Chapter 017, Mycoses and Non-Infectious Diseases (American College of Laboratory Animal Medicine)

Diagnosing Emerging Fungal Threats: A One Health Perspective
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We do not have to look for undescribed fungi in completely new places or tropical regions, however, because they may be in our backyards. My colleagues and I look for new species among the yeasts and other microscopic fungi that are difficult to see. Figure A Diagrammatic representation of relationships of fungal taxa, examples ex. Zoosporic and zygosporic fungi are more diverse than previously recognized on the basis of morphological traits, and they are not monophyletic. Two flagellated taxa, Rozella and Olpidium , are of uncertain taxonomic placement.

Evidence from multilocus sequencing and genomics reveals that microsporidians branch within or near fungi. Ascomycota and Basidiomycota, the most speciose phyla, are each divided into three subphyla. The largest number of fungal species are classified in the subphyla Pezizomycotina and Agaricomycotina. Figure A Images of representative fungal groups. A Hyphae of the blastocladialean fungus, Allomyces sp. Note a terminal zoosporangium ZS containing zoospores. The spiny, dark, thick-walled resting spores RS within the hyphae are those of a zoosporic fungal parasite, Rozella allomycis , of uncertain taxonomic placement.

B Lobosporangium transversale. The zygosporic fungus in the Mortierellales has unusual spiny lobed sporangia Benny and Blackwell, C Sarcoscypha coccinea. The several cm diameter fruiting body of the scarlet cup ascomycete, Sarcoscypha coccinea. Ascospores are formed within asci on the inner surface of the cup. D Mutinus sp. A stinkhorn similar to one mentioned in the text that caused a search for a dead body Anonymous, Stinkhorns produce noxious compounds that attract insect spore dispersers.

The dark slimy mass of spores has been partially removed by flies. James, provided by Meredith Blackwell D photo courtesy of Nhu H. Nguyen, provided by Meredith Blackwell Ascomycetes and basidiomycetes are expected to provide the greatest diversity of additional taxa based on numbers of currently known fungi, but certainly the developing methods using high-throughput sequencing of DNA will lead to the discovery of more of the early diverging groups Figure A Kirk et al.

Examples of large numbers of species isolated into culture from certain substrates include the finding of unique morphotypes of endophytic fungi from 83 leaves in Panama Arnold, , fungal endophyte genotypes in coffee plants Vega et al. Acquiring cultures and specimens will remain important in cases when fungi and cultures are needed for certain purposes, including population studies, environmental remediation, and secondary metabolites.

Taylor and his colleagues used high-throughput sequencing to estimate the presence of more than taxa in a 0. If we are to determine the number of fungi on Earth, environmental sequencing will be necessary to speed fungal exploration and discovery. In addition to new species, entire lineages, some probably at the level of subphylum, may be recognized by DNA sequences such as Soil Clone Group 1 Porter et al.

More work will be needed to determine geographical and substrate ranges in order to obtain more accurate estimates of species numbers. Species discovery is relevant to the topic of this workshop because previously unknown plant and animal pathogenic fungi have been introduced into the United States many times. These fungi probably caused few symptoms and went unnoticed in their native hosts. This scenario certainly is repeated by the fungi discussed in this meeting, including Batrachochytrium dendrobatidis , the pathogenic chytrid of amphibians spread around the world; Geomyces destructans , the pathogen of bats in North America; and Phytophthora ramorum , causing declines of certain plants in North America and Europe.

Prior invasions have included several fungal agents of Dutch elm disease; the chestnut blight fungi; the newly arrived agent of the laurel wilt delivered within the mycangia 10 of its ambrosia beetle vector; and Discula destructans , a pathogen of North American dogwoods Alexopoulos et al. Recently, a new approach to discovering the native ranges of certain fungi has been profitable. Ning Zhang Personal communication, Rutgers University, December 10, designed an efficient assay method using specific primers to detect the dogwood pathogenic fungus in herbarium specimens.

The method promises to greatly reduce the time involved in determining geographical and host ranges and is ideal for working with col-. Because patterns of introduction of pathogens may exist, determination of native ranges is essential in combating invasive organisms. Fungi are important as model systems in research. Saccharomyces cerevisiae Figure A is a supermodel known for its baking and brewing prowess and as the first eukaryote to have its entire genome sequenced.

Note the many budding cells in the stained preparation. Kurtzman, provided by Meredith Blackwell In addition to S. Dodge for his establishment of this Ascomycete as a most suitable organism for genetic studies. He finally persuaded Morgan to take a collection of Neurospora cultures with him from Columbia University to the new Biology Division of the California Institute of Technology, which he established in As mentioned above, S.

This yeast and other species in the Saccharomycotina have relatively small genomes that make them economical candidates for sequencing Mewes et al. In addition, yeasts and other model fungi are easy to grow and complete their lifecycles in culture in a few days; because they are haploid throughout most of their lifecycle, induced mutations are expressed rapidly. Many fungi, including some yeasts, also have a sexual state from which all products of meiosis can be isolated in addition to asexual spores and somatic cells from which uniform populations can be established.

They also are excellent organisms for population studies Anderson et al. Some fungi, including S. For example, yeasts from the gut of wood-feeding beetles have been of particular interest because many of them ferment xylose, a requirement for efficient digestion of lignocellulose in biofuel production. These species have undergone biochemical and metabolic engineering to obtain more information on xylose fermentation pathways, and genome sequencing is important toward this end Jeffries et al.

Humans have used a variety of fungal products for different purposes, including cures. In fact some of the magical fungi mentioned above also have been used for their medicinal properties, which may have been known since prehistoric times. Evidence exists for the use of fungi by early humans. He carried pieces of the fruiting bodies from two species of wood-rotting basidiomycetes, Piptoporus betulinus and Fomes fomentarius , perhaps for medicinal uses Peinter et al. Other writers have suggested that one of the fruiting bodies was used as a strop for sharpening knives and tools, but whatever their use, fungi appear to have been important to Copper Age Europeans.

Some basidiomycetes have been used medicinally in more recent times. Extracts of Inonotus obliquus was used in Europe as a treatment for cancer, and the fruiting bodies of Fomitopsis officinalis the quinine conk , mentioned earlier as grave guardians in the Pacific Northwest, were also harvested for medicinal properties. A different kind of medicinal use by foresters was the application of sheets of mycelium on ax injuries to stop bleeding Gilbertson, Certain ascomycete fungi, previously known as species of Cordyceps , have been used in Asian traditional medicine for several centuries Spatafora et al.

One of these fungi, a parasite of caterpillars, known as Cordyceps sinensis since , now is Ophiocordyceps sinensis based on a phylogenetic study Sung et al. Recent interest in the fungus has provided evidence that it may be effective in the treatment of certain tumors Spatafora et al. The revision of the entire group of insect—pathogenic fungi previously placed in the genus Cordyceps has resulted in the placement of species in three different families Sung et al.

This is an important development because phylogenies are predictive of traits common to closely related fungi, and other Ophiocordyceps species may be targeted for the mining of metabolites. The efforts to develop penicillin for the treatment of bacterial infections at the beginning of World War II resulted in the discovery of a long-sought magic bullet and hastened the rise of the modern pharmaceutical industry. In addition to the fungus-derived drug penicillin, three statin drugs for lowering cholesterol levels e.

Cyclosporine, once critical to transplant surgery, is today used to treat dry eye as well as more serious conditions Blackwell, Fungi also are big business in the food and beverage industries. In addition to the usual fresh fruiting bodies of basidiomycetes mushrooms and a few highly favored ascomycetes truffles and morels , other fungi, such as cuitlacoche corn smut and rice smut, are eaten in Mexico and Asia, respectively. Processed foods also are made from fungi. Several species of Aspergillus are used in the processing of soy sauce, and fungi play a part in the flavoring process of cheeses.

Throughout the world many fermented foods rely on fungi at least in part to increase nutritional value, improve texture and flavor, and preserve the foodstuff. In one short street block in Brussels, I examined shop windows to count the many products that had been touched by fungi: coffee, certain teas, chocolate, cheeses, bread, salami and dry-cured hams, and numerous fermented beverages Tamang and Fleet, As in the case of other fungal products, the making of alcoholic beverages almost certainly was discovered millennia ago, found accidently in prehistoric times when wild yeasts settled into a sugary beverage.

Yeasts are essential to the multibillion-dollar alcoholic beverage industry. The yeasts involved in brewing were first isolated into pure culture by Emil Hansen at the Carlsberg Brewery in Copenhagen, and the brewery lab became an important site of classic yeast genetics and biotechnology research Hansen and Kielland-Brandt, Pretorius suggested that many additional yeast species might be used in winemaking.

In this context my colleagues and I have discovered nearly previously unknown yeasts, many of which have the ability to ferment a variety of sugars, yet are untried for making beverages Suh et al. In addition to its significance in brewing and bread making, S. Fungi interact with all major groups of organisms. Specific interactions with photosynthetic organisms are generally well known Table A About 80 percent of all plant species and 92 percent of plant families form close associations with fungi known as mycorrhizae Smith and Read, ; Trappe, Fungi and plant roots or underground stems form several kinds of mycorrhizae that are classified by the morphology of the interacting fungus in relation to the root.

The associations are important for carbon, mineral, and water exchange, with carbon generally transferred from the plant to the fungus. Arbuscular mycorrhizal AM fungi are known from the million-year-old Rhynie chert. The fungi penetrate the plant cell wall and form a highly branched arbuscule that invaginates the plasma membrane of the root cortex cells.

The members of the asexually reproducing phylum Glomeromycota are obligate fungal partners of about 60 percent of all plant species. Hosts include a variety of crop and forage plants such as maize, rice, alfalfa, and citrus, as well as many non-cultivated plants.

Molecular methods have detected previously unknown host. Ectomycorrhizal fungi FIGURE A are associated with fewer hosts, including certain dominant forest trees such as birch, dipterocarp, eucalyptus, oak, and pine. Greater ectomyccorhizal fungal diversity is evident, and basidiomycetes, ascomycetes, and a few zygomycetes are involved in these associations.

Many of the fungi are generalists, but more specificity occurs than among AM associates. The fungi produce an external mantle over young roots and often cause dramatic shortening and dichotomous branching of the mycorrhizal root Smith and Read, Endophytes are fungi that usually grow within above-ground plant parts without causing disease symptoms in about 95 percent of all plants examined Arnold, The fungi that form the associations have been placed in four groups, depending on host specificity, tissues colonized, and amount of colonization within the plant Rodriguez et al.

Hypocrealean endophytes of grasses and sedges produce alkaloids that have been suggested to deter feeding by insects and vertebrates. Endophyte-infected grasses have enhanced growth and drought resistance Rodriguez et al. A different group of endophytes is more taxonomically diverse and has broad plant host range with restricted growth within the plant, often occupying only a single cell. Some of these horizontally transmitted endophytes convey protection from plant pathogens Arnold et al. About half of the estimated 64, ascomycetes e. Figure A Anaptychia ciliaris.

Small colonies of the lichen-forming fungus on agar medium after 3 months of growth. Schoch et al. Lichens have been used as indicators of pollution. Although the fungal associate can be grown on artificial media, they usually grow very slowly Figure A Lichens are hosts for pathogenic fungi as well as endolichenic fungi, the lichen equivalent of endophytes. Each partner in the lichen has a scientific name, but the name of the lichen as a whole is that of the fungus Ahmadjian, ; Nash, Fungi are heterotrophic and their ability to degrade organic materials and return them to nutrient cycles is an essential activity in almost all ecosystems.

The ability of a fungus to degrade specific substrates depends on the enzymes it produces, and certain fungi are especially important in forest ecosystems where they are the primary decomposers of wood. Basidiomycetes and some ascomycetes are the primary decomposers of plant cell wall carbohydrates cellulose and. Figure A Ectomycorrhizal root.

The hyphae of Rhizopogon rubescens enveloping the young roots of a Virginia pine seedling. The mycelium extends from the roots into the surrounding environment. Anderson, provided by Meredith Blackwell Some wood-decaying fungi invade living trees and attack non-functional tissues, especially heartwood, the non-conducting vascular tissue in the center of a cross section of the trunk.

Few wood-decaying fungi actually cause diseases and most of the damage comes from the weakening of tree trunks so that they fall in wind or ice storms. The loss of weakened trees is a natural process that culls branches and entire trees to create clearings in older forests Gilbertson, The importance of wood-decaying fungi in the formation of nesting holes for wildlife is well known Gilbertson, The red-cockaded woodpecker prefers to nest in mature pines about 60 years old that have been rotted by the basidiomycete Phellinus pini. Old pine stands are a diminishing habitat in regions where pines are grown in plantations on a year rotation or less for commercial use.

The ivory-billed woodpecker may be extinct because the extensive old-growth, bottomland hardwood forests the species inhabited have been lost Gilbertson, A less significant but interesting use of wood decay is the creation of wooden objects that have been modified by wood-decaying fungi. Spalted wood is distinguished by zone lines, the dark lines formed by oxidation at the points of contact between closely related fungal colonies. The patterned wood is often favored by. Even Stradivarius violins may have been made more resonant by the partial decay of the wood Schwarze et al. The importance of many insects in the ecosystem is overlooked, but many of them are important in degradation of course particles, dispersal of bacteria and fungi, and, as is well known, as agents of fungal fertilization.

Fungi clearly provide benefits for insects, although the exact advantages to the fungi beyond providing habitat and a means of dispersal often are not clear Buchner, ; Gilbertson, ; Mueller et al. Few animals have the enzymes necessary to digest refractory plant cell wall materials or to synthesize vitamins. Fungi also may detoxify plant toxins and produce pheromones for insects Table A Dowd, ; Vega and Dowd, ; Wheeler and Blackwell, ; Wilding et al. The best known fungus—insect associations include the farming interactions of basidiomycetes with Old World termites Macrotermitinae Aanen.

The females of another insect group, siricid wood wasps Siricidae , are less well studied, but they have been considered by some to form farming interactions with fungi see Gilbertson, The farming association of the basidiomycete Termitomyces with Old World macrotermitine termites arose once in Africa. Since that event no additional fungal lineages have been domesticated and no reversals of the fungus to a free-living state have been found. Repeated host switching, however, has occurred within termite clades as reflected in the phylogenetic trees of termites and associated fungi Aanen et al.

Nest initiation by both males and females of certain species has been suggested to have influenced the mode of transmission of the fungus, usually acquired from the environment or some source other than a parent horizontal transmission Aanen et al. In the New World it is not termites, but attine ants that are involved with basidiomycetes in farming interactions, and Aanen and his colleagues compared the associations. The attines have become associated with several clades of fungi, and in contrast to termite transmission, transmission of the fungi is usually directly from parent to offspring vertical except in the early diverging ant lineages.

Another important difference is that the ant-associated fungi apparently do not reproduce sexually. The work on the fungus—attine ant associations have revealed that ants have evolved with several groups of fungi on several different occasions. Although the best-known fungal mutalists are species of Leucocoprinus , other fungal groups, including certain species of Pterulaceae, have an association with ants in the Apterostigma pilosum clade Munkacsi et al.

The intensive studies of the fungi and attine ant associations have led to the discovery of other organisms that participate in the complex interactions. Species of hypocrealean ascomycetes in the genus Escovopsis are parasites of the cultivated fungus. Actinomycete associates of the ants produce antibiotics that have been reported to be specific in inhibiting Escovopsis Currie et al. The association of a fourth component of the association is black yeasts that apparently reduce the efficiency of the antibiotics Little and Currie, This attine and—cultivated fungus— Escovopsis parasite associations provide the best example of coevolution, in this case tripartite association, among fungi and associates Currie et al.

Unlike the termite and ant interactions, fungus-beetle associations have arisen multiple times. Some bark and ambrosia beetles have mycangia already mentioned above in which they carry inoculum of certain fungi Malloch and Blackwell, The fungi, often Ceratocystis and Ophiostoma or relatives, may be the agents of plant diseases, and some of the fungi have been introduced. Figure A Excavation of deeply entrenched nest of the ant Atta texana requires heavy equipment or, alternatively, ground-penetrating radar to map such nests.

The ant is native to adjacent parts of Texas and Louisiana, and the nests are said to be able to contain a three-story house. Ophiostoma ulmi and similar fungi have been introduced into the United States, where they are virulent pathogens of trees, including American elms. The most efficient dispersers of some of these fungi actually were introduced before the fungus, Ophiostoma ulmi Alexopoulos et al. In this discussion of beneficial fungi, these interactions benefit the insects and call attention to potential devastating effects of efficient insect dispersal in the context of emerging plant diseases.

Other beneficial fungal associates of insects involve siricid wood wasps and wood-decaying basidiomycetes, species of Amylostereum , Stereum , and Daedalea. The wasps lay their eggs through long ovipositors, tube-shaped organs at the posterior of the abdomen, and the larvae probably rely on fungal enzymes to decompose and detoxify the wood they ingest Gilbertson, ; Martin, Many more fungi are associated with insects as necrotrophic parasites FIGURE A , and some of these deadly fungi have potential for development as biological control agents Vega et al.

In addition, many of about 1, described yeast species have close associations with insects Table A , and the yeasts provide important services to the insects Vega and Dowd, Figure A Hirsutella citriformis Ophiostomataceae on a delphacid planthopper. The asexual fruiting structure of this fungus erupted through the cuticle of the parasitized insect soon after its death.

About species of Septobasidium in the Septobasidiales are known as associates of scale insects; only a few related species of Pachnocybe grow on wood Henk and Vilgalys, The use of insect hosts is unusual for fungi that are related to the plant pathogenic rust fungi. The fungi are parasites of a few of the scale individuals, but in general benefit the entire insect colony by providing a protective covering against parasitic wasps Henk and Vilgalys, Two orders of zygomycetes, Harpellales and Asellariales, were previously placed in a polyphyletic group known as Trichomycetes.

The results of several studies indicate that these gut fungi produce vitamins and perhaps other benefits for their aquatic insect hosts Lichtwardt et al. One species is known to parasitize simulid black flies Lichtwardt et al. Another nutritional interaction between fungi and animals is only briefly noted here, but is extremely important. An early diverging lineage of obligately anaerobic multiflagellated fungi, the Neocallimastigomycota, and vertebrate herbivores are closely associated Griffith et al.

The fungi reside in the host rumen or another anaerobic part of the gut, where they are important in supplying cellulases and other enzymes for the degradation of the large quantities of cellulose ingested by the herbivore James et al. Many fungi are obligate, beneficial associates of other groups of organisms. More often it is the effects of the fungi that we observe when they ferment fruit juice, or fitting to this volume, cause dramatic new outbreaks of disease.

The Robert Frost poem quoted in the prologue of this publication describes the costs of the introduction of the disease caused by the chestnut blight fungus, Cryphonectria parasitica. The poem predicts that the disease will ravage until a new pathogen comes to kill the fungus, and in fact a virus did appear to suppress the fungus. In , however, yet another pathogen, the oriental chestnut gall wasp, was introduced to attack the trees, an additional turn not predicted by the verse. Today, as one out of every six or seven humans on Earth is reported to be malnourished or hungry FAO, , the war against pathogenic diseases of plants and animals is as important as ever.

An earlier writer, Jonathan Swift — addressed the topic of hunger with his essay, A Modest Proposal , written to bring attention to the starvation of Irish tenant farmers during the potato famine.


This volume, Fungal Diseases: An Emerging Threat to Human, Animal, and Plant Health , provides a discussion of new fungal diseases of plants and the animals that we strive to overcome at a time when introduced diseases contribute to hunger. I am grateful to Dr. Fernando Vega, who improved the original manuscript through his careful editing. Several colleagues provided images, and Dr. Matthew Brown kindly prepared the plate. Aanen, D. Eggleton, C. Rosendahl, and J. The evolution of fungus-growing termites and their mutualistic fungal symbionts.

Aime, M. Largent, T. Henkel, and T. Mycologia — Alexopoulos, C. Mims, and M. Introductory mycology. New York: John Wiley and Sons. Amend, A. Seifert, R. Samson, and T. Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Anderson, J. Funt, D. Thompson, S.

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Table of Contents

EU Health Programme This program supports mentored research training leading to a doctoral degree in the biomedical, behavioral, or clinical sciences for individuals from diverse population groups, with the goal of enhancing diversity of the research workforce in the US. Worldwide emergence of a highly destructive and undescribed pathogen, identified by isolation from infected amphibians Longcore et al. PCR was performed based on the protocols of Mirhendi et al. Chung, and B. The blast fungus decoded: genomes in flux. Lumbsch, R.

McLaughlin, M. Powell, S. Redhead, C. Schoch, J. Spatafora, J. Stalpers, R. Vilgalys, M. Biological endpoints included monocyte and neutrophil counts and cytokine levels. VGCV patients experienced a greater improvement by MFI at 9 months from baseline compared to placebo patients but this difference was not statistically significant. VGCV patients experienced these improvements within the first 3 months and maintained that benefit over the remaining 9 months. Patients in the VGCV arm were 7.

Incidence, characteristics, and risk-factors for invasive aspergillosis IA -associated immune reconstitution syndrome IRS in lung transplant recipients are not known. IRS was defined based on previously proposed criteria. In all, 7. Three out of 5 patients with IRS died and 2 of 3 deaths in this group were due to chronic rejection. Human herpesvirus-6 HHV-6 A and 6B are ubiquitous betaherpesviruses viruses with lymphotropic and neurotropic potential.

As reported earlier, these viruses establish latency by integration into the telomeres of host chromosomes. HHV-6 replication was detected by reverse transcriptase polymerase chain reaction amplification of a late envelope glycoprotein. The prevalence of CIHHV-6 in this cohort of adult patients from the USA suffering from a wide range of neurological symptoms including long-term fatigue were found significantly greater than the reported 0.

Sequence comparison of the mRNA and the inherited viral genome revealed that the transcript is produced by an exogenous virus. In conclusion, the data presented here document that some individuals with CIHHV-6 are infected persistently with exogenous HHV-6 strains that lead to a wide range of neurological symptoms; the proposed name for this condition is inherited herpesvirus 6 syndrome or IHS.

J Med. Objectives: To describe and discuss the utility and potential pitfalls of ribosomal RNA locus sequencing for direct identification of invasive fungi from fresh and formalin-fixed, paraffin-embedded specimens. Cycle sequencing was performed on PCR products, and the identity of sequences was determined using a public database.

Results: Four clinical cases of invasive fungal infection are presented to illustrate the utility of DNA sequencing for determining etiology when microbiological culture is negative, for shortening the time to identification of slow-growing fungi, for guiding antifungal therapy, and for shedding light on the pathogenesis of disseminated fungal infection.

Conclusions: Fungal ribosomal RNA locus sequencing from fresh or formalin-fixed, paraffin-embedded specimens is a powerful tool for rapid and accurate diagnosis of patients with culture-negative or uncultured invasive mycosis. If fetal infection occurs early in gestation, severe inflammation and necrosis can cause brain lesions, chorioretinitis, and hearing loss. Hearing loss in congenital toxoplasmosis may be preventable with early diagnosis and treatment.

Cytocochleograms were constructed for hair cells, the stria vascularis, and cochlear neuronal cells. The organism was identified in the internal auditory canal, the spiral ligament, stria vascularis, and saccular macula. The cystic form of the parasite was not associated with the inflammatory response seen in the active tachyzoite form. Our findings have implications for the early identification and management of Toxoplasmosis. Whether nodular lesions have specific risk-factors or influence outcomes in lung transplant recipients with invasive aspergillosis, is not fully known. The study population consisted of 64 consecutive lung transplant recipients with proven or probable invasive aspergillosis.

Outcomes assessed were response rate successful versus unsuccessful outcome and all-cause mortality at 12 weeks. Overall, 34 patients had nodular and 30 had non-nodular lesions. Presence of nodular lesions was less likely to be associated with renal failure at baseline adjusted OR 0. Successful outcome and mortality rates in the study patients were Nodular aspergillosis was associated with significantly higher successful outcome adjusted OR 3. Lung transplant recipients with nodular lesions due to invasive aspergillosis had better outcomes than those without such lesions.

Chronic fatigue syndrome CFS is a debilitating disorder characterized by persistent fatigue that is not alleviated by rest. The lack of a clearly identified underlying mechanism has hindered the development of effective treatments. Studies have demonstrated elevated levels of inflammatory factors in patients with CFS, but findings are contradictory across studies and no biomarkers have been consistently supported.

Single time-point approaches potentially overlook important features of CFS, such as fluctuations in fatigue severity. We have observed that individuals with CFS demonstrate significant day-to-day variability in their fatigue severity. Therefore, to complement previous studies, we implemented a novel longitudinal study design to investigate the role of cytokines in CFS pathophysiology. Ten women meeting the Fukuda diagnostic criteria for CFS and ten healthy age- and body mass index BMI -matched women underwent 25 consecutive days of blood draws and self-reporting of symptom severity.

A plex cytokine panel via Luminex was performed for each of the serum samples collected. Our primary hypothesis was that daily fatigue severity would be significantly correlated with the inflammatory adipokine leptin, in the women with CFS and not in the healthy control women. As a post-hoc analysis, a machine learning algorithm using all 51 cytokines was implemented to determine whether immune factors could distinguish high from low fatigue days. Self-reported fatigue severity was significantly correlated with leptin levels in six of the participants with CFS and one healthy control, supporting our primary hypothesis.

The machine learning algorithm distinguished high from low fatigue days in the CFS group with Our results support the role of cytokines in the pathophysiology of CFS. An uncontrolled, unblinded retrospective chart review was performed on 61 CFS patients treated with mg valganciclovir daily 55 of whom took an induction dose of 1, mg daily for the first 3 weeks. Patients self-rated physical and cognitive functioning as a percentage of their functioning prior to illness.

Baseline antibody titers showed no significant association with response. Patients with cancer are at increased risk for developing infectious complications during the course of their disease and treatment. The following sections of the NCCN Clinical Practice Guidelines in Oncology NCCN Guidelines for Prevention and Treatment of Cancer-Related Infections provide an overview of the risk factors for infectious complications, recommendations for infectious risk categorization, and strategies for prevention of infections in high-risk patient populations with cancer.

Individualized risk evaluation for infections and incorporation of preventative measures are essential components of the overall spectrum of cancer care, and may contribute to optimizing treatment outcomes for patients. Human herpesvirus 6 HHV-6 is a neurotropic virus implicated in central nervous system CNS dysfunction, multiple sclerosis, seizures and encephalitis. We previously reported that integrated HHV-6 can be reactivated by trichostatin A in vitro. Therefore, we hypothesized that a broad array of neurological symptoms of CIHHV-6 patients may respond to antiviral drug treatment.

The patients have been treated with antiviral drugs and monitored for viral load, late mRNA, and clinical improvement. However, both patients relapsed on multiple occasions within months of cessation of antiviral therapy. Successful antiviral drug treatment suggests that clinical symptoms of these patients were due to symptomatic reactivation of CIHHV Alternatively, some CIHHV-6 patients may have a reduced resistance to community-acquired HHV-6 strains due to tolerance leading to persistent infections. Although the associations were not confirmed in subsequent studies by other investigators, patients continue to question the consensus of the scientific community in rejecting the validity of the association.

Here, the original investigators who found XMRV and pMLV polytropic murine leukemia virus in blood of subjects with this disorder report that this association is not confirmed in a blinded analysis of samples from rigorously characterized subjects. The increasing frequency with which molecular methods are used for pathogen discovery poses new challenges to public health and support of science.

It is imperative that strategies be developed to rapidly and coherently address discoveries so that they can be carried forward for translation to clinical medicine or abandoned to focus resource investment more productively. Our study provides a paradigm for pathogen dediscovery that may be helpful to others working in this field. Toxoplasma gondii is an unicellular coccidian parasite with worldwide distribution. It is estimated that more than a third of the world's population has been infected with the parasite, but seroprevalence is unevenly distributed across countries and different socioeconomic strata.

Congenital toxoplasmosis can also cause fetal death, stillbirths or long-term disabling sequelae, particularly among untreated infants. The disease appears to be more frequent and severe at certain latitudes. Congenital toxoplasmosis can be prevented and treated during gestation. Less severe disease is commonly reported in countries where prenatal screening and treatment have been systematically implemented.

By contrast, severe disease appears to be observed primarily in infants born to untreated mothers. For definition purposes, it is best to use the term toxoplasma or Toxoplasma gondii infection when referring to asymptomatic patients with primary or chronic infection, and toxoplasmosis when referring to patients with symptoms or signs. Chromosomally integrated human herpesvirus 6 ciHHV-6 is a condition in which the complete HHV-6 genome is integrated into the host germ line genome and is vertically transmitted in a Mendelian manner.

HHV-6 levels in whole blood that exceed 5. Transplant recipients with ciHHV-6 may be at increased risk for bacterial infection and graft rejection. It is not known whether ciHHV-6 individuals are put at clinical risk by the use of drugs that have been associated with HHV-6 reactivation in vivo or in vitro. Nonetheless, we urge careful observation when use of such drugs is indicated in individuals known to have ciHHV Little is known about whether individuals with ciHHV-6 develop immune tolerance for viral proteins. Further research is needed to determine the role of ciHHV-6 in disease.

Congenital toxoplasmosis can cause significant neurologic manifestations and other untoward sequelae. The Palo Alto Medical Foundation Toxoplasma Serology Laboratory database was searched for data on infants 0 to days old, in whom congenital toxoplasmosis had been confirmed and who had been tested for Toxoplasma gondii-specific immunoglobulin G IgG , IgM, and IgA antibodies, between and Their clinical findings were confirmed at the National Collaborative Chicago-based Congenital Toxoplasmosis Study center.

We reviewed available clinical data and laboratory profiles of infants with congenital toxoplasmosis whose mothers had not been treated for the parasite during gestation. In IgM and IgA antibodies were still present in Laboratory tests, including serologic and polymerase chain reaction tests, were critical for diagnosis in the infants.

Our results contrast remarkably with those of European investigators who rarely observe severe clinical signs in infants with congenital toxoplasmosis. Toxoplasmic retinochoroiditis is deemed a local event, which may fail to evoke a detectable systemic immune response. A correct diagnosis of the disease is a necessary basis for estimating its clinical burden. This is not so difficult in a typical clinical picture. In atypical cases, further diagnostic efforts are to be installed.

Although the aqueous humor may be analyzed for specific antibodies or the presence of parasitic DNA, the DNA burden therein is low, and in rare instances a confirmation would necessitate vitreous sampling. A laboratory confirmation of the diagnosis is frustrated by individual differences in the time elapsing between clinical symptoms and activation of specific antibody production, which may result in false negatives. In congenital ocular toxoplasmosis, a delay in the onset of specific local antibody production could reflect immune tolerance. Herein, the authors attempt to provide a simple and practicable algorithm for a clinically tailored diagnostic approach in atypical instances.

Haematological patients with neutropenic fever are frequently evaluated with chest computed tomography CT to rule out invasive fungal infections IFI. We retrospectively analysed data from consecutive patients with neutropenic fever and abnormal chest CT from to to evaluate their chest CT findings and the yield of diagnostic approaches employed.

Fifty-six patients received diagnostic procedures, including 46 bronchoscopies, 25 lung biopsies and seven sinus biopsies, with a diagnostic yield for IFI of In conclusion, chest CT plays an important role in the evaluation of haematological patients with febrile neutropenia and often leads to a change in antimicrobial therapy. Pulmonary nodules are the most common radiological abnormality. Sinus or lung biopsies have a high-diagnostic yield for IFI as compared to bronchoscopy. Previous research has suggested that human herpesvirus-6 HHV-6 may integrate into host cell chromosomes and be vertically transmitted in the germ line, but the evidence--primarily fluorescence in situ hybridization FISH --is indirect.

We sought, first, to definitively test these two hypotheses. Peripheral blood mononuclear cells PBMCs were isolated from families in which several members, including at least one parent and child, had unusually high copy numbers of HHV-6 DNA per milliliter of blood. Partial sequencing of the viral genome identified the same integrated HHV-6A strain within members of families, confirming vertical transmission of the viral genome.

Reactivation of integrated HHV-6A virus from individuals' PBMCs as well as cell lines was successfully accomplished by compounds known to induce latent herpesvirus replication. Finally, no circular episomal forms were detected even by PCR. Taken together, the data suggest that HHV-6 is unique among human herpesviruses: it specifically and efficiently integrates into telomeres of chromosomes during latency rather than forming episomes, and the integrated viral genome is capable of producing virions. During the past 25 years, advances in immunosuppression and the use of selective anti-microbial prophylaxis have progressively reduced the risk of infection after heart transplantation.

This study presents a historical perspective of the changing trends of infectious disease after heart transplantation. Infectious complications in 4 representative eras of immunosuppression and anti-microbial prophylaxis were analyzed: 1 38 in the pre-cyclosporine era , 2 72 in the early cyclosporine era , where maintenance immunosuppression included high-dose cyclosporine and corticosteroid therapy; 3 in the cyclosporine era , where maintenance immunosuppression included cyclosporine, azathioprine, and lower corticosteroid doses; and 4 in the more recent era , where maintenance immunosuppression included cyclosporine and mycophenolate mofetil.

The overall incidence of infections decreased in the 4 cohorts from 3. Toxoplasmosis can cause severe ocular and neurological disease. We sought to determine risk factors for Toxoplasma gondii infection in the United States. We conducted a case-control study of adults recently infected with T.

Case patients were selected from the Palo Alto Medical Foundation Toxoplasma Serology Laboratory from August through May ; control patients were randomly selected from among T. Data were obtained from serological testing and patient questionnaires. We evaluated case patients with recent T. In multivariate analysis, an elevated risk of recent T. Eating raw oysters, clams, or mussels aOR, 2. Subgroup results are also provided for women and for pregnant women. In the United States, exposure to certain raw or undercooked foods and exposure to kittens are risk factors for T.

Knowledge of these risk factors will help to target prevention efforts. Although invasive candidiasis IC causes significant morbidity and mortality in patients who undergo heart, lung, or heart-lung transplantation, a systematic study in a large cohort of thoracic organ transplant recipients has not been reported to date. Clinical and microbiological data were reviewed for patients who underwent thoracic organ transplantation at Stanford University Medical Center between and We identified and analyzed 76 episodes of IC in 68 patients overall incidence 5.

The incidence of IC decreased over time in all thoracic organ transplant recipients, decreasing from 6. The most common site of infection differed between the HTx and LTx cohorts, with bloodstream or disseminated disease in the former and tracheobronchitis in the latter. Despite the advantages of providing an early presumptive diagnosis, fungal classification by histopathology can be difficult and may lead to diagnostic error.

To assess the accuracy of histologic diagnosis of fungal infections vs culture "gold standard" , we performed a year retrospective review at our institution. Errors resulted from morphologic mimics, use of inappropriate terminology, and incomplete knowledge in mycology. Among 8 discrepancies with clinical follow-up available, 2 potential adverse clinical consequences resulted. While histopathologic identification of fungi in tissue sections and cytologic preparations is prone to error, implementation of a standardized reporting format should improve diagnostic accuracy and prevent adverse outcomes.

Human herpesvirus 6 has rarely been identified as a cause of encephalitis in immunocompetent adults. We describe a patient who had severe encephalomyelitis, hypoglycorrhachia, and human herpesvirus 6 identified in his cerebrospinal fluid and serum and who recovered after treatment with foscarnet and ganciclovir.

Human herpesvirus 6 should be considered in immunocompetent patients with encephalitis. Acute infection with Toxoplasma gondii during pregnancy and its potentially tragic outcome for the fetus and newborn continue to occur in the United States, as well as worldwide, despite the fact that it can be prevented. The infection can be acquired through ingestion of infected, undercooked meat or contaminated food or water. Transmission to the fetus occurs almost solely in women who acquire their primary infection during gestation and can result in visual and hearing loss, mental and psychomotor retardation, seizures, hematological abnormalities, hepatosplenomegaly, or death.

Systematic education and serological screening of pregnant women are the most reliable and currently available strategies for the prevention, diagnosis, and early treatment of the infection in the offspring; this is largely because toxoplasmosis in pregnant women most often goes unrecognized. Treatment of the infection in the fetus and infant during the first year of life has been demonstrated to significantly improve the clinical outcome.

The aim of this study was to determine the prevalence of toxoplasma antibodies among pregnant women in Cali, Colombia.


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In , pregnant women were tested for IgG and IgM antibodies and sociodemographic information was collected. Their average age was Seroprevalence increased significantly with age, There was a significant trend toward a higher seroprevalence in the lower socioeconomic strata SES low: Our results suggest a higher prevalence when compared with those of the national In contrast to reports from other regions of the world, Cali has not seen a decrease in T.

Lymphadenopathy LN is the most common clinical manifestation of acute acquired toxoplasma infection in humans. One hundred nine consecutive patients serum samples diagnosed serologically and by lymph node biopsy as having TL were studied. Equivocal patterns were observed up to 36 months after COLN. Nonacute patterns were observed only for serum samples drawn at least 13 months after COLN. In such cases, investigation for alternative causes, including malignancy, should be instigated. Disseminated Fusarium infection can cause significant morbidity and mortality in immunocompromised patients.

We present a case of disseminated fusariosis in a patient with neutropenic fever successfully treated using both liposomal amphotericin B and voriconazole. Combination anti-fungal therapy may be considered for such patients, particularly for those failing single-drug therapy. Acanthamoeba species are known to cause 2 well-described entities: 1 granulomatous amoebic encephalitis GAE , which usually affects immunocompromised hosts, and 2 keratitis, which typically follows trauma associated with contamination of water or contact lenses.

Less common manifestations include pneumonitis and a subacute granulomatous dermatitis. We describe a case of granulomatous dermatitis secondary to Acanthamoeba infection in a lung transplant recipient and a successful outcome following treatment with lipid formulation of amphotericin B and voriconazole. We believe this is the second case report describing disseminated Acanthamoeba infection in a lung transplant recipient.

We also describe successful outcome with a combination of lipid formulation of amphotericin B and voriconazole, drugs that have not been previously reported to treat Acanthamoeba. Pulmonary infection with Nocardia is an uncommon but serious infection found in immunocompromised patients. We describe a rapidly progressive pulmonary nocardiosis in a heart transplant patient. We then review the common clinical features of Nocardia infection in transplant recipients, outlining the challenges in its diagnosis and management.

We also review the differences between Pneumocystis jiroveci prophylaxis regimens with respect to concomitant prophylaxis of Nocardia and other opportunistic infections. All patients had four or more of the following neurocognitive symptoms: impaired cognitive functioning, slowed processing speed, sleep disturbance, short-term memory deficit, fatigue and symptoms consistent with depression. We sought to determine whether elevated antibodies to EBV and HHV-6 indicated chronic viral activation in patients with CNS dysfunction and if their symptoms could be improved by suppressing viral activity with oral valganciclovir.

Patients with high IgG antibody titers against HHV-6 and EBV who were suffering from central nervous system dysfunction and debilitating fatigue for more than one year median 3 years, range years were treated with 6 months of valganciclovir in an open label study. Clinically significant hematological toxicity or serious adverse events were not observed among the 12 patients.

These preliminary clinical and laboratory observations merit additional studies to establish whether this clinical response is mediated by an antiviral effect of the drug, indirectly via immunomodulation or by placebo effect. We assessed predictive factors and characteristics of patients with late-onset invasive aspergillosis in the current era of novel immunosuppressive agents.

Forty transplant recipients with invasive aspergillosis were included in this prospective, observational study initiated in at our institutions. The use of depleting or non-depleting T or B-cell antibodies, either as induction or as antirejection therapy did not correlate with time to onset of invasive aspergillosis.

Thus, nearly one-half of the Aspergillus infections in transplant recipients in the current era are late-occurring. These data have implications relevant for prophylactic strategies and guiding clinical management of transplant recipients presenting with pulmonary infiltrates. In vitro antifungal testing of Aspergillus isolates to combination therapy was correlated with clinical outcome.

However, in transplant recipients with renal failure adjusted HR 0. No correlation was found between in vitro antifungal interactions of the Aspergillus isolates to the combination of voriconazole and caspofungin and clinical outcome. This article discusses the diagnosis and management of toxoplasmosis. Congenital toxoplasmosis continues to be a tragic outcome of a preventable and treatable infection.

Education of patients, physicians and health policy makers on the primary and secondary preventive measures of the disease, and their execution, will undoubtedly result in lower incidence, morbidity, and mortality rates from congenital disease due to Toxoplasma gondii. Using a single serum sample for testing for immunoglobulin G IgG Toxoplasma antibodies, differences in sensitivity of the dye test which measures primarily IgG antibodies and an IgG enzyme immunoassay were found useful for very early diagnosis of acute Toxoplasma gondii infection. An immunocompromised patient with an invasive soft tissue infection due to Scedosporium apiospermum was successfully treated with voriconazole and surgical debridement.

After transition from intravenous to oral therapy, successive adjustments of the oral dose were required to achieve complete resolution. For soft tissue infections due to molds characterized by thin, septate hyphae branching at acute angles, voriconazole should be considered a first-line antifungal agent. The potential usefulness of plasma voriconazole levels for guiding optimal therapy should be investigated. Toxoplasmic lymphadenopathy TL is the most common clinical manifestation of acute acquired toxoplasma infection in normal individuals. The diagnosis is established by serologic methods and lymph node biopsy.

Recently, tests for avidity of toxoplasma immunoglobulin G IgG antibodies have been introduced to help discriminate between recently acquired and distant infection with the parasite. We studied an avidity test to define the usefulness of this method and to determine the evolution of the IgG avidity in TL. Seventy-three consecutive patients diagnosed as having TL were studied. IgG avidity test titers were noted to be time dependent from the clinical onset of lymphadenopathy.

Low IgG avidity test results were observed in patients who had developed lymphadenopathy from View details for DOI Significant progress has been made in managing fever and neutropenia in patients with cancer. Although initial empiric antimicrobial treatment remains the foundation of therapy for such patients, improved diagnostic modalities, models of risk assessment, and an understanding of the various clinical situations in which infections occur have required that treatment approaches and options evolve. The development of broad-spectrum antibiotics with decreased toxicity has improved patient outcomes.

Nevertheless, the increasing prevalence of antibiotic-resistant pathogens has challenged the clinician to use antimicrobial therapy wisely. Infection control should not rely exclusively on antimicrobial prophylaxis but, rather, should continue to incorporate standard infection control measures and demand careful handwashing by all health care professionals who come into contact with immunocompromised patients.

Invasive fungal pathogens have increased and remain a major concern. Diagnostic and therapeutic modalities for fungal infections remain limited, but careful clinical investigation of new approaches will be needed to define the proper use of these probably expensive new therapeutic additions. Toxoplasma gondii is a protozoan parasite that infects up to a third of the world's population. Infection is mainly acquired by ingestion of food or water that is contaminated with oocysts shed by cats or by eating undercooked or raw meat containing tissue cysts.

Primary infection is usually subclinical but in some patients cervical lymphadenopathy or ocular disease can be present. Infection acquired during pregnancy may cause severe damage to the fetus. In immunocompromised patients, reactivation of latent disease can cause life-threatening encephalitis. Diagnosis of toxoplasmosis can be established by direct detection of the parasite or by serological techniques.

The most commonly used therapeutic regimen, and probably the most effective, is the combination of pyrimethamine with sulfadiazine and folinic acid. This Seminar provides an overview and update on management of patients with acute infection, pregnant women who acquire infection during gestation, fetuses or infants who are congenitally infected, those with ocular disease, and immunocompromised individuals. Controversy about the effectiveness of primary and secondary prevention in pregnant women is discussed.

Important topics of current and future research are presented. Among patients undergoing heart transplantation, Aspergillus is the opportunistic pathogen with the highest attributable mortality. The median time of onset from transplantation for invasive pulmonary aspergillosis IPA was 46 days, but the median time to first positive culture result was days among patients with Aspergillus colonization but no invasive disease.

Most patients with IPA presented with fever and cough within the first 90 days of transplantation and with single or multiple pulmonary nodules.

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Post-transplantation lymphoproliferative disease PTLD is an important source of morbidity and mortality in transplant recipients, with a reported incidence of 0. Risk factors are thought to include immunosuppressive agents and viral infection. This study attempts to evaluate the impact of different immunosuppressive regimens, ganciclovir prophylaxis and other potential risk factors in the development of PTLD.

We reviewed the records of heart, heart-lung patients who underwent transplantation at Stanford between and Of these, 57 heart and 8 heart-lung recipients developed PTLD. During this interval, 4 different immunosuppressive regimens were utilized sequentially. In January , ganciclovir prophylaxis for cytomegalovirus serologic-positive patients was introduced. Other potential risk factors evaluated included age, gender, prior cardiac diagnoses, HLA match, rejection frequency and calcium-channel blockade.

No correlation of development of PTLD was found with different immunosuppression regimens consisting of azathioprine, prednisone, cyclosporine, OKT3 induction, tacrolimus and mycophenolate mofetil. Recipient age and rejection frequency, as well as high-dose cyclosporine immunosuppression, were significantly p View details for DOI Because congenital toxoplasmosis is almost solely the result of maternal infection acquired during gestation, it is critical to determine whether infection during pregnancy has occurred.

In the United States, definitive diagnosis of the acute infection and the time of its occurrence have been compromised by a lack of systematic screening and the fact that only a single serum sample is submitted for testing. In studies in Europe, and depending on the method used, the demonstration of high-avidity immunoglobulin G IgG toxoplasma antibodies has been shown to exclude infection having occurred in the first 3 to 5 months of pregnancy. Sera samples from women in the first 16 weeks of pregnancy were chosen because at least one test in the toxoplasma serological profile TSP suggested or was equivocal for a recently acquired infection.

Of 39 women for whom treatment with spiramycin had been suggested to attempt to prevent congenital transmission, 19 These findings highlight the value of the VIDAS IgG avidity kit when used in combination with the TSP to exclude recent infection, especially when only a single serum sample is available. In order to track the evolution of primary protease inhibitor PI resistance mutations in human immunodeficiency virus type 1 HIV-1 isolates, baseline and follow-up protease sequences were obtained from patients undergoing salvage PI therapy who presented initially with isolates containing a single primary PI resistance mutation.

Jack's leadership and vision created, defined, and significantly contributed to the development of laboratory methods for the diagnosis of the infection and diseases caused by T. A total of infectious episodes IEs that occurred in consecutive heart transplantation patients at Stanford Medical Center between 16 December and 30 June were reviewed.

Infectious complications were a major cause of morbidity and mortality, second only to rejection as the cause of early deaths and the most common cause of late deaths. Of the IEs, The largest number of IEs occurred in the lungs [ A significant reduction in the incidence of IEs and a delay in presentation after transplantation were observed; these were most likely related to the introduction of new chemoprophylactic regimens during the study period and prevention of significant disease caused by cytomegalovirus.

The usefulness of testing for IgG avidity in association with Toxoplasma gondii was evaluated in a US reference laboratory. European investigators have reported that high-avidity IgG toxoplasma antibodies exclude acute infection in the preceding 3 months. Of 93 Of 87 Forty women were given spiramycin, to prevent congenital transmission, and 7 These findings highlight the value of testing a single serum sample obtained in the first trimester of pregnancy for IgG avidity.

Results obtained with commercial testing kits for immunoglobulin M Toxoplasma antibodies may be inaccurate or may be inaccurately interpreted, which may influence whether a woman decides to terminate the pregnancy. This study was undertaken to determine whether confirmatory testing at a reference laboratory and communication of the results and an expert interpretation to the patient's physician would affect the rate of induced abortions among pregnant women with positive results of testing for immunoglobulin M Toxoplasma antibodies in outside laboratories.

A frequently applied mass spectrometry based diagnostic for pathogen detection is matrix assisted laser desorption ionization time of flight mass spectrometry MALDI-ToF MS which detects microbe specific proteins. While MALDI-ToF offers rapid results in a laboratory setting, its application as a diagnostic for outbreaks of unknown fungal pathogens is limited since microbial culture and reference spectra are required. Direct analysis of microbes from biological samples have yielded significant improvements in diagnosis time Lockwood et al.

Finally, while the test time is rapid and the analysis cost per sample is cheap, initial equipment acquisition is expensive Tran et al. More recently other mass spectrometry methods have been developed that hold potential as fungal diagnostics. Infrared spectroscopy Quintelas et al. Refinements for direct sample analysis and high sensitivity in discriminating pathogens in complex microbial communities would benefit the diagnosis of fungal pathogen outbreaks.

LFAs are normally designed to detect antigens or host-produced antibodies specific to a pathogen of interest and are often used to generate rapid test results in human clinical settings Marot-Leblond et al. LFAs have also been developed to test for several wildlife diseases such as amphibian chytridiomycosis Dillon et al. Recently, LFA based diagnostics have diversified to include nucleic acid detection. Detection of a pathogen is indicated by a color change as the target DNA or antigen is bound by the LFA antibody or probe. The intensity of color change is proportional to the amount of target present, enabling the development of semi-quantitative tests using smartphone devices which have been used in a range of applications including detection of fungal toxins and antifungal resistance alleles Lee et al.

The low cost of LFAs makes them an ideal front line diagnostic. LFA drawbacks include long development time, false positives and lower sensitivity compared to other methods Kozel and Burnham-Marusich, It is therefore generally recommended that test results should be corroborated using more sensitive lab-based diagnostics.

Microfluidic biosensors are also increasingly being applied for point of care diagnosis of human pathogens, and could be excellent candidates for application to wildlife epidemiology. Microfluidic devices are often chip based, and channel samples through a series of miniaturized components including those for sample preparation, target detection and data processing Jayamohan et al. An ideal microfluidic biosensor diagnostic should be cheap [for example, it is possible to make microfluidic devices from wax and paper Nilghaz et al. This has been demonstrated for several human pathogens, including for Plasmodium falciparum Fraser et al.

New technology has enabled collection of greater quantities of field data. The question then follows — how to manage, interrogate and visualize it all? Wildlife epidemiological fieldwork often takes place in resource poor environments and under time sensitive conditions. It may be necessary to have multiple teams sampling in different places, requiring easily collatable, consistent sample collection and recording. EpiCollect Aanensen et al. Multiple phones can be linked to a project, with geotagging capabilities.

Users, regardless of location, can view, edit, analyze or download data with a smartphone. However so far, aside from its application to B. The question of how to visualize and present large volumes of complex data has also become pressing. Now, MLST databases are being superseded by the next generation of online genotyping databases that upload, map, analyze and display genome sequence data.

In tools such as WGSA 4 , the sequence data can be directly uploaded via the web application along with metadata and interrogated via an interactive user-friendly interface. While the number of pathogens that can be analyzed in this manner is currently limited, it is only a matter of time before online databases for more, including key mycoses, are developed. Even if such databases have not been created, the phylogeographic output of pathogen genomic analyses can be displayed within the context of its metadata in flexible online resources such as Microreact 5.

Microreact is not alone in presenting a novel way of approaching the management and visualization of genomic and epidemiological data. TransPhylo is an R package that computes the probability of an observed transmission tree for a pathogen given the phylogenetic tree even under circumstances of incomplete sampling or an ongoing epidemic Didelot et al. TreeBreaker has been built for the evolutionary inference of phenotype distribution and has already been used to investigate the association between HIV genetic variation and human leukocyte antigens Ansari and Didelot, ; Didelot et al.

It is clear that fungal disease outbreak analysis increasingly occupies an informatic space where the development of open source toolkits that facilitate rapid analysis and dissemination of diverse data types are central to effective disease management. It is more urgent to monitor EFPs in wildlife now than ever before. In recent years mycoses have ravaged swathes of species, sometimes with catastrophic effects on biodiversity Fisher et al. Globalization resulting in species redistribution and increased contact between hosts will inevitably enhance disease transmission, posing environmental and public health challenges on a worldwide scale.

Specialists from a diverse range of fields including veterinary professionals, researchers and public health workers will need to work cooperatively and vigilantly to mitigate future disease outbreaks. Fundamental to any successful action plan will be the implementation of rapid and reliable diagnostics to identify the aetiological agent of disease, and subsequently monitor the spread of an epidemic. Diagnostics should be reproducible, straightforward to use, generate rapid results and be cost-effective. For example, in a scenario where the pathogen is unknown, common methods that require a priori reference data e.

In such instances, rapid and culture-free sequence based methods such as MinIon may be the first port of call in order to construct a reference genome Farrer and Fisher, ; Langner et al. Once sequence-based pathogen identification is complete, it may be easier to isolate the fungus by inferring ideal culture conditions. At this point development of DNA based rapid diagnostics such as LAMP assays would be possible using the assembled whole genome sequence data. Once cultured, reference mass spectra in addition to development of LFAs for the pathogen could be developed. When a novel rapid diagnostic is validated to meet sensitivity and reproducibility requirements it can be rolled out to practitioners in the field.

Effective modeling of disease dynamics and subsequent management strategies will be dependent on integrating multiple data types collected from different geographic regions as well as clinical microbiology laboratories. Once online, data can easily be disseminated for downstream analysis. Outline of tools applicable to different stages of a pathogen outbreak. While diagnostics for fungal pathogens have come a long way, a great deal more could be done to improve preparation for future outbreaks.

Funding more projects that characterize the huge unknown fungal diversity will provide better genomic and mass spectrometry databases that may enhance the way in which EFPs are first classified through identifying pathogen-associated characteristics using comparative approaches Farrer and Fisher, ; Farrer et al. The development of standardized, cost-effective diagnostics combined with greater collaboration and data sharing will yield faster, more reliable information that is relevant to the rapid assessment and response to outbreaks.

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This will in turn enable more effective mitigation strategies to be implemented and in doing so help to stem future outbreaks of EFPs. All authors wrote and researched the manuscript and contributed to editing. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. National Center for Biotechnology Information , U. Journal List Front Genet v. Front Genet. Published online Sep Pria N.

Fisher , 1 and Kieran A. Bates 1, 3. Matthew C. Kieran A. Author information Article notes Copyright and License information Disclaimer. Ghosh, ku. This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Genetics. Received May 31; Accepted Aug The use, distribution or reproduction in other forums is permitted, provided the original author s and the copyright owner s are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

This article has been cited by other articles in PMC. Abstract Emerging fungal pathogens are a growing threat to global health, ecosystems, food security, and the world economy. Keywords: emerging fungal pathogens, mycoses, one health, disease ecology, epidemiology, diagnostics, genomics, next generation sequencing.

Introduction Emerging fungal pathogens EFPs present an increasing threat to public health, food security, and ecosystems. Loop Mediated Isothermal Amplification LAMP Polymerase Chain Reaction based applications are still often viewed as the gold standard for rapid pathogen diagnosis, but require an expensive and cumbersome thermocycler, refrigeration of costly reagents, and trained personnel. Chemical Characterization Analysis of the chemical composition of microbial cells for taxonomic identification is routine in microbiological laboratories.

Data Collection and Collation New technology has enabled collection of greater quantities of field data.

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Conclusion It is more urgent to monitor EFPs in wildlife now than ever before.