MicrobiologyBytes

Rabies has been one of the most feared diseases throughout human history and has the highest human case-fatality proportion of any infectious disease. Every year over 7 million people receive post-exposure prophylaxis, and an estimated 55,000 people die from rabies. Over 99% of these deaths occur in developing countries where rabies is endemic in domestic dog populations. However, the impacts of canine rabies are often overlooked, largely because human rabies deaths are now extremely rare in Western Europe and North America, where mass vaccination successfully eliminated the disease from domestic dog populations.

Although canine rabies has been successfully eliminated from Western Europe and North America, in the developing world someone dies every ten minutes from this horrific disease, which is primarily spread by domestic dogs. A quantitative understanding of rabies transmission dynamics in domestic dog populations is crucial to determining whether global elimination can be achieved. The unique pathology of rabies allowed researchers to trace case-to-case transmission directly during a rabies outbreak in northern Tanzania. From these unusual data, they generated a detailed analysis of rabies transmission biology and found evidence for surprisingly low levels of transmission. They also analysed outbreak data from around the world and found that the transmission of canine rabies has been inherently low throughout its global historic range, explaining the success of control efforts in developed countries. However, they show that when birth and death rates in domestic dog populations are high, such as in the study populations in Tanzania, it is more difficult to maintain population-level immunity in between vaccination campaigns. Nonetheless, although the level of vaccination coverage required is higher than would be predicted from naïve transmission models, global elimination of canine rabies can be achieved through appropriately designed, sustained domestic dog vaccination campaigns.

Transmission dynamics and prospects for the elimination of canine rabies. PLoS Biol. 2009 Mar 10;7(3):e53
Rabies has been eliminated from domestic dog populations in Western Europe and North America, but continues to kill many thousands of people throughout Africa and Asia every year. A quantitative understanding of transmission dynamics in domestic dog populations provides critical information to assess whether global elimination of canine rabies is possible. We report extensive observations of individual rabid animals in Tanzania and generate a uniquely detailed analysis of transmission biology, which explains important epidemiological features, including the level of variation in epidemic trajectories. We found that the basic reproductive number for rabies, R0, is very low in our study area in rural Africa (approximately 1.2) and throughout its historic global range (<2). This finding provides strong support for the feasibility of controlling endemic canine rabies by vaccination, even near wildlife areas with large wild carnivore populations. However, we show that rapid turnover of domestic dog populations has been a major obstacle to successful control in developing countries, thus regular pulse vaccinations will be required to maintain population-level immunity between campaigns. Nonetheless our analyses suggest that with sustained, international commitment, global elimination of rabies from domestic dog populations, the most dangerous vector to humans, is a realistic goal.

Related:

• Simplified rabies vaccination
• Negative sense RNA viruses

On MicrobiologyBytes I’ve often discussed dangerous antibiotic-resistant superbugs such as Staphylococcus aureus MRSA and Clostridium difficile, and what can be done about them. Manuka honey is gathered in New Zealand and Australia from bees which have fed on the manuka bush, Leptospermum scoparium. Recent research has shown that this particular honey has antibacterial activity due primarily to the presence of methylglyoxal (Identification and quantification of methylglyoxal as the dominant antibacterial constituent of Manuka (Leptospermum scoparium) honeys from New Zealand. Mol Nutr Food Res. 2008 Apr;52(4):483-9). This substance originates from dihydroxyacetone, which is present in the nectar of manuka flowers in varying amounts (The origin of methylglyoxal in New Zealand manuka (Leptospermum scoparium) honey. Carbohydr Res. 2009 May 26;344(8):1050-3). Nectar washed from manuka flowers contained high levels of dihydroxyacetone and no detectable methylglyoxal. Storage of manuka honey at 37°C leads to a decrease in the dihydroxyacetone content and a related increase in methylglyoxal. Addition of dihydroxyacetone to clover honey followed by incubation results in methylglyoxal levels similar to those found in manuka honey.

So why the fuss? Dressings containing manuka honey have been shown to be clinically effective against a wide range of bacteria which cause skin ulcers and chronic wound infections, a big problem in hospitals (PubMed: latest research). But manuka honey is in relatively short supply, and so expensive. Manuka honey is now being made in the UK from bushes brought to the Tregothnan Estate near Truro, Cornwall, in 1888. It goes well with a Cornish cream tea, but at £55 a pot, it’s still not cheap.

Subscribe to podcasts (free):
[iTunes] Enhanced podcasts & videos
[RSS] mp3 podcasts (audio only)
Play this episode: Enhanced version | Audio only

Related:

• Honey, I killed the superbug
• Flesh Eating Bacteria
• Staphylococcus aureus: superbug

The FDA is considering whether the USA should offer the Gardasil vaccine that helps prevent cervical cancer in women – to men. That’s because men also carry and transmit human papilloma virus (HPV).

Seems like a no-brainer:

Adeno-Associated Viruses (AAV) are human parvoviruses widely used as a recombinant vector for gene transfer in animal studies and clinical trials designed to treat acquired or inherited genetic diseases. Wild type AAV is defined as a defective virus because it requires the presence of a helper virus to efficiently replicate. Although many viruses can provide helper functions to AAV, only those of Adenovirus were extensively studied, leading to the generation of molecular tools for recombinant AAV vector production. This study focuses on the helper activities of another virus, Herpes Simplex Virus type-1 (HSV-1), and demonstrates that nine HSV-1 proteins are able to fully and efficiently support the early steps of AAV replication. This study provides new information critical for the understanding of AAV replication and also opens the way for new biotechnological developments in the field of recombinant AAV vectors.

Definition of Herpes Simplex Virus Type 1 Helper Activities for Adeno-Associated Virus Early Replication Events. PLoS Pathog 5(3): e1000340. doi:10.1371/journal.ppat.1000340
The human parvovirus Adeno-Associated Virus (AAV) type 2 can only replicate in cells co-infected with a helper virus, such as Adenovirus or Herpes Simplex Virus type 1 (HSV-1); whereas, in the absence of a helper virus, it establishes a latent infection. Previous studies demonstrated that the ternary HSV-1 helicase/primase (HP) complex (UL5/8/52) and the single-stranded DNA-Binding Protein (ICP8) were sufficient to induce AAV-2 replication in transfected cells. We independently showed that, in the context of a latent AAV-2 infection, the HSV-1 ICP0 protein was able to activate rep gene expression. The present study was conducted to integrate these observations and to further explore the requirement of other HSV-1 proteins during early AAV replication steps, i.e. rep gene expression and AAV DNA replication. Using a cellular model that mimics AAV latency and composite constructs coding for various sets of HSV-1 genes, we first confirmed the role of ICP0 for rep gene expression and demonstrated a synergistic effect of ICP4 and, to a lesser extent, ICP22. Conversely, ICP27 displayed an inhibitory effect. Second, our analyses showed that the effect of ICP0, ICP4, and ICP22 on rep gene expression was essential for the onset of AAV DNA replication in conjunction with the HP complex and ICP8. Third, and most importantly, we demonstrated that the HSV-1 DNA polymerase complex (UL30/UL42) was critical to enhance AAV DNA replication to a significant level in transfected cells and that its catalytic activity was involved in this process. Altogether, this work represents the first comprehensive study recapitulating the series of early events taking place during HSV-1–induced AAV replication.

Related:

• Adeno-associated virus vectors in gene therapy

What is a prokaryote? Does anyone really know? In this article in Microbiology Today (pdf) Norman Pace says not, and believes that the term has stuck since it was first coined in the late 19th century, but with no scientific foundation. He would like all microbiologists to join him in scrapping this anachronism in modern biology:

Experimental results rarely upset the common wisdom of a scientific discipline, but that happened to biology late in the 20th century. The common wisdom in deep evolution and how we classify organisms was rendered sorely in need of modernization. And that modern-ization is happening too slowly. The anachronism here is the notion of “prokaryote” and the model of biological organization and evolution that it elicits. This model, which I term the “prokaryote–eukaryote” model, posits that fundamentally there are two kinds of organisms, prokaryotes and eukaryotes, defined by the presence or absence of a nucleus (more properly nuclear membrane). Additionally, the model proposes that prokaryotes gave rise to eukaryotes, as shown in the figure overleaf. The problem, however, is that the prokaryote concept has been undermined critically by sequence-based phylogenetic results. Indeed, the notion of prokaryote was scientifically illogical from the beginning because the definition, an “organism without a nucleus”, is a negative definition. No-one can tell you what a prokaryote is, they can only tell you what it is not. Yet, institutional biology embraced the notion of prokaryote and it came to dominate textbooks, journals and discourse in matters of deep evolution. But the hypothesis of the prokaryote was never tested…

Read more

Related:

• What is a bacterial species?
• Genomic islands in bacterial evolution
• Evolution of root nodule symbiosis with nitrogen-fixing bacteria

The best ways of managing patients with influenza H5N1 infection are debated by experts in this week’s PLoS Medicine (What Is the Optimal Therapy for Patients with H5N1 Influenza? PLoS Med 6(6): e1000091 doi:10.1371/journal.pmed.1000091). In 2007 the World Health Organization described a new process for rapidly developing clinical management guidelines in emergency situations. This guideline recommends giving the antiviral drug oseltamivir (Tamiflu) at a dose of 75 mg twice daily for five days. Doses higher than this recommended amount should be used to fight H5N1 influenza, argues Nicholas White.  In contrast to the current WHO guidelines, he argues that higher doses should be given for H5N1 infection to avoid any possibility of under-dosing those patients with unusual pharmacokinetics and more resistant organisms. This will come at the expense of increased toxicity, he says, but is necessary given the mortality burden of H5N1 infection and the fact that H5N1 replicates more rapidly than seasonal influenza viruses, reaches much greater viral burdens than do other human influenza viruses, and resistance develops swiftly.

Robert Webster and Elena Govorkova disagree. They argue that we must instead consider a multidrug approach to managing patients with H5N1, an approach that is supported by animal data and “can guard against the emergence of resistant strains.”  Tim Uyeki from the Centers for Disease Control and Prevention in Atlanta, USA, emphasizes theneed for more data to help inform clinical management of patients with H5N1 infections. In the absence of these data, he argues, we need a multipronged strategy: pharmacological strategies including combination antiviral treatment, anti-inflammatory agents, and immunotherapy, and non-pharmacological strategies such as the standardization of optimal ventilator and fluid management, especially for acute respiratory distress syndrome, and management of other complications.

Related:

• MicrobiologyBytes: H5N1 | Influenza | Oseltamivir

Millions of years of coevolution of plants and microbial pathogens have shaped both the abilities of microbial pathogens to overcome plant disease resistance and the abilities of plants to cope with microbial invasion. Phytopathogens from different taxonomic origins secrete structurally unrelated effectors into plants to establish infection and to suppress host defences. In addition, phytopathogenic micro-organisms produce a wide range of cytolytic toxins that function as virulence determinants.

Microbial pattern recognition is a prerequisite for the initiation of antimicrobial defenses in all multicellular organisms, including plants. The bipartite plant immune system is based upon recognition of pathogen-associated molecular patterns by pattern-recognition receptors as well as upon the activities of resistance proteins that have evolved to recognize the presence or activities of microbial effectors. In addition to the recognition of microbial patterns and effectors, plants also possess capacities to sense host-derived damage patterns that originate, for example, from the degradation of the plant cell wall by microbial hydrolytic enzymes.

Paradoxically, some phytopathogenic microbe-derived cytolytic toxins have also been reported to elicit plant defences. However, for virtually all microbial toxins with plant defence-stimulating potential, it is unknown whether activation of plant defences results from toxin-induced cellular distress or, independently of toxin action, from recognition of toxins as microbial patterns by plant pattern-recognition receptors.

Subscribe to podcasts (free):
[iTunes] Enhanced podcasts & videos
[RSS] mp3 podcasts (audio only)
Play this episode: Enhanced version | Audio only

NLPs are a superfamily of proteins that are produced by various phytopathogenic micro-organisms, both prokaryotes and eukaryotes. Necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) trigger leaf necrosis that is genetically distinct from immunity-associated programmed cell death and stimulate immunity associated defences in all dicotyledonous plants tested, but not in monocotyledons such as grasses. Hence, NLPs were proposed to have dual functions in plant pathogen interactions, acting both as triggers of immune responses and as toxin-like virulence factors. The broad taxonomic distribution of NLPs, in particular their occurrence in both prokaryotic and eukaryotic species, is unusual for known microbial phytotoxins, the production of which is restricted to a narrow range of microbial species.

Recent work has determined the crystal structure of an NLP from a phytopathogenic fungus (A common toxin fold mediates microbial attack and plant defense. PNAS USA June 11 2009, doi: 10.1073/pnas.0902362106). Computational modeling of the three-dimensional structure of NLPs from another fungus and from a phytopathogenic bacterium reveals a high degree of conservation. Expression of the fungus NLPs in an NLP-deficient phytopathogenic bacteria restored bacterial virulence.

Mutation analysis revealed that identical structural properties were required to cause plasma membrane permeabilization and cytolysis in plant cells, as well as to restore bacterial virulence. The conclusion is that NLPs are conserved virulence factors whose wide taxonomic distribution is exceptional for microbial phytotoxins, and that contribute to host infection by plasma membrane destruction and cytolysis. Phytotoxin-induced cellular damage-associated activation of plant defenses is reminiscent of microbial toxin-induced inflammatory activation in vertebrates and may constitute another conserved element in animal and plant innate immunity.

Related:

• Toll-Like Receptors
• Bacterial toxins

Neisseria meningitidis (meningococcus) and Neisseria gonorrhoeae (gonococcus) are the causative agents of epidemic meningitis and gonorrhoea, respectively. Both are Gram-negative bacteria that specifically infect humans, although they prefer to inhabit distinct human mucosal niches and cause markedly different diseases. One important difference between these pathogens is that almost all clinically important N. meningitidis strains are encapsulated, whereas N. gonorrhoeae strains lack capsule biosynthetic genes. N. meningitidis is a frequent asymptomatic colonizer of the human upper respiratory tract, and most adults are resistant to infection through acquired immunity. However, in susceptible individuals N. meningitidis can cause serious blood and brain infections that are usually manifested as meningitis and septicaemia. It also seems that meningococcal strains vary in their ability to cause sporadic or epidemic outbreaks. The outcomes of meningococcal infection may be devastating and, in the absence of timely intervention, can lead to neurological disorders and death. N. gonorrhoeae is a sexually transmitted pathogen that primarily infects the urogenital tract, giving rise to intense local inflammation and a range of clinical manifestations. A signature property of the two pathogens is their ability to modulate their surface antigenic make up with remarkable speed. This is the basis of their success as human-specific pathogens, as constant surface modulation and point mutations enable the bacteria to evade human immune mechanisms. Extensive surface variation also poses a substantial problem in developing effective vaccines against several strains of N. meningitidis and against N. gonorrhoeae. Although multicomponent vaccines are being developed, the available vaccines fall short of combating all virulent strains.

Pathogenic neisseriae: surface modulation, pathogenesis and infection control. Nature Reviews Microbiology 7, 274 (2009). doi:10.1038/nrmicro2097
Although renowned as a lethal pathogen, Neisseria meningitidis has adapted to be a commensal of the human nasopharynx. It shares extensive genetic and antigenic similarities with the urogenital pathogen Neisseria gonorrhoeae but displays a distinct lifestyle and niche preference. Together, they pose a considerable challenge for vaccine development as they modulate their surface structures with remarkable speed. Nonetheless, their host-cell attachment and invasion capacity is maintained, a property that could be exploited to combat tissue infiltration. With the primary focus on N. meningitidis, this review examines the known mechanisms used by these pathogens for niche establishment and the challenges such mechanisms pose for infection control.

Related:

• Neisseria gonorrhoeae: the video

Some canyons in Israel have north and south-facing slopes that have completely different environments, despite their close proximity. In this article in Microbiology Today (pdf) Johannes Sikorski looks at the micro-organisms that live in these habitats and come to some surprising conclusions that might help us understand micro-evolution rather better:

Bacteria and archaea are genetically, phylogenetically and physiologically very diverse. But how does such diversity start to evolve? How do the first subtle and tender lineages begin to accrue? Oh, you might say, that’s trivial. Have a look at the textbooks and you will find everything there about the evolutionary interplay of mutation, recombination, natural selection and genetic drift. The theoretical framework of population genetics is extremely well-developed. Even more, you insist, microbial microevolution has and still is being analysed in very elegant laboratory experiments, where microbes are allowed to mutate, adapt and evolve in test tubes under very stringent and therefore reproducible and adjustable conditions. But may I remind you that the majority of bacteria are neither evolving in a computer, nor are they living in the pencils of mathe-maticians and theoretical population geneticists, nor in laboratory test tubes, although all these approaches yield tremendous results. Most bacteria live outside in the environment, in water, soil, rocks, plants, etc. Here, where they face a great plethora of biotic and abiotic challenges, they evolve and speciate. Shouldn’t we look at how evolution happens in nature, even though as passive observers, we researchers cannot control this process? What are the decisive factors? Is it possible to catch a glimpse of such a natural evolutionary experiment?

Read more

Related:

• What is a bacterial species?
• Genomic islands in bacterial evolution
• Evolution of root nodule symbiosis with nitrogen-fixing bacteria