Posts Tagged ‘Emerging disease’

Climate change influences infectious disease in the Arctic and the tropics

Wednesday, January 13th, 2010

Climate Climate change is incontestably a phenomenon of global causes and impacts. However, as the contribution of different regions and countries to climate change differs, so do the impacts. This paper examines the current and potential impact of climate change on infectious diseases in regions that could not be more different: the Arctic and the tropics. Despite obvious differences in environmental and socio-economic contexts, there are commonalities between these areas, both in the mechanisms through which climate change influences disease transmission and in the adaptation responses health systems can and should mount. The authors consider five main common characteristics and requirements, respectively, regarding climate-sensitive infectious diseases:

  1. Exposure to new patterns of climate-sensitive infectious diseases.
  2. Disease surveillance and early warning systems.
  3. Health system preparedness.
  4. Enhanced global efforts towards developing drugs and vaccines.
  5. Common challenges for research.

Climate change influences infectious diseases both in the Arctic and the tropics: joining the dots. Glob Health Action 2: 11 November 2009. doi: 10.3402/gha.v2i0.2106

Related:

Clustering of MRSA strains across Europe

Tuesday, January 12th, 2010

map Staphylococcus aureus is the main cause of purulent infection in humans. S. aureus has the potential for local as well as disseminated infection and can cause lesions in all tissues and anatomical sites. Infections can be either acquired in the community or in association with health care. The position of S. aureus as one of the most important human pathogens is largely due to its virulence potential and ubiquitous occurrence as a coloniser in humans, domestic animals, and livestock. Between 25% and 35% of healthy human individuals carry S. aureus on the skin or mucous membranes. Any injury that compromises epithelial integrity, trauma, medical or surgical interventions, as well as viral infections, can lead to tissue invasion. It is assumed that severity and outcome depend largely on the virulence of the introduced strain and the immune repertoire of the host. Occasionally, S. aureus acquires enhanced virulence and antimicrobial resistance through horizontal DNA transfer and maintains these mobile genetic elements in a predominantly clonal genomic background. Thus, clones of S. aureus are relatively stable and mainly diversify by the accumulation of single nucleotide substitutions in the absence of frequent interstrain recombination. It is therefore possible to discern different clones and clonal lineages by molecular typing. This method allows several important observations to be made regarding the evolution, epidemiology, and spread of clones with particular public health importance, such as hospital-, community- , and livestock-associated methicillin-resistant S. aureus (MRSA).

A new study finds that methicillin-resistant S. aureus (MRSA), responsible for several difficult-to-treat infections including blood poisoning and pneumonia and a particular problem in hospitals, occurs in distinct geographical clusters across Europe, indicating that MRSA is being diffused by patients moving between hospitals rather than spreading freely in the community. The study used an interactive Web tool to map different strains of the Staphylococcus aureus bacterium across the continent. MRSA infections have become more prevalent in hospitals over the past ten years, and information about its geographical distribution could help us to understand how it spreads and how to control it.

Since 2006 a large group of collaborators in 450 European hospitals located in 26 different countries collected both MRSA and methicillin-sensitive S. aureus (MSSA) isolates from infected patients. National laboratories identified specific strains of S. aureus by molecular typing and entered this information into a Web-based mapping application which is publicly available. The results show that strains of MRSA tend to cluster within regional borders and, in several instances, were associated with individual hospitals. This suggests that MRSA is mainly spread by patients who are repeatedly admitted to different hospitals. Control efforts aimed at interrupting the spread within and between health care institutions may not only be feasible but ultimately successful.

Geographic Distribution of Staphylococcus aureus Causing Invasive Infections in Europe: A Molecular-Epidemiological Analysis. PLoS Med 7(1): e1000215 doi:10.1371/journal.pmed.1000215:
Staphylococcus aureus is one of the most important human pathogens and methicillin-resistant variants (MRSAs) are a major cause of hospital and community-acquired infection. We aimed to map the geographic distribution of the dominant clones that cause invasive infections in Europe. In each country, staphylococcal reference laboratories secured the participation of a sufficient number of hospital laboratories to achieve national geo-demographic representation. Participating laboratories collected successive methicillin-susceptible (MSSA) and MRSA isolates from patients with invasive S. aureus infection using an agreed protocol. All isolates were sent to the respective national reference laboratories and characterised by quality-controlled sequence typing of the variable region of the staphylococcal spa gene (spa typing), and data were uploaded to a central database. Relevant genetic and phenotypic information was assembled for interactive interrogation by a purpose-built Web-based mapping application. Between September 2006 and February 2007, 357 laboratories serving 450 hospitals in 26 countries collected 2,890 MSSA and MRSA isolates from patients with invasive S. aureus infection. A wide geographical distribution of spa types was found with some prevalent in all European countries. MSSA were more diverse than MRSA. Genetic diversity of MRSA differed considerably between countries with dominant MRSA spa types forming distinctive geographical clusters. We provide evidence that a network approach consisting of decentralised typing and visualisation of aggregated data using an interactive mapping tool can provide important information on the dynamics of MRSA populations such as early signalling of emerging strains, cross border spread, and importation by travel. In contrast to MSSA, MRSA spa types have a predominantly regional distribution in Europe. This finding is indicative of the selection and spread of a limited number of clones within health care networks, suggesting that control efforts aimed at interrupting the spread within and between health care institutions may not only be feasible but ultimately successful and should therefore be strongly encouraged.

Related:

The Bornavirus in all of us

Thursday, January 7th, 2010

Bornavirus Even before I wrote my online notes about Bornaviruses over 10 years ago, this group of viruses was always a bit of a mystery. Considerable controversy still surrounds the role of these viruses in human pathogenesis, so it is of great interest that a report has just been published in Nature describing how Bornavirus-like sequences have been repeatedly incorporated into the genome during mammalian evolution. BDV infection might create a source of mutation in infected individuals, which allows a testable hypothesis for the alleged, but still controversial, causative association of BDV infection with certain psychiatric disorders, such as schizophrenia and mood disorders.

Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature 463, 84, (2010). doi:10.1038/nature08695
Retroviruses are the only group of viruses known to have left a fossil record, in the form of endogenous proviruses, and approximately 8% of the human genome is made up of these elements. Although many other viruses, including non-retroviral RNA viruses, are known to generate DNA forms of their own genomes during replication, none has been found as DNA in the germline of animals. Bornaviruses, a genus of non-segmented, negative-sense RNA virus, are unique among RNA viruses in that they establish persistent infection in the cell nucleus. Here we show that elements homologous to the nucleoprotein (N) gene of bornavirus exist in the genomes of several mammalian species, including humans, non-human primates, rodents and elephants. These sequences have been designated endogenous Borna-like N (EBLN) elements. Some of the primate EBLNs contain an intact open reading frame (ORF) and are expressed as mRNA. Phylogenetic analyses showed that EBLNs seem to have been generated by different insertional events in each specific animal family. Furthermore, the EBLN of a ground squirrel was formed by a recent integration event, whereas those in primates must have been formed more than 40 million years ago. We also show that the N mRNA of a current mammalian bornavirus, Borna disease virus (BDV), can form EBLN-like elements in the genomes of persistently infected cultured cells. Our results provide the first evidence for endogenization of non-retroviral virus-derived elements in mammalian genomes and give novel insights not only into generation of endogenous elements, but also into a role of bornavirus as a source of genetic novelty in its host.

Related:

Disease-driven declines in global amphibian biodiversity

Monday, December 14th, 2009

Batrachochytrium dendrobatidis Amphibians such as frogs and toads are being driven to extinction by an aquatic fungus. This microbe, commonly called Bd, is spreading rapidly around the world and contributing to the decline in the biodiversity of the animals. In this article in Microbiology Today (pdf) Matthew Fisher believes that if control measures are not implemented, one-third of amphibian species could disappear:

Amphibians became the most ancient class of land-dwelling vertebrates when, 360 million years ago, Ichthyostega first hauled itself onto what was then Greenland. Since then, the amphibia have diversified into over 6,300 species that not only settled all continents except Antarctica, but also survived the catastrophic extinction events that overwhelmed their sister group, the dinosaurs. However, longevity of species is no guarantee of their future success; modern-day amphibians are suffering rates of extinction that far exceed those of any other class of vertebrates, including mammals and birds. Nearly one-third of amphibian species are threatened. The question of why amphibians are becoming extinct at these accelerated rates has puzzled scientists for three decades. While it is now clear that we are heading for a new anthropocene mass-extinction event as a consequence of human-driven planetary degradation, it has not been clear why this should be affecting amphibians more than other taxa. Further, many amphibian declines and extinctions were observed to occur in pristine environments that are relatively untouched by humans, such as rainforests and montane systems. A clue to the mystery came about when scientists working in Central America noted that the declines in amphibian biodiversity appeared to be occurring in a wave-like manner, with the initial losses being observed in Costa Rica, then spreading southwards towards the Panama Canal at rates of up to 43 km per year. These patterns of decline were suggestive of an epidemic, spreading pathogen, and in 1997 an international team of scientists discovered a new organism that appeared to be associated with many previously ‘enigmatic’ amphibian extinctions in two regions: Central America and north-eastern Australia. In 1999, the mycologist Joyce Longcore formally described this organism as new species of aquatic fungus and named it Batrachochytrium dendrobatidis.

Read more

Related:

Severity of swine flu in the USA

Tuesday, December 8th, 2009

Influenza virus Research published this week in PLoS Medicine presents the most accurate assessment to date of the severity of the swine flu (H1N1) pandemic in the US. Scientists need to measure the severity of swine flu (how often infection with the swine flu virus results in symptoms leading to illness, hospitalization or death) so that appropriate pandemic plans can be put into place. Severity of swine flu has been difficult to measure for two main reasons: first, people with severe influenza are more likely than those with mild cases to seek care, making it difficult to estimate how many total cases have occurred, and second, the sheer number of cases means that recording routine case data can be difficult due to overburdening of public health systems. In this study, researchers from from Milwaukee (where all medically attended cases were recorded, whether hospitalized or not) and New York City (where only hospitalizations, intensive care admission and deaths were recorded, and a telephone survey of flu-like illness was conducted), along with earlier results from studies by the US CDC, used a statistical approach called Bayesian evidence synthesis. This enabled accurate estimations of severity to be made. Their analyses reveal that the autumn-winter pandemic wave of swine flu should have a death toll only slightly higher than, or considerably lower than, that caused by seasonal influenza in an average year, provided swine flu continues to behave as it did during the summer. Seasonal influenza mainly kills elderly adults, but the authors reveal that most deaths from swine flu will occur in non-elderly adults, a shift in age distribution that has been seen in previous pandemics.

The Severity of Pandemic H1N1 Influenza in the United States, from April to July 2009: A bayesian Analysis. PLoS Med 6(12): e1000207 doi:10.1371/journal.pmed.1000207
Accurate measures of the severity of pandemic (H1N1) 2009 influenza (pH1N1) are needed to assess the likely impact of an anticipated resurgence in the autumn in the Northern Hemisphere. Severity has been difficult to measure because jurisdictions with large numbers of deaths and other severe outcomes have had too many cases to assess the total number with confidence. Also, detection of severe cases may be more likely, resulting in overestimation of the severity of an average case. We sought to estimate the probabilities that symptomatic infection would lead to hospitalization, ICU admission, and death by combining data from multiple sources. We used complementary data from two US cities: Milwaukee attempted to identify cases of medically attended infection whether or not they required hospitalization, while New York City focused on the identification of hospitalizations, intensive care admission or mechanical ventilation (hereafter, ICU), and deaths. New York data were used to estimate numerators for ICU and death, and two sources of data – medically attended cases in Milwaukee or self-reported influenza-like illness (ILI) in New York – were used to estimate ratios of symptomatic cases to hospitalizations. Combining these data with estimates of the fraction detected for each level of severity, we estimated the proportion of symptomatic patients who died (symptomatic case-fatality ratio, sCFR), required ICU (sCIR), and required hospitalization (sCHR), overall and by age category. Evidence, prior information, and associated uncertainty were analyzed in a Bayesian evidence synthesis framework. Using medically attended cases and estimates of the proportion of symptomatic cases medically attended, we estimated an sCFR of 0.048% (95% credible interval [CI] 0.026%–0.096%), sCIR of 0.239% (0.134%–0.458%), and sCHR of 1.44% (0.83%–2.64%). Using self-reported ILI, we obtained estimates approximately 7–96lower. sCFR and sCIR appear to be highest in persons aged 18 y and older, and lowest in children aged 5–17 y. sCHR appears to be lowest in persons aged 5–17; our data were too sparse to allow us to determine the group in which it was the highest. These estimates suggest that an autumn–winter pandemic wave of pH1N1 with comparable severity per case could lead to a number of deaths in the range from considerably below that associated with seasonal influenza to slightly higher, but with the greatest impact in children aged 0–4 and adults 18–64. These estimates of impact depend on assumptions about total incidence of infection and would be larger if incidence of symptomatic infection were higher or shifted toward adults, if viral virulence increased, or if suboptimal treatment resulted from stress on the health care system; numbers would decrease if the total proportion of the population symptomatically infected were lower than assumed.

Related:

UK HIV cases higher than ever

Friday, November 27th, 2009

More people than ever before are living with HIV in the UK but more than a quarter do not know they have it, figures show. The number of estimated cases rose by 8% between 2007 and 2008, says the Health Protection Agency. But it is thought 22,000 of the 83,000 people with HIV do not know they are infected.

More people than ever before are living with HIV in the UK but more than a quarter do not know they have it, figures show. The number of estimated cases rose by 8% between 2007 and 2008, says the Health Protection Agency. But it is thought 22,000 of the 83,000 people with HIV do not know they are infected.

Read more

Related:

Replication cycle of chikungunya virus

Monday, November 2nd, 2009

Chikungunya virus The unprecedented 2005-2006 epidemics of chikungunya virus (CHIKV) in the French Reunion Island in the Indian Ocean, followed by several outbreaks in other parts of the world such as India, have attracted the attention of clinicians, scientists, and state authorities about the risks linked to this re-emerging mosquito-borne virus. CHIKV, which belongs to the Alphaviruses genus, was not previously regarded as a highly pathogenic arbovirus. However, this opinion was challenged by the death of several CHIKV-infected persons in Reunion Island. The epidemic episode began in December 2005 and four months later the seroprevalence survey report indicated that 236,000 persons, more than 30% of Reunion Island population, had been infected with CHIKV, among which 0.4-0.5% of cases were fatal. Since the epidemic peak, the infection case number has continued to increase to almost 40% of the population, with a total of more than 250 fatalities.

Although information available on CHIKV is growing quite rapidly, we are still far from understanding the strategies required for the ecologic success of this virus, virus replication, its interactions with its vertebrate hosts and arthropod vectors, and its genetic evolution. This paper summarizes the current knowledge of CHIKV genomic organization, cell tropism, and the virus replication cycle, and evaluate the possibility to predict its future evolution. Such understanding may be applied in order to anticipate future epidemics and reduce the incidence by development and application of, for example, vaccination and antiviral therapy.

Replication cycle of chikungunya: A re-emerging arbovirus. Virology. Sep 2 2009

Related:

Rethinking dengue hemorrhagic fever

Wednesday, October 28th, 2009

Dengue virus Dengue virus infection usually causes a severe flu like illness, although symptoms may be mild in young children. DHF, however, is a severe and sometimes fatal complication of dengue virus infection that affects about half a million people every year after infection with any one of the four dengue virus (DENV) serotypes. DHF patients usually fall into two groups; children and adults who become infected with a second dengue virus serotype after an initial primary dengue virus infection with a different serotype, and infants with primary dengue virus infections born to mothers who have some dengue virus immunity. The widely accepted explanation for the pathogenesis of DHF in these settings, particularly during infancy, is antibody-dependent enhancement (ADE) of DENV infection.

Researchers conducted a prospective nested case-control study of DENV infections during infancy. Clinical data and blood samples were collected from 4,441 mothers and infants in up to two pre-illness study visits, and surveillance was performed for symptomatic and inapparent DENV infections. Pre-illness plasma samples were used to measure the associations between maternally derived anti-DENV3 antibody-neutralizing and enhancing capacities at the time of DENV3 infection and development of infant DHF. The study examined 60 infants with DENV infections across a wide spectrum of disease severity. DENV3 was the predominant serotype among the infants with symptomatic (35/40) and inapparent (15/20) DENV infections, and 59/60 infants had a primary DENV infection. The estimated in vitro anti-DENV3 neutralizing capacity at birth positively correlated with the age of symptomatic primary DENV3 illness in infants. At the time of symptomatic DENV3 infection, essentially all infants had low anti-DENV3 neutralizing activity and measurable DENV3 ADE activity. The infants who developed DHF did not have significantly higher frequencies or levels of DENV3 ADE activity compared to symptomatic infants without DHF. A higher weight-for-age in the first 3 mo of life and at illness presentation was associated with a greater risk for DHF from a primary DENV infection during infancy. This prospective nested case-control study of primarily DENV3 infections during infancy has shown that infants exhibit a full range of disease severity after primary DENV infections.

The current model for development of DHF in infants around 6 months old is that anti-dengue virus antibodies transferred from a dengue-immune mother to her child somehow enhance dengue virus infection, resulting in more severe symptoms (the  antibody-dependent enhancement  model). These results support an initial in vivo protective role for maternally derived antibody. There was no significant association between DENV3 ADE activity at illness onset and the development of DHF compared with less severe symptomatic illness. The results of this study should encourage rethinking or refinement of the current ADE pathogenesis model for infant DHF and stimulate new directions of research into mechanisms responsible for the development of DHF during infancy.

A Prospective Nested Case-Control Study of Dengue in Infants: Rethinking and Refining the Antibody-Dependent Enhancement Dengue Hemorrhagic Fever Model. PLoS Med 6(10): e1000171 doi:10.1371/journal.pmed.1000171

Related:

Will genomics help prevent the next pandemic?

Tuesday, October 27th, 2009

PLoS The Public Library of Science has published The Genomics of Emerging Infectious Disease, a collection of essays, perspectives, and reviews that explores how genomics – with all its associated tools and techniques – can provide insights into our understanding of emerging infectious disease. As pandemic H1N1 2009 influenza (swine flu) continues to spread around the globe, people want to know if this virus poses more of a threat than other seasonal flu strains, how fast it is spreading (and where), and what can be done to contain it. The increasing speed at which complete genome sequences and other genome-scale data can be generated provides tremendous opportunities to address these questions by identifying the molecular changes in disease agents such as influenza viruses that will enable us to track their spread and evolution and to generate the vaccines and drugs necessary to combat them.  The Genomics of Emerging Infectious Disease collection discusses the challenges involved and how scientists and public health professionals might take advantage of these opportunities and advances to prevent the next pandemic.

Emerging infectious diseases are caused by a wide range of organisms, but they are perhaps best typified by zoonotic viral diseases, which cross from animal to human hosts and can have a devastating impact on human health. These zoonotic diseases include monkeypox, Hendra virus, Nipah virus, and severe acute respiratory syndrome coronavirus (SARS-CoV), in addition to influenza A and the lentiviruses (HIV) that cause AIDS.  The apparent increased transmission of pathogens from animals to humans over recent decades can be attributed to the unintended consequences of globalization as well as environmental factors and changes in agricultural practices. Articles in the collection also shine a spotlight on specific pathogens, some familiar and widespread, such as influenza A virus, some “re-emerging”, such as the Mycobacterium tuberculosis complex that causes tuberculosis, and some identified only relatively recently, such as the bacterium Helicobacter pylori, which is associated with peptic ulcers and gastric cancer. Others discuss the broader implications of genomics research in this area, such as what it means for researchers in developing countries or for our biosecurity. Genomics can and should be used proactively to build our preparedness for and responsiveness to biological threats: