MicrobiologyBytes

Paleontologists have found that Tyrannosaurus rex and its close relatives suffered from a potentially life-threatening infectious disease similar to one that occurs in living birds known as trichomonosis. Trichomonas gallinae infections are most prevalent in pigeons which are generally immune.  Birds of prey are particularly susceptible to trichomonosis if they eat infected pigeons. Adult birds can then pass the disease to their nestlings through beak-to-beak contact. Tell-tale symptoms of trichomonosis include swellings and holes in the back of the lower jaw.  The disease is prevented from infecting the entire interior of the bone by the innate immune response that localizes infections as a result of the actions of a unique avian white blood cell called the heterophil. Some of the world’s most famous T. rex specimens, such as “Sue” at the Field Museum in Chicago, and the holotype specimen at the Carnegie Museum of Natural History in Pittsburgh have holes like these in their lower jaw. The holes in tyrannosaur jaws occur in exactly the same place as in modern birds with trichomonosis.  The shape of the holes and the way that they merge into the surrounding bone is very similar in both animals. The cause of these holes in tyrannosaurs has previously been attributed to tooth gouges from biting or bacterial infections, but a trichomonosis-type disease is more likely given the position and nature of the holes.

The disease appeared to be quite common in tyrannosaurs and could have been deadly to those that were infected. As the parasites take hold in serious infections, lesions form around the jaw and inside the throat, eventually eating away the bone. As the lesions grow, the animal has trouble swallowing food and may eventually starve to death. Tyrannosaurs are so far the only dinosaurs that appear to have had this disease.  The researchers therefore faced the problem of explaining how it was spread. In addition to other routes through which infection may have spread, tyrannosaurs might have facilitated infection by biting each other or even through cannibalism. Cannibalism has been tentatively suggested in other studies of theropod behaviour and this certainly could have been a route of transmission for the infection, but other scenarios were more frequent. Fighting and specifically head-biting would have been an ideal mechanism for spreading the disease among tyrannosaurs. It is unlikely to be a coincidence that a significant number of adult tyrannosaur specimens show both face-biting marks and evidence of a trichomonosis-like disease.  Previous studies have shown that up to 60% of tyrannosaur specimens display evidence of face-biting. Bone pathology is hard to find in any specimen, and bone diseases are relatively uncommon.  Finding both types of pathologies in a high proportion of individuals strongly suggests that they could be linked.

There are similarities with what has been happening to Tasmanian devils recently, where a debilitating oral cancer is being spread by animals fighting and biting each other’s faces.  This disease may eventually wipe out this iconic Australian mammal. It is ironic to think that an animal as mighty as T. rex probably died as a result of a parasitic infection. The link in disease is not surprising given the evolutionary relationship of dinosaurs to birds.  But the discovery of a likely candidate for such a disease represents a major step forward in our understanding of disease origins in birds and their dinosaur precursors. The discovery gives us an insight into the dinosaur immune system.  The response of tyrannosaurs to this trichomonosis-like disease is almost identical to that found in living birds. These simple holes in tyrannosaur jaws give us a dramatic example of an avian-like defence system in action.

Common Avian Infection Plagued the Tyrant Dinosaurs. PLoS ONE 4(9): e7288 doi:10.1371/journal.pone.0007288
Tyrannosaurus rex and other tyrannosaurid fossils often display multiple, smooth-edged full-thickness erosive lesions on the mandible, either unilaterally or bilaterally. The cause of these lesions in the Tyrannosaurus rex specimen FMNH PR2081 (known informally by the name ‘Sue’) has previously been attributed to actinomycosis, a bacterial bone infection, or bite wounds from other tyrannosaurids. We conducted an extensive survey of tyrannosaurid specimens and identified ten individuals with full-thickness erosive lesions. These lesions were described, measured and photographed for comparison with one another. We also conducted an extensive survey of related archosaurs for similar lesions. We show here that these lesions are consistent with those caused by an avian parasitic infection called trichomonosis, which causes similar abnormalities on the mandible of modern birds, in particular raptors. This finding represents the first evidence for the ancient evolutionary origin of an avian transmissible disease in non-avian theropod dinosaurs. It also provides a valuable insight into the palaeobiology of these now extinct animals. Based on the frequency with which these lesions occur, we hypothesize that tyrannosaurids were commonly infected by a Trichomonas gallinae-like protozoan. For tyrannosaurid populations, the only non-avian dinosaur group that show trichomonosis-type lesions, it is likely that the disease became endemic and spread as a result of antagonistic intraspecific behavior, consumption of prey infected by a Trichomonas gallinae-like protozoan and possibly even cannibalism. The severity of trichomonosis-related lesions in specimens such as Tyrannosaurus rex FMNH PR2081 and Tyrannosaurus rex MOR 980, strongly suggests that these animals died as a direct result of this disease, mostly likely through starvation.

Related:

• Trichomonas
• The Island of Fossil Viruses
• Phoenix from the ashes: The 5 million year old virus

The first modern clinical description of leptospirosis was published by Weil in 1886, hence leptospirosis is frequently known as Weil’s disease. Over the past decade, outbreaks during sporting events, adventure tourism and disasters have underscored its ability to become a public health problem in non-traditional settings. However, leptospirosis is a neglected disease that places its greatest burden on impoverished populations from developing countries and tropical regions. In addition to being an endemic disease of subsistence farmers, leptospirosis has emerged as a widespread problem in urban slums, where inadequate sanitation has produced the conditions for rat-borne transmission. More than 500,000 cases of severe leptospirosis are reported each year, with case fatality rates exceeding 10%.

Leptospirosis is a zoonotic disease, transmitted from rats to humans via rodent urine, that has emerged as an important cause of morbidity and mortality among impoverished populations. One hundred years after the discovery of the causative spirochaetal agent, little is understood about Leptospira pathogenesis, which in turn has hampered the development of new intervention strategies to address this neglected disease. However, the recent availability of complete genome sequences for Leptospira spp. and the discovery of genetic tools for their transformation have led to important insights into the biology of these pathogens and their pathogenesis. This review discusses the life cycle of the bacterium, recent advances in understanding and the implications for the future prevention of leptospirosis.

Leptospira: the dawn of the molecular genetics era for an emerging zoonotic pathogen. 2009 Nature Reviews Microbiology 7: 736-747 doi:10.1038/nrmicro2208

Related:

• Leptospirosis

The urinary tract is among the most common sites of bacterial infection. Over half (53%) of all women and 14% of men experience at least one urinary tract infection (UTI) in their lifetime, leading to an average of 6.8 million physician office visits, 1.3 million emergency room visits, and 245,000 hospitalizations per year, with an annual cost of over US$2.4 billion in the United States alone. Escherichia coli is the infectious agent in more than 80% of uncomplicated UTIs, which occur in patients with a normal urinary tract devoid of structural abnormalities or inflammatory lesions.

In light of the recent E. coli outbreak in the UK, the news that scientists have made an important step toward what could become the first vaccine to prevent urinary tract infections is interesting. To help combat this common health issue, the scientists used a novel systematic approach combining bioinformatics, genomics and proteomics to look for key parts of the E. coli bacterium that could be used in a vaccine to elicit an effective immune response. The team screened 5,379 possible bacterial proteins and identified three strong candidates to use in a vaccine to prime the body to fight E. coli, the cause of most uncomplicated urinary tract infections. The vaccine produced prevented infection and produced key types of immunity when tested in mice.

Scientists have attempted to develop a vaccine for UTIs over the past two decades. This latest potential vaccine has features that may better its chances of success. It alerts the immune system to iron receptors on the surface of bacteria that perform a critical function allowing infection to spread. Administered via the nose rather than injected, it induces an immune response in the body’s mucosa, a first line of defense against invading pathogens. The protective immune response, which also produced in mucosal tissue in the urinary tract, should help the body fight infection where it starts. The research team is currently testing more strains of E. coli. Most of the strains produce the same iron-related proteins that the vaccine targets, an encouraging sign that the vaccine could work against many urinary tract infections.

Iron acquisition is a critical function required by bacteria in order to cause infections. In uropathogenic E. coli, this function is mediated by a repertoire of systems that scavenge iron from the host during infection. Vaccination with certain iron receptors from these systems is sufficient to elicit protective immunity from experimental urinary tract infection. Induction of an antibody response played a key role in protection from infection because antibody class-switching and the production of antibodies in urine correlated with reduced numbers of bacteria in the bladder. By targeting an entire class of molecules involved in iron acquisition instead of a single protein, it was possible to successfully identify components of a protective UTI vaccine. This strategy could be a useful approach in the development of vaccines to prevent infections caused by other pathogenic bacteria.

However, this is still early clinical research and this candidate vaccine has not yet undegone even a phase 1 safety trial in humans. And even if that were successful, the vaccine would take several more years to reach the market, even if manufacturers decided they could make a profit from producing it. So the next time you’re down on the farm, wash your hands – and make sure that burger is properly cooked through.

Mucosal Immunization with Iron Receptor Antigens Protects against Urinary Tract Infection. 2009PLoS Pathog 5(9): e1000586 doi:10.1371/journal.ppat.1000586
Uncomplicated infections of the urinary tract, caused by uropathogenic Escherichia coli, are among the most common diseases requiring medical intervention. A preventive vaccine to reduce the morbidity and fiscal burden these infections have upon the healthcare system would be beneficial. Here, we describe the results of a large-scale selection process that incorporates bioinformatic, genomic, transcriptomic, and proteomic screens to identify six vaccine candidates from the 5379 predicted proteins encoded by uropathogenic E. coli strain CFT073. The vaccine candidates, ChuA, Hma, Iha, IreA, IroN, and IutA, all belong to a functional class of molecules that is involved in iron acquisition, a process critical for pathogenesis in all microbes. Intranasal immunization of CBA/J mice with these outer membrane iron receptors elicited a systemic and mucosal immune response that included the production of antigen-specific IgM, IgG, and IgA antibodies. The cellular response to vaccination was characterized by the induction and secretion of IFN-c and IL-17. Of the six potential vaccine candidates, IreA, Hma, and IutA provided significant protection from experimental infection. In immunized animals, class-switching from IgM to IgG and production of antigen-specific IgA in the urine represent immunological correlates of protection from E. coli bladder colonization. These findings are an important first step toward the development of a subunit vaccine to prevent urinary tract infections and demonstrate how targeting an entire class of molecules that are collectively required for pathogenesis may represent a fundamental strategy to combat infections.

Related:

• Microbiology Video Library: Escherichia coli
• E. coli O157:H7 – getting to the bottom of the burger bug
• The continuing evolution of E. coli O157:H7
• Bacterial toxins

via Wired

The Great Flu is a free online game designed to introduce players to the nature of virus epidemics and means of controlling them. The game offers players the choice of five levels of flu severity (game difficulty), a €2 billion budget and a range of actions of varying effectiveness, such as sending researchers to afflicted areas, distribution of facemasks, stockpiling vaccines and antivirals, and closing schools, airports and public markets.  Taking various actions triggers various pieces of supporting material such as mocked-up news coverage and messages from governments or regional authorities, and also provides information on the nature and spread of earlier flu pandemics.

Leprosy is a debilitating but treatable disease caused by infection with Mycobacterium leprae. Although popular conceptions of leprosy are focused primarily on images from Biblical or Medieval times, one quarter of a million people worldwide were still suffering from the disease in 2007. The history of leprosy is “interwoven with civilization itself”. An understanding of the origin and transmission routes of this disease can potentially lead to new insights about the evolution of infectious diseases and eradication efforts. However, the organism responsible is difficult to culture in the laboratory and much about leprosy is still poorly understood, including the origin, initial transmission routes and timing of the spread of the disease in the Old World.

A new cross-disciplinary report describes the analysis of a 4000-year-old skeleton from India bearing evidence of leprosy. This skeleton represents both the earliest archaeological evidence for human infection with M. leprae in the world and the first evidence for the disease in prehistoric India. This work demonstrates that leprosy was present in human populations in India by the end of the mature phase of the Indus Civilization (2000 B.C.) and provides support for one hypothesis about prehistoric transmission routes for the disease. The findings also support the hypothesis that the Sanskrit Atharva Veda, composed before the first millennium B.C., is the earliest written reference to the disease and that burial traditions in the second millennium B.C. in one northwestern Indian village bear some resemblance to practices in Hindu tradition today.

As infectious diseases go, leprosy is still one of the least well-understood, in part because the M. leprae is difficult to culture for research and it has only one other animal host, the nine banded armadillo. An Indian or African origin for the disease has often been assumed based on historical sources that support an initial spread of the disease from Asia to Europe with Alexander the Great’s army after 400 B.C. Skeletal evidence for the disease was previously limited to 300-400 B.C. in Egypt and Thailand. A report on genomics of Mycobacterium published in the magazine Science in 2005 suggested the disease may have originated in Africa during the Late Pleistocene and that M. leprae spread out of Africa sometime after 40,000 years ago, when human population densities were small. A counter hypothesis was proposed in the same volume of Science by Pinhasi and colleagues suggesting that the same data could be interpreted as evidence for a Late Holocene migration of the disease out of India after the development of large urban centers. The new work describes a case of leprosy recorded in a skeleton buried around 2000 B.C. in Rajasthan, India, at the site of Balathal. From 3700-1800 B.C. Balathal was a large agrarian settlement at the margins of the Indus Civilization. The mature phase of the Indus Civilization during the latter half of the third millennium B.C., was a period of social complexity characterized by urbanization, a system of writing, standardized weights and measures, monumental architecture, and trade networks that stretched to Mesopotamia and beyond. The presence of leprosy in India toward the end of this period indicates that M. leprae existed in South Asia at least 4000 years ago. This suggests that there may be some validity to the hypothesis that the disease spread between Africa and Asia during a period of incipient urbanization, increasing population density, and regular inter-continental trade networks.

The team is currently attempting to recover ancient DNA from the skeleton to determine if the strain of M. leprae infecting the individual from Balathal is similar to strains common in Africa, Asia and Europe today. If it is successful, this work could shed additional light on the origin and transmission routes of this disease. Understanding more about the disease can help clear up some of the many popular misconceptions about leprosy. It is generally associated with outcast and neglected people suffering their contagion on the margins of urban centers in late Biblical or Medieval times. In reality, leprosy is transmitted only through prolonged close contact with nasal droplets or infected regions of the body. It is not highly contagious and the infection can remain latent for decades. In fact, most people infected with M. leprae have few or very mild symptoms. Because leprosy is not highly contagious and its survival is likely dependent upon dense populations, the association with urban environments is possibly the only accurate part of the popular perception.

The presence of leprosy at Balathal 4000 years ago also supports translations of the Eber’s papyrus in Egypt and a Sanskrit text in India (the Atharva Veda) that refer to the disease as early as 1550 B.C. The Atharva Veda is a set of Sanskrit hymns devoted to describing health problems, their causes and treatments available in ancient India. Translations of leprosy have been questioned because it is difficult to perform a differential diagnosis on descriptions in such ancient texts particularly since diagnosis was not why the conditions were being described. The evidence from Balathal indicates that it is possible that the authors were describing leprosy as the disease was present in the subcontinent in prehistoric times. Furthermore, in contemporary Hindu tradition burial is uncommon unless an individual is a highly respected member of the community (like an ascetic) or is an individual seen as unfit to be sacrificed through cremation. These latter individuals are buried, including outcastes, pregnant women, children under 5, victims of magic or curses, and lepers. During the second millennium B.C., when there was disintegration of Indus settlements and new, smaller settlements sprang up all over the western half of peninsular India, adult burial becomes rare, children under 5 begin to predominate in the skeletal assemblages, and this early leper was one of only five individuals buried at the site of Balathal. Thus there is a similarity in terms of the demography of the burial populations from the second millennium and Vedic tradition. In addition, another feature of this burial that resembles Vedic symbolism is the burial site itself. The leper’s skeleton was interred within a large stone enclosure that had been filled with vitrified ash from burned cow dung, the most sacred and purifying of substances in Vedic tradition. The presence of this skeleton at Balathal, the manner in which it was interred, and the preponderance of children in burial assemblages from this time period throughout western India suggest deep time for the origin of these practices still common in Vedic tradition today.

Ancient Skeletal Evidence for Leprosy in India (2000 BC). 2009 PLoS ONE 4(5): e5669
Leprosy is a chronic infectious disease caused by Mycobacterium leprae that affects almost 250,000 people worldwide. The timing of first infection, geographic origin, and pattern of transmission of the disease are still under investigation. Comparative genomics research has suggested M. leprae evolved either in East Africa or South Asia during the Late Pleistocene before spreading to Europe and the rest of the World. The earliest widely accepted evidence for leprosy is in Asian texts dated to 600 B.C. We report an analysis of pathological conditions in skeletal remains from the second millennium B.C. in India. A middle aged adult male skeleton demonstrates pathological changes in the rhinomaxillary region, degenerative joint disease, infectious involvement of the tibia (periostitis), and injury to the peripheral skeleton. The presence and patterning of lesions was subject to a process of differential diagnosis for leprosy including treponemal disease, leishmaniasis, tuberculosis, osteomyelitis, and non-specific infection. Results indicate that lepromatous leprosy was present in India by 2000 B.C. This evidence represents the oldest documented skeletal evidence for the disease. Our results indicate that Vedic burial traditions in cases of leprosy were present in northwest India prior to the first millennium B.C. Our results also support translations of early Vedic scriptures as the first textual reference to leprosy. The presence of leprosy in skeletal material dated to the post-urban phase of the Indus Age suggests that if M. leprae evolved in Africa, the disease migrated to India before the Late Holocene, possibly during the third millennium B.C. at a time when there was substantial interaction among the Indus Civilization, Mesopotamia, and Egypt. This evidence should be impetus to look for additional skeletal and molecular evidence of leprosy in India and Africa to confirm the African origin of the disease.

Related:

• New hope for leprosy?

In 1928, by chance, Alexander Fleming discovered penicillin, which was subsequently developed and saved millions from death by infectious disease. In this article in Microbiology Today, Kevin Brown recounts the story of this amazing antibiotic and tells something of the man who found it:

In many ways Fleming could have only discovered the original wonder drug in his musty, dusty, overcrowded, cluttered laboratory at St Mary’s Hospital. After all, if there was no possibility of contamination there could have been no penicillin. Some might argue that without Fleming, there would have been none either. Certainly, the chance contamination of culture plates was common, but Fleming’s genius was to notice something unusual and act upon it. As a scientist, he was very much in the tradition of the 19th-century lone researcher interested in unusual phenomena. This approach was to pay dividends when in September 1928 he returned from a 6-week holiday to find not only that a plate of staphylococci, he had been working on before his holiday had become contaminated by a fungus, but that there was the now classic zone of inhibition around the mould. Ever the master of understatement, Fleming’s response was typical of the man: “That’s funny!”

Read more

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• Towards The Next 80 Years of Penicillin Production
• Penicillin: Triumph and Tragedy
• Antibiotics will not get rid of your cold

discovermagazine.com

It was just a matter of time before someone discovered that Madagascar is a museum for viruses. The discovery came when a team of American and English scientists perused the genome of the gray mouse lemur. Nestled among its genes were segments of DNA that bore a remarkable resemblance to HIV. How on Earth could a deadly virus’s genes become part of a primate’s own genome? Some kinds of viruses, known as retroviruses, replicate by inserting their DNA into host cells, where their DNA can guide the production of new viruses. But many studies indicate that sometimes these viruses infect the cells that will give rise to sperm and eggs. The virus ends up in a fertilized egg and gets passed down to ever cell in the developing embryo–including its own sex cells. Now the virus gets passed down through the generations. It may still retain the ability to infect other cells for a while, but mutations typically knock out that ability. Instead, the virus can only insert copies of its DNA back into its own host cell’s genome. Over millions of years, this viral DNA spreads through the host genome. Our own DNA contains 98,000 stretches of this virus DNA, plus 150,000 tiny viral fragments, making up about 8% of our genome – about five times more DNA than the DNA that encodes proteins.

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Related:

• Phoenix from the ashes: The 5 million year old virus

Understanding the evolutionary history of human viruses, along with the factors that have shaped their spatial distributions, is one of the most active areas of study in the field of microbial evolution. This reviews give an overview of our current knowledge of the genetic diversity of human viruses using comparative studies of viral populations, particularly those with RNA genomes, to highlight important generalities in the patterns and processes of viral evolution. Special emphasis is given to the major dichotomy between RNA and DNA viruses in their epidemiological dynamics and the different types of phylogeographic pattern exhibited by human viruses. It also considers a central paradox in studies of virus evolution: Although epidemiological theory predicts that RNA viruses have ancestries dating back millennia, with major ecological transitions facilitating their emergence, the genetic diversity in currently circulating viral populations has a far more recent ancestry, indicative of continual lineage turnover.

Evolutionary history and phylogeography of human viruses. Annu Rev Microbiol. 2008 62: 307-328

Related:

• Do viruses evolve to protect their hosts?
• Global migration of influenza viruses