MicrobiologyBytes

I’m in Edinburgh today, taling at the annual meeting of Eurosurveillance, so as a warm up, here’s an intereting story from Eurosurveillance:

Climate and environmental changes are suspected as major determinants that alter the distribution and transmission patterns of certain communicable diseases, especially those transmitted by arthropods, such as ticks (e.g. tick-borne encephalitis (TBE) and Lyme disease), mosquitoes, (e.g. Chikungunya and Dengue fever), or sandflies (e.g. visceral leishmaniasis). Apart from the effect on the natural conditions and favouring a wider distribution of vectors which may carry diseases, they can also influence occupational and recreational human behaviour and lead to an increased exposure to the risk of infectious diseases e.g. through increased time spent outdoors and harvesting food in woodlands with high concentrations of ticks.

In the European Union (EU), climate and environmental changes are believed to be a cause for the recent resurgence of ‘old suspects’ such as malaria, as well as the geographic expansion of diseases like West Nile fever or TBE. On 5 September 2012, TBE was included in the list of notifiable diseases in the EU. The main European Commission Decisions on communicable diseases were amended to include TBE in the list of diseases for EU notification, along with its own new case definition.

Tick-borne encephalitis joins the diseases under surveillance in the European Union. Euro Surveill. 2012; 17(42): pii=20299

Oceans cover approximately 70% of Earth’s surface and play fundamental roles in processes that have global ecological and socioeconomic impacts. They are a vital component of the climate system and are suffering and partially attenuating climate change. Life originated in the oceans, which have been the main sites of evolution. Photosynthesis is a critical process that allows life on Earth, and interestingly, half the global primary production occurs in the sea, mostly by planktonic microorganisms that account for only 0.2% of global primary producer biomass. This has many consequences for the functioning of marine ecosystems, influencing carbon and energy fluxes through organisms (food webs), affecting carbon fluxes to deep waters (biological pump), and fine-tuning of all biogeochemical cycles.

Planktonic microorganisms are categorized into classes based on size for operational purposes. Initially, only prokaryotes were included in the smallest class (picoplankton: cells 0.2 to 2 μm) and microbial eukaryotes (protists) were included in the nanoplankton (2 to 20 μm) or microplankton (20 to 200 μm). However, minute eukaryotes were soon detected by epifluorescence microscopy and flow cytometry. Picoeukaryotes are now known to be ubiquitous in surface oceans and form, together with prokaryotes, an ocean’s veil above which larger protists and metazoans might bloom. They exemplify the ecological success of miniaturized cells prepared for independent life by keeping only the minimal cellular components, typically one mitochondrion, one Golgi apparatus, and optionally one chloroplast and flagellum. Molecular methods today offer new tools for studying picoplankton biogeography, activity, biological interactions, and population control mechanisms.

Eukaryotic picoplankton in surface oceans. Annu Rev Microbiol. (2011) 65: 91-110
The eukaryotic picoplankton is a heterogeneous collection of small protists 1 to 3 µm in size populating surface oceans at abundances of 10(^2) to 10(^4) cells ml(^1). Pigmented cells are important primary producers that are at the base of food webs. Colorless cells are mostly bacterivores and play key roles in channeling bacteria to higher trophic levels as well as in nutrient recycling. Mixotrophy and parasitism are relevant but less investigated trophic paths. Molecular surveys of picoeukaryotes have unveiled a large phylogenetic diversity and new lineages, and it is critical to understand the ecological and evolutionary significance of this large and novel diversity. A main goal is to assess how individuals are organized in taxonomic units and how they participate in ecological processes. Picoeukaryotes are convincingly integral members of marine ecosystems in terms of cell abundance, biomass, activity, and diversity and they play crucial roles in food webs and biogeochemical cycles.

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From the first molecules of oxygen produced by marine cyanobacteria ~3.5 billion years ago to the methanogens luxuriating in the warm, carbon-rich swamps of the Carboniferous period, microbial processes have long been key drivers of, and responders to, climate change. It is widely accepted that microorganisms have played a key part in determining the atmospheric concentrations of greenhouse gases, including carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) (which have the greatest impact on radiative forcing), throughout much of Earth’s history. What is more open to debate is the part that they will play in the coming decades and centuries, the climate feedbacks that will be important, and how humankind might harness microbial processes to manage climate change. The feedback responses of microorganisms to climate change in terms of greenhouse gas flux may either amplify (positive feedback) or reduce (negative feedback) the rate of climate change. With the twenty-first century projected to experience some of the most rapid climatic changes in our planet’s history, and with biogenic fluxes of the main anthropogenic greenhouse gases being tied integrally to microorganisms, improving our understanding of microbial processes has never been so important.

Microorganisms and climate change: terrestrial feedbacks and mitigation options. (2010) Nature Reviews Microbiology 8, 779 doi:10.1038/nrmicro2439
Microbial processes have a central role in the global fluxes of the key biogenic greenhouse gases (carbon dioxide, methane and nitrous oxide) and are likely to respond rapidly to climate change. Whether changes in microbial processes lead to a net positive or negative feedback for greenhouse gas emissions is unclear. To improve the prediction of climate models, it is important to understand the mechanisms by which microorganisms regulate terrestrial greenhouse gas flux. This involves consideration of the complex interactions that occur between microorganisms and other biotic and abiotic factors. The potential to mitigate climate change by reducing greenhouse gas emissions through managing terrestrial microbial processes is a tantalizing prospect for the future.

Related:

• Calcifying cyanobacteria and carbon capture
• Climate change influences infectious disease in the Arctic and the tropics
• Extreme Weather Events And Epidemics

Strategies to reduce emissions of carbon dioxide (CO₂) from fossil fuels, and hence mitigate climate change, include energy savings, development of renewable biofuels, and carbon capture and storage (CCS). For CCS, several scenarios are being considered. One approach is capture of point-source CO₂ from power plants or other industrial sources and subsequent injection of the concentrated CO₂ underground or into the ocean. An alternative to this point-source CCS method is expansion of biological carbon sequestration of atmospheric CO₂ by measures such as reforestation, changes in land use practices, increased carbon allocation to underground biomass, production of biochar, and enhanced biomineralization. In addition to geological or oceanic CO₂ injection, novel models for point-source CCS based on accelerated weathering and biomineralization are emerging, utilizing either abiotic or biotic processes. Biomineralization of CO₂ by calcium carbonate (CaCO3) precipitation is a common phenomenon in marine, freshwater, and terrestrial ecosystems and is a fundamental process in the global carbon cycle.

Employment of cyanobacteria in biomineralization of carbon dioxide by calcium carbonate precipitation offers novel and self-sustaining strategies for point-source carbon capture and sequestration. Although details of this process remain to be elucidated, a carbon-concentrating mechanism, and chemical reactions in exopolysaccharide or proteinaceous surface layers are assumed to be of crucial importance. Cyanobacteria can utilize solar energy through photosynthesis to convert carbon dioxide to recalcitrant calcium carbonate. Calcium can be derived from sources such as gypsum or industrial brine. A better understanding of the biochemical and genetic mechanisms that carry out and regulate cynaobacterial biomineralization should put us in a position where we can further optimize these steps by exploiting the powerful techniques of genetic engineering, directed evolution, and biomimetics.

Calcifying cyanobacteria-the potential of biomineralization for carbon capture and storage. Curr Opin Biotechnol. Apr 22 2010

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• Growing Algae to Mop Up CO₂ off Antarctica
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Emerging and reemerging infectious diseases are increasing worldwide and represent a major public health concern. One class of emerging human and animal diseases is caused by fungi. A new study examines an outbreak of a fungal infection, Cryptococcus gattii, in the Pacific Northwest of the United States. This fungus has been considered a tropical fungus, but emerged to cause an outbreak in the temperate climes of Vancouver Island in 1999 that is now causing disease in humans and animals in the United States. Because of the way an Oregon-specific strain of the fungus is reproducing and spreading, it will likely move into California and other adjacent areas. This novel fungus is worrisome because it appears to be a threat to otherwise healthy people. Typically, we more often see this fungal disease associated with transplant recipients and HIV-infected patients, but that is not what we are seeing in this case. VGIIc, the new Oregon strain, has yielded dozens of isolates from many specimens, including domesticated animals like cats, dogs and sheep – even an unlucky alpaca. Most of those are nonmigratory animals, which suggests that the animals probably didn’t bring the pathogen from some other region but, rather, acquired it locally. Using molecular techniques, the geneticists uncovered clues that showed the Oregon-only fungal strain most likely arose recently, parallel to the outbreak of C. gattii that began in Canada in 1999 that has now spread into Washington and Oregon.

The researchers found that the novel genotype (VGIIc) is now a major source of C. gattii illness in Oregon. Because C. gattii types had previously been found in tropical areas, the authors speculate that environmental changes may be responsible for the evolution and emergence of this pathogen. Determining the exact origin of the VGIIc type is difficult, and sampling thus far has failed to turn up isolates in Oregon soil, water or trees. The mortality rate for recent C. gattii cases in the Pacific Northwest is running at approximately 25 percent, or 5 out of 21 cases analyzed in the United States, compared to a mortality rate of 8.7 percent of 218 cases in British Columbia, Canada. Most C. gattii infections follow a more complicated clinical course in people than does the more common Cryptococcus neoformans. Symptoms can appear two to several months after exposure, and while most people never develop symptoms, those infected may have a cough lasting weeks, sharp chest pain, shortness of breath, headache (related to meningitis), fever, night time sweats and weight loss. In animals the symptoms are a runny nose, breathing problems, nervous system problems and raised bumps under the skin. While C. gattii can be treated, it cannot be prevented; there is no vaccine. Because the strain is so virulent when it infects some humans and animals, the researchers are calling for greater awareness and vigilance in testing. Some strains of C. gattii are not more virulent than C. neoformans, for example, but doctors need to know what type they are dealing with.

Emergence and Pathogenicity of Highly Virulent Cryptococcus gattii Genotypes in the Northwest United States. PLoS Pathog 6(4): e1000850. doi:10.1371/journal.ppat.1000850
Cryptococcus gattii causes life-threatening disease in otherwise healthy hosts and to a lesser extent in immunocompromised hosts. The highest incidence for this disease is on Vancouver Island, Canada, where an outbreak is expanding into neighboring regions including mainland British Columbia and the United States. This outbreak is caused predominantly by C. gattii molecular type VGII, specifically VGIIa/major. In addition, a novel genotype, VGIIc, has emerged in Oregon and is now a major source of illness in the region. Through molecular epidemiology and population analysis of MLST and VNTR markers, we show that the VGIIc group is clonal and hypothesize it arose recently. The VGIIa/IIc outbreak lineages are sexually fertile and studies support ongoing recombination in the global VGII population. This illustrates two hallmarks of emerging outbreaks: high clonality and the emergence of novel genotypes via recombination. In macrophage and murine infections, the novel VGIIc genotype and VGIIa/major isolates from the United States are highly virulent compared to similar non-outbreak VGIIa/major-related isolates. Combined MLST-VNTR analysis distinguishes clonal expansion of the VGIIa/major outbreak genotype from related but distinguishable less-virulent genotypes isolated from other geographic regions. Our evidence documents emerging hypervirulent genotypes in the United States that may expand further and provides insight into the possible molecular and geographic origins of the outbreak.

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• All About Fungi: Part 1
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There is strong evidence to suggest that climate change has, and will continue to affect the occurrence, distribution and prevalence of livestock diseases in Great Britain (GB). This paper reviews how climate change could affect livestock diseases in GB. Factors influenced by climate change and that could affect livestock diseases include the molecular biology of the pathogen itself; vectors (if any); farming practice and land use; zoological and environmental factors; and the establishment of new microenvironments and microclimates. The interaction of these factors is an important consideration in forecasting how livestock diseases may be affected. Risk assessments should focus on looking for combinations of factors that may be directly affected by climate change, or that may be indirectly affected through changes in human activity, such as land use (e.g. deforestation), transport and movement of animals, intensity of livestock farming and habitat change. A risk assessment framework is proposed, based on modules that accommodate these factors. This framework could be used to screen for the emergence of unexpected disease events.

The effect of climate change on the occurrence and prevalence of livestock diseases in Great Britain: a review. J Appl Microbiol. (2009) 106(5): 1409-1423

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Tropical coral reefs harbour a reservoir of enormous biodiversity that is increasingly threatened by direct human activities and indirect global climate shifts. Emerging coral diseases are one serious threat implicated in extensive reef deterioration through disruption of the integrity of the coral holobiont – a complex symbiosis between the coral animal, endobiotic alga and an array of microorganisms. In this article, the authors review the current understanding of the role of microorganisms in coral health and disease, and highlight the pressing interdisciplinary research priorities required to elucidate the mechanisms of disease. They advocate an approach that applies knowledge gained from experiences in human and veterinary medicine, integrated into multidisciplinary studies that investigate the interactions between host, agent and environment of a given coral disease. These approaches include robust and precise disease diagnosis, standardised ecological methods and application of rapidly developing DNA, RNA and protein technologies, alongside established histological, microbial ecology and ecological expertise. Such approaches will allow a better understanding of the causes of coral mortality and coral reef declines and help assess potential management options to mitigate their effects in the longer term.

The role of the environment in coral disease epizootics has been a major focus of investigations because coral reefs are the ecosystem facing the most rapidly advancing threat from climate change. Corals are sessile organisms and have the advantage that individual animals can be tracked in the wild to monitor disease progression. Significant challenges in framing the scale, complexity and natural variability of emerging coral diseases throughout the world’s oceans include a lack of historical baseline data sets and a wide diversity of ecological factors that influence disease patterns on both regional and global scales. Progress has been made to clarify the effects and drivers of coral disease on local and regional scales, and the field continues to refine the methods of coral disease assessment. However, developing a meaningful understanding of the interactions between the environment, the agent and the host is still required.

Microbial disease and the coral holobiont. Trends in Microbiology 17 (12) 554-562, 2009. doi:10.1016/j.tim.2009.09.004

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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

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Dengue fever is a major public health problem in many tropical regions of the world. It is a vector-borne disease, transmitted most often by the mosquito Aedes aegypti. According to the WHO, the prevalence of dengue is highest in tropical areas of Asia and the Americas, with 50-100 million estimated cases of dengue fever and 250,000-500,000 cases of dengue hemorrhagic fever occurring annually worldwide as explosive outbreaks in urban areas.

In Brazil, three dengue virus serotypes (DENV) have been introduced in the past three decades. In 2007-2008, a dengue fever epidemic in Rio de Janeiro led to 240 deaths registered (100 deaths due to dengue hemorrhagic fever and 140 due to other dengue-related complications). This populous city presents highly favorable conditions for transmission of dengue. Dengue surveillance and control in large urban areas with high levels of dengue transmission pose important challenges. Therefore, consistent knowledge of the dynamics of this disease that integrates epidemiological and entomological data is essential.

Human movement is a key factor of dengue virus inflow in Rio de Janeiro, Brazil. The results published in a new paper, based on data from a severe epidemic in 2007-2008, contribute to new understanding on the dynamics of dengue fever in the second largest city in Brazil. This research combines data on dengue fever seroprevalence, recent dengue infection, and vector density in three neighborhoods of Rio de Janeiro: an urban, a suburban, and a slum area. Serological surveys were conducted before and during the epidemic period. Entomological surveys consisted of weekly collections of A. aegypti eggs and adults from traps. This integrated entomological-serological survey showed evidence of silent transmission even during a severe epidemic. No association was observed between household infestation index and risk of dengue infection in these areas, raising new questions about where transmission occurs – in the household, at work or elsewhere. When combined, the neighborhood-specific seroprevalence maps correlated significantly higher risk with areas of intense people traffic. These results add to previous epidemiological studies of dengue virus infections and contribute to the understanding of A. aegypti habits. The conclusions may provide a basis for new studies that could further identify the higher seroprevalence risk areas and help to develop and implement dengue-control programs.

Spatial Evaluation and Modeling of Dengue Seroprevalence and Vector Density in Rio de Janeiro, Brazil. PLoS Negl Trop Dis 3(11): e545. doi:10.1371/journal.pntd.0000545
Rio de Janeiro, Brazil, experienced a severe dengue fever epidemic in 2008. This was the worst epidemic ever, characterized by a sharp increase in case-fatality rate, mainly among younger individuals. A combination of factors, such as climate, mosquito abundance, buildup of the susceptible population, or viral evolution, could explain the severity of this epidemic. The main objective of this study is to model the spatial patterns of dengue seroprevalence in three neighborhoods with different socioeconomic profiles in Rio de Janeiro. As blood sampling coincided with the peak of dengue transmission, we were also able to identify recent dengue infections and visually relate them to Aedes aegypti spatial distribution abundance. We analyzed individual and spatial factors associated with seroprevalence using Generalized Additive Model (GAM). Three neighborhoods were investigated: a central urban neighborhood, and two isolated areas characterized as a slum and a suburban area. Weekly mosquito collections started in September 2006 and continued until March 2008. In each study area, 40 adult traps and 40 egg traps were installed in a random sample of premises, and two infestation indexes calculated: mean adult density and mean egg density. Sera from individuals living in the three neighborhoods were collected before the 2008 epidemic (July through November 2007) and during the epidemic (February through April 2008). Sera were tested for DENV-reactive IgM, IgG, Nested RT-PCR, and Real Time RT-PCR. From the before– after epidemics paired data, we described seroprevalence, recent dengue infections (asymptomatic or not), and seroconversion. Recent dengue infection varied from 1.3% to 14.1% among study areas. The highest IgM seropositivity occurred in the slum, where mosquito abundance was the lowest, but household conditions were the best for promoting contact between hosts and vectors. By fitting spatial GAM we found dengue seroprevalence hotspots located at the entrances of the two isolated communities, which are commercial activity areas with high human movement. No association between recent dengue infection and household’s high mosquito abundance was observed in this sample. This study contributes to better understanding the dynamics of dengue in Rio de Janeiro by assessing the relationship between dengue seroprevalence, recent dengue infection, and vector density. In conclusion, the variation in spatial seroprevalence patterns inside the neighborhoods, with significantly higher risk patches close to the areas with large human movement, suggests that humans may be responsible for virus inflow to small neighborhoods in Rio de Janeiro. Surveillance guidelines should be further discussed, considering these findings, particularly the spatial patterns for both human and mosquito populations.

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