MicrobiologyBytes

Human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) are the most prevalent deadly chronic viral diseases. HIV is treated by small molecule inhibitors. HBV is treated by immunomodulation and small molecule inhibitors. HCV is currently treated primarily by immunomodulation but many small molecules are in clinical development. Although HIV is a retrovirus, HBV is a double-stranded DNA virus, and HCV is a single-stranded RNA virus, antiviral drug resistance complicates the development of drugs and the successful treatment of each of these viruses. Although their replication cycles, therapeutic targets, and evolutionary mechanisms are different, the fundamental approaches to identifying and characterizing HIV, HBV, and HCV drug resistance are similar. This review describes the evolution of HIV, HBV, and HCV within individuals and populations and the genetic mechanisms associated with drug resistance to each of the antiviral drug classes used for their treatment.

Comparison of the Mechanisms of Drug Resistance among HIV, Hepatitis B, and Hepatitis C. Viruses. 2010; 2(12):2696-2739. doi:10.3390/v2122696

Related:

• Update on HBV and HCV Therapy
• Can HIV infection be eradicated through use of potent antiviral agents?
• Plugging the holes in hepatitis C virus antiviral therapy

A new study examines how bacterial and archaeal genomic repertoires evolve to face new challenges by acquiring genes from other individuals. Microbes live and thrive in incredibly diverse and harsh conditions, from boiling or freezing water to the human immune system. This remarkable adaptability results from their ability to quickly modify their repertoire of protein functions by gaining, losing and modifying their genes. Microbes were known to modify genes to expand their repertoire of protein families in two ways: via duplication processes followed by slow functional specialization, in the same way as large multicellular organisms like us, and by acquiring different genes directly from other microbes. The latter process, known as horizontal gene transfer (HGT), is notoriously conspicuous in the spread of antibiotic resistance, turning some bacteria into drug-resistant ‘superbugs’ such as MRSA (methicillin-resistant Staphylococcus aureus), a serious public health concern.

The researchers examined a large database of microbial genomes, including some of the most virulent human pathogens, to discover whether duplication or HGT was the most common expansion method. They show that gene family expansion can indeed follow both routes, but unlike large multicellular organisms, it predominantly takes place by horizontal transfer. Thus, quick diversification of microbial functions results from the recruitment by microbes of pre-existing adaptations from other microbes. The study concludes with the observation that, since microbes invented the majority of life’s biochemical diversity, from respiration to photosynthesis, we should recognize the predominant role of HGT in the diversification of all protein families.

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes. (2011) PLoS Genet 7(1): e1001284. doi:10.1371/journal.pgen.1001284
Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. We analyzed closely related prokaryote strains or species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus), average-sized genomes (Bacillus, Enterobacteriaceae), and large genomes (Pseudomonas, Bradyrhizobiaceae) to untangle the effects of duplication and horizontal transfer. After removing the effects of transposable elements and phages, we show that the vast majority of expansions of protein families are due to transfer, even among large genomes. Transferred genes — xenologs — persist longer in prokaryotic lineages possibly due to a higher/longer adaptive role. On the other hand, duplicated genes — paralogs — are expressed more, and, when persistent, they evolve slower. This suggests that gene transfer and gene duplication have very different roles in shaping the evolution of biological systems: transfer allows the acquisition of new functions and duplication leads to higher gene dosage. Accordingly, we show that paralogs share most protein–protein interactions and genetic regulators, whereas xenologs share very few of them. Prokaryotes invented most of life’s biochemical diversity. Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families.

Related:

• Barriers to Horizontal Gene Transfer
• Evolution of Clostridium difficile

Researchers have found that the nematode Caenorhabditis elegans, a millimeter-long worm used extensively for decades to study many aspects of biology, can be targeted by naturally occurring virus infections. The discovery means C. elegans is likely to help scientists study the way viruses and their hosts interact.

Marie-Anne Felix at the Centre National de la Recherche Scientifique (CNRS, France), who studies the evolution of nematodes at the Jacques Monod Institute, began the study by gathering C. elegans from rotting fruit in French orchards. Felix noted that some of her sample worms appeared to be sick. Treatment with antibiotics failed to cure them. She then repeated a classic biological experiment that led to the discovery of viruses. Sick worms were ground up and passed through a filter fine enough to remove any bacterial or parasitic infectious agents. A new batch of worms was exposed to the ground-up remains of the first batch. When the new batch got sick, a viral infection was likely to be present. David Wang, at Washington University School of Medicine in St. Louis, found the worms had been suffering infections from two viruses related to nodaviruses, a class of viruses previously found to infect insects and fish. Nodaviruses are not currently known to infect humans. Tests showed one of the new viruses can infect the strain of C. elegans most commonly used in research.

Several fundamental phenomena of human biology were first revealed using C. elegans – including the ability of cells to self-destruct to prevent cancer, and the process of RNA interference, which operates to destroy double helices of RNA coming from outside the organism. RNA interference was discovered by Andy Fire and Craig Mello (Nobel Prize 2006) and is widely used as a tool to inactivate genes, yet its natural role in C. elegans remained a mystery. The new nematode-infecting virus provides the first evidence in a completely natural setting and without any artificial manipulations that RNA interference in C. elegans has an important role in defending the worm against viruses.

“Model organisms are essential to important steps forward in biology, and we’re eager to see what C. elegans can teach us about the way hosts and viruses interact,” Wang says. “We can easily disable any of C. elegans genes, confront the worm with a virus and watch to see if this makes the infection worse, better or has no effect,” says Wang. “If it changes the worm’s response to infection, we will look to see if similar genes are present in humans and other mammals.”

Natural and Experimental Infection of Caenorhabditis Nematodes by Novel Viruses Related to
Nodaviruses. (2011) PLoS Biol 9(1): e1000586. doi:10.1371/journal.pbio.1000586
An ideal model system to study antiviral immunity and host-pathogen co-evolution would combine a genetically tractable small animal with a virus capable of naturally infecting the host organism. The use of C. elegans as a model to define host- viral interactions has been limited by the lack of viruses known to infect nematodes. From wild isolates of C. elegans and C. briggsae with unusual morphological phenotypes in intestinal cells, we identified two novel RNA viruses distantly related to known nodaviruses, one infecting specifically C. elegans (Orsay virus), the other C. briggsae (Santeuil virus). Bleaching of embryos cured infected cultures demonstrating that the viruses are neither stably integrated in the host genome nor transmitted vertically. 0.2 mm filtrates of the infected cultures could infect cured animals. Infected animals continuously maintained viral infection for 6 mo (50 generations), demonstrating that natural cycles of horizontal virus transmission were faithfully recapitulated in laboratory culture. In addition to infecting the natural C. elegans isolate, Orsay virus readily infected laboratory C. elegans mutants defective in RNAi and yielded higher levels of viral RNA and infection symptoms as compared to infection of the corresponding wild-type N2 strain. These results demonstrated a clear role for RNAi in the defense against this virus. Furthermore, different wild C. elegans isolates displayed differential susceptibility to infection by Orsay virus, thereby affording genetic approaches to defining antiviral loci. This discovery establishes a bona fide viral infection system to explore the natural ecology of nematodes, host-pathogen co-evolution, the evolution of small RNA responses, and innate antiviral mechanisms.

Related:

• Nematode provides new animal model for emerging pathogen
• Trojan horses and other dirty tricks

Typically, viruses are considered to be small particles that easily pass through 0.2 µm filters and have small genomes containing a few protein-encoding genes. However, large viruses with huge dsDNA genomes that encode hundreds of proteins are being discovered with increasing frequency. These large viruses have also been referred to as giruses in order to emphasize their unique properties. Examples of giruses include:

1. Mimivirus and its close relative Mamavirus, which infect amoebae and have the largest genomes (~1.2 Mb). Mimivirus has 979 protein-encoding sequences (CDSs), six tRNA genes and 33 non-coding RNA genes.
2. Viruses that infect algae (phycodnaviruses) and have genomes up to ~560 kb.
3. Viruses, such as bacterophage G, that infect bacteria and have genomes up to ~670 kb (~498 kb is unique sequence).

A recent report describes the newest girus, a lytic virus (named CroV) that infects the marine microzooplankton Cafeteria roenbergensis. CroV has a ~730 kb genome and contains 544 CDSs and 22 tRNAs encoding genes in the 618 kb central region of its genome. Viruses with genomes ranging from 100 to 280 kb, such as herpesviruses and baculoviruses, are not discussed in this commentary, and poxviruses, asfarviruses, iridoviruses, and ascoviruses are only briefly mentioned because of their evolutionary connection to some giruses. Another group of viruses with dsDNA genomes >500 kb are the polydnaviruses.

To place the size of these large viruses into perspective, the smallest free-living bacterium, Mycoplasma genitalium, encodes ~470 CDSs. Although estimates of the minimum genome size required to support life are ~250 CDSs, some symbiotic bacteria such as Carsonella ruddii and Hodgkinia cicadicola have genomes of 160 kb and 144 kb, respectively. Thus, many large viruses have more CDSs than some single-celled organisms.

Another Really, Really Big Virus. (2011) Viruses 3(1): 32-46; doi:10.3390/v3010032
Viruses with genomes larger than 300 kb and up to 1.2 Mb, which encode hundreds of proteins, are being discovered and characterized with increasing frequency. Most, but not all, of these large viruses (often referred to as giruses) infect protists that live in aqueous environments. Bioinformatic analyses of metagenomes of aqueous samples indicate that large DNA viruses are quite common in nature and await discovery. One issue that is perhaps not appreciated by the virology community is that large viruses, even those classified in the same family, can differ significantly in morphology, lifestyle, and gene complement. This brief commentary, which will mention some of these unique properties, was stimulated by the characterization of the newest member of this club, virus CroV (Fischer, M.G.; Allen, M.J.; Wilson, W.H.; Suttle, C.A. Giant virus with a remarkable complement of genes infects marine zooplankton. PNAS USA 2010, 107, 19508-19513). CroV has a 730 kb genome (with ~544 protein-encoding genes) and infects the marine microzooplankton Cafeteria roenbergensis producing a lytic infection.

Related:

• DNA Viruses – Really Big Ones
• Marvellous mimivirus
• Marine mimivirus relatives are large algal viruses

The current UK National Framework for Pandemic Influenza states that during a pandemic, domestic travel should continue to operate normally but users should adopt good hygiene measures, stagger journeys where possible to reduce overcrowding; and stay at home altogether if symptomatic with pandemic influenza. This advice reflects the need to maintain, as far as possible, business continuity and near normal functioning of society, but acknowledges that some data exist about the transmission of influenza on board public transport, notably commercial airliners. Until very recently, there were no data that directly supported or refuted an association between the use of public ground transportation and the risk of acute respiratory infection. The risk posed by large numbers of transient casual human contacts has not been adequately defined. The current uncertainty makes the formulation of pandemic transport policies difficult. So what’s the risk?

Is public transport a risk factor for acute respiratory infection? BMC Infectious Diseases 2011, 11:16doi:10.1186/1471-2334-11-16
Background: The relationship between public transport use and acquisition of acute respiratory infection (ARI) is not well understood but potentially important during epidemics and pandemics.
Methods: A case-control study performed during the 2008/09 influenza season. Cases (n=72) consulted a General Practitioner with ARI, and controls with another non-respiratory acute condition (n=66). Data were obtained on bus or tram usage in the five days preceding illness onset (cases) or the five days before consultation (controls) alongside demographic details. Multiple logistic regression modelling was used to investigate the association between bus or tram use and ARI, adjusting for potential confounders.
Results: Recent bus or tram use within five days of symptom onset was associated with an almost six-fold increased risk of consulting for ARI (adjusted OR=5.94 95% CI 1.33-26.5). The risk of ARI appeared to be modified according to the degree of habitual bus and tram use, but this was not statistically significant (1-3 times/week: adjusted OR=0.54 (95% CI 0.15-1.95; >3 times/week: 0.37 (95% CI 0.13-1.06).
Conclusions: We found a statistically significant association between ARI and bus or tram use in the five days before symptom onset. The risk appeared greatest among occasional bus or tram users, but this trend was not statistically significant. However, these data are plausible in relation to the greater likelihood of developing protective antibodies to common respiratory viruses if repeatedly exposed. The findings have differing implications for the control of seasonal acute respiratory infections and for pandemic influenza.

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• Dirty Money
• Influenza virus transmission is dependent on humidity and temperature
• Global migration of influenza viruses

The availability of nitrogen (N) is one of the factors that controls the productivity of the oceans, and there has been great interest in determining the magnitudes and pathways of N inputs to the world’s oceans through biological N₂ fixation. Biological N₂ fixation is the reduction of N₂ gas to biologically available ammonium, and this is performed by a diverse but limited number of bacterial and archaeal genera. Cyanobacteria are generally assumed to be the major N₂-fixing microorganisms in the open ocean. Atmospheric N₂ is one of the important external sources of N to the surface waters of the oceans, and thus provides the stoichiometric nutrient flux to support the export of carbon to the deep ocean. This is of importance in ocean–atmosphere fluxes and feedbacks that help to constrain the atmospheric concentrations of the greenhouse gas CO₂. There continues to be controversy over whether the oceanic denitrification losses of N are balanced by N₂ fixation inputs. There are large uncertainties in the estimates of basin- and global-scale denitrification and N₂ fixation rates from biogeochemical calculations, perhaps due to the many assumptions required to scale these processes globally from either biogeochemical or biological data. Conversely, there is also a general lack of data on the distributions and activities of N₂-fixing microorganisms over the vast scales of the ocean. At the core of resolving these issues is the identification of the organisms involved and determining how they function, the factors that limit their growth, and their roles in food webs. The difficulties in determining the roles of open ocean microorganisms in N₂ fixation are the nature of N₂-fixing microorganisms themselves, the dilute nature of microbial populations in the oligotrophic ocean, and the general difficulty in cultivating microorganisms from the ocean. Despite these hurdles, over the past few years much has been learned about the microorganisms primarily responsible for N₂ fixation in the surface waters of the open ocean.

Nitrogen fixation by marine cyanobacteria. Trends Microbiol. Jan 10 2011
Discrepancies between estimates of oceanic N₂ fixation and nitrogen (N) losses through denitrification have focused research on identifying N₂-fixing cyanobacteria and quantifying cyanobacterial N₂ fixation. Previously unrecognized cultivated and uncultivated unicellular cyanobacteria have been discovered that are widely distributed, and some have very unusual properties. Uncultivated unicellular N₂-fixing cyanobacteria (UCYN-A) lack major metabolic pathways including the tricarboxylic acid cycle and oxygen-evolving photosystem II. Genomes of the oceanic N₂-fixing cyanobacteria are highly conserved at the DNA level, and genetic diversity is maintained by genome rearrangements. The major cyanobacterial groups have different physiological and ecological constraints that result in highly variable geographic distributions, with implications for the marine N-cycle budget.

Related:

• Cyanobacteria
• Calcifying cyanobacteria and carbon capture
• A day in the life of a cyanobacterium

Antibiotics can have ecological effects that impact the efficacy of other antimicrobial agents or facilitate the development of secondary infections. When antibiotics are administered, particularly when they are overused or misused, they change the environment and the biome, which in turn can lead to the selection or development of bacterial strains resistant to a wide range of antibiotic agents, extending beyond the particular antibiotic or antibiotic class initially administered. Certain antibiotic agents also change the normal bacterial flora or environment within the gastrointestinal tract, which in turn can promote the colonization and overgrowth of particular bacteria (e.g. Clostridium difficile), and increase the risk of gastrointestinal infections associated with these bacteria. Antibiotic usage can also have an impact on skin and mucosa colonization (such as for methicillin-resistant Staphylococcus aureus) with significantly increased risk of subsequent infections. These forms of ‘collateral damage’ associated with antibiotic use are important considerations when deciding how best to use antibiotics to prevent or treat infections in the hospital (and community) setting. This review looks at some of the ecological effects of antibiotics used in the hospital and their potential for collateral damage of the nosocomial environment. Collateral damage is becoming an increasing problem due to the increasing severity of illness in hospitalized patients and the increasing use of broad-spectrum antibiotics. The ultimate goal is to understand how to better use antibiotics to optimize their beneficial effects, while minimizing risk of collateral damage, in other words, to improve antibiotic stewardship within hospitals and other institutions.

Beyond the target pathogen: ecological effects of the hospital formulary. (2011) Curr Opin Infect Dis. 24 Suppl 1: S21-31
Antibiotic therapy has the potential for intended as well as unintended consequences due to ecological effects that extend beyond the target pathogen. This review examines some of the collateral damage and collateral benefit that may occur when using antibiotic therapy. Antibiotics excreted in the gastrointestinal tract cause alterations of the indigenous flora. Such disruptions may increase the risk of colonization and overgrowth of pathogenic bacteria, including resistant species, with the potential for serious infection for an individual patient as well as possible hospital-wide dissemination resulting in local outbreaks of infection. For example, Clostridium difficile infection (CDI), and particularly associated diarrhea and colitis, is a potentially serious and growing problem in hospitals worldwide, and is associated with disruption of gut flora through use of broad-spectrum antibiotics, especially those with antianaerobic activity. Infection control measures and improved antibiotic stewardship are key measures for CDI prevention. Another example is the risk of intestinal colonization and overgrowth with resistant bacteria, which is heightened in surgical patients requiring antimicrobial therapy for intraabdominal infections. Results from two Optimizing Intra-Abdominal Surgery with Invanz studies (OASIS-I and OASIS-II) suggested emergence of resistant Enterobacteriaceae was less likely in these patients treated with ertapenem than in those treated with ceftriaxone/metronidazole or piperacillin/tazobactam. Finally, recent studies have reported that increased use of a nonpseudomonal carbapenem such as ertapenem does not reduce the susceptibility of Pseudomonas aeruginosa to pseudomonal carbapenems, for example, imipenem or meropenem. In fact, data from one study showed increased ertapenem/decreased imipenem use was associated with improved susceptibility of P. aeruginosa to imipenem, probably due to decreased selective pressure for resistant species. Improper antibiotic use can be associated with detrimental effects related to the ecological impacts of these drugs. Improved antibiotic stewardship and appropriate infection control measures are key to minimization of the collateral damage associated with antibiotic therapy and may even have collateral benefits.

Emerging infectious diseases arise by a range of distinct phenomena, such as the resurgence or upsurge of pre-existing endemic infections, the arrival of exotic microorganisms and the appearance of genetically new microorganisms. The evolutionary emergence of new human pathogens is driven by changes in the biological barriers that determine host-pathogen interactions and therefore the transmission competence of any new partnership. True evolutionary emergence is rare. Among emerging infectious diseases other than infection by drug-resistant bacteria, there is a high percentage of zoonoses. This review focuses on infectious diseases that have emerged recently in new areas, where selection may favour microbial genetic novelties. Among these, vector-borne pathogens are particularly common.

The arrival, establishment and spread of exotic diseases: patterns and predictions. Nature Rev Microbiol. 2010 8(5): 361-371 doi: 10.1038/nrmicro2336
The impact of human activities on the principles and processes governing the arrival, establishment and spread of exotic pathogens is illustrated by vector-borne diseases such as malaria, dengue, chikungunya, West Nile, bluetongue and Crimean-Congo haemorrhagic fevers. Competent vectors, which are commonly already present in the areas, provide opportunities for infection by exotic pathogens that are introduced by travel and trade. At the same time, the correct combination of environmental conditions (both abiotic and biotic) makes many far-flung parts of the world latently and predictably, but differentially, permissive to persistent transmission cycles. Socioeconomic factors and nutritional status determine human exposure to disease and resistance to infection, respectively, so that disease incidence can vary independently of biological cycles.

Related:

• Emerging and re-emerging infectious diseases
• Hantaviruses as Emerging Pathogens
• Where do viruses come from?

Although viruses are most often studied as pathogens, many are beneficial to their hosts, providing essential functions in some cases and conditionally beneficial functions in others. Beneficial viruses have been discovered in many different hosts, including bacteria, insects, plants, fungi and animals. How these beneficial interactions evolve is still a mystery in many cases but, as discussed in this review, the mechanisms of these interactions are beginning to be understood in more detail.

The good viruses: viral mutualistic symbioses. (2011) Nature Reviews Microbiology 9, 99-108 doi:10.1038/nrmicro2491