The challenge of emerging and re-emerging infectious diseases

Emerging and re-emerging infections at the turn of the millennium

After World War II, mankind believed that infectious diseases were on the way to being defeated. Unfortunately, they still are the second worldwide cause of death. Globalization changes promote the emergence of new infections and pandemics; international deliveries and travelling facilitate the dissemination of infectious agents; man-induced environmental changes create new opportunities for contacts between species, leading to infections in aberrant hosts, including man; global warming enables insects, a major vector of pathogens, to thrive in more countries. The main pandemics have been caused by viruses, such as HIV and novel subtypes of influenza viruses. In addition, prion proteins are a threat. The transmission of the Creutzfeld Jakob disease variant through blood transfusion and the recent discovery of prion protein in the spleen of a haemophilia patient are a matter of further concern. The end of the war against infectious diseases is not in sight. Mankind's battle with pathogens has lasted millennia and is destined to continue.

Genomic Approaches to the Host Response to Pathogens

The need to better understand host–pathogen interactions has risen with the expansion in genomics and related technologies. This chapter focuses on two aspects of the host response to pathogens where major advances are being made using genomic approaches. The availability of complete genomic sequences of an expanding number of pathogens, the human and mouse genome sequences, and the advent of genome-wide genotyping and gene expression profiling has opened up new avenues of investigation in the field. The genotype of the pathogen plays a major role in the response of the host to infection with more virulent pathogenic strains possessing the capability to interfere with the host immune response. In addition, different individuals in a population can have very different responses to a genetically identical pathogen. Part of the differential response is governed by the underlying genetic differences between individuals. The advent of genome-wide genotyping using single nucleotide polymorphisms or microsatellite markers is leading to major advances in molecular epidemiology. The future impact of genomic approaches on the development of diagnostics and therapeutics is discussed for infectious diseases. This includes defining the basis of genetic susceptibility to infection and system-wide molecular response to a pathogen.

How Ebola impacts genetics of Western lowland gorilla populations

Background

Emerging infectious diseases in wildlife are major threats for both human health and biodiversity conservation. Infectious diseases can have serious consequences for the genetic diversity of populations, which could enhance the species' extinction probability. The Ebola epizootic in western and central Africa induced more than 90% mortality in Western lowland gorilla population. Although mortality rates are very high, the impacts of Ebola on genetic diversity of Western lowland gorilla have never been assessed.

Methodology/Principal Findings

We carried out long term studies of three populations of Western lowland gorilla in the Republic of the Congo (Odzala-Kokoua National Park, Lossi gorilla sanctuary both affected by Ebola and Lossi's periphery not affected). Using 17 microsatellite loci, we compared genetic diversity and structure of the populations and estimate their effective size before and after Ebola outbreaks. Despite the effective size decline in both populations, we did not detect loss in genetic diversity after the epizootic. We revealed temporal changes in allele frequencies in the smallest population.

Conclusions/Significance

Immigration and short time elapsed since outbreaks could explain the conservation of genetic diversity after the demographic crash. Temporal changes in allele frequencies could not be explained by genetic drift or random sampling. Immigration from genetically differentiated populations and a non random mortality induced by Ebola, i.e., selective pressure and cost of sociality, are alternative hypotheses. Understanding the influence of Ebola on gorilla genetic dynamics is of paramount importance for human health, primate evolution and conservation biology.

Plant-made vaccine antigens and biopharmaceuticals

Plant cells are ideal bioreactors for the production and oral delivery of vaccines and biopharmaceuticals, eliminating the need for expensive fermentation, purification, cold storage, transportation and sterile delivery. Plant-made vaccines have been developed for two decades but none has advanced beyond Phase I. However, two plant-made biopharmaceuticals are now advancing through Phase II and Phase III human clinical trials. In this review, we evaluate the advantages and disadvantages of different plant expression systems (stable nuclear and chloroplast or transient viral) and their current limitations or challenges. We provide suggestions for advancing this valuable concept for clinical applications and conclude that greater research emphasis is needed on large-scale production, purification, functional characterization, oral delivery and preclinical evaluation.

Plant-made vaccine antigens and biopharmaceuticals

Plant cells are ideal bioreactors for the production and oral delivery of vaccines and biopharmaceuticals, eliminating the need for expensive fermentation, purification, cold storage, transportation and sterile delivery. Plant-made vaccines have been developed for two decades but none has advanced beyond Phase I. However, two plant-made biopharmaceuticals are now advancing through Phase II and Phase III human clinical trials. In this review, we evaluate the advantages and disadvantages of different plant expression systems (stable nuclear and chloroplast or transient viral) and their current limitations or challenges. We provide suggestions for advancing this valuable concept for clinical applications and conclude that greater research emphasis is needed on large-scale production, purification, functional characterization, oral delivery and preclinical evaluation.

The European network of Biosafety-Level-4 laboratories: enhancing European preparedness for new health threats

Emerging and re-emerging infections and possible bioterrorism acts will continue to challenge both the medical community and civilian populations worldwide, urging health authorities to respond rapidly and effectively. Established in 2005, the European Community (EC)-funded European Network of Biosafety-Level-4 laboratories (Euronet-P4), which brings together the laboratories in Porton Down, London, Hamburg, Marburg, Solna, Lyon and Rome, seeks to increase international collaboration in the areas of high containment laboratory biosafety and viral diagnostic capability, to strengthen Europe's capacity to respond to an infectious disease emergency, and to offer assistance to countries not equipped with such costly facilities. Network partners have agreed on a common strategy to fill the gaps identified in the field of risk group-4 agents’ laboratory diagnosis, namely the lack of standardization and of reference samples. The network has received a further 3-year funding, to offer assistance to external laboratories, and to start the planning of field activities.

Crows break off live camphor twigs: an avian disturbance effect on plants

Birds are usually considered beneficial partners for plants, acting as predators on herbivorous insects, pollinators and seed dispersal agents. However, in an urban area of central Japan, birds break off large quantities of live camphor tree (Cinnamomum camphora) twigs in winter. This loss of vegetative parts was examined quantitatively to estimate the impact on the trees. I also observed bird foraging behaviour to determine the species involved and the possible reasons underlying this destructive activity. Broken twigs on the forest floor were found to have numerous leaves and spring buds. The densities of leaves and buds in the litter were 288.5 and 54.4 m(-2), respectively. The jungle crow (Corvus macrorhynchos) may have broken off the twigs either to peck the fruits while perching on stable branches, or possibly to remove twigs obstructing access to fruit. In contrast, brown-eared bulbuls (Hypsipetes amaurotis), oriental turtle doves (Streptopelia orientalis) and rove doves (Columba livia) ate fruits without breaking twigs. The interaction between C. camphora and C. macrorhynchos only extends back for about 20 years in urban Japan, indicating that this is unlikely to be a stable, co-evolved relationship.

Acute hepatitis E virus infection in Taiwan 2002-2006 revisited: PCR shows frequent co-infection with multiple hepatitis viruses

Sporadic cases of acute hepatitis E virus (HEV) infection with production of anti-HEV IgM have been reported occasionally in Taiwan despite no reported outbreaks in the past. This study was undertaken to determine whether serological markers correlated with virus detection. From 2002 to 2006, 72 reported cases of acute hepatitis E seropositive for anti-HEV IgM in Taiwan were enrolled for investigation. Acute phase serum samples were collected for detection of HEV RNA, HBV DNA, HCV RNA, and GBV-C RNA by PCR. The results showed that viral sequences of HEV, HBV, HCV and GBV-C were detected in 54 (75%), 21 (29.2%), 9 (12.5%), and 22 (30.6%) of cases, respectively. Acute hepatitis A co-infection was excluded in all patients because none were seropositive for anti-HAV IgM and, nine patients (12.5%) did not seroconvert to anti-HEV IgG. These results suggest that serum markers did not correlate completely with viremia in the diagnosis of acute HEV infection. Multiple viruses may co-infect with acute hepatitis E virus in Taiwan. Detection of hepatitis E viremia together with seropositivity for anti-HEV IgM and followed by seroconversion to anti-HEV IgG should be included in the diagnostic criteria for HEV infection.

Point of care strategy for rapid diagnosis of novel A/H1N1 influenza virus

In late June 2009, we implemented for public hospitals of Marseille Point Of Care strategy for rapid diagnosis of novel A/H1N1 influenza virus. During two months, we have tested more than 900 specimens in both Point Of Care laboratories. We believe that implementation of Point of Care strategy for the largest number of suspects cases may improve quality of patients care and our knowledge of the epidemiology of the pandemic.

Ixodes ricinus ticks are reservoir hosts for Rickettsia helvetica and potentially carry flea-borne Rickettsia species

BACKGROUND

Hard ticks have been identified as important vectors of rickettsiae causing the spotted fever syndrome. Tick-borne rickettsiae are considered to be emerging, but only limited data are available about their presence in Western Europe, their natural life cycle and their reservoir hosts. Ixodes ricinus, the most prevalent tick species, were collected and tested from different vegetation types and from potential reservoir hosts. In one biotope area, the annual and seasonal variability of rickettsiae infections of the different tick stages were determined for 9 years.

RESULTS

The DNA of the human pathogen R. conorii as well as R. helvetica, R. sp. IRS and R. bellii-like were found. Unexpectedly, the DNA of the highly pathogenic R. typhi and R. prowazekii and 4 other uncharacterized Rickettsia spp. related to the typhus group were also detected in I. ricinus. The presence of R. helvetica in fleas isolated from small rodents supported our hypothesis that cross-infection can occur under natural conditions, since R. typhi/prowazekii and R. helvetica as well as their vectors share rodents as reservoir hosts. In one biotope, the infection rate with R. helvetica was ~66% for 9 years, and was comparable between larvae, nymphs, and adults. Larvae caught by flagging generally have not yet taken a blood meal from a vertebrate host. The simplest explanation for the comparable prevalence of R. helvetica between the defined tick stages is, that R. helvetica is vertically transmitted through the next generation with high efficiency. The DNA of R. helvetica was also present in whole blood from mice, deer and wild boar.

CONCLUSION

Besides R. helvetica, unexpected rickettsiae are found in I. ricinus ticks. We propose that I. ricinus is a major reservoir host for R. helvetica, and that vertebrate hosts play important roles in the further geographical dispersion of rickettsiae.

Using satellite images of environmental changes to predict infectious disease outbreaks

Recent events clearly illustrate a continued vulnerability of large populations to infectious diseases, which is related to our changing human-constructed and natural environments. A single person with multidrug-resistant tuberculosis in 2007 provided a wake-up call to the United States and global public health infrastructure, as the health professionals and the public realized that today's ease of airline travel can potentially expose hundreds of persons to an untreatable disease associated with an infectious agent. Ease of travel, population increase, population displacement, pollution, agricultural activity, changing socioeconomic structures, and international conflicts worldwide have each contributed to infectious disease events. Today, however, nothing is larger in scale, has more potential for long-term effects, and is more uncertain than the effects of climate change on infectious disease outbreaks, epidemics, and pandemics. We discuss advances in our ability to predict these events and, in particular, the critical role that satellite imaging could play in mounting an effective response.

Evolution and emergence of novel human infections

Some zoonotic pathogens cause sporadic infection in humans but rarely propagate further, while others have succeeded in overcoming the species barrier and becoming established in the human population. Adaptation, driven by selection pressure in human hosts, can play a significant role in allowing pathogens to cross this species barrier. Here we use a simple mathematical model to study potential epidemiological markers of adaptation. We ask: under what circumstances could ongoing adaptation be signalled by large clusters of human infection? If a pathogen has caused hundreds of cases but with little transmission, does this indicate that the species barrier cannot be crossed? Finally, how can case reports be monitored to detect an imminent emergence event? We distinguish evolutionary scenarios under which adaptation is likely to be signalled by large clusters of infection and under which emergence is likely to occur without any prior warning. Moreover, we show that a lack of transmission never rules out adaptability, regardless of how many zoonoses have occurred. Indeed, after the first 100 zoonotic cases, continuing sporadic zoonotic infections without onward, human-to-human transmission offer little extra information on pathogen adaptability. Finally, we present a simple method for monitoring outbreaks for signs of emergence and discuss public health implications.

Infectious causes of cancer and their detection

Molecular techniques for identifying pathogens associated with cancer continue to be developed, including one reported recently in BMC Medical Genomics. Identifying a causal infectious agent helps in understanding the biology of these cancers and can lead ultimately to the development of antimicrobial drugs and vaccines for their treatment and prevention.

Isolation rooms for highly infectious diseases: an inventory of capabilities in European countries

Isolation of patients with highly infectious diseases (HIDs) in hospital rooms with adequate technical facilities is essential to reduce the risk of spreading disease. The European Network for Infectious Diseases (EUNID), a project co-funded by European Commission and involving 16 European Union member states, performed an inventory of high level isolation rooms (HIRs, hospital rooms with negative pressure and anteroom). In participating countries, HIRs are available in at least 211 hospitals, with at least 1789 hospital beds. The adequacy of this number is not known and will depend on prevailing circumstances. Sporadic HID cases can be managed in the available HIRs. HIRs could also have a role in the initial phases of an influenza pandemic. However, large outbreaks due to natural or to bioterrorist events will need management strategies involving healthcare facilities other than HIRs.

Crosstalk between components of the innate immune system: promoting anti-microbial defenses and avoiding immunopathologies

Because it reaches full functional efficacy rapidly upon encounter with a pathogen, the innate immune system is considered as the first line of defense against infections. The sensing of microbes or of transformed or infected cells, through innate immune recognition receptors (referred to as activating I2R2), initiates pro-inflammatory responses and innate immune effector functions. Other I2R2 with inhibitory properties bind self-ligands constitutively expressed in host. However, this dichotomy in the recognition of foreign or induced self versus constitutive self by I2R2 is not always respected in certain non-infectious conditions reminiscent of immunopathologies. In this review, we discuss that immune mechanisms have evolved to avoid inappropriate inflammatory disorders in individuals. Molecular crossregulation exists between components of I2R2 signaling pathways, and intricate interactions between cells from both innate and adaptive immune systems set the bases of controlled immune responses. We also pinpoint that, like T or B cells, some cells of the innate immune system must go through education processes to prevent autoreactivity. In addition, we illustrate how gene expression profiling of immune cell types is a useful tool to find functional homologies between cell subsets of different species and to speculate about unidentified functions of these cells in the responses to pathogen infections.

Use of unstructured event-based reports for global infectious disease surveillance

Free or low-cost sources of unstructured information, such as Internet news and online discussion sites, provide detailed local and near real-time data on disease outbreaks, even in countries that lack traditional public health surveillance. To improve public health surveillance and, ultimately, interventions, we examined 3 primary systems that process event-based outbreak information: Global Public Health Intelligence Network, HealthMap, and EpiSPIDER. Despite similarities among them, these systems are highly complementary because they monitor different data types, rely on varying levels of automation and human analysis, and distribute distinct information. Future development should focus on linking these systems more closely to public health practitioners in the field and establishing collaborative networks for alert verification and dissemination. Such development would further establish event-based monitoring as an invaluable public health resource that provides critical context and an alternative to traditional indicator-based outbreak reporting.

Microfluidic systems for pathogen sensing: a review

Rapid pathogen sensing remains a pressing issue today since conventional identification methodsare tedious, cost intensive and time consuming, typically requiring from 48 to 72 h. In turn, chip based technologies, such as microarrays and microfluidic biochips, offer real alternatives capable of filling this technological gap. In particular microfluidic biochips make the development of fast, sensitive and portable diagnostic tools possible, thus promising rapid and accurate detection of a variety of pathogens. This paper will provide a broad overview of the novel achievements in the field of pathogen sensing by focusing on methods and devices that compliment microfluidics.

A novel approach to real-time risk prediction for emerging infectious diseases: a case study in Avian Influenza H5N1

Mathematical simulation modelling of epidemic processes has recently become a popular tool in guiding policy decisions for potential disease outbreaks. Such models all rely on various parameters in order to specify quantities such as transmission and detection rates. However, the values of these parameters are peculiar to an individual outbreak, and estimating them in advance of an epidemic has been the major difficulty in the predictive credibility of such approaches. The obstruction to classical approaches in estimating model parameters has been that of missing data: (i) an infected individual is only detected after the onset of clinical signs, we never observe the time of infection directly; (ii) if we wish to make inference on an epidemic while it is in progress (in order to predict how it might unfold in the future), we must take into account the fact that there may be individuals who are infected but not yet detected. In this paper we apply a reversible-jump Markov chain Monte Carlo algorithm to a combined spatial and contact network model constructed in a Bayesian context to provide a real-time risk prediction during an epidemic. Using the example of a potential Avian H5N1 epidemic in the UK poultry industry, we demonstrate how such a technique can be used to give real-time predictions of quantities such as the probability of individual poultry holdings becoming infected, the risk that individual holdings pose to the population if they become infected, and the number and whereabouts of infected, but not yet detected, holdings. Since the methodology generalises easily to many epidemic situations, we anticipate its use as a real-time decision-support tool for targetting disease control to critical transmission processes, and for monitoring the efficacy of current control policy.

First reported case of Cryptococcus gattii in the Southeastern USA: implications for travel-associated acquisition of an emerging pathogen

In 2007, the first confirmed case of Cryptococcus gattii was reported in the state of North Carolina, USA. An otherwise healthy HIV negative male patient presented with a large upper thigh cryptococcoma in February, which was surgically removed and the patient was started on long-term high-dose fluconazole treatment. In May of 2007, the patient presented to the Duke University hospital emergency room with seizures. Magnetic resonance imaging revealed two large CNS lesions found to be cryptococcomas based on brain biopsy. Prior chest CT imaging had revealed small lung nodules indicating that C. gattii spores or desiccated yeast were likely inhaled into the lungs and dissemination occurred to both the leg and CNS. The patient's travel history included a visit throughout the San Francisco, CA region in September through October of 2006, consistent with acquisition during this time period. Cultures from both the leg and brain biopsies were subjected to analysis. Based on phenotypic and molecular methods, both isolates were C. gattii, VGI molecular type, and distinct from the Vancouver Island outbreak isolates. Based on multilocus sequence typing of coding and noncoding regions and virulence in a heterologous host model, the leg and brain isolates are identical, but the two differed in mating fertility. Two clinical isolates, one from a transplant recipient in San Francisco and the other from Australia, were identical to the North Carolina clinical isolate at all markers tested. Closely related isolates that differ at only one or a few noncoding markers are present in the Australian environment. Taken together, these findings support a model in which C. gattii VGI was transferred from Australia to California, possibly though an association with its common host plant E. camaldulensis, and the patient was exposed in San Francisco and returned to present with disease in North Carolina.

Lost in transcription--inhibition of RNA polymerase

Form and function: The natural product myxopyronin A provides the key to understanding the inhibition of bacterial RNA polymerase and should spark new ideas for the design of new antibiotics against tuberculosis and other infectious diseases.

Silencing viral microRNA as a novel antiviral therapy?

Viruses are intracellular parasites that ensure their existence by converting host cells into viral particle producing entities or into hiding places rendering the virus invisible to the host immune system. Some viruses may also survive by transforming the infected cell into an immortal tumour cell. MicroRNAs are small non-coding transcripts that function as posttranscriptional regulators of gene expression. Viruses encode miRNAs that regulate expression of both cellular and viral genes, and contribute to the pathogenic properties of viruses. Hence, neutralizing the action of viral miRNAs expression by complementary single-stranded oligonucleotides or so-called anti-miRNAs may represent a strategy to combat viral infections and viral-induced pathogenesis. This review describes the miRNAs encoded by human viruses, and discusses the possible therapeutic applications of anti-miRNAs against viral diseases.

Identification of microbial DNA in human cancer

BACKGROUND

Microorganisms have been associated with many types of human diseases; however, a significant number of clinically important microbial pathogens remain to be discovered.

METHODS

We have developed a genome-wide approach, called Digital Karyotyping Microbe Identification (DK-MICROBE), to identify genomic DNA of bacteria and viruses in human disease tissues. This method involves the generation of an experimental DNA tag library through Digital Karyotyping (DK) followed by analysis of the tag sequences for the presence of microbial DNA content using a compiled microbial DNA virtual tag library.

RESULTS

To validate this technology and to identify pathogens that may be associated with human cancer pathogenesis, we used DK-MICROBE to determine the presence of microbial DNA in 58 human tumor samples, including brain, ovarian, and colorectal cancers. We detected DNA from Human herpesvirus 6 (HHV-6) in a DK library of a colorectal cancer liver metastasis and in normal tissue from the same patient.

CONCLUSION

DK-MICROBE can identify previously unknown infectious agents in human tumors, and is now available for further applications for the identification of pathogen DNA in human cancer and other diseases.

Host mixing and disease emergence

Recent cases of emergent diseases have renewed interest in the evolutionary and ecological mechanisms that promote parasite adaptation to novel hosts [1-6]. Crucial to adaptation is the degree of mixing of original, susceptible hosts, and novel hosts. An increase in the frequency of the original host has two opposing effects on adaptation: an increase in the supply of mutant pathogens with improved performance on the novel host [7-9]; and reduced selection to infect novel hosts, caused by fitness costs commonly observed to be associated with host switching [10-17]. The probability of disease emergence will therefore peak at intermediate frequencies of the original host. We tested these predictions by following the evolution of a virus grown under a range of different frequencies of susceptible (original) and resistant (novel) host bacteria. Viruses that evolved to infect resistant hosts were only detected when susceptible hosts were at frequencies between 0.1% and 1%. Subsequent experiments supported the predictions that there was reduced selection and mutation supply at higher and lower frequencies, respectively. These results suggest that adaptation to novel hosts can occur only under very specific ecological conditions, and that small changes in contact rates between host species might help to mitigate disease emergence.

Emerging trends in plasma-free manufacturing of recombinant protein therapeutics expressed in mammalian cells

Mammalian cells are the expression system of choice for therapeutic proteins, especially those requiring complex post‐translational modifications. Traditionally, these cells are grown in medium supplemented with serum and other animal‐ or human‐derived components to support viability and productivity. Such proteins are also typically added as excipients and stabilizers in the final drug formulation. However, the transmission of hepatitis B in the 1970s and of hepatitis C and HIV in the 1980s through plasma‐derived factor VIII concentrates had catastrophic consequences for hemophilia patients. Thus, due to regulatory concerns about the inherent potential for transmission of infectious agents as well as the heterogeneity and lack of reliability of the serum supply, a trend has emerged to eliminate the use of plasma‐derived additives in the production and formulation of recombinant protein therapeutics. This practice began with products used in the treatment of hemophilia and is progressively expanding throughout the entire industry. The plasma‐free method of producing recombinant therapeutics is accomplished by the use of both cell culture media and final product formulations that do not contain animal‐ or human‐derived additives. A number of recombinant therapeutic proteins for the treatment of several different diseases have been produced by plasma‐free processes, with the objective of improving safety by eliminating blood‐borne pathogens or by reducing immunogenicity. This review describes the factors that drove the development of plasma‐free protein therapeutics and provides examples of advances in manufacturing that have made possible the removal of human and animal‐derived products from all steps of recombinant protein production.

Lamivudine monotherapy for chronic hepatitis B infection with acute exacerbation revisited

BACKGROUND

Acute exacerbation (AE) of chronic hepatitis B virus (HBV) infection in cancer chemotherapy patients and in organ transplant recipients receiving immunosuppressants may cause catastrophe and high mortality. Hence, immediate treatment with nucleoside analogues for such patients has become a consensus. Anti-HBV therapeutic trials in Asia have shown that AE of chronic hepatitis B (CH-B) may result in increased sustained remission (SR) rate with lamivudine monotherapy. Nonetheless, AE episodes in CH-B patients may evolve uneventfully and lead to spontaneous remission. Thus, the policy of immediate anti-HBV therapy for AE patients reaches an impasse. Once treatment is initiated, life long HBV suppression may be necessary.

OBJECTIVE

To determine whether lamivudine monotherapy during an AE of CH-B results in an increase in SR compared with no therapy.

METHODS

A cohort of 154 CH-B patients seropositive for hepatitis B e antigen with AE formed the study group. This included 102 cases receiving a nationwide therapeutic trial of 18-month lamivudine monotherapy that were compared with 52 cases with no therapy. All were observed for at least 30 months, which encompassed the 18-month on treatment period and a 12-month posttreatment follow-up.

RESULTS

No significant increase was observed in the SR rate in the lamivudine treatment group compared with the spontaneous remission rate in the untreated patients (P=0.782, Fisher's exact test).

CONCLUSION

AE does not increase the SR rate during 18-month lamivudine monotherapy. Immediate lamivudine therapy for AE patients is not justified as mandatory. The policy should be only applied to AE patients with impending liver failure.

Emergence of infectious diseases: when hidden pathogens break out

Our understanding of disease emergence is largely limited by the assumption that disease emergence is the result of increased exposure to pathogenic agents. Pathogen exposure is thought to arise through an increase in the number of interactions between humans and their natural environment, changes in demography and mobility, or through genetic variation in the infectious agents which may alter virulence or ability to infect new host species. The study of new diseases (which are often revealed by unusually severe symptoms or atypical epidemiological patterns) applies the most effort to the research of new pathogens. Here, using examples, we discuss alternative but non-exclusive mechanisms that may either reveal the presence of long-term circulating pathogens or explain changes in their nosologic properties in relation to their pattern of circulation and infection conditions. A better understanding of the ecology of pathogenic organisms and their host populations should help to define more efficient health management strategies.

Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy

Antimicrobial drug development is increasingly lagging behind the evolution of antibiotic resistance, and as a result, there is a pressing need for new antibacterial therapies that can be readily designed and implemented. In this work, we engineered bacteriophage to overexpress proteins and attack gene networks that are not directly targeted by antibiotics. We show that suppressing the SOS network in Escherichia coli with engineered bacteriophage enhances killing by quinolones by several orders of magnitude in vitro and significantly increases survival of infected mice in vivo. In addition, we demonstrate that engineered bacteriophage can enhance the killing of antibiotic-resistant bacteria, persister cells, and biofilm cells, reduce the number of antibiotic-resistant bacteria that arise from an antibiotic-treated population, and act as a strong adjuvant for other bactericidal antibiotics (e.g., aminoglycosides and beta-lactams). Furthermore, we show that engineering bacteriophage to target non-SOS gene networks and to overexpress multiple factors also can produce effective antibiotic adjuvants. This work establishes a synthetic biology platform for the rapid translation and integration of identified targets into effective antibiotic adjuvants.

Generating aptamers for recognition of virus-infected cells

BACKGROUND

The development of molecular probes capable of recognizing virus-infected cells is essential to meet the serious clinical, therapeutic, and national-security challenges confronting virology today. We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells.

METHODS

To create aptamer probes capable of recognizing virus-infected cells, we used cell-SELEX (systematic evolution of ligands via exponential enrichment), which uses intact infected live cells as targets for aptamer selection. In this study, vaccinia virus-infected and -uninfected lung cancer A549 cells were chosen to develop our model probes.

RESULTS

A panel of aptamers has been evolved by means of the infected cell-SELEX procedure. The results demonstrate that the aptamers bind selectively to vaccinia virus-infected A549 cells with apparent equilibrium dissociation constants in the nanomolar range. In addition, these aptamers can specifically recognize a variety of target infected cell lines. The aptamers' target is most likely a viral protein located on the cell surface.

CONCLUSIONS

The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell-SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells.

The heterogeneity of human antibody responses to vaccinia virus revealed through use of focused protein arrays

The renewed interest in strategies to combat infectious agents with epidemic potential has led to a re-examination of vaccination protocols against smallpox. To help define which antigens elicit a human antibody response, we have targeted proteins known or predicted to be presented on the surface of the intracellular mature virion (IMV) or the extracellular enveloped virion (EEV). The predicted ectodomains were expressed in a mammalian in vitro coupled transcription/translation reaction using tRNA(lys) precharged with lysine-epsilon-biotin followed by solid phase immobilization on 384-well neutravidin-coated plates. The generated array is highly specific and sensitive in a micro-ELISA format. By comparison of binding of vaccinia-immune sera to the reticulocyte lysate-produced proteins and to secreted post-translationally modified proteins, we demonstrate that for several proteins including the EEV proteins B5 and A33, proper recognition is dependent upon appropriate folding, with little dependence upon glycosylation per se. We further demonstrate that the humoral immune response to vaccinia among different individuals is not uniform in specificity or strength, as different IMV and EEV targets predominate within the group of immunogenic proteins. This heterogeneity likely results from the diversity of HLA Class II alleles and CD4 T helper cell epitopes stimulating B cell antibody production. Our findings have important implications both for design of new recombinant subunit vaccines as well as for methods of assaying the human antibody response utilizing recombinant proteins produced in vitro.

The cost of simplifying air travel when modeling disease spread

Background

Air travel plays a key role in the spread of many pathogens. Modeling the long distance spread of infectious disease in these cases requires an air travel model. Highly detailed air transportation models can be over determined and computationally problematic. We compared the predictions of a simplified air transport model with those of a model of all routes and assessed the impact of differences on models of infectious disease.

Methodology/Principal Findings

Using U.S. ticket data from 2007, we compared a simplified “pipe” model, in which individuals flow in and out of the air transport system based on the number of arrivals and departures from a given airport, to a fully saturated model where all routes are modeled individually. We also compared the pipe model to a “gravity” model where the probability of travel is scaled by physical distance; the gravity model did not differ significantly from the pipe model. The pipe model roughly approximated actual air travel, but tended to overestimate the number of trips between small airports and underestimate travel between major east and west coast airports. For most routes, the maximum number of false (or missed) introductions of disease is small (<1 per day) but for a few routes this rate is greatly underestimated by the pipe model.

Conclusions/Significance

If our interest is in large scale regional and national effects of disease, the simplified pipe model may be adequate. If we are interested in specific effects of interventions on particular air routes or the time for the disease to reach a particular location, a more complex point-to-point model will be more accurate. For many problems a hybrid model that independently models some frequently traveled routes may be the best choice. Regardless of the model used, the effect of simplifications and sensitivity to errors in parameter estimation should be analyzed.

Metagenomic diagnosis of bacterial infections

To test the ability of high-throughput DNA sequencing to detect bacterial pathogens, we used it on DNA from a patient’s feces during and after diarrheal illness. Sequences showing best matches for Campylobacter jejuni were detected only in the illness sample. Various bacteria may be detectable with this metagenomic approach.

An Ensemble Trajectory Method for Real-Time Modeling and Prediction of Unfolding Epidemics: Analysis of the 2005 Marburg Fever Outbreak in Angola

We propose a new methodology for the modeling and real time prediction of the course of unfolding epidemic outbreaks. The method posits a class of standard epidemic models and explores uncertainty in empirical data to set up a family of possible outbreak trajectories that span the probability distribution of models parameters and initial conditions. A genetic algorithm is used to estimate likely trajectories consistent with the data and reconstruct the probability distribution of model parameters. In this way the ensemble of trajectories allows for temporal extrapolation to produce estimates of future cases and deaths, with quantified levels of uncertainty. We apply this methodology to an outbreak of Marburg hemorrhagic fever in Angola during 2005 in order to estimate disease epidemiological parameters and assess the effects of interventions. Data for cases and deaths was compiled from World Health Organization as the epidemic unfolded. We describe the outbreak through a standard epidemic model used in the past for Ebola, a closely related viral pathogen. The application of our method allows us to make quantitative prognostics as the outbreak unfolds for the expected time to the end of the epidemic and final numbers of cases and fatalities, which were eventually confirmed. We provided a real time analysis of the effects of intervention and possible under reporting and place bounds on population movements necessary to guarantee that the epidemic did not regain momentum.

Investigation of antimicrobial and protease-inhibitory activity from cultured cyanobacteria

A culture collection of cyanobacteria has been established at the University of Illinois at Chicago. This collection includes marine, terrestrial, and freshwater strains and contains representatives of the five orders of cyanobacteria: Chroococcales, Pleurocapsales, Oscillatoriales, Nostocales, and Stigonematales. In this study, extracts from a subset of 61 strains, 16 marine and 45 freshwater/terrestrial, were evaluated against three current protease targets, i.e. 20S proteasome and two SARS viral proteases, two important bacterial targets, i.e. Mycobacterium tuberculosis and Bacillus anthracis, and in the Artemia salina toxicity assay. In total, extracts of 12 strains possessed significant levels of activity in one or more targets. The overwhelming majority of active extracts (11 of 12) were from either freshwater or terrestrial forms of cyanobacteria, with the greater part of these (9 of 12) being heterocyst-forming strains. These results further support the use of cultured cyanobacteria as a source of biologically active natural products.

Predicting undetected infections during the 2007 foot-and-mouth disease outbreak

Active disease surveillance during epidemics is of utmost importance in detecting and eliminating new cases quickly, and targeting such surveillance to high-risk individuals is considered more efficient than applying a random strategy. Contact tracing has been used as a form of at-risk targeting, and a variety of mathematical models have indicated that it is likely to be highly efficient. However, for fast-moving epidemics, resource constraints limit the ability of the authorities to perform, and follow up, contact tracing effectively. As an alternative, we present a novel real-time Bayesian statistical methodology to determine currently undetected (occult) infections. For the UK foot-and-mouth disease (FMD) epidemic of 2007, we use real-time epidemic data synthesized with previous knowledge of FMD outbreaks in the UK to predict which premises might have been infected, but remained undetected, at any point during the outbreak. This provides both a framework for targeting surveillance in the face of limited resources and an indicator of the current severity and spatial extent of the epidemic. We anticipate that this methodology will be of substantial benefit in future outbreaks, providing a compromise between targeted manual surveillance and random or spatially targeted strategies.

Interleukin-15 and NK1.1+ cells provide innate protection against acute Salmonella enterica serovar Typhimurium infection in the gut and in systemic tissues

Control of bacterial colonization at mucosal surfaces depends on rapid activation of the innate immune system. Interleukin-15 (IL-15) directs the development, maturation, and function of a population of cells positive for NK1.1, such as natural killer (NK) cells, which are critical components of the innate immune defense against several viral and bacterial pathogens. Using IL-15-deficient mice, in vivo depletion of NK1.1(+) cells from wild-type mice, and in vivo overexpression of IL-15 from a recombinant adenovirus, we tested the role of IL-15 and NK1.1(+) cells in innate protection of the murine gut and reticuloendothelial system from Salmonella enterica serovar Typhimurium infection. IL-15 and the NK1.1(+) cell population provided innate protection from serovar Typhimurium in mice at the enteric mucosae and in the reticuloendothelial system during murine typhoid. Interestingly, serovar Typhimurium extensively colonized the gut of IL-15(-/-) mice and wild-type C57BL/6 mice depleted of NK1.1(+) cells prior to infection, even though the animals were not pretreated with antibiotics to reduce colonization resistance and there was an absence of overt inflammation in the colon and cecum. Enhanced dissemination of Salmonella from the gut of mice depleted of NK1.1(+) cells correlated with a localized disruption of IL-17 in the colon. These data suggest a relationship between the gut ecosystem and the innate mucosal immune system, which may be linked via IL-15 and NK1.1(+) cells.

Emerging and re-emerging viruses in Malaysia, 1997-2007

Over the past decade, a number of unique zoonotic and non-zoonotic viruses have emerged in Malaysia. Several of these viruses have resulted in significant morbidity and mortality to those affected and they have imposed a tremendous public health and economic burden on the state. Amongst the most devastating was the outbreak of Nipah virus encephalitis in 1998, which resulted in 109 deaths. The culling of more than a million pigs, identified as the amplifying host, ultimately brought the outbreak under control. A year prior to this, and subsequently again in 2000 and 2003, large outbreaks of hand-foot-and-mouth disease due to enterovirus 71, with rare cases of fatal neurological complications, were reported in young children. Three other new viruses – Tioman virus (1999), Pulau virus (1999), and Melaka virus (2006) – whose origins have all been linked to bats, have been added to the growing list of novel viruses being discovered in Malaysia. The highly pathogenic H5N1 avian influenza has also been detected in Malaysia with outbreaks in poultry in 2004, 2006, and 2007. Fortunately, no human infections were reported. Finally, the HIV/AIDS epidemic has seen the emergence of an HIV-1 recombinant form (CRF33_01B) in HIV-infected individuals from various risk groups, with evidence of ongoing and rapid expansion.

Comparison of multiple vaccine vectors in a single heterologous prime-boost trial

The prevention of infectious disease via prophylactic immunization is a mainstay of global public health efforts. Vaccine design would be facilitated by a better understanding of the type and durability of immune responses generated by different vaccine vectors. We report here the results of a comparative immunogenicity trial of six different vaccine vectors expressing the same insert antigen, cowpox virus B5 (CPXV-B5). Of those vectors tested, recombinant adenovirus (rAd5) was the most immunogenic, inducing the highest titer anti-B5 antibodies and conferring protection from sublethal vaccinia virus challenge in mice after a single immunization. We tested select heterologous prime-boost combinations and identified recombinant vesicular stomatitis virus (rVSV) and recombinant Venezuelan equine encephalitis virus replicons (VRP) as the most synergistic regimen. Comparative data such as those presented here are critical to efforts to generate protective vaccines for emerging infectious diseases as well as for biothreat agents.