsets multiple linear regression models predicting prevalence of each pathogen. Corrected Akaike Information Criteria (AICc) were assigned to the alternative models to compare their utility. Competitive models for each response were averaged using AICc weights. Rainfall was most predictive of pathogen prevalence, and EVI also contributed to A. marginale and B. bigemina prevalence. These findings support the utility of environmental data for understanding vector-borne disease epidemiology on a regional level within a tropical environment.

Disaggregating Tropical Disease Prevalence by Climatic and Vegetative Zones within Tropical West Africa

PubMed Central

Beckley, Carl S.; Shaban, Salisu; Palmer, Guy H.; Hudak, Andrew T.; Noh, Susan M.; Futse, James E.

2016-01-01

Tropical infectious disease prevalence is dependent on many socio-cultural determinants. However, rainfall and temperature frequently underlie overall prevalence, particularly for vector-borne diseases. As a result these diseases have increased prevalence in tropical as compared to temperate regions. Specific to tropical Africa, the tendency to incorrectly infer that tropical diseases are uniformly prevalent has been partially overcome with solid epidemiologic data. This finer resolution data is important in multiple contexts, including understanding risk, predictive value in disease diagnosis, and population immunity. We hypothesized that within the context of a tropical climate, vector-borne pathogen prevalence would significantly differ according to zonal differences in rainfall, temperature, relative humidity and vegetation condition. We then determined if these environmental data were predictive of pathogen prevalence. First we determined the prevalence of three major pathogens of cattle, Anaplasma marginale, Babesia bigemina and Theileria spp, in the three vegetation zones where cattle are predominantly raised in Ghana: Guinea savannah, semi-deciduous forest, and coastal savannah. The prevalence of A. marginale was 63%, 26% for Theileria spp and 2% for B. bigemina. A. marginale and Theileria spp. were significantly more prevalent in the coastal savannah as compared to either the Guinea savanna or the semi-deciduous forest, supporting acceptance of the first hypothesis. To test the predictive power of environmental variables, the data over a three year period were considered in best subsets multiple linear regression models predicting prevalence of each pathogen. Corrected Akaike Information Criteria (AICc) were assigned to the alternative models to compare their utility. Competitive models for each response were averaged using AICc weights. Rainfall was most predictive of pathogen prevalence, and EVI also contributed to A. marginale and B. bigemina prevalence. These findings support the utility of environmental data for understanding vector-borne disease epidemiology on a regional level within a tropical environment. PMID:27022740

Development of associations and kinetic models for microbiological data to be used in comprehensive food safety prediction software.

PubMed

Halder, Amit; Black, D Glenn; Davidson, P Michael; Datta, Ashim

2010-08-01

The objective of this study was to use an existing database of food products and their associated processes, link it with a list of the foodborne pathogenic microorganisms associated with those products and finally identify growth and inactivation kinetic parameters associated with those pathogens. The database was to be used as a part of the development of comprehensive software which could predict food safety and quality for any food product. The main issues in building such a predictive system included selection of predictive models, associations of different food types with pathogens (as determined from outbreak histories), and variability in data from different experiments. More than 1000 data sets from published literature were analyzed and grouped according to microorganisms and food types. Final grouping of data consisted of the 8 most prevalent pathogens for 14 different food groups, covering all of the foods (>7000) listed in the USDA Natl. Nutrient Database. Data for each group were analyzed in terms of 1st-order inactivation, 1st-order growth, and sigmoidal growth models, and their kinetic response for growth and inactivation as a function of temperature were reported. Means and 95% confidence intervals were calculated for prediction equations. The primary advantage in obtaining group-specific kinetic data is the ability to extend microbiological growth and death simulation to a large array of product and process possibilities, while still being reasonably accurate. Such simulation capability could provide vital ''what if'' scenarios for industry, Extension, and academia in food safety.

An in-premise model for Legionella exposure during showering events.

PubMed

Schoen, Mary E; Ashbolt, Nicholas J

2011-11-15

An exposure model was constructed to predict the critical Legionella densities in an engineered water system that result in infection from inhalation of aerosols containing the pathogen while showering. The model predicted the Legionella densities in the shower air, water and in-premise plumbing biofilm that might result in a deposited dose of Legionella in the alveolar region of the lungs associated with infection for a routine showering event. Processes modeled included the detachment of biofilm-associated Legionella from the in-premise plumbing biofilm during a showering event, the partitioning of the pathogen from the shower water to the air, and the inhalation and deposition of particles in the lungs. The range of predicted critical Legionella densities in the air and water was compared to the available literature. The predictions were generally within the limited set of observations for air and water, with the exception of Legionella density within in-premise plumbing biofilms, for which there remains a lack of observations for comparison. Sensitivity analysis of the predicted results to possible changes in the uncertain input parameters identified the target deposited dose associated with infections, the pathogen air-water partitioning coefficient, and the quantity of detached biofilm from in-premise pluming surfaces as important parameters for additional data collection. In addition, the critical density of free-living protozoan hosts in the biofilm required to propagate the infectious Legionella was estimated. Together, this evidence can help to identify critical conditions that might lead to infection derived from pathogens within the biofilms of any plumbing system from which humans may be exposed to aerosols. Published by Elsevier Ltd.

DEVELOPING SITE-SPECIFIC MODELS FOR FORECASTING BACTERIA LEVELS AT COASTAL BEACHES

EPA Science Inventory

The U.S.Beaches Environmental Assessment and Coastal Health Act of 2000 authorizes studies of pathogen indicators in coastal recreation waters that develop appropriate, accurate, expeditious, and cost-effective methods (including predictive models) for quantifying pathogens in co...

Implication of global climate change on the distribution and activity of Phytophthora ramorum

Treesearch

Robert C. Venette

2009-01-01

Global climate change is predicted to alter the distribution and activity of several forest pathogens. Boland et al. (2004) suggested that climate change might affect pathogen establishment, rate of disease progress, and the duration of...

Neutral Theory and Rapidly Evolving Viral Pathogens.

PubMed

Frost, Simon D W; Magalis, Brittany Rife; Kosakovsky Pond, Sergei L

2018-06-01

The evolution of viral pathogens is shaped by strong selective forces that are exerted during jumps to new hosts, confrontations with host immune responses and antiviral drugs, and numerous other processes. However, while undeniably strong and frequent, adaptive evolution is largely confined to small parts of information-packed viral genomes, and the majority of observed variation is effectively neutral. The predictions and implications of the neutral theory have proven immensely useful in this context, with applications spanning understanding within-host population structure, tracing the origins and spread of viral pathogens, predicting evolutionary dynamics, and modeling the emergence of drug resistance. We highlight the multiple ways in which the neutral theory has had an impact, which has been accelerated in the age of high-throughput, high-resolution genomics.

Risk Prioritization Tool to Identify the Public Health Risks of Wildlife Trade: The Case of Rodents from Latin America.

PubMed

Bueno, I; Smith, K M; Sampedro, F; Machalaba, C C; Karesh, W B; Travis, D A

2016-06-01

Wildlife trade (both formal and informal) is a potential driver of disease introduction and emergence. Legislative proposals aim to prevent these risks by banning wildlife imports, and creating 'white lists' of species that are cleared for importation. These approaches pose economic harm to the pet industry, and place substantial burden on importers and/or federal agencies to provide proof of low risk for importation of individual species. As a feasibility study, a risk prioritization tool was developed to rank the pathogens found in rodent species imported from Latin America into the United States with the highest risk of zoonotic consequence in the United States. Four formally traded species and 16 zoonotic pathogens were identified. Risk scores were based on the likelihood of pathogen release and human exposure, and the severity of the disease (consequences). Based on the methodology applied, three pathogens (Mycobacterium microti, Giardia spp. and Francisella tularensis) in one species (Cavia porcellus) were ranked as highest concern. The goal of this study was to present a methodological approach by which preliminary management resources can be allocated to the identified high-concern pathogen-species combinations when warranted. This tool can be expanded to other taxa and geographic locations to inform policy surrounding the wildlife trade. © 2015 Blackwell Verlag GmbH.

Novel Mutation in the ATP-Binding Cassette Transporter A3 (ABCA3) Encoding Gene Causes Respiratory Distress Syndrome in A Term Newborn in Southwest Iran

PubMed Central

Rezaei, Farideh; Shafiei, Mohammad; Shariati, Gholamreza; Dehdashtian, Ali; Mohebbi, Maryam; Galehdari, Hamid

2016-01-01

Introduction ABCA3 glycoprotein belongs to the ATP-binding cassette (ABC) superfamily of transporters, which utilize the energy derived from hydrolysis of ATP for the translocation of a wide variety of substrates across the plasma membrane. Mutations in the ABCA3 gene are knowingly causative for fatal surfactant deficiency, particularly respiratory distress syndrome (RDS) in term babies. Case Presentation In this study, Sanger sequencing of the whole ABCA3 gene (NCBI NM_001089) was performed in a neonatal boy with severe RDS. A homozygous mutation has been identified in the patient. Parents were heterozygous for the same missense mutation GGA > AGA at position 202 in exon 6 of the ABCA3 gene (c.604G > A; p.G202R). Furthermore, 70 normal individuals have been analyzed for the mentioned change with negative results. Conclusions Regarding Human Genome Mutation Database (HGMD) and other literature recherche, the detected change is a novel mutation and has not been reported before. Bioinformatics mutation predicting tools prefer it as pathogenic. PMID:27437095

Pathogen evolution under host avoidance plasticity.

PubMed

McLeod, David V; Day, Troy

2015-09-07

Host resistance consists of defences that limit pathogen burden, and can be classified as either adaptations targeting recovery from infection or those focused upon infection avoidance. Conventional theory treats avoidance as a fixed strategy which does not vary from one interaction to the next. However, there is increasing empirical evidence that many avoidance strategies are triggered by external stimuli, and thus should be treated as phenotypically plastic responses. Here, we consider the implications of avoidance plasticity for host-pathogen coevolution. We uncover a number of predictions challenging current theory. First, in the absence of pathogen trade-offs, plasticity can restrain pathogen evolution; moreover, the pathogen exploits conditions in which the host would otherwise invest less in resistance, causing resistance escalation. Second, when transmission trades off with pathogen-induced mortality, plasticity encourages avirulence, resulting in a superior fitness outcome for both host and pathogen. Third, plasticity ensures the sterilizing effect of pathogens has consequences for pathogen evolution. When pathogens castrate hosts, selection forces them to minimize mortality virulence; moreover, when transmission trades off with sterility alone, resistance plasticity is sufficient to prevent pathogens from evolving to fully castrate. © 2015 The Author(s).

Future research needs involving pathogens in groundwater

NASA Astrophysics Data System (ADS)

Bradford, Scott A.; Harvey, Ronald W.

2017-06-01

Contamination of groundwater by enteric pathogens has commonly been associated with disease outbreaks. Proper management and treatment of pathogen sources are important prerequisites for preventing groundwater contamination. However, non-point sources of pathogen contamination are frequently difficult to identify, and existing approaches for pathogen detection are costly and only provide semi-quantitative information. Microbial indicators that are readily quantified often do not correlate with the presence of pathogens. Pathogens of emerging concern and increasing detections of antibiotic resistance among bacterial pathogens in groundwater are topics of growing concern. Adequate removal of pathogens during soil passage is therefore critical for safe groundwater extraction. Processes that enhance pathogen transport (e.g., high velocity zones and preferential flow) and diminish pathogen removal (e.g., reversible retention and enhanced survival) are of special concern because they increase the risk of groundwater contamination, but are still incompletely understood. Improved theory and modeling tools are needed to analyze experimental data, test hypotheses, understand coupled processes and controlling mechanisms, predict spatial and/or temporal variability in model parameters and uncertainty in pathogen concentrations, assess risk, and develop mitigation and best management approaches to protect groundwater.

Future research needs involving pathogens in groundwater

USGS Publications Warehouse

Bradford, Scott A.; Harvey, Ronald W.

2017-01-01

Contamination of groundwater by enteric pathogens has commonly been associated with disease outbreaks. Proper management and treatment of pathogen sources are important prerequisites for preventing groundwater contamination. However, non-point sources of pathogen contamination are frequently difficult to identify, and existing approaches for pathogen detection are costly and only provide semi-quantitative information. Microbial indicators that are readily quantified often do not correlate with the presence of pathogens. Pathogens of emerging concern and increasing detections of antibiotic resistance among bacterial pathogens in groundwater are topics of growing concern. Adequate removal of pathogens during soil passage is therefore critical for safe groundwater extraction. Processes that enhance pathogen transport (e.g., high velocity zones and preferential flow) and diminish pathogen removal (e.g., reversible retention and enhanced survival) are of special concern because they increase the risk of groundwater contamination, but are still incompletely understood. Improved theory and modeling tools are needed to analyze experimental data, test hypotheses, understand coupled processes and controlling mechanisms, predict spatial and/or temporal variability in model parameters and uncertainty in pathogen concentrations, assess risk, and develop mitigation and best management approaches to protect groundwater.

Pathogenicity in POLG syndromes: DNA polymerase gamma pathogenicity prediction server and database.

PubMed

Nurminen, Anssi; Farnum, Gregory A; Kaguni, Laurie S

2017-06-01

DNA polymerase gamma (POLG) is the replicative polymerase responsible for maintaining mitochondrial DNA (mtDNA). Disorders related to its functionality are a major cause of mitochondrial disease. The clinical spectrum of POLG syndromes includes Alpers-Huttenlocher syndrome (AHS), childhood myocerebrohepatopathy spectrum (MCHS), myoclonic epilepsy myopathy sensory ataxia (MEMSA), the ataxia neuropathy spectrum (ANS) and progressive external ophthalmoplegia (PEO). We have collected all publicly available POLG-related patient data and analyzed it using our pathogenic clustering model to provide a new research and clinical tool in the form of an online server. The server evaluates the pathogenicity of both previously reported and novel mutations. There are currently 176 unique point mutations reported and found in mitochondrial patients in the gene encoding the catalytic subunit of POLG, POLG . The mutations are distributed nearly uniformly along the length of the primary amino acid sequence of the gene. Our analysis shows that most of the mutations are recessive, and that the reported dominant mutations cluster within the polymerase active site in the tertiary structure of the POLG enzyme. The POLG Pathogenicity Prediction Server (http://polg.bmb.msu.edu) is targeted at clinicians and scientists studying POLG disorders, and aims to provide the most current available information regarding the pathogenicity of POLG mutations.

Clinical characterisation of pneumonia caused by atypical pathogens combining classic and novel predictors.

PubMed

Masiá, M; Gutiérrez, F; Padilla, S; Soldán, B; Mirete, C; Shum, C; Hernández, I; Royo, G; Martin-Hidalgo, A

2007-02-01

The aim of this study was to characterise community-acquired pneumonia (CAP) caused by atypical pathogens by combining distinctive clinical and epidemiological features and novel biological markers. A population-based prospective study of consecutive patients with CAP included investigation of biomarkers of bacterial infection, e.g., procalcitonin, C-reactive protein and lipopolysaccharide-binding protein (LBP) levels. Clinical, radiological and laboratory data for patients with CAP caused by atypical pathogens were compared by univariate and multivariate analysis with data for patients with typical pathogens and patients from whom no organisms were identified. Two predictive scoring models were developed with the most discriminatory variables from multivariate analysis. Of 493 patients, 94 had CAP caused by atypical pathogens. According to multivariate analysis, patients with atypical pneumonia were more likely to have normal white blood cell counts, have repetitive air-conditioning exposure, be aged <65 years, have elevated aspartate aminotransferase levels, have been exposed to birds, and have lower serum levels of LBP. Two different scoring systems were developed that predicted atypical pathogens with sensitivities of 35.2% and 48.8%, and specificities of 93% and 91%, respectively. The combination of selected patient characteristics and laboratory data identified up to half of the cases of atypical pneumonia with high specificity, which should help clinicians to optimise initial empirical therapy for CAP.

Microbial Survey of Pennsylvania Surface Water Used for Irrigating Produce Crops.

PubMed

Draper, Audrey D; Doores, Stephanie; Gourama, Hassan; LaBorde, Luke F

2016-06-01

Recent produce-associated foodborne illness outbreaks have been attributed to contaminated irrigation water. This study examined microbial levels in Pennsylvania surface waters used for irrigation, relationships between microbial indicator organisms and water physicochemical characteristics, and the potential use of indicators for predicting the presence of human pathogens. A total of 153 samples taken from surface water sources used for irrigation in southeastern Pennsylvania were collected from 39 farms over a 2-year period. Samples were analyzed for six microbial indicator organisms (aerobic plate count, Enterobacteriaceae, coliform, fecal coliforms, Escherichia coli, and enterococci), two human pathogens (Salmonella and E. coli O157), and seven physical and environmental characteristics (pH, conductivity, turbidity, air and water temperature, and sampling day and 3-day-accumulated precipitation levels). Indicator populations were highly variable and not predicted by water and environmental characteristics. Only five samples were confirmed positive for Salmonella, and no E. coli O157 was detected in any samples. Predictive relationships between microbial indicators and the occurrence of pathogens could therefore not be determined.

A robust multiplex real-time PCR method for simultaneous detection of Salmonella spp., Escherichia coli O157 and Listeria monocytogenes in fresh fruits and vegetables

USDA-ARS?s Scientific Manuscript database

Introduction: On average, about 48 million people per year in the U.S. are affected by food borne diseases. A major portion of these illnesses are caused by Salmonella spp., Escherichia coli O157:H7 and Listeria monocytogenes. Hence, it is important to identify the specific pathogens in contaminate...

Pest risk assessment of the importation into the United States of unprocessed Pinus logs and chips from Australia

Treesearch

John T Kliejunas; Harold H. Burdsall; Gregg A. DeNitto; Andris Eglitis; Dennis A. Haugen; Michael I. Haverty; Jessie A. Micales-Glaeser

2006-01-01

The unmitigated pest risk potential for the importation of unprocessed logs and chips of species of Pinus (Pinus radiata, P. elliottii Engelm. var. elliottii, P. taeda L., and P. caribaea var. hondurensis, principally) from Australia into the United States was assessed by estimating the likelihood and consequences of introduction of representative insects and pathogens...

The use of Zero-valent iron biosand filters to reduce E. coli O157:H12 in irrigation water applied to spinach plants in a field setting

USDA-ARS?s Scientific Manuscript database

Contaminated irrigation water is a potential source for the introduction of foodborne pathogens on to produce commodities. Zero-valent iron (ZVI) may provide a simple cheap method to mitigate the contamination of produce groups through irrigation water. A small field scale system was utilized to e...

Development of a real-time RT-PCR assay for squash mosaic virus useful for broad spectrum detection of various serotypes and its incorporation into a multiplex seed health assay

USDA-ARS?s Scientific Manuscript database

Seed-borne pathogens pose a serious threat to modern agricultural cropping systems as they can be disseminated to many geographical regions around the world. With trends of increasing global seed production and trade, seed-health testing is an important quality control step to prevent the introduct...

Confirmation of independent introductions of an exotic plant pathogen of Cornus species, Discula destructiva, on the east and west coasts of North America and subsequent population bottlenecks

USDA-ARS?s Scientific Manuscript database

Cornus florida (eastern flowering dogwood) and C. nuttallii (pacific flowering dogwood) are North American native tree species that belong to the big-bracted group of dogwoods. Cornus species are highly valued for their ornamental characteristics, have fruits that contain high fat content for animal...

A comparative evaluation of the GENE-up assay for the detection of Escherichia coli O157:H7

USDA-ARS?s Scientific Manuscript database

Introduction: Shiga-toxigenic Escherichia coli O157:H7 (STEC O157) remains one of the major food-borne public health threats since it was first identified as a pathogen in 1982. In the US, per year, the CDC estimates ca. 95,000 STEC O157 infections, among which ca. 3700 are lab confirmed cases. STE...

A simulation model for studying the role of pre-slaughter factors on the exposure of beef carcasses to human microbial hazards.

PubMed

Jordan, D; McEwen, S A; Lammerding, A M; McNab, W B; Wilson, J B

1999-06-29

A Monte Carlo simulation model was constructed for assessing the quantity of microbial hazards deposited on cattle carcasses under different pre-slaughter management regimens. The model permits comparison of industry-wide and abattoir-based mitigation strategies and is suitable for studying pathogens such as Escherichia coli O157:H7 and Salmonella spp. Simulations are based on a hierarchical model structure that mimics important aspects of the cattle population prior to slaughter. Stochastic inputs were included so that uncertainty about important input assumptions (such as prevalence of a human pathogen in the live cattle-population) would be reflected in model output. Control options were built into the model to assess the benefit of having prior knowledge of animal or herd-of-origin pathogen status (obtained from the use of a diagnostic test). Similarly, a facility was included for assessing the benefit of re-ordering the slaughter sequence based on the extent of external faecal contamination. Model outputs were designed to evaluate the performance of an abattoir in a 1-day period and included outcomes such as the proportion of carcasses contaminated with a pathogen, the daily mean and selected percentiles of pathogen counts per carcass, and the position of the first infected animal in the slaughter run. A measure of the time rate of introduction of pathogen into the abattoir was provided by assessing the median, 5th percentile, and 95th percentile cumulative pathogen counts at 10 equidistant points within the slaughter run. Outputs can be graphically displayed as frequency distributions, probability densities, cumulative distributions or x-y plots. The model shows promise as an inexpensive method for evaluating pathogen control strategies such as those forming part of a Hazard Analysis and Critical Control Point (HACCP) system.

Investigating Differences across Host Species and Scales to Explain the Distribution of the Amphibian Pathogen Batrachochytrium dendrobatidis

PubMed Central

Peterson, Anna C.; McKenzie, Valerie J.

2014-01-01

Many pathogens infect more than one host species, and clarifying how these different hosts contribute to pathogen dynamics can facilitate the management of pathogens and can lend insight into the functioning of pathogens in ecosystems. In this study, we investigated a suite of native and non-native amphibian hosts of the pathogen Batrachochytrium dendrobatidis (Bd) across multiple scales to identify potential mechanisms that may drive infection patterns in the Colorado study system. Specifically, we aimed to determine if: 1) amphibian populations vary in Bd infection across the landscape, 2) amphibian community composition predicts infection (e.g., does the presence or abundance of any particular species influence infection in others?), 3) amphibian species vary in their ability to produce infectious zoospores in a laboratory infection, 4) heterogeneity in host ability observed in the laboratory scales to predict patterns of Bd prevalence in the landscape. We found that non-native North American bullfrogs (Lithobates catesbeianus) are widespread and have the highest prevalence of Bd infection relative to the other native species in the landscape. Additionally, infection in some native species appears to be related to the density of sympatric L. catesbeianus populations. At the smaller host scale, we found that L. catesbeianus produces more of the infective zoospore stage relative to some native species, but that this zoospore output does not scale to predict infection in sympatric wild populations of native species. Rather, landscape level infection relates most strongly to density of hosts at a wetland as well as abiotic factors. While non-native L. catesbeianus have high levels of Bd infection in the Colorado Front Range system, we also identified Bd infection in a number of native amphibian populations allopatric with L. catesbeianus, suggesting that multiple host species are important contributors to the dynamics of the Bd pathogen in this landscape. PMID:25222375

The prediction of a pathogenesis-related secretome of Puccinia helianthi through high-throughput transcriptome analysis.

PubMed

Jing, Lan; Guo, Dandan; Hu, Wenjie; Niu, Xiaofan

2017-03-11

Many plant pathogen secretory proteins are known to be elicitors or pathogenic factors,which play an important role in the host-pathogen interaction process. Bioinformatics approaches make possible the large scale prediction and analysis of secretory proteins from the Puccinia helianthi transcriptome. The internet-based software SignalP v4.1, TargetP v1.01, Big-PI predictor, TMHMM v2.0 and ProtComp v9.0 were utilized to predict the signal peptides and the signal peptide-dependent secreted proteins among the 35,286 ORFs of the P. helianthi transcriptome. 908 ORFs (accounting for 2.6% of the total proteins) were identified as putative secretory proteins containing signal peptides. The length of the majority of proteins ranged from 51 to 300 amino acids (aa), while the signal peptides were from 18 to 20 aa long. Signal peptidase I (SpI) cleavage sites were found in 463 of these putative secretory signal peptides. 55 proteins contained the lipoprotein signal peptide recognition site of signal peptidase II (SpII). Out of 908 secretory proteins, 581 (63.8%) have functions related to signal recognition and transduction, metabolism, transport and catabolism. Additionally, 143 putative secretory proteins were categorized into 27 functional groups based on Gene Ontology terms, including 14 groups in biological process, seven in cellular component, and six in molecular function. Gene ontology analysis of the secretory proteins revealed an enrichment of hydrolase activity. Pathway associations were established for 82 (9.0%) secretory proteins. A number of cell wall degrading enzymes and three homologous proteins specific to Phytophthora sojae effectors were also identified, which may be involved in the pathogenicity of the sunflower rust pathogen. This investigation proposes a new approach for identifying elicitors and pathogenic factors. The eventual identification and characterization of 908 extracellularly secreted proteins will advance our understanding of the molecular mechanisms of interactions between sunflower and rust pathogen and will enhance our ability to intervene in disease states.

Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors.

PubMed

Williams, Angela H; Sharma, Mamta; Thatcher, Louise F; Azam, Sarwar; Hane, James K; Sperschneider, Jana; Kidd, Brendan N; Anderson, Jonathan P; Ghosh, Raju; Garg, Gagan; Lichtenzveig, Judith; Kistler, H Corby; Shea, Terrance; Young, Sarah; Buck, Sally-Anne G; Kamphuis, Lars G; Saxena, Rachit; Pande, Suresh; Ma, Li-Jun; Varshney, Rajeev K; Singh, Karam B

2016-03-05

Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pisi (Fop-37622), significant pathogens of chickpea and pea respectively, the world's second and third most important grain legumes, and lastly f. sp. medicaginis (Fom-5190a) for which we developed a model legume pathosystem utilising Medicago truncatula. Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publicly available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume-infecting formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified small conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp. We demonstrate that distinction of core and potential dispensable genomic regions of novel F. oxysporum genomes is an effective tool to facilitate effector discovery and the identification of gene content possibly linked to host specificity. While the legume-infecting isolates didn't share large genomic regions of pathogenicity-related content, smaller regions and candidate effector proteins were highly conserved, suggesting that they may play specific roles in inducing disease on legume hosts.

Forecasting invasive pneumococcal disease trends after the introduction of 13-valent pneumococcal conjugate vaccine in the United States, 2010-2020.

PubMed

Link-Gelles, Ruth; Taylor, Thomas; Moore, Matthew R

2013-05-24

Pneumococcal vaccines are highly effective at preventing invasive pneumococcal disease (IPD), a leading cause of global morbidity. Because pneumococcal vaccines can be expensive, it is useful to estimate what impact might be expected from their introduction. Our objective was to develop a statistical model that could predict rates of IPD following introduction of 13-valent pneumococcal conjugate vaccine (PCV13) in the U.S. We used active surveillance data to design and validate a Poisson model forecasting the reductions in IPD observed after U.S. introduction of 7-valent pneumococcal conjugate vaccine (PCV7) in 2000. We used this model to forecast rates of IPD from 2010 to 2020 in the presence of PCV13. Because increases in non-PCV7-type IPD were evident following PCV7 introduction, we evaluated varying levels of increase in non-PCV13-type IPD ("serotype replacement") by sensitivity analyses. A total of 43,507 cases of IPD were identified during 1998-2009; cases from this period were used to develop the model, which accurately predicted indirect effects of PCV7 in adults, as well as serotype replacement. Assuming that PCV13 provides similar protection against PCV13 serotypes as PCV7 did against PCV7 serotypes, the base-case model predicted approximately 168,000 cases of IPD prevented from 2011 to 2020. When serotype replacement was varied in sensitivity analyses from 0 to levels comparable to that seen with serotype 19A (the most common replacement serotype since PCV7 was introduced), the model predicted 167,000-170,000 cases prevented. The base-case model predicted rates of IPD in children under five years of age decreasing from 21.9 to 9.3 cases per 100,000 population. This model provides a "benchmark" for assessing progress in the prevention of IPD in the years after PCV13 introduction. The amount of serotype replacement is unlikely to greatly affect the overall number of cases prevented by PCV13. Published by Elsevier Ltd.

Evaluating High-Throughput Ab Initio Gene Finders to Discover Proteins Encoded in Eukaryotic Pathogen Genomes Missed by Laboratory Techniques

PubMed Central

Goodswen, Stephen J.; Kennedy, Paul J.; Ellis, John T.

2012-01-01

Next generation sequencing technology is advancing genome sequencing at an unprecedented level. By unravelling the code within a pathogen’s genome, every possible protein (prior to post-translational modifications) can theoretically be discovered, irrespective of life cycle stages and environmental stimuli. Now more than ever there is a great need for high-throughput ab initio gene finding. Ab initio gene finders use statistical models to predict genes and their exon-intron structures from the genome sequence alone. This paper evaluates whether existing ab initio gene finders can effectively predict genes to deduce proteins that have presently missed capture by laboratory techniques. An aim here is to identify possible patterns of prediction inaccuracies for gene finders as a whole irrespective of the target pathogen. All currently available ab initio gene finders are considered in the evaluation but only four fulfil high-throughput capability: AUGUSTUS, GeneMark_hmm, GlimmerHMM, and SNAP. These gene finders require training data specific to a target pathogen and consequently the evaluation results are inextricably linked to the availability and quality of the data. The pathogen, Toxoplasma gondii, is used to illustrate the evaluation methods. The results support current opinion that predicted exons by ab initio gene finders are inaccurate in the absence of experimental evidence. However, the results reveal some patterns of inaccuracy that are common to all gene finders and these inaccuracies may provide a focus area for future gene finder developers. PMID:23226328

Using Microbial Source Tracking Markers to Predict Occurrence of Waterborne Pathogens in Urban and Agricultural Watershed

EPA Science Inventory

Runoff from agricultural fields and urban landscapes may carry a variety of microbial contaminants that compromises water quality and increases the possibility of human exposure to pathogenic microorganisms. Establishing the relationship between microbial source tracking (MST) ma...

Biological and serological variability, evolution and molecular epidemiology of Zucchini yellow mosaic virus (ZYMV, Potyvirus) with special reference to Caribbean islands.

PubMed

Desbiez, C; Wipf-Scheibel, C; Lecoq, H

2002-04-23

Zucchini yellow mosaic virus (ZYMV, Potyvirus) emerged as an important pathogen of cucurbits within the last 20 years. Its origins and mechanisms for evolution and worldwide spread represent important questions to understand plant virus emergence. Sequence analysis on a 250 nucleotide fragment including the N-terminal part of the coat protein coding region, revealed one major group of strains, and some highly divergent isolates from distinct origins. Within the major group, three subsets of strains were defined without correlation with geographic origin, year of collection or biological properties. ZYMV was first observed in Martinique and Guadeloupe in 1992 and 1994, respectively. We studied the evolution of ZYMV variability on both islands in the few years following the putative virus introduction. In Martinique, molecular divergence remained low even after 6 years, suggesting a lack of new introductions. Interactions between strains resulted in a stability of the high biological variability, while the serological diversity decreased and molecular divergence remained low. In Guadeloupe, as in Martinique in 1993, serological variability was high shortly after virus introduction. While the first introduction in Guadeloupe was independent from Martinique, the 'Martinique' type was detected in 1998, suggesting further introductions, maybe through viruliferous aphids or imported plant material.

A SPECTRUM OF PATHOGENIC AND NON-PATHOGENIC INTESTINAL PARASITES IN PRE-EMPLOYMENT MEDICAL CHECK-UP FOR WORKERS AND THEIR FAMILIES

PubMed Central

Koshak, Emad A.; Zakai, Haytham A.

2003-01-01

Introduction: Stool analysis plays an important role in pre-employment tests for the screening of intestinal parasites in new workers. Objective: to explore the spectrum of intestinal parasites in stool samples of workers and their families during the pre-employment tests over a one-year period at King Abdulaziz University Hospital (KAUH). Methods: Subjects were selected sequentially from routine single stool analysis forms labeled for pre-employment tests. Stool specimens were examined using the formalin ether technique at the parasitology laboratory at KAUH. Results: Two hundred and ninety two different stool samples of the workers and their families were studied. Their ages ranged from 3 to 72 year old (mean 32 ± 8.5 SD) and females formed 58.6% of the number. Intestinal parasites were detected in 161 workers (55%). The prevalence of intestinal parasites in Saudi workers was significantly lower than non-Saudi nationals, 15.8% versus 57.9% (p<0.001). Of all the positive cases, pathogenic intestinal parasites were found in 40 % of them and the commonest were Trichuris trichuria (39.1%), Hookworm (34.2%), Entamoeba histolytica (16.1%). Non-pathogenic parasites were found in 19.5% and the commonest were Blastocystis hominis (34.8%), Endolimax nana (29.8%), Entamoeba coli (15.5%). One type of parasite was found in 75 (46.6%) and multiple different parasites were found in 86 (53.4%). There was a high significant correlation between the detection of pathogenic and non-pathogenic parasites (p<0.001). Conclusion: Infestation of stools with pathogenic and non-pathogenic intestinal parasites is a common finding in more than half of the new workers and their families. The correlation between non-pathogenic and pathogenic parasites reflects mutual risk factors, and their potential hazards cannot be overlooked. Effective stool screening and eradication strategies for intestinal parasites in new workers should be rigorously enforced. PMID:23011980

Concentration and separation of biological organisms by ultrafiltration and dielectrophoresis

DOEpatents

Simmons, Blake A.; Hill, Vincent R.; Fintschenko, Yolanda; Cummings, Eric B.

2010-10-12

Disclosed is a method for monitoring sources of public water supply for a variety of pathogens by using a combination of ultrafiltration techniques together dielectrophoretic separation techniques. Because water-borne pathogens, whether present due to "natural" contamination or intentional introduction, would likely be present in drinking water at low concentrations when samples are collected for monitoring or outbreak investigations, an approach is needed to quickly and efficiently concentrate and separate particles such as viruses, bacteria, and parasites in large volumes of water (e.g., 100 L or more) while simultaneously reducing the sample volume to levels sufficient for detecting low concentrations of microbes (e.g., <10 mL). The technique is also designed to screen the separated microbes based on specific conductivity and size.

Organization of an optimal adaptive immune system

NASA Astrophysics Data System (ADS)

Walczak, Aleksandra; Mayer, Andreas; Balasubramanian, Vijay; Mora, Thierry

The repertoire of lymphocyte receptors in the adaptive immune system protects organisms from a diverse set of pathogens. A well-adapted repertoire should be tuned to the pathogenic environment to reduce the cost of infections. I will discuss a general framework for predicting the optimal repertoire that minimizes the cost of infections contracted from a given distribution of pathogens. The theory predicts that the immune system will have more receptors for rare antigens than expected from the frequency of encounters and individuals exposed to the same infections will have sparse repertoires that are largely different, but nevertheless exploit cross-reactivity to provide the same coverage of antigens. I will show that the optimal repertoires can be reached by dynamics that describes the competitive binding of antigens by receptors, and selective amplification of stimulated receptors.

Origin and invasion of the emerging infectious pathogen Sphaerothecum destruens

PubMed Central

Sana, Salma; Hardouin, Emilie A; Gozlan, Rodolphe E; Ercan, Didem; Tarkan, Ali Serhan; Zhang, Tiantian; Andreou, Demetra

2017-01-01

Non-native species are often linked to the introduction of novel pathogens with detrimental effects on native biodiversity. Since Sphaerothecum destruens was first discovered as a fish pathogen in the United Kingdom, it has been identified as a potential threat to European fish biodiversity. Despite this parasite’s emergence and associated disease risk, there is still a poor understanding of its origin in Europe. Here, we provide the first evidence to support the hypothesis that S. destruens was accidentally introduced to Europe from China along with its reservoir host Pseudorasbora parva via the aquaculture trade. This is the first study to confirm the presence of S. destruens in China, and it has expanded the confirmed range of S. destruens to additional locations in Europe. The demographic analysis of S. destruens and its host P. parva in their native and invasive range further supported the close association of both species. This research has direct significance and management implications for S. destruens in Europe as a non-native parasite. PMID:28831194

Foodborne general outbreaks of Shiga toxin-producing Escherichia coli O157 in England and Wales 1992-2002: where are the risks?

PubMed

Gillespie, I A; O'Brien, S J; Adak, G K; Cheasty, T; Willshaw, G

2005-10-01

Between 1 January 1992 and 31 December 2002, Shiga toxin-producing Escherichia coli O157 (STEC O157) accounted for 44 of the 1645 foodborne general outbreaks of infectious intestinal disease reported to the Health Protection Agency Communicable Disease Surveillance Centre. These outbreaks, although rare, were characterized by severe infection, with 169 hospital admissions and five deaths reported. STEC O157 outbreaks were compared with other pathogens to identify factors associated with this pathogen. Single risk variable analysis and logistic regression were employed. Two distinct aetiologies were identified. Foodborne outbreaks of STEC O157 infection in England and Wales were independently associated with farms, which related to milk and milk products, and with red meats/meat products, which highlighted butchers' shops as a cause for concern. The introduction and adherence to effective control measures, based on the principles of hazard analysis, provide the best means of minimizing the risk of foodborne infection with this pathogen.

Unravelling the microbiome of eggs of the endangered sea turtle Eretmochelys imbricata identifies bacteria with activity against the emerging pathogen Fusarium falciforme.

PubMed

Sarmiento-Ramírez, Jullie M; van der Voort, Menno; Raaijmakers, Jos M; Diéguez-Uribeondo, Javier

2014-01-01

Habitat bioaugmentation and introduction of protective microbiota have been proposed as potential conservation strategies to rescue endangered mammals and amphibians from emerging diseases. For both strategies, insight into the microbiomes of the endangered species and their habitats is essential. Here, we sampled nests of the endangered sea turtle species Eretmochelys imbricata that were infected with the fungal pathogen Fusarium falciforme. Metagenomic analysis of the bacterial communities associated with the shells of the sea turtle eggs revealed approximately 16,664 operational taxonomic units, with Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes as the most dominant phyla. Subsequent isolation of Actinobacteria from the eggshells led to the identification of several genera (Streptomyces, Amycolaptosis, Micromomospora Plantactinospora and Solwaraspora) that inhibit hyphal growth of the pathogen F. falciforme. These bacterial genera constitute a first set of microbial indicators to evaluate the potential role of microbiota in conservation of endangered sea turtle species.

Swine dysentery: aetiology, pathogenicity, determinants of transmission and the fight against the disease.

PubMed

Alvarez-Ordóñez, Avelino; Martínez-Lobo, Francisco Javier; Arguello, Héctor; Carvajal, Ana; Rubio, Pedro

2013-05-10

Swine Dysentery (SD) is a severe mucohaemorhagic enteric disease of pigs caused by Brachyspira hyodysenteriae, which has a large impact on pig production and causes important losses due to mortality and sub-optimal performance. Although B. hyodysenteriae has been traditionally considered a pathogen mainly transmitted by direct contact, through the introduction of subclinically infected animals into a previously uninfected herd, recent findings position B. hyodysenteriae as a potential threat for indirect transmission between farms. This article summarizes the knowledge available on the etiological agent of SD and its virulence traits, and reviews the determinants of SD transmission. The between-herds and within-herd transmission routes are addressed. The factors affecting disease transmission are thoroughly discussed, i.e., environmental survival of the pathogen, husbandry factors (production system, production stage, farm management), role of vectors, diet influence and interaction of the microorganism with gut microbiota. Finally, prophylactic and therapeutic approaches to fight against the disease are briefly described.

Animal models of highly pathogenic RNA viral infections: encephalitis viruses.

PubMed

Holbrook, Michael R; Gowen, Brian B

2008-04-01

The highly pathogenic RNA viruses that cause encephalitis include a significant number of emerging or re-emerging viruses that are also considered potential bioweapons. Many of these viruses, including members of the family Flaviviridae, the genus Alphavirus in the family Togaviridae, and the genus Henipavirus in the family Paramyxoviridae, circulate widely in their endemic areas, where they are transmitted by mosquitoes or ticks. They use a variety of vertebrate hosts, ranging from birds to bats, in their natural life cycle. As was discovered in the United States, the introduction of a mosquito-borne encephalitis virus such as West Nile virus can cause significant health and societal concerns. There are no effective therapeutics for treating diseases caused by any of these viruses and there is limited, if any, vaccine availability for most. In this review we provide a brief summary of the current status of animal models used to study highly pathogenic encephalitic RNA viruses for the development of antiviral therapeutics and vaccines.

Fleas as parasites of the family Canidae

PubMed Central

2011-01-01

Historically, flea-borne diseases are among the most important medical diseases of humans. Plague and murine typhus are known for centuries while the last years brought some new flea-transmitted pathogens, like R. felis and Bartonella henselae. Dogs may play an essential or an accidental role in the natural transmission cycle of flea-borne pathogens. They support the growth of some of the pathogens or they serve as transport vehicles for infected fleas between their natural reservoirs and humans. More than 15 different flea species have been described in domestic dogs thus far. Several other species have been found to be associated with wild canids. Fleas found on dogs originate from rodents, birds, insectivores and from other Carnivora. Dogs therefore may serve as ideal bridging hosts for the introduction of flea-borne diseases from nature to home. In addition to their role as ectoparasites they cause nuisance for humans and animals and may be the cause for severe allergic reactions. PMID:21767354

Swine Dysentery: Aetiology, Pathogenicity, Determinants of Transmission and the Fight against the Disease

PubMed Central

Alvarez-Ordóñez, Avelino; Martínez-Lobo, Francisco Javier; Arguello, Héctor; Carvajal, Ana; Rubio, Pedro

2013-01-01

Swine Dysentery (SD) is a severe mucohaemorhagic enteric disease of pigs caused by Brachyspira hyodysenteriae, which has a large impact on pig production and causes important losses due to mortality and sub-optimal performance. Although B. hyodysenteriae has been traditionally considered a pathogen mainly transmitted by direct contact, through the introduction of subclinically infected animals into a previously uninfected herd, recent findings position B. hyodysenteriae as a potential threat for indirect transmission between farms. This article summarizes the knowledge available on the etiological agent of SD and its virulence traits, and reviews the determinants of SD transmission. The between-herds and within-herd transmission routes are addressed. The factors affecting disease transmission are thoroughly discussed, i.e., environmental survival of the pathogen, husbandry factors (production system, production stage, farm management), role of vectors, diet influence and interaction of the microorganism with gut microbiota. Finally, prophylactic and therapeutic approaches to fight against the disease are briefly described. PMID:23665849

Reconstructing genome evolution in historic samples of the Irish potato famine pathogen

PubMed Central

Martin, Michael D.; Cappellini, Enrico; Samaniego, Jose A.; Zepeda, M. Lisandra; Campos, Paula F.; Seguin-Orlando, Andaine; Wales, Nathan; Orlando, Ludovic; Ho, Simon Y. W.; Dietrich, Fred S.; Mieczkowski, Piotr A.; Heitman, Joseph; Willerslev, Eske; Krogh, Anders; Ristaino, Jean B.; Gilbert, M. Thomas P.

2013-01-01

Responsible for the Irish potato famine of 1845–49, the oomycete pathogen Phytophthora infestans caused persistent, devastating outbreaks of potato late blight across Europe in the 19th century. Despite continued interest in the history and spread of the pathogen, the genome of the famine-era strain remains entirely unknown. Here we characterize temporal genomic changes in introduced P. infestans. We shotgun sequence five 19th-century European strains from archival herbarium samples—including the oldest known European specimen, collected in 1845 from the first reported source of introduction. We then compare their genomes to those of extant isolates. We report multiple distinct genotypes in historical Europe and a suite of infection-related genes different from modern strains. At virulence-related loci, several now-ubiquitous genotypes were absent from the historical gene pool. At least one of these genotypes encodes a virulent phenotype in modern strains, which helps explain the 20th century’s episodic replacements of European P. infestans lineages. PMID:23863894

An Interspecies Comparative Analysis of the Predicted Secretomes of the Necrotrophic Plant Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

PubMed Central

2015-01-01

Phytopathogenic fungi form intimate associations with host plant species and cause disease. To be successful, fungal pathogens communicate with a susceptible host through the secretion of proteinaceous effectors, hydrolytic enzymes and metabolites. Sclerotinia sclerotiorum and Botrytis cinerea are economically important necrotrophic fungal pathogens that cause disease on numerous crop species. Here, a powerful bioinformatics pipeline was used to predict the refined S. sclerotiorum and B. cinerea secretomes, identifying 432 and 499 proteins respectively. Analyses focusing on S. sclerotiorum revealed that 16% of the secretome encoding genes resided in small, sequence heterogeneous, gene clusters that were distributed over 13 of the 16 predicted chromosomes. Functional analyses highlighted the importance of plant cell hydrolysis, oxidation-reduction processes and the redox state to the S. sclerotiorum and B. cinerea secretomes and potentially host infection. Only 8% of the predicted proteins were distinct between the two secretomes. In contrast to S. sclerotiorum, the B. cinerea secretome lacked CFEM- or LysM-containing proteins. The 115 fungal and oomycete genome comparison identified 30 proteins specific to S. sclerotiorum and B. cinerea, plus 11 proteins specific to S. sclerotiorum and 32 proteins specific to B. cinerea. Expressed sequence tag (EST) and proteomic analyses showed that 246 S. sclerotiorum secretome encoding genes had EST support, including 101 which were only expressed in vitro and 49 which were only expressed in planta, whilst 42 predicted proteins were experimentally proven to be secreted. These detailed in silico analyses of two important necrotrophic pathogens will permit informed choices to be made when candidate effector proteins are selected for function analyses in planta. PMID:26107498

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.

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.

Linking microbial community structure to function in representative simulated systems.

PubMed

Marcus, Ian M; Wilder, Hailey A; Quazi, Shanin J; Walker, Sharon L

2013-04-01

Pathogenic bacteria are generally studied as a single strain under ideal growing conditions, although these conditions are not the norm in the environments in which pathogens typically proliferate. In this investigation, a representative microbial community along with Escherichia coli O157:H7, a model pathogen, was studied in three environments in which such a pathogen could be found: a human colon, a septic tank, and groundwater. Each of these systems was built in the lab in order to retain the physical/chemical and microbial complexity of the environments while maintaining control of the feed into the models. The microbial community in the colon was found to have a high percentage of bacteriodetes and firmicutes, while the septic tank and groundwater systems were composed mostly of proteobacteria. The introduction of E. coli O157:H7 into the simulated systems elicited a shift in the structures and phenotypic cell characteristics of the microbial communities. The fate and transport of the microbial community with E. coli O157:H7 were found to be significantly different from those of E. coli O157:H7 studied as a single isolate, suggesting that the behavior of the organism in the environment was different from that previously conceived. The findings in this study clearly suggest that to gain insight into the fate of pathogens, cells should be grown and analyzed under conditions simulating those of the environment in which the pathogens are present.

Linking Microbial Community Structure to Function in Representative Simulated Systems

PubMed Central

Marcus, Ian M.; Wilder, Hailey A.; Quazi, Shanin J.

2013-01-01

Pathogenic bacteria are generally studied as a single strain under ideal growing conditions, although these conditions are not the norm in the environments in which pathogens typically proliferate. In this investigation, a representative microbial community along with Escherichia coli O157:H7, a model pathogen, was studied in three environments in which such a pathogen could be found: a human colon, a septic tank, and groundwater. Each of these systems was built in the lab in order to retain the physical/chemical and microbial complexity of the environments while maintaining control of the feed into the models. The microbial community in the colon was found to have a high percentage of bacteriodetes and firmicutes, while the septic tank and groundwater systems were composed mostly of proteobacteria. The introduction of E. coli O157:H7 into the simulated systems elicited a shift in the structures and phenotypic cell characteristics of the microbial communities. The fate and transport of the microbial community with E. coli O157:H7 were found to be significantly different from those of E. coli O157:H7 studied as a single isolate, suggesting that the behavior of the organism in the environment was different from that previously conceived. The findings in this study clearly suggest that to gain insight into the fate of pathogens, cells should be grown and analyzed under conditions simulating those of the environment in which the pathogens are present. PMID:23396331

Evidence for common ancestry among viruses isolated from wild birds in Beringia and highly pathogenic intercontinental reassortant H5N1 and H5N2 influenza A viruses

USGS Publications Warehouse

Ramey, Andy M.; Reeves, Andrew; Teslaa, Joshua L.; Nashold, Sean W.; Donnelly, Tyrone F.; Bahl, Justin; Hall, Jeffrey S.

2016-01-01

Highly pathogenic clade 2.3.4.4 H5N8, H5N2, and H5N1 influenza A viruses were first detected in wild, captive, and domestic birds in North America in November–December 2014. In this study, we used wild waterbird samples collected in Alaska prior to the initial detection of clade 2.3.4.4 H5 influenza A viruses in North America to assess the evidence for: (1) dispersal of highly pathogenic influenza A viruses from East Asia to North America by migratory birds via Alaska and (2) ancestral origins of clade 2.3.4.4 H5 reassortant viruses in Beringia. Although we did not detect highly pathogenic influenza A viruses in our sample collection from western Alaska, we did identify viruses that contained gene segments sharing recent common ancestry with intercontinental reassortant H5N2 and H5N1 viruses. Results of phylogenetic analyses and estimates for times of most recent common ancestry support migratory birds sampled in Beringia as maintaining viral diversity closely related to novel highly pathogenic influenza A virus genotypes detected in North America. Although our results do not elucidate the route by which highly pathogenic influenza A viruses were introduced into North America, genetic evidence is consistent with the hypothesized trans-Beringian route of introduction via migratory birds.

Contrasting epidemic histories reveal pathogen-mediated balancing selection on class II MHC diversity in a wild songbird.

PubMed

Hawley, Dana M; Fleischer, Robert C

2012-01-01

The extent to which pathogens maintain the extraordinary polymorphism at vertebrate Major Histocompatibility Complex (MHC) genes via balancing selection has intrigued evolutionary biologists for over half a century, but direct tests remain challenging. Here we examine whether a well-characterized epidemic of Mycoplasmal conjunctivitis resulted in balancing selection on class II MHC in a wild songbird host, the house finch (Carpodacus mexicanus). First, we confirmed the potential for pathogen-mediated balancing selection by experimentally demonstrating that house finches with intermediate to high multi-locus MHC diversity are more resistant to challenge with Mycoplasma gallisepticum. Second, we documented sequence and diversity-based signatures of pathogen-mediated balancing selection at class II MHC in exposed host populations that were absent in unexposed, control populations across an equivalent time period. Multi-locus MHC diversity significantly increased in exposed host populations following the epidemic despite initial compromised diversity levels from a recent introduction bottleneck in the exposed host range. We did not observe equivalent changes in allelic diversity or heterozygosity across eight neutral microsatellite loci, suggesting that the observations reflect selection rather than neutral demographic processes. Our results indicate that a virulent pathogen can exert sufficient balancing selection on class II MHC to rescue compromised levels of genetic variation for host resistance in a recently bottlenecked population. These results provide evidence for Haldane's long-standing hypothesis that pathogens directly contribute to the maintenance of the tremendous levels of genetic variation detected in natural populations of vertebrates.

Advances on plant-pathogen interactions from molecular toward systems biology perspectives.

PubMed

Peyraud, Rémi; Dubiella, Ullrich; Barbacci, Adelin; Genin, Stéphane; Raffaele, Sylvain; Roby, Dominique

2017-05-01

In the past 2 decades, progress in molecular analyses of the plant immune system has revealed key elements of a complex response network. Current paradigms depict the interaction of pathogen-secreted molecules with host target molecules leading to the activation of multiple plant response pathways. Further research will be required to fully understand how these responses are integrated in space and time, and exploit this knowledge in agriculture. In this review, we highlight systems biology as a promising approach to reveal properties of molecular plant-pathogen interactions and predict the outcome of such interactions. We first illustrate a few key concepts in plant immunity with a network and systems biology perspective. Next, we present some basic principles of systems biology and show how they allow integrating multiomics data and predict cell phenotypes. We identify challenges for systems biology of plant-pathogen interactions, including the reconstruction of multiscale mechanistic models and the connection of host and pathogen models. Finally, we outline studies on resistance durability through the robustness of immune system networks, the identification of trade-offs between immunity and growth and in silico plant-pathogen co-evolution as exciting perspectives in the field. We conclude that the development of sophisticated models of plant diseases incorporating plant, pathogen and climate properties represent a major challenge for agriculture in the future. © 2016 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Aquatic Pseudomonads Inhibit Oomycete Plant Pathogens of Glycine max

PubMed Central

Wagner, Andrew; Norris, Stephen; Chatterjee, Payel; Morris, Paul F.; Wildschutte, Hans

2018-01-01

Seedling root rot of soybeans caused by the host-specific pathogen Phytophthora sojae, and a large number of Pythium species, is an economically important disease across the Midwest United States that negatively impacts soybean yields. Research on biocontrol strategies for crop pathogens has focused on compounds produced by microbes from soil, however, recent studies suggest that aquatic bacteria express distinct compounds that efficiently inhibit a wide range of pathogens. Based on these observations, we hypothesized that freshwater strains of pseudomonads might be producing novel antagonistic compounds that inhibit the growth of oomycetes. To test this prediction, we utilized a collection of 330 Pseudomonas strains isolated from soil and freshwater habitats, and determined their activity against a panel of five oomycetes: Phytophthora sojae, Pythium heterothalicum, Pythium irregulare, Pythium sylvaticum, and Pythium ultimum, all of which are pathogenic on soybeans. Among the bacterial strains, 118 exhibited antagonistic activity against at least one oomycete species, and 16 strains were inhibitory to all pathogens. Antagonistic activity toward oomycetes was significantly more common for aquatic isolates than for soil isolates. One water-derived strain, 06C 126, was predicted to express a siderophore and exhibited diverse antagonistic profiles when tested on nutrient rich and iron depleted media suggesting that more than one compound was produced that effectively inhibited oomycetes. These results support the concept that aquatic strains are an efficient source of compounds that inhibit pathogens. We outline a strategy to identify other strains that express unique compounds that may be useful biocontrol agents. PMID:29896163

Rapid acquisition of polymorphic virulence markers during adaptation of highly pathogenic avian influenza H5N8 virus in the mouse.

PubMed

Choi, Won-Suk; Baek, Yun Hee; Kwon, Jin Jung; Jeong, Ju Hwan; Park, Su-Jin; Kim, Young-Il; Yoon, Sun-Woo; Hwang, Jungwon; Kim, Myung Hee; Kim, Chul-Joong; Webby, Richard J; Choi, Young Ki; Song, Min-Suk

2017-01-17

Emergence of a highly pathogenic avian influenza (HPAI) H5N8 virus in Asia and its spread to Europe and North America has caused great concern for human health. Although the H5N8 virus has been only moderately pathogenic to mammalian hosts, virulence can still increase. We evaluated the pathogenic potential of several H5N8 strains via the mouse-adaptation method. Two H5N8 viruses were sequentially passaged in BALB/c mice and plaque-purified from lung samples. The viruses rapidly obtained high virulence (MLD 50 , up to 0.5 log10 PFU/mL) within 5 passages. Sequence analysis revealed the acquisition of several virulence markers, including the novel marker P708S in PB1 gene. Combinations of markers synergistically enhanced viral replication and polymerase activity in human cell lines and virulence and multiorgan dissemination in mice. These results suggest that H5N8 viruses can rapidly acquire virulence markers in mammalian hosts; thus, rapid spread as well as repeated viral introduction into the hosts may significantly increase the risk of human infection and elevate pandemic potential.

Rapid acquisition of polymorphic virulence markers during adaptation of highly pathogenic avian influenza H5N8 virus in the mouse

PubMed Central

Choi, Won-Suk; Baek, Yun Hee; Kwon, Jin Jung; Jeong, Ju Hwan; Park, Su-Jin; Kim, Young-il; Yoon, Sun-Woo; Hwang, Jungwon; Kim, Myung Hee; Kim, Chul-Joong; Webby, Richard J.; Choi, Young Ki; Song, Min-Suk

2017-01-01

Emergence of a highly pathogenic avian influenza (HPAI) H5N8 virus in Asia and its spread to Europe and North America has caused great concern for human health. Although the H5N8 virus has been only moderately pathogenic to mammalian hosts, virulence can still increase. We evaluated the pathogenic potential of several H5N8 strains via the mouse-adaptation method. Two H5N8 viruses were sequentially passaged in BALB/c mice and plaque-purified from lung samples. The viruses rapidly obtained high virulence (MLD50, up to 0.5 log10 PFU/mL) within 5 passages. Sequence analysis revealed the acquisition of several virulence markers, including the novel marker P708S in PB1 gene. Combinations of markers synergistically enhanced viral replication and polymerase activity in human cell lines and virulence and multiorgan dissemination in mice. These results suggest that H5N8 viruses can rapidly acquire virulence markers in mammalian hosts; thus, rapid spread as well as repeated viral introduction into the hosts may significantly increase the risk of human infection and elevate pandemic potential. PMID:28094780

A microfluidic platform with integrated arrays for immunologic assays for biological pathogen detection

NASA Astrophysics Data System (ADS)

Klemm, Richard; Becker, Holger; Hlawatsch, Nadine; Julich, Sandra; Miethe, Peter; Moche, Christian; Schattschneider, Sebastian; Tomaso, Herbert; Gärtner, Claudia

2014-05-01

The ability to integrate complete assays on a microfluidic chip helps to greatly simplify instrument requirements and allows the use of lab-on-a-chip technology in the field. A core application for such field-portable systems is the detection of pathogens in a CBRN scenario such as permanent monitoring of airborne pathogens, e.g. in subway stations or hospitals etc. An immunological assay was chosen as method for the pathogen identification. The conceptual approach was its realization as a lab-on-a-chip system, enabling an easy handling of the sample in an automated manner. The immunological detection takes place on an antibody array directly implemented in the microfluidic network. Different immobilization strategies will be presented showing the performance of the system. Central elements of the disposable microfluidic device like fluidic interface, turning valves, liquid introduction and waste storage, as well as the architecture of measurement and control fluidic network, will be introduced. Overall process times of about 30 minutes were achieved and assays for the detection of Francisella tularensis and Yersinia pestis are presented. An important feature of the integrated lab-on-a-chip approach is that all waste liquids remain on-chip and contamination risks can be avoided.

Temporal and spatial scaling of the genetic structure of a vector-borne plant pathogen.

PubMed

Coletta-Filho, Helvécio D; Francisco, Carolina S; Almeida, Rodrigo P P

2014-02-01

The ecology of plant pathogens of perennial crops is affected by the long-lived nature of their immobile hosts. In addition, changes to the genetic structure of pathogen populations may affect disease epidemiology and management practices; examples include local adaptation of more fit genotypes or introduction of novel genotypes from geographically distant areas via human movement of infected plant material or insect vectors. We studied the genetic structure of Xylella fastidiosa populations causing disease in sweet orange plants in Brazil at multiple scales using fast-evolving molecular markers (simple-sequence DNA repeats). Results show that populations of X. fastidiosa were regionally isolated, and that isolation was maintained for populations analyzed a decade apart from each other. However, despite such geographic isolation, local populations present in year 2000 were largely replaced by novel genotypes in 2009 but not as a result of migration. At a smaller spatial scale (individual trees), results suggest that isolates within plants originated from a shared common ancestor. In summary, new insights on the ecology of this economically important plant pathogen were obtained by sampling populations at different spatial scales and two different time points.

IPMP 2013 - A comprehensive data analysis tool for predictive microbiology

USDA-ARS?s Scientific Manuscript database

Predictive microbiology is an area of applied research in food science that uses mathematical models to predict the changes in the population of pathogenic or spoilage microorganisms in foods undergoing complex environmental changes during processing, transportation, distribution, and storage. It f...

A Mycobacterium avium subsp. paratuberculosis predicted serine protease is associated with acid stress and intraphagosomal survival

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) is an intracellular pathogen that persists inside host macrophages despite severe oxidative stress and nutrient deprivation. Intrabacterial pH homeostasis is vital to pathogenic mycobacteria to preserve cellular biological processes and stability of ...

Response of coliform populations in streambed sediment and water column to changes in nutrient concentrations in water.

PubMed

Shelton, D R; Pachepsky, Y A; Kiefer, L A; Blaustein, R A; McCarty, G W; Dao, T H

2014-08-01

As sediments increasingly become recognized as reservoirs of indicator and pathogen microorganisms, an understanding of the persistence of indicator organisms becomes important for assessment and predictions of microbial water quality. The objective of this work was to observe the response of water column and sediment coliform populations to the change in nutrient concentrations in the water column. Survival experiments were conducted in flow-through chambers containing sandy sediments. Bovine feces were collected fresh and introduced into sediment. Sixteen days later, the same fecal material was autoclaved and diluted to provide three levels - 1×, 0.5×, and 0.1× of nutrient concentrations - spike in water column. Total coliforms, Escherichia coli, and total aerobic heterotrophic bacterial concentrations were monitored in water and sediment. Bacteria responded to the nutrient spike with initial growth both in the water column and in sediment. The response of bacterial concentrations in water column was nonlinear, with no significant changes at 0.1 and .5× spikes, but a substantial change at 1× spike. Bacteria in sediment responded to the spikes at all added nutrient levels. Coliform inactivation rates both in sediment and in water after the initial growth occurred, were not significantly different from the inactivation rates before spike. These results indicate that introduction of nutrients into the water column results in nonlinear response of E. coli concentrations both in water and in sediments, followed by the inactivation with the same rate as before introduction of nutrients. Published by Elsevier Ltd.

An introduction to joint research by the USEPA and USGS on ...

EPA Pesticide Factsheets

Improvements in analytical methodology have allowed low-level detection of an ever increasing number of pharmaceuticals, personal care products, hormones, pathogens and other contaminants of emerging concern (CECs). The use of these improved analytical tools has allowed researchers to document the global presence of CECs derived from a wide range of urban (e.g. wastewater treatment plants, onsite septic systems, landfills) and agricultural (e.g. livestock and crop production) sources. In addition, such research has documented that CECs are sufficiently mobile and persistent to be transported to all environmental compartments (e.g. surface water, stream bed sediment, groundwater, soil, tissue). This paper is an introduction to a series of papers being published in Science of the Total Environment

Visibility from roads predict the distribution of invasive fishes in agricultural ponds.

PubMed

Kizuka, Toshikazu; Akasaka, Munemitsu; Kadoya, Taku; Takamura, Noriko

2014-01-01

Propagule pressure and habitat characteristics are important factors used to predict the distribution of invasive alien species. For species exhibiting strong propagule pressure because of human-mediated introduction of species, indicators of introduction potential must represent the behavioral characteristics of humans. This study examined 64 agricultural ponds to assess the visibility of ponds from surrounding roads and its value as a surrogate of propagule pressure to explain the presence and absence of two invasive fish species. A three-dimensional viewshed analysis using a geographic information system quantified the visual exposure of respective ponds to humans. Binary classification trees were developed as a function of their visibility from roads, as well as five environmental factors: river density, connectivity with upstream dam reservoirs, pond area, chlorophyll a concentration, and pond drainage. Traditional indicators of human-mediated introduction (road density and proportion of urban land-use area) were alternatively included for comparison instead of visual exposure. The presence of Bluegill (Lepomis macrochirus) was predicted by the ponds' higher visibility from roads and pond connection with upstream dam reservoirs. Results suggest that fish stocking into ponds and their dispersal from upstream sources facilitated species establishment. Largemouth bass (Micropterus salmoides) distribution was constrained by chlorophyll a concentration, suggesting their lower adaptability to various environments than that of Bluegill. Based on misclassifications from classification trees for Bluegill, pond visual exposure to roads showed greater predictive capability than traditional indicators of human-mediated introduction. Pond visibility is an effective predictor of invasive species distribution. Its wider use might improve management and mitigate further invasion. The visual exposure of recipient ecosystems to humans is important for many invasive species that spread with frequent instances of human-mediated introduction.

Substitutions near the Hemagglutinin Receptor-Binding Site Determine the Antigenic Evolution of Influenza A H3N2 Viruses in U.S. Swine

PubMed Central

Lewis, Nicola S.; Anderson, Tavis K.; Kitikoon, Pravina; Skepner, Eugene; Burke, David F.

2014-01-01

ABSTRACT Swine influenza A virus is an endemic and economically important pathogen in pigs, with the potential to infect other host species. The hemagglutinin (HA) protein is the primary target of protective immune responses and the major component in swine influenza A vaccines. However, as a result of antigenic drift, vaccine strains must be regularly updated to reflect currently circulating strains. Characterizing the cross-reactivity between strains in pigs and seasonal influenza virus strains in humans is also important in assessing the relative risk of interspecies transmission of viruses from one host population to the other. Hemagglutination inhibition (HI) assay data for swine and human H3N2 viruses were used with antigenic cartography to quantify the antigenic differences among H3N2 viruses isolated from pigs in the United States from 1998 to 2013 and the relative cross-reactivity between these viruses and current human seasonal influenza A virus strains. Two primary antigenic clusters were found circulating in the pig population, but with enough diversity within and between the clusters to suggest updates in vaccine strains are needed. We identified single amino acid substitutions that are likely responsible for antigenic differences between the two primary antigenic clusters and between each antigenic cluster and outliers. The antigenic distance between current seasonal influenza virus H3 strains in humans and those endemic in swine suggests that population immunity may not prevent the introduction of human viruses into pigs, and possibly vice versa, reinforcing the need to monitor and prepare for potential incursions. IMPORTANCE Influenza A virus (IAV) is an important pathogen in pigs and humans. The hemagglutinin (HA) protein is the primary target of protective immune responses and the major target of vaccines. However, vaccine strains must be updated to reflect current strains. Characterizing the differences between seasonal IAV in humans and swine IAV is important in assessing the relative risk of interspecies transmission of viruses. We found two primary antigenic clusters of H3N2 in the U.S. pig population, with enough diversity to suggest updates in swine vaccine strains are needed. We identified changes in the HA protein that are likely responsible for these differences and that may be useful in predicting when vaccines need to be updated. The difference between human H3N2 viruses and those in swine is enough that population immunity is unlikely to prevent new introductions of human IAV into pigs or vice versa, reinforcing the need to monitor and prepare for potential introductions. PMID:24522915

Growth rate, transmission mode and virulence in human pathogens.

PubMed

Leggett, Helen C; Cornwallis, Charlie K; Buckling, Angus; West, Stuart A

2017-05-05

The harm that pathogens cause to hosts during infection, termed virulence, varies across species from negligible to a high likelihood of rapid death. Classic theory for the evolution of virulence is based on a trade-off between pathogen growth, transmission and host survival, which predicts that higher within-host growth causes increased transmission and higher virulence. However, using data from 61 human pathogens, we found the opposite correlation to the expected positive correlation between pathogen growth rate and virulence. We found that (i) slower growing pathogens are significantly more virulent than faster growing pathogens, (ii) inhaled pathogens and pathogens that infect via skin wounds are significantly more virulent than pathogens that are ingested, but (iii) there is no correlation between symptoms of infection that aid transmission (such as diarrhoea and coughing) and virulence. Overall, our results emphasize how virulence can be influenced by mechanistic life-history details, especially transmission mode, that determine how parasites infect and exploit their hosts.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'. © 2017 The Authors.

Insight of Genus Corynebacterium: Ascertaining the Role of Pathogenic and Non-pathogenic Species

PubMed Central

Oliveira, Alberto; Oliveira, Leticia C.; Aburjaile, Flavia; Benevides, Leandro; Tiwari, Sandeep; Jamal, Syed B.; Silva, Arthur; Figueiredo, Henrique C. P.; Ghosh, Preetam; Portela, Ricardo W.; De Carvalho Azevedo, Vasco A.; Wattam, Alice R.

2017-01-01

This review gathers recent information about genomic and transcriptomic studies in the Corynebacterium genus, exploring, for example, prediction of pathogenicity islands and stress response in different pathogenic and non-pathogenic species. In addition, is described several phylogeny studies to Corynebacterium, exploring since the identification of species until biological speciation in one species belonging to the genus Corynebacterium. Important concepts associated with virulence highlighting the role of Pld protein and Tox gene. The adhesion, characteristic of virulence factor, was described using the sortase mechanism that is associated to anchorage to the cell wall. In addition, survival inside the host cell and some diseases, were too addressed for pathogenic corynebacteria, while important biochemical pathways and biotechnological applications retain the focus of this review for non-pathogenic corynebacteria. Concluding, this review broadly explores characteristics in genus Corynebacterium showing to have strong relevance inside the medical, veterinary, and biotechnology field. PMID:29075239

Insight of Genus Corynebacterium: Ascertaining the Role of Pathogenic and Non-pathogenic Species.

PubMed

Oliveira, Alberto; Oliveira, Leticia C; Aburjaile, Flavia; Benevides, Leandro; Tiwari, Sandeep; Jamal, Syed B; Silva, Arthur; Figueiredo, Henrique C P; Ghosh, Preetam; Portela, Ricardo W; De Carvalho Azevedo, Vasco A; Wattam, Alice R

2017-01-01

This review gathers recent information about genomic and transcriptomic studies in the Corynebacterium genus, exploring, for example, prediction of pathogenicity islands and stress response in different pathogenic and non-pathogenic species. In addition, is described several phylogeny studies to Corynebacterium , exploring since the identification of species until biological speciation in one species belonging to the genus Corynebacterium . Important concepts associated with virulence highlighting the role of Pld protein and Tox gene. The adhesion, characteristic of virulence factor, was described using the sortase mechanism that is associated to anchorage to the cell wall. In addition, survival inside the host cell and some diseases, were too addressed for pathogenic corynebacteria, while important biochemical pathways and biotechnological applications retain the focus of this review for non-pathogenic corynebacteria. Concluding, this review broadly explores characteristics in genus Corynebacterium showing to have strong relevance inside the medical, veterinary, and biotechnology field.

Pathogen prevalence, group bias, and collectivism in the standard cross-cultural sample.

PubMed

Cashdan, Elizabeth; Steele, Matthew

2013-03-01

It has been argued that people in areas with high pathogen loads will be more likely to avoid outsiders, to be biased in favor of in-groups, and to hold collectivist and conformist values. Cross-national studies have supported these predictions. In this paper we provide new pathogen codes for the 186 cultures of the Standard Cross-Cultural Sample and use them, together with existing pathogen and ethnographic data, to try to replicate these cross-national findings. In support of the theory, we found that cultures in high pathogen areas were more likely to socialize children toward collectivist values (obedience rather than self-reliance). There was some evidence that pathogens were associated with reduced adult dispersal. However, we found no evidence of an association between pathogens and our measures of group bias (in-group loyalty and xenophobia) or intergroup contact.

Evolutionary conservation analysis increases the colocalization of predicted exonic splicing enhancers in the BRCA1 gene with missense sequence changes and in-frame deletions, but not polymorphisms

PubMed Central

Pettigrew, Christopher; Wayte, Nicola; Lovelock, Paul K; Tavtigian, Sean V; Chenevix-Trench, Georgia; Spurdle, Amanda B; Brown, Melissa A

2005-01-01

Introduction Aberrant pre-mRNA splicing can be more detrimental to the function of a gene than changes in the length or nature of the encoded amino acid sequence. Although predicting the effects of changes in consensus 5' and 3' splice sites near intron:exon boundaries is relatively straightforward, predicting the possible effects of changes in exonic splicing enhancers (ESEs) remains a challenge. Methods As an initial step toward determining which ESEs predicted by the web-based tool ESEfinder in the breast cancer susceptibility gene BRCA1 are likely to be functional, we have determined their evolutionary conservation and compared their location with known BRCA1 sequence variants. Results Using the default settings of ESEfinder, we initially detected 669 potential ESEs in the coding region of the BRCA1 gene. Increasing the threshold score reduced the total number to 464, while taking into consideration the proximity to splice donor and acceptor sites reduced the number to 211. Approximately 11% of these ESEs (23/211) either are identical at the nucleotide level in human, primates, mouse, cow, dog and opossum Brca1 (conserved) or are detectable by ESEfinder in the same position in the Brca1 sequence (shared). The frequency of conserved and shared predicted ESEs between human and mouse is higher in BRCA1 exons (2.8 per 100 nucleotides) than in introns (0.6 per 100 nucleotides). Of conserved or shared putative ESEs, 61% (14/23) were predicted to be affected by sequence variants reported in the Breast Cancer Information Core database. Applying the filters described above increased the colocalization of predicted ESEs with missense changes, in-frame deletions and unclassified variants predicted to be deleterious to protein function, whereas they decreased the colocalization with known polymorphisms or unclassified variants predicted to be neutral. Conclusion In this report we show that evolutionary conservation analysis may be used to improve the specificity of an ESE prediction tool. This is the first report on the prediction of the frequency and distribution of ESEs in the BRCA1 gene, and it is the first reported attempt to predict which ESEs are most likely to be functional and therefore which sequence variants in ESEs are most likely to be pathogenic. PMID:16280041

PCPPI: a comprehensive database for the prediction of Penicillium-crop protein-protein interactions

USDA-ARS?s Scientific Manuscript database

Penicillium expansum, the causal agent of blue mold, is one of the most prevalent postharvest pathogens infecting a wide range of crops after harvest. In response, crops have evolved various defense systems to protect themselves against this and other pathogens. Penicillium-crop interaction is a m...

PREDICTING VIRUS LOADING TO STREAMS FROM GROUNDWATER: NONPOINT SOURCE APPLICATIONS FOR TMDL EVALUATIONS

EPA Science Inventory

Density of septic systems in watersheds has been identified as a contributor to pathogen loading in streams. At present, little work has been done to provide simple models to assist in evaluating groundwater loading for pathogen TMDLs. A compartmental model is being developed for...

Environmental interactions that influence secondary metabolism and development in the saprophytic crop pathogen Aspergillus flavus

USDA-ARS?s Scientific Manuscript database

Aspergillus flavus is a pathogenic and opportunistic fungus that can infect several crops of agricultural importance and has the potential to produce carcinogenic mycotoxins such as aflatoxin. Predicted changes in global temperatures, precipitation patterns and carbon dioxide levels are expected to ...

SCREENING MODELS TO PREDICT PROBABILITY OF CONTAMINATION BY PATHOGENIC VIRUSES IN DRINKING WATER AQUIFERS

EPA Science Inventory

The Safe Drinking Water Act's 1996 Amendments broadened the definition of public water systems (PWS) to include systems which serve drinking water to as few as 25 individuals. Implementation of the proposed Ground Water Rule for Pathogens will place an increased burden on utiliti...

Review of pathogen treatment reductions for onsite non-potable reuse of alternative source waters

EPA Science Inventory

Communities face a challenge when implementing onsite reuse of collected waters for non-potable purposes given the lack of national microbial standards. Quantitative Microbial Risk Assessment (QMRA) can be used to predict the pathogen risks associated with the non-potable reuse o...

Analysis of genome sequences from plant pathogenic Rhodococcus reveals genetic novelties in virulence loci

USDA-ARS?s Scientific Manuscript database

Members of Gram-positive Actinobacteria cause economically important diseases to plants. Within the Rhodococcus genus, some members can cause growth deformities and persist as pathogens on a wide range of host plants. The current model predicts that phytopathogenic isolates require a cluster of thre...

Glacial Refugia in Pathogens: European Genetic Structure of Anther Smut Pathogens on Silene latifolia and Silene dioica

PubMed Central

Vercken, Elodie; Fontaine, Michael C.; Gladieux, Pierre; Hood, Michael E.; Jonot, Odile; Giraud, Tatiana

2010-01-01

Climate warming is predicted to increase the frequency of invasions by pathogens and to cause the large-scale redistribution of native host species, with dramatic consequences on the health of domesticated and wild populations of plants and animals. The study of historic range shifts in response to climate change, such as during interglacial cycles, can help in the prediction of the routes and dynamics of infectious diseases during the impending ecosystem changes. Here we studied the population structure in Europe of two Microbotryum species causing anther smut disease on the plants Silene latifolia and Silene dioica. Clustering analyses revealed the existence of genetically distinct groups for the pathogen on S. latifolia, providing a clear-cut example of European phylogeography reflecting recolonization from southern refugia after glaciation. The pathogen genetic structure was congruent with the genetic structure of its host species S. latifolia, suggesting dependence of the migration pathway of the anther smut fungus on its host. The fungus, however, appeared to have persisted in more numerous and smaller refugia than its host and to have experienced fewer events of large-scale dispersal. The anther smut pathogen on S. dioica also showed a strong phylogeographic structure that might be related to more northern glacial refugia. Differences in host ecology probably played a role in these differences in the pathogen population structure. Very high selfing rates were inferred in both fungal species, explaining the low levels of admixture between the genetic clusters. The systems studied here indicate that migration patterns caused by climate change can be expected to include pathogen invasions that follow the redistribution of their host species at continental scales, but also that the recolonization by pathogens is not simply a mirror of their hosts, even for obligate biotrophs, and that the ecology of hosts and pathogen mating systems likely affects recolonization patterns. PMID:21187901

Prevalence of pathogenic germline variants detected by multigene sequencing in unselected Japanese patients with ovarian cancer

PubMed Central

Hirasawa, Akira; Imoto, Issei; Naruto, Takuya; Akahane, Tomoko; Yamagami, Wataru; Nomura, Hiroyuki; Masuda, Kiyoshi; Susumu, Nobuyuki; Tsuda, Hitoshi; Aoki, Daisuke

2017-01-01

Pathogenic germline BRCA1, BRCA2 (BRCA1/2), and several other gene variants predispose women to primary ovarian, fallopian tube, and peritoneal carcinoma (OC), although variant frequency and relevance information is scarce in Japanese women with OC. Using targeted panel sequencing, we screened 230 unselected Japanese women with OC from our hospital-based cohort for pathogenic germline variants in 75 or 79 OC-associated genes. Pathogenic variants of 11 genes were identified in 41 (17.8%) women: 19 (8.3%; BRCA1), 8 (3.5%; BRCA2), 6 (2.6%; mismatch repair genes), 3 (1.3%; RAD51D), 2 (0.9%; ATM), 1 (0.4%; MRE11A), 1 (FANCC), and 1 (GABRA6). Carriers of BRCA1/2 or any other tested gene pathogenic variants were more likely to be diagnosed younger, have first or second-degree relatives with OC, and have OC classified as high-grade serous carcinoma (HGSC). After adjustment for these variables, all 3 features were independent predictive factors for pathogenic variants in any tested genes whereas only the latter two remained for variants in BRCA1/2. Our data indicate similar variant prevalence in Japanese patients with OC and other ethnic groups and suggest that HGSC and OC family history may facilitate genetic predisposition prediction in Japanese patients with OC and referring high-risk patients for genetic counseling and testing. PMID:29348823

Prevalence of pathogenic germline variants detected by multigene sequencing in unselected Japanese patients with ovarian cancer.

PubMed

Hirasawa, Akira; Imoto, Issei; Naruto, Takuya; Akahane, Tomoko; Yamagami, Wataru; Nomura, Hiroyuki; Masuda, Kiyoshi; Susumu, Nobuyuki; Tsuda, Hitoshi; Aoki, Daisuke

2017-12-22

Pathogenic germline BRCA1 , BRCA2 ( BRCA1/2 ), and several other gene variants predispose women to primary ovarian, fallopian tube, and peritoneal carcinoma (OC), although variant frequency and relevance information is scarce in Japanese women with OC. Using targeted panel sequencing, we screened 230 unselected Japanese women with OC from our hospital-based cohort for pathogenic germline variants in 75 or 79 OC-associated genes. Pathogenic variants of 11 genes were identified in 41 (17.8%) women: 19 (8.3%; BRCA1 ), 8 (3.5%; BRCA2 ), 6 (2.6%; mismatch repair genes), 3 (1.3%; RAD51D ), 2 (0.9%; ATM ), 1 (0.4%; MRE11A ), 1 ( FANCC ), and 1 ( GABRA6 ). Carriers of BRCA1/2 or any other tested gene pathogenic variants were more likely to be diagnosed younger, have first or second-degree relatives with OC, and have OC classified as high-grade serous carcinoma (HGSC). After adjustment for these variables, all 3 features were independent predictive factors for pathogenic variants in any tested genes whereas only the latter two remained for variants in BRCA1/2 . Our data indicate similar variant prevalence in Japanese patients with OC and other ethnic groups and suggest that HGSC and OC family history may facilitate genetic predisposition prediction in Japanese patients with OC and referring high-risk patients for genetic counseling and testing.

Identification of Hotspots in the European Union for the Introduction of Four Zoonotic Arboviroses by Live Animal Trade

PubMed Central

Durand, Benoit; Lecollinet, Sylvie; Beck, Cécile; Martínez-López, Beatriz; Balenghien, Thomas; Chevalier, Véronique

2013-01-01

Live animal trade is considered a major mode of introduction of viruses from enzootic foci into disease-free areas. Due to societal and behavioural changes, some wild animal species may nowadays be considered as pet species. The species diversity of animals involved in international trade is thus increasing. This could benefit pathogens that have a broad host range such as arboviruses. The objective of this study was to analyze the risk posed by live animal imports for the introduction, in the European Union (EU), of four arboviruses that affect human and horses: Eastern and Western equine encephalomyelitis, Venezuelan equine encephalitis and Japanese encephalitis. Importation data for a five-years period (2005-2009, extracted from the EU TRACES database), environmental data (used as a proxy for the presence of vectors) and horses and human population density data (impacting the occurrence of clinical cases) were combined to derive spatially explicit risk indicators for virus introduction and for the potential consequences of such introductions. Results showed the existence of hotspots where the introduction risk was the highest in Belgium, in the Netherlands and in the north of Italy. This risk was higher for Eastern equine encephalomyelitis (EEE) than for the three other diseases. It was mainly attributed to exotic pet species such as rodents, reptiles or cage birds, imported in small-sized containments from a wide variety of geographic origins. The increasing species and origin diversity of these animals may have in the future a strong impact on the risk of introduction of arboviruses in the EU. PMID:23894573

Identification of hotspots in the European union for the introduction of four zoonotic arboviroses by live animal trade.

PubMed

Durand, Benoit; Lecollinet, Sylvie; Beck, Cécile; Martínez-López, Beatriz; Balenghien, Thomas; Chevalier, Véronique

2013-01-01

Live animal trade is considered a major mode of introduction of viruses from enzootic foci into disease-free areas. Due to societal and behavioural changes, some wild animal species may nowadays be considered as pet species. The species diversity of animals involved in international trade is thus increasing. This could benefit pathogens that have a broad host range such as arboviruses. The objective of this study was to analyze the risk posed by live animal imports for the introduction, in the European Union (EU), of four arboviruses that affect human and horses: Eastern and Western equine encephalomyelitis, Venezuelan equine encephalitis and Japanese encephalitis. Importation data for a five-years period (2005-2009, extracted from the EU TRACES database), environmental data (used as a proxy for the presence of vectors) and horses and human population density data (impacting the occurrence of clinical cases) were combined to derive spatially explicit risk indicators for virus introduction and for the potential consequences of such introductions. Results showed the existence of hotspots where the introduction risk was the highest in Belgium, in the Netherlands and in the north of Italy. This risk was higher for Eastern equine encephalomyelitis (EEE) than for the three other diseases. It was mainly attributed to exotic pet species such as rodents, reptiles or cage birds, imported in small-sized containments from a wide variety of geographic origins. The increasing species and origin diversity of these animals may have in the future a strong impact on the risk of introduction of arboviruses in the EU.

Effect of calcium hydroxide application to cattle feedlot pens on Escherichia coli O157:H7 and total E. coli in pen surface manure

USDA-ARS?s Scientific Manuscript database

Introduction: Cattle and beef products are sources of the pathogen Escherichia coli O157:H7. Lime products have a long history of use in cattle production as disinfectants for sick pens, calving pens, and muddy areas, to control the spread of diseases. Lime may also be useful as a preharvest trea...

Agribusiness Industry, 2006

DTIC Science & Technology

2006-01-01

countries. An economic boost of this magnitude would also go a long ways toward eliminating rural poverty around the globe, as trade is universally...World Bank estimates that 140 million people could be lifted out of poverty by 2015 if members of the World Trade Organization ended subsidies and...contaminated beef with a nicotine -based insecticide, poisoning 111 people. This type of post-kill step introduction of a poison or pathogen presents perhaps

Gene Gun-Delivered DNA Vaccines for Hemorrhagic Fever With Renal Syndrome: Advancement to Clinical Trials

DTIC Science & Technology

2008-12-01

bioterrorism pathogens that threaten troops. 1. INTRODUCTION Hantaviruses are RNA viruses belonging to the family Bunyaviridae, and are...the etiologic agents of hemorrhagic fever with renal syndrome (HFRS) in the Old World and hantavirus pulmonary syndrome in the New World. The...viruses are carried by persistently infected rodents and are found worldwide. There are no licensed vaccines for hantaviruses ; thus, they continue to

Integrated inference and evaluation of host–fungi interaction networks

PubMed Central

Remmele, Christian W.; Luther, Christian H.; Balkenhol, Johannes; Dandekar, Thomas; Müller, Tobias; Dittrich, Marcus T.

2015-01-01

Fungal microorganisms frequently lead to life-threatening infections. Within this group of pathogens, the commensal Candida albicans and the filamentous fungus Aspergillus fumigatus are by far the most important causes of invasive mycoses in Europe. A key capability for host invasion and immune response evasion are specific molecular interactions between the fungal pathogen and its human host. Experimentally validated knowledge about these crucial interactions is rare in literature and even specialized host–pathogen databases mainly focus on bacterial and viral interactions whereas information on fungi is still sparse. To establish large-scale host–fungi interaction networks on a systems biology scale, we develop an extended inference approach based on protein orthology and data on gene functions. Using human and yeast intraspecies networks as template, we derive a large network of pathogen–host interactions (PHI). Rigorous filtering and refinement steps based on cellular localization and pathogenicity information of predicted interactors yield a primary scaffold of fungi–human and fungi–mouse interaction networks. Specific enrichment of known pathogenicity-relevant genes indicates the biological relevance of the predicted PHI. A detailed inspection of functionally relevant subnetworks reveals novel host–fungal interaction candidates such as the Candida virulence factor PLB1 and the anti-fungal host protein APP. Our results demonstrate the applicability of interolog-based prediction methods for host–fungi interactions and underline the importance of filtering and refinement steps to attain biologically more relevant interactions. This integrated network framework can serve as a basis for future analyses of high-throughput host–fungi transcriptome and proteome data. PMID:26300851

Sexual Disgust Trumps Pathogen Disgust in Predicting Voter Behavior During the 2016 U.S. Presidential Election.

PubMed

Billingsley, Joseph; Lieberman, Debra; Tybur, Joshua M

2018-01-01

Why is disgust sensitivity associated with socially conservative political views? Is it because socially conservative ideologies mitigate the risks of infectious disease, whether by promoting out-group avoidance or by reinforcing norms that sustain antipathogenic practices? Or might it be because socially conservative ideologies promote moral standards that advance a long-term, as opposed to a short-term, sexual strategy? Recent attempts to test these two explanations have yielded differing results and conflicting interpretations. Here, we contribute to the literature by examining the relationship between disgust sensitivity and political orientation, political party affiliation, and an often overlooked outcome-actual voter behavior. We focus on voter behavior and affiliation for the 2016 U.S. presidential election to determine whether pathogen or sexual disgust better predicts socially conservative ideology. Although many prominent aspects of Donald Trump's campaign-particularly his anti-foreign message-align with the pathogen-avoidance model of conservatism, we found that pathogen-related disgust sensitivity exerted no influence on political ideology, political party affiliation, or voter behavior, after controlling for sexual disgust sensitivity. In contrast, sexual disgust sensitivity was associated with increased odds of voting for Donald Trump versus each other major presidential candidate, as well as with increased odds of affiliating with the Republican versus the Democratic or Libertarian parties. In fact, for every unit increase in sexual disgust sensitivity, the odds of a participant voting for Trump versus Clinton increased by approximately 30%. It seems, then, that sexual disgust trumps pathogen disgust in predicting socially conservative voting behavior.

Difference between Japanese Secondary and Tertiary Medical Facilities Regarding Changes in the Hospitalization of Children for Pneumonia after the Introduction of the Pneumococcal Conjugate Vaccine.

PubMed

Haro, Kaoru; Ogawa, Masato; Hoshina, Takayuki; Kojiro, Masumi; Kusuhara, Koichi

2017-05-24

This study aimed to compare hospitalization of children for pneumonia between secondary and tertiary medical facilities, which hospitalize many children without and with underlying diseases, respectively, after the introduction of the pneumococcal conjugate vaccine (PCV). Our retrospective study included children admitted to the Department of Pediatrics at Kitakyushu General Hospital, a secondary medical facility, and the Hospital of the University of Occupational and Environment Health, Japan, a tertiary medical facility, from 2009 to 2013 for pneumonia. We compared the change in the rate of hospitalization for pneumonia after the introduction of the 7-valent PCV between the secondary and tertiary medical facilities. Hospitalization of patients with pneumonia declined by 28.8% in our secondary medical facility. In particular, hospitalization for pneumonia other than confirmed mycoplasmal or viral pneumonia was significantly reduced by 49.2%. In contrast, hospitalization of patients with pneumonia did not decline in our tertiary medical facility. After the introduction of PCV, hospitalization of children for pneumonia was not reduced at the tertiary medical facility. Various other pathogens besides pneumococcus may be associated with the development of pneumonia in children with underlying diseases.

Effect of route of introduction and host cultivar on the colonization, internalization, and movement of the human pathogen Escherichia coli O157:H7 in spinach.

PubMed

Mitra, R; Cuesta-Alonso, E; Wayadande, A; Talley, J; Gilliland, S; Fletcher, J

2009-07-01

Human pathogens can contaminate leafy produce in the field by various routes. We hypothesized that interactions between Escherichia coli O157:H7 and spinach are influenced by the route of introduction and the leaf microenvironment. E. coli O157:H7 labeled with green fluorescent protein was dropped onto spinach leaf surfaces, simulating bacteria-laden raindrops or sprinkler irrigation, and survived on the phylloplane for at least 14 days, with increasing titers and areas of colonization over time. The same strains placed into the rhizosphere by soil infiltration remained detectable on very few plants and in low numbers (10(2) to 10(6) CFU/g fresh tissue) that decreased over time. Stem puncture inoculations, simulating natural wounding, rarely resulted in colonization or multiplication. Bacteria forced into the leaf interior survived for at least 14 days in intercellular spaces but did not translocate or multiply. Three spinach cultivars with different leaf surface morphologies were compared for colonization by E. coli O157:H7 introduced by leaf drop or soil drench. After 2 weeks, cv. Bordeaux hosted very few bacteria. More bacteria were seen on cv. Space and were dispersed over an area of up to 0.3 mm2. The highest bacterial numbers were observed on cv. Tyee but were dispersed only up to 0.15 mm2, suggesting that cv. Tyee may provide protected niches or more nutrients or may promote stronger bacterial adherence. These findings suggest that the spinach phylloplane is a supportive niche for E. coli O157:H7, but no conclusive evidence was found for natural entry into the plant interior. The results are relevant for interventions aimed at minimizing produce contamination by human pathogens.

Whole Gene Capture Analysis of 15 CRC Susceptibility Genes in Suspected Lynch Syndrome Patients.

PubMed

Jansen, Anne M L; Geilenkirchen, Marije A; van Wezel, Tom; Jagmohan-Changur, Shantie C; Ruano, Dina; van der Klift, Heleen M; van den Akker, Brendy E W M; Laros, Jeroen F J; van Galen, Michiel; Wagner, Anja; Letteboer, Tom G W; Gómez-García, Encarna B; Tops, Carli M J; Vasen, Hans F; Devilee, Peter; Hes, Frederik J; Morreau, Hans; Wijnen, Juul T

2016-01-01

Lynch Syndrome (LS) is caused by pathogenic germline variants in one of the mismatch repair (MMR) genes. However, up to 60% of MMR-deficient colorectal cancer cases are categorized as suspected Lynch Syndrome (sLS) because no pathogenic MMR germline variant can be identified, which leads to difficulties in clinical management. We therefore analyzed the genomic regions of 15 CRC susceptibility genes in leukocyte DNA of 34 unrelated sLS patients and 11 patients with MLH1 hypermethylated tumors with a clear family history. Using targeted next-generation sequencing, we analyzed the entire non-repetitive genomic sequence, including intronic and regulatory sequences, of 15 CRC susceptibility genes. In addition, tumor DNA from 28 sLS patients was analyzed for somatic MMR variants. Of 1979 germline variants found in the leukocyte DNA of 34 sLS patients, one was a pathogenic variant (MLH1 c.1667+1delG). Leukocyte DNA of 11 patients with MLH1 hypermethylated tumors was negative for pathogenic germline variants in the tested CRC susceptibility genes and for germline MLH1 hypermethylation. Somatic DNA analysis of 28 sLS tumors identified eight (29%) cases with two pathogenic somatic variants, one with a VUS predicted to pathogenic and LOH, and nine cases (32%) with one pathogenic somatic variant (n = 8) or one VUS predicted to be pathogenic (n = 1). This is the first study in sLS patients to include the entire genomic sequence of CRC susceptibility genes. An underlying somatic or germline MMR gene defect was identified in ten of 34 sLS patients (29%). In the remaining sLS patients, the underlying genetic defect explaining the MMRdeficiency in their tumors might be found outside the genomic regions harboring the MMR and other known CRC susceptibility genes.

Occurrence of waterborne pathogens and Escherichia coli at offshore drinking water intakes in lake Ontario.

PubMed

Edge, T A; Khan, I U H; Bouchard, R; Guo, J; Hill, S; Locas, A; Moore, L; Neumann, N; Nowak, E; Payment, P; Yang, R; Yerubandi, R; Watson, S

2013-10-01

The occurrence of waterborne pathogens was investigated at three drinking water intakes located about 2 km offshore in Lake Ontario. Water sampling was conducted over 3 years for Campylobacter spp., Cryptosporidium spp., Giardia spp., cultivable enteric viruses, and water quality parameters. All pathogens were detected in the offshore source water for each water treatment plant (WTP1 to WTP3), although at relatively low frequencies and concentrations. Giardia was the most common pathogen, occurring in 36% of water samples from the influent of WTP1 (n = 46), and with a maximum concentration of 0.70 cysts/liter in this influent. Cryptosporidium occurred as frequently as 15% in the WTP2 influent (n = 35), with a maximum concentration of 0.40 oocysts/liter in the WTP1 influent. The human Bacteroidales HF183 DNA marker was most common in the WTP1 influent (19%), and this was the only WTP where the Cryptosporidium hominis genotype was detected. No water quality parameter was predictive of pathogen occurrence across all three WTP influents. Escherichia coli was often below detection when pathogens were detected, and spikes in E. coli concentrations often did not coincide with pathogen occurrence. After summer rain events, river plumes had E. coli concentrations as high as 222 CFU/100 ml in surface waters 2 km offshore, without impacting drinking water intakes below the thermocline on the lake bottom. At times, prechlorination to control mussels at offshore intake cribs compromised the use of E. coli for "raw" water quality assessment, particularly for chlorine-resistant Cryptosporidium. E. coli measured by standard methods did not reliably predict pathogen occurrence at drinking water intakes in offshore ecosystems.

Occurrence of Waterborne Pathogens and Escherichia coli at Offshore Drinking Water Intakes in Lake Ontario

PubMed Central

Khan, I. U. H.; Bouchard, R.; Guo, J.; Hill, S.; Locas, A.; Moore, L.; Neumann, N.; Nowak, E.; Payment, P.; Yang, R.; Yerubandi, R.; Watson, S.

2013-01-01

The occurrence of waterborne pathogens was investigated at three drinking water intakes located about 2 km offshore in Lake Ontario. Water sampling was conducted over 3 years for Campylobacter spp., Cryptosporidium spp., Giardia spp., cultivable enteric viruses, and water quality parameters. All pathogens were detected in the offshore source water for each water treatment plant (WTP1 to WTP3), although at relatively low frequencies and concentrations. Giardia was the most common pathogen, occurring in 36% of water samples from the influent of WTP1 (n = 46), and with a maximum concentration of 0.70 cysts/liter in this influent. Cryptosporidium occurred as frequently as 15% in the WTP2 influent (n = 35), with a maximum concentration of 0.40 oocysts/liter in the WTP1 influent. The human Bacteroidales HF183 DNA marker was most common in the WTP1 influent (19%), and this was the only WTP where the Cryptosporidium hominis genotype was detected. No water quality parameter was predictive of pathogen occurrence across all three WTP influents. Escherichia coli was often below detection when pathogens were detected, and spikes in E. coli concentrations often did not coincide with pathogen occurrence. After summer rain events, river plumes had E. coli concentrations as high as 222 CFU/100 ml in surface waters 2 km offshore, without impacting drinking water intakes below the thermocline on the lake bottom. At times, prechlorination to control mussels at offshore intake cribs compromised the use of E. coli for “raw” water quality assessment, particularly for chlorine-resistant Cryptosporidium. E. coli measured by standard methods did not reliably predict pathogen occurrence at drinking water intakes in offshore ecosystems. PMID:23835181

Evaluating the pathogenic potential of environmental Escherichia coli by using the Caenorhabditis elegans infection model.

PubMed

Merkx-Jacques, Alexandra; Coors, Anja; Brousseau, Roland; Masson, Luke; Mazza, Alberto; Tien, Yuan-Ching; Topp, Edward

2013-04-01

The detection and abundance of Escherichia coli in water is used to monitor and mandate the quality of drinking and recreational water. Distinguishing commensal waterborne E. coli isolates from those that cause diarrhea or extraintestinal disease in humans is important for quantifying human health risk. A DNA microarray was used to evaluate the distribution of virulence genes in 148 E. coli environmental isolates from a watershed in eastern Ontario, Canada, and in eight clinical isolates. Their pathogenic potential was evaluated with Caenorhabditis elegans, and the concordance between the bioassay result and the pathotype deduced by genotyping was explored. Isolates identified as potentially pathogenic on the basis of their complement of virulence genes were significantly more likely to be pathogenic to C. elegans than those determined to be potentially nonpathogenic. A number of isolates that were identified as nonpathogenic on the basis of genotyping were pathogenic in the infection assay, suggesting that genotyping did not capture all potentially pathogenic types. The detection of the adhesin-encoding genes sfaD, focA, and focG, which encode adhesins; of iroN2, which encodes a siderophore receptor; of pic, which encodes an autotransporter protein; and of b1432, which encodes a putative transposase, was significantly associated with pathogenicity in the infection assay. Overall, E. coli isolates predicted to be pathogenic on the basis of genotyping were indeed so in the C. elegans infection assay. Furthermore, the detection of C. elegans-infective environmental isolates predicted to be nonpathogenic on the basis of genotyping suggests that there are hitherto-unrecognized virulence factors or combinations thereof that are important in the establishment of infection.

Microbes and masculinity: Does exposure to pathogenic cues alter women's preferences for male facial masculinity and beardedness?

PubMed

McIntosh, Toneya L; Lee, Anthony J; Sidari, Morgan J; Stower, Rebecca E; Sherlock, James M; Dixson, Barnaby J W

2017-01-01

Women's preferences for men's androgen dependent secondary sexual traits are proposed to be phenotypically plastic in response to exposure to pathogens and pathogen disgust. While previous studies report that masculinity in facial shape is more attractive to women who have recently been exposed to pathogenic cues and who are high in self-reported pathogen disgust, facial hair may reduce male attractiveness under conditions of high pathogens as beards are a possible breeding ground for disease carrying ectoparasites. In the present study, we test whether women's preferences for beardedness and facial masculinity vary due to exposure to different pathogenic cues. Participants (N = 688, mean age + 1SD = 31.94 years, SD = 6.69, range = 18-67) rated the attractiveness of facial composite stimuli of men when they were clean-shaven or fully bearded. These stimuli were also manipulated in order to vary sexual dimorphism by ±50%. Ratings were conducted before and after exposure to one of four experimental treatments in which participants were primed to either high pathogens (e.g. infected cuts), ectoparasites (e.g. body lice), a mixture of pathogens and ectoparasites, or a control condition (e.g. innocuous liquids). Participants then completed the three-domain disgust scale measuring attitudes to moral, sexual and pathogen disgust. We predicted that women would prefer facial masculinity following exposure to pathogenic cues, but would show reduced preferences for facial hair following exposure to ectoparasites. Women preferred full beards over clean-shaven faces and masculinised over feminised faces. However, none of the experimental treatments influenced the direction of preferences for facial masculinity or beardedness. We also found no association between women's self-reported pathogen disgust and their preferences for facial masculinity. However, there was a weak positive association between moral disgust scores and preferences for facial masculinity, which might reflect conservatism and preferences for gender typicality in faces. Women's preferences for beards were positively associated with their pathogen disgust, which runs contrary to our predictions and may reflect preferences for high quality individuals who can withstand any costs of beardedness, although further replications are necessary before firm conclusions can be made. We conclude that there is little support for pathogenic exposure being a mechanism that underpins women's directional preferences for masculine traits.

Microbes and masculinity: Does exposure to pathogenic cues alter women’s preferences for male facial masculinity and beardedness?

PubMed Central

McIntosh, Toneya L.; Lee, Anthony J.; Sidari, Morgan J.; Stower, Rebecca E.; Sherlock, James M.

2017-01-01

Women’s preferences for men’s androgen dependent secondary sexual traits are proposed to be phenotypically plastic in response to exposure to pathogens and pathogen disgust. While previous studies report that masculinity in facial shape is more attractive to women who have recently been exposed to pathogenic cues and who are high in self-reported pathogen disgust, facial hair may reduce male attractiveness under conditions of high pathogens as beards are a possible breeding ground for disease carrying ectoparasites. In the present study, we test whether women’s preferences for beardedness and facial masculinity vary due to exposure to different pathogenic cues. Participants (N = 688, mean age + 1SD = 31.94 years, SD = 6.69, range = 18–67) rated the attractiveness of facial composite stimuli of men when they were clean-shaven or fully bearded. These stimuli were also manipulated in order to vary sexual dimorphism by ±50%. Ratings were conducted before and after exposure to one of four experimental treatments in which participants were primed to either high pathogens (e.g. infected cuts), ectoparasites (e.g. body lice), a mixture of pathogens and ectoparasites, or a control condition (e.g. innocuous liquids). Participants then completed the three-domain disgust scale measuring attitudes to moral, sexual and pathogen disgust. We predicted that women would prefer facial masculinity following exposure to pathogenic cues, but would show reduced preferences for facial hair following exposure to ectoparasites. Women preferred full beards over clean-shaven faces and masculinised over feminised faces. However, none of the experimental treatments influenced the direction of preferences for facial masculinity or beardedness. We also found no association between women’s self-reported pathogen disgust and their preferences for facial masculinity. However, there was a weak positive association between moral disgust scores and preferences for facial masculinity, which might reflect conservatism and preferences for gender typicality in faces. Women’s preferences for beards were positively associated with their pathogen disgust, which runs contrary to our predictions and may reflect preferences for high quality individuals who can withstand any costs of beardedness, although further replications are necessary before firm conclusions can be made. We conclude that there is little support for pathogenic exposure being a mechanism that underpins women’s directional preferences for masculine traits. PMID:28594843

Predicting and understanding law-making with word vectors and an ensemble model.

PubMed

Nay, John J

2017-01-01

Out of nearly 70,000 bills introduced in the U.S. Congress from 2001 to 2015, only 2,513 were enacted. We developed a machine learning approach to forecasting the probability that any bill will become law. Starting in 2001 with the 107th Congress, we trained models on data from previous Congresses, predicted all bills in the current Congress, and repeated until the 113th Congress served as the test. For prediction we scored each sentence of a bill with a language model that embeds legislative vocabulary into a high-dimensional, semantic-laden vector space. This language representation enables our investigation into which words increase the probability of enactment for any topic. To test the relative importance of text and context, we compared the text model to a context-only model that uses variables such as whether the bill's sponsor is in the majority party. To test the effect of changes to bills after their introduction on our ability to predict their final outcome, we compared using the bill text and meta-data available at the time of introduction with using the most recent data. At the time of introduction context-only predictions outperform text-only, and with the newest data text-only outperforms context-only. Combining text and context always performs best. We conducted a global sensitivity analysis on the combined model to determine important variables predicting enactment.

Predicting and understanding law-making with word vectors and an ensemble model

PubMed Central

Nay, John J.

2017-01-01

Out of nearly 70,000 bills introduced in the U.S. Congress from 2001 to 2015, only 2,513 were enacted. We developed a machine learning approach to forecasting the probability that any bill will become law. Starting in 2001 with the 107th Congress, we trained models on data from previous Congresses, predicted all bills in the current Congress, and repeated until the 113th Congress served as the test. For prediction we scored each sentence of a bill with a language model that embeds legislative vocabulary into a high-dimensional, semantic-laden vector space. This language representation enables our investigation into which words increase the probability of enactment for any topic. To test the relative importance of text and context, we compared the text model to a context-only model that uses variables such as whether the bill’s sponsor is in the majority party. To test the effect of changes to bills after their introduction on our ability to predict their final outcome, we compared using the bill text and meta-data available at the time of introduction with using the most recent data. At the time of introduction context-only predictions outperform text-only, and with the newest data text-only outperforms context-only. Combining text and context always performs best. We conducted a global sensitivity analysis on the combined model to determine important variables predicting enactment. PMID:28489868

Predicting essential genes for identifying potential drug targets in Aspergillus fumigatus.

PubMed

Lu, Yao; Deng, Jingyuan; Rhodes, Judith C; Lu, Hui; Lu, Long Jason

2014-06-01

Aspergillus fumigatus (Af) is a ubiquitous and opportunistic pathogen capable of causing acute, invasive pulmonary disease in susceptible hosts. Despite current therapeutic options, mortality associated with invasive Af infections remains unacceptably high, increasing 357% since 1980. Therefore, there is an urgent need for the development of novel therapeutic strategies, including more efficacious drugs acting on new targets. Thus, as noted in a recent review, "the identification of essential genes in fungi represents a crucial step in the development of new antifungal drugs". Expanding the target space by rapidly identifying new essential genes has thus been described as "the most important task of genomics-based target validation". In previous research, we were the first to show that essential gene annotation can be reliably transferred between distantly related four Prokaryotic species. In this study, we extend our machine learning approach to the much more complex Eukaryotic fungal species. A compendium of essential genes is predicted in Af by transferring known essential gene annotations from another filamentous fungus Neurospora crassa. This approach predicts essential genes by integrating diverse types of intrinsic and context-dependent genomic features encoded in microbial genomes. The predicted essential datasets contained 1674 genes. We validated our results by comparing our predictions with known essential genes in Af, comparing our predictions with those predicted by homology mapping, and conducting conditional expressed alleles. We applied several layers of filters and selected a set of potential drug targets from the predicted essential genes. Finally, we have conducted wet lab knockout experiments to verify our predictions, which further validates the accuracy and wide applicability of the machine learning approach. The approach presented here significantly extended our ability to predict essential genes beyond orthologs and made it possible to predict an inventory of essential genes in Eukaryotic fungal species, amongst which a preferred subset of suitable drug targets may be selected. By selecting the best new targets, we believe that resultant drugs would exhibit an unparalleled clinical impact against a naive pathogen population. Additional benefits that a compendium of essential genes can provide are important information on cell function and evolutionary biology. Furthermore, mapping essential genes to pathways may also reveal critical check points in the pathogen's metabolism. Finally, this approach is highly reproducible and portable, and can be easily applied to predict essential genes in many more pathogenic microbes, especially those unculturable. Copyright © 2014 Elsevier Ltd. All rights reserved.

Bacterial meningitis in Malawian adults, adolescents, and children during the era of antiretroviral scale-up and Haemophilus influenzae type b vaccination, 2000-2012.

PubMed

Wall, Emma C; Everett, Dean B; Mukaka, Mavuto; Bar-Zeev, Naor; Feasey, Nicholas; Jahn, Andreas; Moore, Mike; van Oosterhout, Joep J; Pensalo, Paul; Baguimira, Kenneth; Gordon, Stephen B; Molyneux, Elizabeth M; Carrol, Enitan D; French, Neil; Molyneux, Malcolm E; Heyderman, Robert S

2014-05-01

We documented bacterial meningitis trends among adults and children presenting to a large teaching hospital in Malawi during introduction of Haemophilus influenzae type b (Hib) vaccination and the rollout of antiretroviral therapy (ART). We analyzed data from 51 000 consecutive cerebrospinal fluid (CSF) samples obtained from adults, adolescents, and children with suspected meningitis admitted to the Queen Elizabeth Central Hospital, Blantyre, Malawi, between 2000 and 2012. There was a significant decline in the total number of CSF isolates over 12 years (incident rate ratio [IRR], 0.93; 95% CI, .92-.94; P < .001). This decline was entirely in children aged <5 years (IRR, 0.87; 95% CI, .85-.88; P < .001) and coincided with the introduction of Hib vaccination. The number of adult isolates has remained unchanged (IRR, 0.99; 95% CI, .97-1.0; P = .135) despite rapid scale-up of ART provision. In children aged <5 years, Streptococcus pneumoniae, nontyphoidal salmonellae (NTS), and Hib were the most frequently isolated pathogens, and have declined over this time period. Streptococcus pneumoniae was the most frequently isolated pathogen in older children and adults. Estimated incidence of bacterial meningitis in 2012 was 20 per 100,000 cases in children aged <14 years, 6 per 100,000 adolescents, and 10 per 100,000 adults. Rates of bacterial meningitis have declined in children, but not adults, coinciding with the introduction of Hib vaccination. The highly successful rollout of ART has not yet resulted in a reduction in the incidence in adults where the burden remains high. Long-term surveillance of bacterial meningitis outside of the epidemic "meningitis belt" in Africa is essential.

Development of a hydrolysis probe-based real-time assay for the detection of tropical strains of Fusarium oxysporum f. sp. cubense race 4.

PubMed

Aguayo, Jaime; Mostert, Diane; Fourrier-Jeandel, Céline; Cerf-Wendling, Isabelle; Hostachy, Bruno; Viljoen, Altus; Ioos, Renaud

2017-01-01

Fusarium oxysporum f. sp. cubense (Foc) is one of the most important threats to global banana production. Strategies to control the pathogen are lacking, with plant resistance offering the only long-term solution, if sources of resistance are available. Prevention of introduction of Foc into disease-free areas thus remains a key strategy to continue sustainable banana production. In recent years, strains of Foc affecting Cavendish bananas have destroyed plantations in a number of countries in Asia and in the Middle East, and one African country. One vegetative compatibility group (VCG), 01213/16, is considered the major threat to bananas in tropical and subtropical climatic conditions. However, other genetically related VCGs, such as 0121, may potentially jeopardize banana cultures if they were introduced into disease-free areas. To prevent the introduction of these VCGs into disease-free Cavendish banana-growing countries, a real-time PCR test was developed to accurately detect both VCGs. A previously described putative virulence gene was used to develop a specific combination of hydrolysis probe/primers for the detection of tropical Foc race 4 strains. The real-time PCR parameters were optimized by following a statistical approach relying on orthogonal arrays and the Taguchi method in an attempt to enhance sensitivity and ensure high specificity of the assay. This study also assessed critical performance criteria, such as repeatability, reproducibility, robustness, and specificity, with a large including set of 136 F. oxysporum isolates, including 73 Foc pathogenic strains representing 24 VCGs. The validation data demonstrated that the new assay could be used for regulatory testing applications on banana plant material and can contribute to preventing the introduction and spread of Foc strains affecting Cavendish bananas in the tropics.

Bacterial Meningitis in Malawian Adults, Adolescents, and Children During the Era of Antiretroviral Scale-up and Haemophilus influenzae Type b Vaccination, 2000–2012

PubMed Central

Wall, Emma C.; Everett, Dean B.; Mukaka, Mavuto; Bar-Zeev, Naor; Feasey, Nicholas; Jahn, Andreas; Moore, Mike; van Oosterhout, Joep J.; Pensalo, Paul; Baguimira, Kenneth; Gordon, Stephen B.; Molyneux, Elizabeth M.; Carrol, Enitan D.; French, Neil; Molyneux, Malcolm E.; Heyderman, Robert S.

2014-01-01

Background. We documented bacterial meningitis trends among adults and children presenting to a large teaching hospital in Malawi during introduction of Haemophilus influenzae type b (Hib) vaccination and the rollout of antiretroviral therapy (ART). Methods. We analyzed data from 51 000 consecutive cerebrospinal fluid (CSF) samples obtained from adults, adolescents, and children with suspected meningitis admitted to the Queen Elizabeth Central Hospital, Blantyre, Malawi, between 2000 and 2012. Results. There was a significant decline in the total number of CSF isolates over 12 years (incident rate ratio [IRR], 0.93; 95% CI, .92–.94; P < .001). This decline was entirely in children aged <5 years (IRR, 0.87; 95% CI, .85–.88; P < .001) and coincided with the introduction of Hib vaccination. The number of adult isolates has remained unchanged (IRR, 0.99; 95% CI, .97–1.0; P = .135) despite rapid scale-up of ART provision. In children aged <5 years, Streptococcus pneumoniae, nontyphoidal salmonellae (NTS), and Hib were the most frequently isolated pathogens, and have declined over this time period. Streptococcus pneumoniae was the most frequently isolated pathogen in older children and adults. Estimated incidence of bacterial meningitis in 2012 was 20 per 100 000 cases in children aged <14 years, 6 per 100 000 adolescents, and 10 per 100 000 adults. Conclusions. Rates of bacterial meningitis have declined in children, but not adults, coinciding with the introduction of Hib vaccination. The highly successful rollout of ART has not yet resulted in a reduction in the incidence in adults where the burden remains high. Long-term surveillance of bacterial meningitis outside of the epidemic “meningitis belt” in Africa is essential. PMID:24496208

Implementation of innovative pulsed xenon ultraviolet (PX-UV) environmental cleaning in an acute care hospital.

PubMed

Fornwalt, Lori; Riddell, Brad

2014-01-01

It is widely acknowledged that the hospital environment is an important reservoir for many of the pathogenic microbes associated with health care-associated infections (HAIs). Environmental cleaning plays an important role in the prevention and containment of HAIs, in patient safety, and the overall experience of health care facilities. New technologies, such as pulsed xenon ultraviolet (PX-UV) light systems are an innovative development for enhanced cleaning and decontamination of hospital environments. A portable PX-UV disinfection device delivers pulsed UV light to destroy microbial pathogens and spores, and can be used in conjunction with manual environmental cleaning. In addition, this technology facilitates thorough disinfection of hospital rooms in 10-15 minutes. The current study was conducted to evaluate whether the introduction of the PX-UV device had a positive impact on patient satisfaction. Satisfaction was measured using the Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) survey. In 2011, prior to the introduction of the PX-UV system, patient HCAHPS scores for cleanliness averaged 75.75%. In the first full quarter after enhanced cleaning of the facility was introduced, this improved to 83%. Overall scores for the hospital rose from 76% (first quarter, 2011) to 87.6% (fourth quarter, 2012). As a result of this improvement, the hospital received 1% of at-risk reimbursement from the inpatient prospective payment system as well as additional funding. Cleanliness of the hospital environment is one of the questions included in the HCAHPS survey and one measure of patient satisfaction. After the introduction of the PX-UV system, the score for cleanliness and the overall rating of the hospital rose from below the fiftieth to the ninety-ninth percentile. This improvement in the patient experience was associated with financial benefits to the hospital.

Evidence for the benefits of food chain interventions on E. coli 0157:H7/NM prevalence in retail ground beef and human disease incidence: A success story.

PubMed

Pollari, Frank; Christidis, Tanya; Pintar, Katarina D M; Nesbitt, Andrea; Farber, Jeff; Lavoie, Marie-Claude; Gill, Alex; Kirsch, Penelope; Johnson, Roger P

2017-04-20

Human infection with Escherichia coli O157:H7/NM has historically been associated with consumption of undercooked ground beef. The purpose of this paper is to investigate the correlation of the decline in E. coli O157:H7/NM infections in Canada with the introduction of control efforts in ground beef by industry. The human incidence of E. coli O157:H7/NM, prevalence in ground beef and interventions from 1996 to 2014 were analyzed. Pathogen prevalence data were obtained from federal government and industry surveillance and inspection/compliance programs. A survey of the largest ground beef producers in Canada was conducted to identify when interventions were implemented. The incidence of E. coli O157:H7/NM infections in Canada declined from ∼4 cases/100 000 to ∼1 case/100 000 from 2000 to 2010. Verotoxigenic Escherichia coli (VTEC) prevalence in ground beef sold at retail declined from about 30% around the year 2000 to <2% since 2012. Other measures of the prevalence of E. coli, VTEC, and E. coli O157:H7/NM in beef and ground beef also declined. The number and types of interventions implemented in the major beef processing establishments in Canada increased from 1996 to 2016. The observed decline in human illnesses and pathogen levels in relation to retail meats was associated with the introduction of control efforts by industry, federal and provincial/territorial governments, and the general population. Industry-led changes in beef processing along with the introduction of food safety policies, regulations, and public education have led to improved food safety in Canada.

Development of a hydrolysis probe-based real-time assay for the detection of tropical strains of Fusarium oxysporum f. sp. cubense race 4

PubMed Central

Cerf-Wendling, Isabelle; Hostachy, Bruno; Viljoen, Altus; Ioos, Renaud

2017-01-01

Fusarium oxysporum f. sp. cubense (Foc) is one of the most important threats to global banana production. Strategies to control the pathogen are lacking, with plant resistance offering the only long-term solution, if sources of resistance are available. Prevention of introduction of Foc into disease-free areas thus remains a key strategy to continue sustainable banana production. In recent years, strains of Foc affecting Cavendish bananas have destroyed plantations in a number of countries in Asia and in the Middle East, and one African country. One vegetative compatibility group (VCG), 01213/16, is considered the major threat to bananas in tropical and subtropical climatic conditions. However, other genetically related VCGs, such as 0121, may potentially jeopardize banana cultures if they were introduced into disease-free areas. To prevent the introduction of these VCGs into disease-free Cavendish banana-growing countries, a real-time PCR test was developed to accurately detect both VCGs. A previously described putative virulence gene was used to develop a specific combination of hydrolysis probe/primers for the detection of tropical Foc race 4 strains. The real-time PCR parameters were optimized by following a statistical approach relying on orthogonal arrays and the Taguchi method in an attempt to enhance sensitivity and ensure high specificity of the assay. This study also assessed critical performance criteria, such as repeatability, reproducibility, robustness, and specificity, with a large including set of 136 F. oxysporum isolates, including 73 Foc pathogenic strains representing 24 VCGs. The validation data demonstrated that the new assay could be used for regulatory testing applications on banana plant material and can contribute to preventing the introduction and spread of Foc strains affecting Cavendish bananas in the tropics. PMID:28178348

Using the genome aggregation database, computational pathogenicity prediction tools, and patch clamp heterologous expression studies to demote previously published long QT syndrome type 1 mutations from pathogenic to benign.

PubMed

Clemens, Daniel J; Lentino, Anne R; Kapplinger, Jamie D; Ye, Dan; Zhou, Wei; Tester, David J; Ackerman, Michael J

2018-04-01

Mutations in the KCNQ1-encoded Kv7.1 potassium channel cause long QT syndrome (LQTS) type 1 (LQT1). It has been suggested that ∼10%-20% of rare LQTS case-derived variants in the literature may have been published erroneously as LQT1-causative mutations and may be "false positives." The purpose of this study was to determine which previously published KCNQ1 case variants are likely false positives. A list of all published, case-derived KCNQ1 missense variants (MVs) was compiled. The occurrence of each MV within the Genome Aggregation Database (gnomAD) was assessed. Eight in silico tools were used to predict each variant's pathogenicity. Case-derived variants that were either (1) too frequently found in gnomAD or (2) absent in gnomAD but predicted to be pathogenic by ≤2 tools were considered potential false positives. Three of these variants were characterized functionally using whole-cell patch clamp technique. Overall, there were 244 KCNQ1 case-derived MVs. Of these, 29 (12%) were seen in ≥10 individuals in gnomAD and are demotable. However, 157 of 244 MVs (64%) were absent in gnomAD. Of these, 7 (4%) were predicted to be pathogenic by ≤2 tools, 3 of which we characterized functionally. There was no significant difference in current density between heterozygous KCNQ1-F127L, -P477L, or -L619M variant-containing channels compared to KCNQ1-WT. This study offers preliminary evidence for the demotion of 32 (13%) previously published LQT1 MVs. Of these, 29 were demoted because of their frequent sighting in gnomAD. Additionally, in silico analysis and in vitro functional studies have facilitated the demotion of 3 ultra-rare MVs (F127L, P477L, L619M). Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Time evolution of predictability of epidemics on networks.

PubMed

Holme, Petter; Takaguchi, Taro

2015-04-01

Epidemic outbreaks of new pathogens, or known pathogens in new populations, cause a great deal of fear because they are hard to predict. For theoretical models of disease spreading, on the other hand, quantities characterizing the outbreak converge to deterministic functions of time. Our goal in this paper is to shed some light on this apparent discrepancy. We measure the diversity of (and, thus, the predictability of) outbreak sizes and extinction times as functions of time given different scenarios of the amount of information available. Under the assumption of perfect information-i.e., knowing the state of each individual with respect to the disease-the predictability decreases exponentially, or faster, with time. The decay is slowest for intermediate values of the per-contact transmission probability. With a weaker assumption on the information available, assuming that we know only the fraction of currently infectious, recovered, or susceptible individuals, the predictability also decreases exponentially most of the time. There are, however, some peculiar regions in this scenario where the predictability decreases. In other words, to predict its final size with a given accuracy, we would need increasingly more information about the outbreak.

Time evolution of predictability of epidemics on networks

NASA Astrophysics Data System (ADS)

Holme, Petter; Takaguchi, Taro

2015-04-01

Epidemic outbreaks of new pathogens, or known pathogens in new populations, cause a great deal of fear because they are hard to predict. For theoretical models of disease spreading, on the other hand, quantities characterizing the outbreak converge to deterministic functions of time. Our goal in this paper is to shed some light on this apparent discrepancy. We measure the diversity of (and, thus, the predictability of) outbreak sizes and extinction times as functions of time given different scenarios of the amount of information available. Under the assumption of perfect information—i.e., knowing the state of each individual with respect to the disease—the predictability decreases exponentially, or faster, with time. The decay is slowest for intermediate values of the per-contact transmission probability. With a weaker assumption on the information available, assuming that we know only the fraction of currently infectious, recovered, or susceptible individuals, the predictability also decreases exponentially most of the time. There are, however, some peculiar regions in this scenario where the predictability decreases. In other words, to predict its final size with a given accuracy, we would need increasingly more information about the outbreak.

Stratifying risk factors for multidrug-resistant pathogens in hospitalized patients coming from the community with pneumonia.

PubMed

Aliberti, Stefano; Di Pasquale, Marta; Zanaboni, Anna Maria; Cosentini, Roberto; Brambilla, Anna Maria; Seghezzi, Sonia; Tarsia, Paolo; Mantero, Marco; Blasi, Francesco

2012-02-15

 Not all risk factors for acquiring multidrug-resistant (MDR) organisms are equivalent in predicting pneumonia caused by resistant pathogens in the community. We evaluated risk factors for acquiring MDR bacteria in patients coming from the community who were hospitalized with pneumonia. Our evaluation was based on actual infection with a resistant pathogen and clinical outcome during hospitalization.  An observational, prospective study was conducted on consecutive patients coming from the community who were hospitalized with pneumonia. Data on admission and during hospitalization were collected. Logistic regression models were used to evaluate risk factors for acquiring MDR bacteria independently associated with the actual presence of a resistant pathogen and in-hospital mortality.  Among the 935 patients enrolled in the study, 473 (51%) had at least 1 risk factor for acquiring MDR bacteria on admission. Of all risk factors, hospitalization in the preceding 90 days (odds ratio [OR], 4.87 95% confidence interval {CI}, 1.90-12.4]; P = .001) and residency in a nursing home (OR, 3.55 [95% CI, 1.12-11.24]; P = .031) were independent predictors for an actual infection with a resistant pathogen. A score able to predict pneumonia caused by a resistant pathogen was computed, including comorbidities and risk factors for MDR. Hospitalization in the preceding 90 days and residency in a nursing home were also independent predictors for in-hospital mortality.  Risk factors for acquiring MDR bacteria should be weighted differently, and a probabilistic approach to identifying resistant pathogens among patients coming from the community with pneumonia should be embraced.

The effects of demographic, social, and environmental characteristics on pathogen prevalence in wild felids across a gradient of urbanization

PubMed Central

Logan, Kenneth A.; Alldredge, Mat W.; Carver, Scott; Bevins, Sarah N.; Lappin, Michael; VandeWoude, Sue; Crooks, Kevin R.

2017-01-01

Transmission of pathogens among animals is influenced by demographic, social, and environmental factors. Anthropogenic alteration of landscapes can impact patterns of disease dynamics in wildlife populations, increasing the potential for spillover and spread of emerging infectious diseases in wildlife, human, and domestic animal populations. We evaluated the effects of multiple ecological mechanisms on patterns of pathogen exposure in animal populations. Specifically, we evaluated how ecological factors affected the prevalence of Toxoplasma gondii (Toxoplasma), Bartonella spp. (Bartonella), feline immunodeficiency virus (FIV), and feline calicivirus (FCV) in bobcat and puma populations across wildland-urban interface (WUI), low-density exurban development, and wildland habitat on the Western Slope (WS) and Front Range (FR) of Colorado during 2009–2011. Samples were collected from 37 bobcats and 29 pumas on the WS and FR. As predicted, age appeared to be positively related to the exposure to pathogens that are both environmentally transmitted (Toxoplasma) and directly transmitted between animals (FIV). In addition, WS bobcats appeared more likely to be exposed to Toxoplasma with increasing intraspecific space-use overlap. However, counter to our predictions, exposure to directly-transmitted pathogens (FCV and FIV) was more likely with decreasing space-use overlap (FCV: WS bobcats) and potential intraspecific contacts (FIV: FR pumas). Environmental factors, including urbanization and landscape covariates, were generally unsupported in our models. This study is an approximation of how pathogens can be evaluated in relation to demographic, social, and environmental factors to understand pathogen exposure in wild animal populations. PMID:29121060

Method for concentration and separation of biological organisms by ultrafiltration and dielectrophoresis

DOEpatents

Simmons, Blake A.; Hill, Vincent R.; Fintschenko, Yolanda; Cummings, Eric B.

2012-09-04

Disclosed is a method for monitoring sources of public water supply for a variety of pathogens by using a combination of ultrafiltration techniques together dielectrophoretic separation techniques. Because water-borne pathogens, whether present due to "natural" contamination or intentional introduction, would likely be present in drinking water at low concentrations when samples are collected for monitoring or outbreak investigations, an approach is needed to quickly and efficiently concentrate and separate particles such as viruses, bacteria, and parasites in large volumes of water (e.g., 100 L or more) while simultaneously reducing the sample volume to levels sufficient for detecting low concentrations of microbes (e.g., <10 mL). The technique is also designed to screen the separated microbes based on specific conductivity and size.

Per capita invasion probabilities: A linear model to predict rates of invasion via ballast water

EPA Science Inventory

Ballast water discharges are a major source of species introductions into marine, estuarine, and freshwater ecosystems. To mitigate the introduction of new invaders into these ecosystems, many agencies are proposing discharge standards that establish upper concentration limits f...

CURRENT VFARS ONGOING RESEARCH AND WHAT NEEDS TO BE DONE TO EVALUATE THE VFARS CONCEPT AND DETERMINE ITS FEASIBILITY

EPA Science Inventory

The VFARs concept predicts that pathogens can be identified using structural similarities among virulence genes from diverse species. This concept is of interest to the EPA for several reasons: the Agency's need to discriminate between virulent and avirulent isolates of pathogen...

Bacteriophages as biocontrol agents of food pathogens.

PubMed

Mahony, Jennifer; McAuliffe, Olivia; Ross, R Paul; van Sinderen, Douwe

2011-04-01

Bacteriophages have long been recognized for their potential as biotherapeutic agents. The recent approval for the use of phages of Listeria monocytogenes for food safety purposes has increased the impetus of phage research to uncover phage-mediated applications with activity against other food pathogens. Areas of emerging and growing significance, such as predictive modelling and genomics, have shown their potential and impact on the development of new technologies to combat food pathogens. This review will highlight recent advances in the research of phages that target food pathogens and that promote their use in biosanitation, while it will also discuss its limitations. Copyright © 2010 Elsevier Ltd. All rights reserved.

Herd diagnosis of low pathogen diarrhoea in growing pigs - a pilot study.

PubMed

Pedersen, Ken Steen; Johansen, Markku; Angen, Oystein; Jorsal, Sven Erik; Nielsen, Jens Peter; Jensen, Tim K; Guedes, Roberto; Ståhl, Marie; Bækbo, Poul

2014-01-01

The major indication for antibiotic use in Danish pigs is treatment of intestinal diseases post weaning. Clinical decisions on antibiotic batch medication are often based on inspection of diarrhoeic pools on the pen floor. In some of these treated diarrhoea outbreaks, intestinal pathogens can only be demonstrated in a small number of pigs within the treated group (low pathogen diarrhoea). Termination of antibiotic batch medication in herds suffering from such diarrhoea could potentially reduce the consumption of antibiotics in the pig industry. The objective of the present pilot study was to suggest criteria for herd diagnosis of low pathogen diarrhoea in growing pigs. Data previously collected from 20 Danish herds were used to create a case series of clinical diarrhoea outbreaks normally subjected to antibiotic treatment. In the present study, these diarrhoea outbreaks were classified as low pathogen (<15% of the pigs having bacterial intestinal disease) (n =5 outbreaks) or high pathogen (≥15% of the pigs having bacterial intestinal disease) (n =15 outbreaks). Based on the case series, different diagnostic procedures were explored, and criteria for herd diagnosis of low pathogen diarrhoea were suggested. The effect of sampling variation was explored by simulation. The diagnostic procedure with the highest combined herd-level sensitivity and specificity was qPCR testing of a pooled sample containing 20 randomly selected faecal samples. The criteria for a positive test result (high pathogen diarrhoea outbreak) were an average of 1.5 diarrhoeic faecal pools on the floor of each pen in the room under investigation and a pathogenic bacterial load ≥35,000 per gram in the faecal pool tested by qPCR. The bacterial load was the sum of Lawsonia intracellularis, Brachyspira pilosicoli and Escherichia coli F4 and F18 bacteria per gram faeces. The herd-diagnostic performance was (herd-level) diagnostic sensitivity =0.99, diagnostic specificity =0.80, positive predictive value =0.94 and negative predictive value =0.96. The pilot study suggests criteria for herd diagnosis of low pathogen diarrhoea in growing pigs. The suggested criteria should now be evaluated, and the effect of terminating antibiotic batch medication in herds identified as suffering from low pathogen diarrhoea should be explored.

Modelling the seasonality of Lyme disease risk and the potential impacts of a warming climate within the heterogeneous landscapes of Scotland.

PubMed

Li, Sen; Gilbert, Lucy; Harrison, Paula A; Rounsevell, Mark D A

2016-03-01

Lyme disease is the most prevalent vector-borne disease in the temperate Northern Hemisphere. The abundance of infected nymphal ticks is commonly used as a Lyme disease risk indicator. Temperature can influence the dynamics of disease by shaping the activity and development of ticks and, hence, altering the contact pattern and pathogen transmission between ticks and their host animals. A mechanistic, agent-based model was developed to study the temperature-driven seasonality of Ixodes ricinus ticks and transmission of Borrelia burgdorferi sensu lato across mainland Scotland. Based on 12-year averaged temperature surfaces, our model predicted that Lyme disease risk currently peaks in autumn, approximately six weeks after the temperature peak. The risk was predicted to decrease with increasing altitude. Increases in temperature were predicted to prolong the duration of the tick questing season and expand the risk area to higher altitudinal and latitudinal regions. These predicted impacts on tick population ecology may be expected to lead to greater tick-host contacts under climate warming and, hence, greater risks of pathogen transmission. The model is useful in improving understanding of the spatial determinants and system mechanisms of Lyme disease pathogen transmission and its sensitivity to temperature changes. © 2016 The Author(s).

Modelling the seasonality of Lyme disease risk and the potential impacts of a warming climate within the heterogeneous landscapes of Scotland

PubMed Central

Gilbert, Lucy; Harrison, Paula A.; Rounsevell, Mark D. A.

2016-01-01

Lyme disease is the most prevalent vector-borne disease in the temperate Northern Hemisphere. The abundance of infected nymphal ticks is commonly used as a Lyme disease risk indicator. Temperature can influence the dynamics of disease by shaping the activity and development of ticks and, hence, altering the contact pattern and pathogen transmission between ticks and their host animals. A mechanistic, agent-based model was developed to study the temperature-driven seasonality of Ixodes ricinus ticks and transmission of Borrelia burgdorferi sensu lato across mainland Scotland. Based on 12-year averaged temperature surfaces, our model predicted that Lyme disease risk currently peaks in autumn, approximately six weeks after the temperature peak. The risk was predicted to decrease with increasing altitude. Increases in temperature were predicted to prolong the duration of the tick questing season and expand the risk area to higher altitudinal and latitudinal regions. These predicted impacts on tick population ecology may be expected to lead to greater tick–host contacts under climate warming and, hence, greater risks of pathogen transmission. The model is useful in improving understanding of the spatial determinants and system mechanisms of Lyme disease pathogen transmission and its sensitivity to temperature changes. PMID:27030039

Role of India's wildlife in the emergence and re-emergence of zoonotic pathogens, risk factors and public health implications.

PubMed

Singh, B B; Gajadhar, A A

2014-10-01

Evolving land use practices have led to an increase in interactions at the human/wildlife interface. The presence and poor knowledge of zoonotic pathogens in India's wildlife and the occurrence of enormous human populations interfacing with, and critically linked to, forest ecosystems warrant attention. Factors such as diverse migratory bird populations, climate change, expanding human population and shrinking wildlife habitats play a significant role in the emergence and re-emergence of zoonotic pathogens from India's wildlife. The introduction of a novel Kyasanur forest disease virus (family flaviviridae) into human populations in 1957 and subsequent occurrence of seasonal outbreaks illustrate the key role that India's wild animals play in the emergence and reemergence of zoonotic pathogens. Other high priority zoonotic diseases of wildlife origin which could affect both livestock and humans include influenza, Nipah, Japanese encephalitis, rabies, plague, leptospirosis, anthrax and leishmaniasis. Continuous monitoring of India's extensively diverse and dispersed wildlife is challenging, but their use as indicators should facilitate efficient and rapid disease-outbreak response across the region and occasionally the globe. Defining and prioritizing research on zoonotic pathogens in wildlife are essential, particularly in a multidisciplinary one-world one-health approach which includes human and veterinary medical studies at the wildlife-livestock-human interfaces. This review indicates that wild animals play an important role in the emergence and re-emergence of zoonotic pathogens and provides brief summaries of the zoonotic diseases that have occurred in wild animals in India. Copyright © 2014 Elsevier B.V. All rights reserved.

V/STOL Aerodynamics

DTIC Science & Technology

1974-10-01

jet exhaust, m (ft) Ro radius of engine exhaust, m (ft) 1. INTRODUCTION free deg S wing area, m2 (ft2) t time, see T Thrust, N (lb) u...dimensional potential flow method to lift prediction for a wing with internally blown flaps is described. INTRODUCTION The objectives of this paper are...twofold. The first is to provide an introduction to this session on research into the aerodynamics of powered high lift systems. This will be

Inter-kingdom prediction certainty evaluation of protein subcellular localization tools: microbial pathogenesis approach for deciphering host microbe interaction.

PubMed

Khan, Abdul Arif; Khan, Zakir; Kalam, Mohd Abul; Khan, Azmat Ali

2018-01-01

Microbial pathogenesis involves several aspects of host-pathogen interactions, including microbial proteins targeting host subcellular compartments and subsequent effects on host physiology. Such studies are supported by experimental data, but recent detection of bacterial proteins localization through computational eukaryotic subcellular protein targeting prediction tools has also come into practice. We evaluated inter-kingdom prediction certainty of these tools. The bacterial proteins experimentally known to target host subcellular compartments were predicted with eukaryotic subcellular targeting prediction tools, and prediction certainty was assessed. The results indicate that these tools alone are not sufficient for inter-kingdom protein targeting prediction. The correct prediction of pathogen's protein subcellular targeting depends on several factors, including presence of localization signal, transmembrane domain and molecular weight, etc., in addition to approach for subcellular targeting prediction. The detection of protein targeting in endomembrane system is comparatively difficult, as the proteins in this location are channelized to different compartments. In addition, the high specificity of training data set also creates low inter-kingdom prediction accuracy. Current data can help to suggest strategy for correct prediction of bacterial protein's subcellular localization in host cell. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Epidemiology of whooping cough & typing of Bordetella pertussis.

PubMed

Hegerle, Nicolas; Guiso, Nicole

2013-11-01

Bordetella pertussis is a Gram-negative human-restricted bacterium that evolved from the broad-range mammalian pathogen, Bordetella bronchiseptica. It causes whooping cough or pertussis in humans, which is the most prevalent vaccine-preventable disease worldwide. The introduction of the pertussis whole-cell vaccination for young children, followed by the introduction of the pertussis acellular vaccination (along with booster vaccination) for older age groups, has affected the bacterial population and epidemiology of the disease. B. pertussis is relatively monomorphic worldwide, but nevertheless, different countries are facing different epidemiological evolutions of the disease. Although it is tempting to link vaccine-driven phenotypic and genotypic evolution of the bacterium to epidemiology, many other factors should be considered and surveillance needs to continue, in addition to studies investigating the impact of current clinical isolates on vaccine efficacy.

SARS and MERS: recent insights into emerging coronaviruses.

PubMed

de Wit, Emmie; van Doremalen, Neeltje; Falzarano, Darryl; Munster, Vincent J

2016-08-01

The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 marked the second introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The continuing introductions of MERS-CoV from dromedary camels, the subsequent travel-related viral spread, the unprecedented nosocomial outbreaks and the high case-fatality rates highlight the need for prophylactic and therapeutic measures. Scientific advancements since the 2002-2003 severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic allowed for rapid progress in our understanding of the epidemiology and pathogenesis of MERS-CoV and the development of therapeutics. In this Review, we detail our present understanding of the transmission and pathogenesis of SARS-CoV and MERS-CoV, and discuss the current state of development of measures to combat emerging coronaviruses.

Sin Nombre Virus and Rodent Species Diversity: A Test of the Dilution and Amplification Hypotheses

PubMed Central

Clay, Christine A.; Lehmer, Erin M.; Jeor, Stephen St.; Dearing, M. Denise

2009-01-01

Background Species diversity is proposed to greatly impact the prevalence of pathogens. Two predominant hypotheses, the “Dilution Effect” and the “Amplification Effect”, predict divergent outcomes with respect to the impact of species diversity. The Dilution Effect predicts that pathogen prevalence will be negatively correlated with increased species diversity, while the Amplification Effect predicts that pathogen prevalence will be positively correlated with diversity. For many host-pathogen systems, the relationship between diversity and pathogen prevalence has not be empirically examined. Methodology/Principal Findings We tested the Dilution and Amplification Effect hypotheses by examining the prevalence of Sin Nombre virus (SNV) with respect to diversity of the nocturnal rodent community. SNV is directly transmitted primarily between deer mice (Peromyscus maniculatus). Using mark-recapture sampling in the Spring and Fall of 2003–2005, we measured SNV prevalence in deer mice at 16 landscape level sites (3.1 hectares each) that varied in rodent species diversity. We explored several mechanisms by which species diversity may affect SNV prevalence, including reduced host density, reduced host persistence, the presence of secondary reservoirs and community composition. We found a negative relationship between species diversity and SNV prevalence in deer mice, thereby supporting the Dilution Effect hypothesis. Deer mouse density and persistence were lower at sites with greater species diversity; however, only deer mouse persistence was positively correlated with SNV prevalence. Pinyon mice (P. truei) may serve as dilution agents, having a negative effect on prevalence, while kangaroo rats (Dipodomys ordii), may have a positive effect on the prevalence of SNV, perhaps through effects on deer mouse behavior. Conclusions/Significance While previous studies on host-pathogen systems have found patterns of diversity consistent with either the Dilution or Amplification Effects, the mechanisms by which species diversity influences prevalence have not been investigated. Our study indicates that changes in host persistence, coupled with interspecific interactions, are important mechanisms through which diversity may influence patterns of pathogens. Our results reveal the complexity of rodent community interactions with respect to SNV dynamics. PMID:19649283

Surveillance for Enteric Pathogens in a Case-Control Study of Acute Diarrhea in Western Kenya

DTIC Science & Technology

2012-11-01

isolates was ascertained using the MicroScan WalkAway 40 Plus. An enzyme immunoassay kit was used to detect rotavirus , and ova and parasite...examination was conducted by micros- copy and an enzyme immunoassay. Results: Rotavirus (10.2% and 10.5%) and Shigella (11% and 8%) were isolated significantly...Keywords: Gastroenteritis, Protozoa, Rotavirus , Shigella, Escherichia coli, Antimicrobial resistance Introduction Diarrheal disease continues to be a

The re-emergency and persistence of vaccine preventable diseases.

PubMed

Borba, Rodrigo C N; Vidal, Vinícius M; Moreira, Lilian O

2015-08-01

The introduction of vaccination worldwide dramatically reduced the incidence of pathogenic bacterial and viral diseases. Despite the highly successful vaccination strategies, the number of cases among vaccine preventable diseases has increased in the last decade and several of those diseases are still endemic in different countries. Here we discuss some epidemiological aspects and possible arguments that may explain why ancient diseases such as, measles, polio, pertussis, diphtheria and tuberculosis are still with us.

The introduction of dengue vaccine may temporarily cause large spikes in prevalence.

PubMed

Pandey, A; Medlock, J

2015-04-01

A dengue vaccine is expected to be available within a few years. Once vaccine is available, policy-makers will need to develop suitable policies to allocate the vaccine. Mathematical models of dengue transmission predict complex temporal patterns in prevalence, driven by seasonal oscillations in mosquito abundance. In particular, vaccine introduction may induce a transient period immediately after vaccine introduction where prevalence can spike higher than in the pre-vaccination period. These spikes in prevalence could lead to doubts about the vaccination programme among the public and even among decision-makers, possibly impeding the vaccination programme. Using simple dengue transmission models, we found that large transient spikes in prevalence are robust phenomena that occur when vaccine coverage and vaccine efficacy are not either both very high or both very low. Despite the presence of transient spikes in prevalence, the models predict that vaccination does always reduce the total number of infections in the 15 years after vaccine introduction. We conclude that policy-makers should prepare for spikes in prevalence after vaccine introduction to mitigate the burden of these spikes and to accurately measure the effectiveness of the vaccine programme.

Probability-based collaborative filtering model for predicting gene-disease associations.

PubMed

Zeng, Xiangxiang; Ding, Ningxiang; Rodríguez-Patón, Alfonso; Zou, Quan

2017-12-28

Accurately predicting pathogenic human genes has been challenging in recent research. Considering extensive gene-disease data verified by biological experiments, we can apply computational methods to perform accurate predictions with reduced time and expenses. We propose a probability-based collaborative filtering model (PCFM) to predict pathogenic human genes. Several kinds of data sets, containing data of humans and data of other nonhuman species, are integrated in our model. Firstly, on the basis of a typical latent factorization model, we propose model I with an average heterogeneous regularization. Secondly, we develop modified model II with personal heterogeneous regularization to enhance the accuracy of aforementioned models. In this model, vector space similarity or Pearson correlation coefficient metrics and data on related species are also used. We compared the results of PCFM with the results of four state-of-arts approaches. The results show that PCFM performs better than other advanced approaches. PCFM model can be leveraged for predictions of disease genes, especially for new human genes or diseases with no known relationships.

Cheating, trade-offs and the evolution of aggressiveness in a natural pathogen population

PubMed Central

Barrett, Luke; Bell, Thomas; Dwyer, Greg; Bergelson, Joy

2011-01-01

The evolutionary dynamics of pathogens are critically important for disease outcomes, prevalence and emergence. In this study we investigate ecological conditions that may promote the long-term maintenance of virulence polymorphisms in pathogen populations. Recent theory predicts that evolution towards increased virulence can be reversed if less aggressive social ‘cheats’ exploit more aggressive ‘cooperator’ pathogens. However, there is no evidence that social exploitation operates within natural pathogen populations. We show that for the bacterium Pseudomonas syringae, major polymorphisms for pathogenicity are maintained at unexpectedly high frequencies in populations infecting the host Arabidopsis thaliana. Experiments reveal that less aggressive strains substantially increase their growth potential in mixed infections and have a fitness advantage in non-host environments. These results suggest that niche differentiation can contribute to the maintenance of virulence polymorphisms, and that both within-host and between-host growth rates modulate cheating and cooperation in P. syringae populations. PMID:21951910

De novo Transcriptome Analysis of Rhizoctonia solani AG1 IA Strain Early Invasion in Zoysia japonica Root.

PubMed

Zhu, Chen; Ai, Lin; Wang, Li; Yin, Pingping; Liu, Chenglan; Li, Shanshan; Zeng, Huiming

2016-01-01

Zoysia japonica brown spot was caused by necrotrophic fungus Rhizoctonia solani invasion, which led to severe financial loss in city lawn and golf ground maintenance. However, little was known about the molecular mechanism of R. solani pathogenicity in Z. japonica. In this study we examined early stage interaction between R. solani AG1 IA strain and Z. japonica cultivar "Zenith" root by cell ultra-structure analysis, pathogenesis-related proteins assay and transcriptome analysis to explore molecular clues for AG1 IA strain pathogenicity in Z. japonica. No obvious cell structure damage was found in infected roots and most pathogenesis-related protein activities showedg a downward trend especially in 36 h post inoculation, which exhibits AG1 IA strain stealthy invasion characteristic. According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database classification, most DEGs in infected "Zenith" roots dynamically changed especially in three aspects, signal transduction, gene translation, and protein synthesis. Total 3422 unigenes of "Zenith" root were predicted into 14 kinds of resistance (R) gene class. Potential fungal resistance related unigenes of "Zenith" root were involved in ligin biosynthesis, phytoalexin synthesis, oxidative burst, wax biosynthesis, while two down-regulated unigenes encoding leucine-rich repeat receptor protein kinase and subtilisin-like protease might be important for host-derived signal perception to AG1 IA strain invasion. According to Pathogen Host Interaction (PHI) database annotation, 1508 unigenes of AG1 IA strain were predicted and classified into 37 known pathogen species, in addition, unigenes encoding virulence, signaling, host stress tolerance, and potential effector were also predicted. This research uncovered transcriptional profiling during the early phase interaction between R. solani AG1 IA strain and Z. japonica, and will greatly help identify key pathogenicity of AG1 IA strain.

Using cure models for analyzing the influence of pathogens on salmon survival

USGS Publications Warehouse

Ray, Adam R; Perry, Russell W.; Som, Nicholas A.; Bartholomew, Jerri L

2014-01-01

Parasites and pathogens influence the size and stability of wildlife populations, yet many population models ignore the population-level effects of pathogens. Standard survival analysis methods (e.g., accelerated failure time models) are used to assess how survival rates are influenced by disease. However, they assume that each individual is equally susceptible and will eventually experience the event of interest; this assumption is not typically satisfied with regard to pathogens of wildlife populations. In contrast, mixture cure models, which comprise logistic regression and survival analysis components, allow for different covariates to be entered into each part of the model and provide better predictions of survival when a fraction of the population is expected to survive a disease outbreak. We fitted mixture cure models to the host–pathogen dynamics of Chinook Salmon Oncorhynchus tshawytscha and Coho Salmon O. kisutch and the myxozoan parasite Ceratomyxa shasta. Total parasite concentration, water temperature, and discharge were used as covariates to predict the observed parasite-induced mortality in juvenile salmonids collected as part of a long-term monitoring program in the Klamath River, California. The mixture cure models predicted the observed total mortality well, but some of the variability in observed mortality rates was not captured by the models. Parasite concentration and water temperature were positively associated with total mortality and the mortality rate of both Chinook Salmon and Coho Salmon. Discharge was positively associated with total mortality for both species but only affected the mortality rate for Coho Salmon. The mixture cure models provide insights into how daily survival rates change over time in Chinook Salmon and Coho Salmon after they become infected with C. shasta.

Dr Jekyll and Mrs Hyde: Risky hybrid sex by amphibian-parasitizing chytrids in the Brazilian Atlantic Forests.

PubMed

Ghosh, Pria; Fisher, Matthew C

2016-07-01

In their article in this issue of Molecular Ecology, Jenkinson et al. () and colleagues address a worrying question-how could arguably the most dangerous pathogen known to science, Batrachochytrium dendrobatidis (Bd), become even more virulent? The answer: start having sex. Jenkinson et al. present a case for how the introduction into Brazil of the globally invasive lineage of Bd, BdGPL, has disrupted the relationship between native amphibians and an endemic Bd lineage, BdBrazil. BdBrazil is hypothesized to be native to the Atlantic Forest and so have a long co-evolutionary history with biodiverse Atlantic Forest amphibian community. The authors suggest that this has resulted in a zone of hybrid Bd genotypes which are potentially more likely to cause fatal chytridiomycosis than either parent lineage. The endemic-nonendemic Bd hybrid genotypes described in this study, and the evidence for pathogen translocation via the global amphibian trade presented, highlights the danger of anthropogenic pathogen dispersal. This research emphasizes that biosecurity regulations may have to refocus on lineages within species if we are to mitigate against the danger of new, possibly hypervirulent genotypes of pathogens emerging as phylogeographic barriers are breached. © 2016 John Wiley & Sons Ltd.

Reconstructing the emergence of a lethal infectious disease of wildlife supports a key role for spread through translocations by humans

PubMed Central

Cunningham, Andrew A.; Langton, Tom E. S.

2016-01-01

There have been few reconstructions of wildlife disease emergences, despite their extensive impact on biodiversity and human health. This is in large part attributable to the lack of structured and robust spatio-temporal datasets. We overcame logistical problems of obtaining suitable information by using data from a citizen science project and formulating spatio-temporal models of the spread of a wildlife pathogen (genus Ranavirus, infecting amphibians). We evaluated three main hypotheses for the rapid increase in disease reports in the UK: that outbreaks were being reported more frequently, that climate change had altered the interaction between hosts and a previously widespread pathogen, and that disease was emerging due to spatial spread of a novel pathogen. Our analysis characterized localized spread from nearby ponds, consistent with amphibian dispersal, but also revealed a highly significant trend for elevated rates of additional outbreaks in localities with higher human population density—pointing to human activities in also spreading the virus. Phylogenetic analyses of pathogen genomes support the inference of at least two independent introductions into the UK. Together these results point strongly to humans repeatedly translocating ranaviruses into the UK from other countries and between UK ponds, and therefore suggest potential control measures. PMID:27683363

Predictive models for Escherichia coli concentrations at inland lake beaches and relationship of model variables to pathogen detection

USGS Publications Warehouse

Francy, Donna S.; Stelzer, Erin A.; Duris, Joseph W.; Brady, Amie M.G.; Harrison, John H.; Johnson, Heather E.; Ware, Michael W.

2013-01-01

Predictive models, based on environmental and water quality variables, have been used to improve the timeliness and accuracy of recreational water quality assessments, but their effectiveness has not been studied in inland waters. Sampling at eight inland recreational lakes in Ohio was done in order to investigate using predictive models for Escherichia coli and to understand the links between E. coli concentrations, predictive variables, and pathogens. Based upon results from 21 beach sites, models were developed for 13 sites, and the most predictive variables were rainfall, wind direction and speed, turbidity, and water temperature. Models were not developed at sites where the E. coli standard was seldom exceeded. Models were validated at nine sites during an independent year. At three sites, the model resulted in increased correct responses, sensitivities, and specificities compared to use of the previous day's E. coli concentration (the current method). Drought conditions during the validation year precluded being able to adequately assess model performance at most of the other sites. Cryptosporidium, adenovirus, eaeA (E. coli), ipaH (Shigella), and spvC (Salmonella) were found in at least 20% of samples collected for pathogens at five sites. The presence or absence of the three bacterial genes was related to some of the model variables but was not consistently related to E. coli concentrations. Predictive models were not effective at all inland lake sites; however, their use at two lakes with high swimmer densities will provide better estimates of public health risk than current methods and will be a valuable resource for beach managers and the public.