MicrobiologyBytes

Phages are now acknowledged as the most abundant microorganisms on the planet and are also possibly the most diversified. This diversity is mostly driven by their dynamic adaptation when facing selective pressure such as phage resistance mechanisms, which are widespread in bacterial hosts. When infecting bacterial cells, phages face a range of antiviral mechanisms, and they have evolved multiple tactics to avoid, circumvent or subvert these mechanisms in order to thrive in most environments. This review highlights the most important antiviral mechanisms of bacteria as well as the counter-attacks used by phages to evade these systems.

Bacteriophage resistance mechanisms. Nature Reviews Microbiology 8: 317-327 (2010). doi:10.1038/nrmicro2315

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Nanobacteria are supposedly exotic, slow-growing, pleomorphic, infectious, pathogenic, sub-micrometer-sized (50–500 nm) bacteria coated with hydroxyapatite. These anomalous characteristics, considered unprecedented for any microorganism known to date, have been refuted on many grounds. In experiments, nanobacteria are shown to be no more than organic-mineral complexes. And yet, despite the large body of evidence directly contradicting the claims for nanobacteria as living microorganisms, studies implicating NB as infectious agents of disease continue to be published.

A new paper In PLoS ONE provides further evdience for the non-living nature of these non-bacteria, but because it is impossible to prove a negative hypothesis (they don’t exist) and because some people like a good conspiracy theory, I doubt this will be the end of the nonobacteria saga.

Critical Evaluation of Gamma-Irradiated Serum Used as Feeder in the Culture and Demonstration of Putative Nanobacteria and Calcifying Nanoparticles. PLoS ONE 5(4): e10343. doi:10.1371/journal.pone.0010343
The culture and demonstration of putative nanobacteria (NB) and calcifying nanoparticles (CNP) from human and animal tissues has relied primarily on the use of a culture supplement consisting of FBS that had been γ-irradiated at a dose of 30 kGy (γ-FBS). The use of γ-FBS is based on the assumption that this sterilized fluid has been rid entirely of any residual NB/CNP, while it continues to promote the slow growth in culture of NB/CNP from human/animal tissues. We show here that γ-irradiation (5–50 kGy) produces extensive dose-dependent serum protein breakdown as demonstrated through UV and visible light spectrophotometry, fluorometry, Fourier-transformed infrared spectroscopy, and gel electrophoresis. Yet, both γ-FBS and γ-irradiated human serum (γ-HS) produce NB/CNP in cell culture conditions that are morphologically and chemically indistinguishable from their normal serum counterparts. Contrary to earlier claims, γ-FBS does not enhance the formation of NB/CNP from several human body fluids (saliva, urine, ascites, and synovial fluid) tested. In the presence of additional precipitating ions, both γ-irradiated serum (FBS and HS) and γ-irradiated proteins (albumin and fetuin-A) retain the inherent dual NB inhibitory and seeding capabilities seen also with their untreated counterparts. By gel electrophoresis, the particles formed from both γ-FBS and γ-HS are seen to have assimilated into their scaffold the same smeared protein profiles found in the γ-irradiated sera. However, their protein compositions as identified by proteomics are virtually identical to those seen with particles formed from untreated serum. Moreover, particles derived from human fluids and cultured in the presence of γ-FBS contain proteins derived from both γ-FBS and the human fluid under investigation—a confusing and unprecedented scenario indicating that these particles harbor proteins from both the host tissue and the FBS used as feeder. Thus, the NB/CNP described in the literature clearly bear hybrid protein compositions belonging to different species. We conclude that there is no basis to justify the use of γ-FBS as a feeder for the growth and demonstration of NB/CNP or any NB-like particles in culture. Moreover, our results call into question the validity of the entire body of literature accumulated to date on NB and CNP.

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It is estimated that marine microscopic algae – phytoplankton – are responsible for half of the Earth’s photosynthesis. In 2000, American scientists discovered that many marine bacteria contain a gene in their genome that encodes a new kind of light-harvesting pigment: proteorhodopsin. Proteorhodopsin is related to the pigment in the retina that enables human vision in less intense light. As many as half of the surface ocean bacteria have proteorhodopsins, which are membrane proteins that allow harvesting of energy from sunlight, implying a potentially significant role of non–chlorophyll-based phototrophy in oceanic carbon cycling and energy flows. Evidence of specific roles for proteorhodopsins in marine bacteria and the marine environment remains surprisingly scarce. One reason for this is the lack of marine bacteria (containing proteorhodopsin genes) that can be maintained in laboratory culture and that are tractable to genetic manipulation. Now, a decade later, the first direct evidence for the functioning of proteorhodopsin in native marine bacteria is published, based on mutational analysis in a marine bacterium.

A new study shows that a proteorhodopsin-containing member of the widespread marine genus Vibrio displays light-enhanced survival during starvation in seawater. At the same time the new study shows that proteorhodopsin-mediated phototrophy (the process of acquiring energy from light) allows marine bacteria to better survive periods of starvation in an often nutrient-depleted ocean. Growth recovery experiments showed that bacteria starving in the light could more rapidly respond to improved growth conditions than those incubated in the dark. A proteorhodopsin deficient Vibrio strain confirms that light-dependent survival of starvation is mediated by the proteorhodopsin. Proteorhodopsin phototrophy thus provides a physiological mechanism that allows surface ocean bacteria to manage an environment where resource availability fluctuates markedly.

The importance of understanding novel mechanisms for marine bacteria to efficiently use solar energy is obvious if one considers that a litre of seawater on average contains around a billion bacteria, many of which contain proteorhodopsin. The activity of these bacteria play a crucial role in the global carbon cycle by determining oceanic production of CO₂ through respiration and determining how the fluxes of energy that are fixed by photosynthesis are channeled through marine food chains. Bacteria at the ocean surface are swimming in a sea of light, and it may not be all that surprising that evolution has favored microorganisms that can use this abundant energy source most efficiently.

Proteorhodopsin Phototrophy Promotes Survival of Marine Bacteria during Starvation. PLoS Biol 8(4): e1000358. doi:10.1371/journal.pbio.1000358
Proteorhodopsins are globally abundant photoproteins found in bacteria in the photic zone of the ocean. Although their function as proton pumps with energy-yielding potential has been demonstrated, the ecological role of proteorhodopsins remains largely unexplored. Here, we report the presence and function of proteorhodopsin in a member of the widespread genus Vibrio, uncovered through whole-genome analysis. Phylogenetic analysis suggests that the Vibrio strain AND4 obtained proteorhodopsin through lateral gene transfer, which could have modified the ecology of this marine bacterium. We demonstrate an increased long-term survival of AND4 when starved in seawater exposed to light rather than held in darkness. Furthermore, mutational analysis provides the first direct evidence, to our knowledge, linking the proteorhodopsin gene and its biological function in marine bacteria. Thus, proteorhodopsin phototrophy confers a fitness advantage to marine bacteria, representing a novel mechanism for bacterioplankton to endure frequent periods of resource deprivation at the ocean’s surface.

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Lyme borreliosis (Lyme disease) first came to prominence about 30 years ago, following its emergence in the area of Lyme, Connecticut, USA, but its major clinical features had been described in Europe during the previous century. It is the most common vector-borne bacterial infection in temperate regions of the northern hemisphere, caused by several genospecies of Borrelia burgdorferi, a spirochaete transmitted by ticks of the Ixodes ricinus complex. In Europe, it has a widespread distribution throughout forested and woodland areas from southern Scandinavia to some parts of northern Mediterranean countries. Incidence rises from west to east. Many of the most highly endemic regions are found in central and eastern Europe. As many as 200 000 cases may occur annually. Over 35,000 confirmed or probable cases were notified in the United States in 2008. Most occur in 10 north-eastern and north-central states.

Lyme disease has been perceived as difficult to diagnose and treat, but much is now known about its clinical presentations, which largely fall into well defined categories in both adults and children. This review features recent publications on clinical diagnosis and management. The reported incidence of Lyme borreliosis has increased markedly in many countries. Many recent publications have focused on clinical and laboratory aspects of paediatric and adult neuroborreliosis, and there is now strong evidence for the efficacy of oral doxycycline for most presentations of neuroborreliosis. Serological tests have improved significantly. Several studies have confirmed that patients treated for early Lyme borreliosis have good overall long-term outcomes. Studies of patients with persistent symptoms following treatment have not shown evidence for active infection or for sustained benefit from prolonged antibiotic treatment. Greater efforts are needed to provide education for prevention and early diagnosis to avoid late complications. Further improvements in diagnostic tests would be welcomed. More research is required to assess the causes and management of post-Lyme symptoms.

Lyme borreliosis: current issues in diagnosis and management. Curr Opin Infect Dis. Apr 17 2010

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Human noroviruses in the family Caliciviridae are a major cause of epidemic gastroenteritis. They are responsible for at least 95% of viral outbreaks and over 50% of all outbreaks worldwide. Transmission of these highly infectious plus-stranded RNA viruses occurs primarily through contaminated food or water, but also through person-to-person contact and exposure to fomites. Norovirus infections are typically acute and self-limited. However, disease can be much more severe and prolonged in infants, elderly, and immunocompromised individuals. Norovirus outbreaks frequently occur in semi-closed communities such as nursing homes, military settings, schools, hospitals, cruise ships, and disaster relief situations. Noroviruses are classified as Category B biodefense agents because they are highly contagious, extremely stable in the environment, resistant to common disinfectants, and associated with debilitating illness. The number of reported norovirus outbreaks has risen sharply since 2002 suggesting the emergence of more infectious strains. There has also been increased recognition that noroviruses are important causes of childhood hospitalization. Moreover, noroviruses have recently been associated with multiple clinical outcomes other than gastroenteritis. It is unclear whether these new observations are due to improved norovirus diagnostics or to the emergence of more virulent norovirus strains. Regardless, it is clear that human noroviruses cause considerable morbidity worldwide, have significant economic impact, and are clinically important emerging pathogens. Despite the impact of human norovirus-induced disease and the potential for emergence of highly virulent strains, the pathogenic features of infection are not well understood due to the lack of a cell culture system and previous lack of animal models. This review summarizes the current understanding of norovirus pathogenesis from the histological to the molecular level, including contributions from new model systems.

Pathogenesis of Noroviruses, Emerging RNA Viruses. Viruses 2010, 2(3), 748-781 doi:10.3390/v2030748

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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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The Antarctic continent is one of the most physically and chemically extreme terrestrial environments to be inhabited by microorganisms. Although most of the continent is covered by glacial ice sheets, ice-free areas comprising ~0.4% of the continental land mass are discontinuously distributed around the coastal margins, and many of these areas seem to have been ice free since at least the last glacial maximum2. The McMurdo Dry Valleys are a series of generally west-to-east-oriented, glacially carved valleys located between the Polar Plateau and the Ross Sea in Southern Victoria Land, Antarctica. Dry Valley soil ecosystems are characterized by large variations in temperature and light regimes, steep chemical gradients and a high incidence of solar radiation with an elevated ultraviolet B light component. The microorganisms inhabiting these ice-free, cold-soil environments exist under conditions of low nutrient status and low bioavailability of water, this being further compromised by high levels of salinity. The additive effects of the extreme aridity and widely fluctuating physiochemical conditions of these cold deserts are expected to have a great impact on the adaptations and life cycle strategies used by resident biota.

Recent applications of molecular methods have revealed a dramatically contrasting picture – a very wide diversity of microbial taxa, many of which are uncultured and taxonomically unique, and a community that seems to be structured solely by abiotic processes. This article reviews these extreme Antarctic terrestrial microbial communities, with particular emphasis on the factors that are involved in their development, distribution and maintenance in these cold desert environments.

On the rocks: the microbiology of Antarctic Dry Valley soils. Nat Rev Microbiol. 2010 8(2): 129-138

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Whether it is in the setting of disease or in a healthy state, the human body contains a diverse range of microorganisms, including bacteria and fungi. The interactions between these taxonomically diverse microorganisms are highly dynamic and dependent on a multitude of microorganism and host factors. Human disease can develop from an imbalance between commensal bacteria and fungi or from invasion of particular host niches by opportunistic bacterial and fungal pathogens. This Review describes the clinical and molecular characteristics of bacterial–fungal interactions that are relevant to human disease.

Medically important bacterial–fungal interactions. 2010 Nature Reviews Microbiology 8, 340-349 doi:10.1038/nrmicro2313

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Neurotropic viruses, including herpesviruses, rabies virus, and poliovirus, initiate infection in the periphery and can move through peripheral neurons to reach the central nervous system (CNS). Since peripheral neurons can be up to one meter long, inefficient neural transport could dramatically affect pathogenesis of neurotropic viruses. This study uses a novel viral “bar-coding” assay to quantify the efficiency of poliovirus transport from the periphery to the CNS in mice. Only 20% of the poliovirus population successfully moved from the periphery to the CNS. Transport of poliovirus in peripheral neurons was very inefficient, and the innate immune response also limited viral movement. Surprisingly, the neural transport barrier was as strong as the innate immune response barrier. Importantly, by overcoming both the neural transport and innate immune barriers, 80% of the poliovirus population successfully moved from the periphery to the CNS, and mice succumbed to disease three times faster than mice with intact barriers. This study identifies inefficient neural transport as a substantial barrier to viral movement in peripheral neurons, which may limit CNS access for many viruses. Peripheral nervous system barriers may contribute to the low incidence of paralytic poliomyelitis in humans, and may also contribute to inefficient trafficking of other neurotropic viruses.

Limited Trafficking of a Neurotropic Virus Through Inefficient Retrograde Axonal Transport and the Type I Interferon Response. 2010 PLoS Pathog 6(3): e1000791. doi:10.1371/journal.ppat.1000791