California Institute for Medical Research

San Jose, CA, United States

California Institute for Medical Research

San Jose, CA, United States
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Burco J.D.,University of California at Davis | Ziccardi M.H.,University of California at Davis | Clemons K.V.,California Institute for Medical Research | Tell L.A.,University of California at Davis
Avian Diseases | Year: 2012

Avian aspergillosis, most often caused by Aspergillus fumigatus, is a common and devastating disease affecting a range of bird species. Early diagnosis is difficult and often unreliable. The current study evaluated the utility of measuring (1→3)-β-D-glucan (BG) concentrations in avian plasma samples to aid in the diagnosis of aspergillosis. We evaluated a commercially available BG assay (Fungitell®, Beacon Diagnostics) using 178 plasma samples from naturally infected, experimentally infected, and aspergillosis-free birds. Although there was variation in BG concentration, as reflected by high standard deviations, seabirds with confirmed aspergillosis had the highest mean BG concentrations (M = 3098.7 pg/dl, SD = 5022.6, n = 22) followed by companion avian species and raptors with confirmed aspergillosis (M =1033.8 pg/dl, SD = 1531.6, n = 19) and experimentally infected Japanese quail (Coturnix japonica; M = 1066.5 pg/dl, SD = 1348.2, n = 17). Variation in severity of disease, differences among species of birds with and without disease, and also different levels in environmental exposure likely contribute to the differences among avian groups. The overall sensitivity and specificity of the BG test for diagnosis of aspergillosis in birds was 60.0 and 92.7%, respectively, with an overall optimized avian cut-off value of ≥461 pg/dl for positive disease. Our findings suggest that, although BG concentrations are highly variable between and within different avian groups, it could serve as a useful adjunctive diagnostic test for aspergillosis that is applicable to multiple avian species in some settings, particularly as a negative predictor of infection. © 2012 American Association of Avian Pathologists.

Song J.C.,Santa Clara Valley Medical Center | Song J.C.,California Institute for Medical Research | Stevens D.A.,California Institute for Medical Research | Stevens D.A.,Stanford University
Critical Reviews in Microbiology | Year: 2016

Abstract: Over the past decade, echinocandins have emerged as first-line antifungal agents for many Candida infections. The echinocandins have a unique mechanism of action, inhibiting the synthesis of β-1,3-d-glucan polymers, key components of the cell wall in pathogenic fungi. Caspofungin was the first echinocandin antifungal agent to become licensed for use. The objectives of this review are to summarize the existing published data on caspofungin, under the subject headings of chemistry and mechanism of action, spectrum of activity, pharmacodynamics, pharmacokinetics, clinical studies, safety, drug interactions, dosing, and an overview of the drug’s current place in therapy. © 2015 Taylor & Francis.

Sabino R.,University of Minho | Sabino R.,Instituto Nacional Of Saude Dr Ricardo Jorge | Sampaio P.,University of Minho | Rosado L.,Instituto Nacional Of Saude Dr Ricardo Jorge | And 5 more authors.
Journal of Clinical Microbiology | Year: 2010

Among the Candida species causing bloodstream infections, Candida parapsilosis is one of the most frequently isolated. The objective of the present work was the identification of new microsatellite loci able to distinguish among C. parapsilosis isolates. DNA sequences with trinucleotide repeats were selected from the C. parapsilosis genome database. PCR primer sets flanking the microsatellite repeats were designed and tested with 20 independent isolates. On the basis of the amplification efficiency, specificity, and observed polymorphism, four of the sequences were selected for strain typing. Two hundred thirty-three independent C. parapsilosis sensu stricto isolates were genotyped by using these markers. The polymorphic loci exhibited from 20 to 42 alleles and 39 to 92 genotypes. In a multiplex analysis, 192 genotypes were obtained and the combined discriminatory power of the four microsatellites was 0.99. Reproducibility was demonstrated by submission of subcultures of 4 isolates each, in triplicate, interspersed with unique numbers among a group of 30 isolates for blind testing. Comparison of the genotypes obtained by microsatellite analysis and those obtained by randomly amplified polymorphic DNA analysis, restriction fragment length polymorphism analysis, and internal transcribed sequence grouping was performed and showed that the microsatellite method could distinguish individual isolates; none of the other methods could do that. Related species, C. orthopsilosis and C. metapsilosis, were not confused with C. parapsilosis sensu stricto. These new microsatellites are a valuable tool for use for the differentiation of C. parapsilosis sensu stricto strains, vital in epidemiology to answer questions of strain relatedness and determine pathways of transmission. Copyright © 2010, American Society for Microbiology. All Rights Reserved.

Shankar J.,California Institute for Medical Research | Shankar J.,Santa Clara Valley Medical Center | Shankar J.,Stanford University | Restrepo A.,Corporacion para Investigaciones Biologicas | And 6 more authors.
Clinical Microbiology Reviews | Year: 2011

Paracoccidioidomycosis, one of the most important endemic and systemic mycoses in Latin America, presents several clinical pictures. Epidemiological studies indicate a striking rarity of disease (but not infection) in females, but only during the reproductive years. This suggested a hormonal interaction between female hormones and the etiologic dimorphic fungus Paracoccidioides brasiliensis. Many fungi have been shown to use hormonal (pheromonal) fungal molecules for intercellular communication, and there are increasing numbers of examples of interactions between mammalian hormones and fungi, including the specific binding of mammalian hormones by fungal proteins, and suggestions of mammalian hormonal modulation of fungal behavior. This suggests an evolutionary conservation of hormonal receptor systems. We recount studies showing the specific hormonal binding of mammalian estrogen to proteins in P. brasiliensis and an action of estrogen to specifically block the transition from the saprophytic form to the invasive form of the fungus in vitro. This block has been demonstrated to occur in vivo in animal studies. These unique observations are consistent with an estrogen-fungus receptor-mediated effect on pathogenesis. The fungal genes responsive to estrogen action are under study. © 2011, American Society for Microbiology. All Rights Reserved.

Stevens D.A.,Santa Clara Valley Medical Center | Stevens D.A.,California Institute for Medical Research | Stevens D.A.,Stanford University
Clinics in Dermatology | Year: 2012

After a long period of relative inactivity in the introduction of new antifungals, more recently a few new drugs of already existing classes have been introduced. These represent small or large advantages and differences compared with existing available alternative therapy for deep and systemic mycoses. The 3 newest drugs include posaconazole, micafungin, and anidulafungin, whose pharmacology, toxicology, and indications are presented. © 2012 Elsevier Inc.

Clemons K.V.,California Institute for Medical Research | Clemons K.V.,Santa Clara Valley Medical Center | Clemons K.V.,Stanford University | Schwartz J.A.,Charles River Associates | And 3 more authors.
Antimicrobial Agents and Chemotherapy | Year: 2012

We have shown previously that high-dose lipid amphotericin preparations are not more efficacious than lower doses in aspergillosis. We studied toxicity, drug concentrations and localization, and quantitative infection concurrently, using a 4-day model of central nervous system (CNS) aspergillosis to assess early events. Mice given Aspergillus fumigatus conidia intracerebrally, under a cyclophosphamide immunosuppressive regimen, were treated for 3 days (AmBisome at 3 or 10 mg/kg of body weight, Abelcet at 10 mg/kg, amphotericin B deoxycholate at 1 mg/kg, caspofungin at 5 mg/kg, or voriconazole at 40 mg/kg). Sampling 24 h after the last treatment showed that AmBisome at 3 but not at 10 mg/kg, as well as Abelcet, caspofungin, and voriconazole, reduced brain CFU. All regimens reduced renal infection. Minor renal tubular changes occurred with AmBisome or Abelcet therapy, whereas heart, lung, and brain showed no drug toxicity. Amphotericin B tissue and serum concentrations did not correlate with efficacy. Endothelial cell activation (ICAM-1 and P-selectin in cerebral capillaries) occurred during infection. Amphotericin B derived from AmBisome and Abelcet localized in activated endothelium and from Abelcet in intravascular monocytes. In 10-day studies dosing uninfected mice, minor renal tubular changes occurred after AmBisome or Abelcet at 1, 5, or 10 mg/kg with or without cyclophosphamide treatment; nephrosis occurred only with Abelcet in cyclophosphamide-treated mice. Hepatotoxicity occurred with AmBisome and Abelcet but was reduced in cyclophosphamide-treated mice. Marked CFU reduction by AmBisome at 3 mg/kg occurred in association with relatively more intense inflammation. Abelcet renal localization appears to be a precursor to late nephrotoxicity. Hepatotoxicity may contribute to high-dose Abelcet and AmBisome failures. Our novel observation of endothelial amphotericin localization during infection may contribute to amphotericin mechanism of efficacy. Copyright © 2012, American Society for Microbiology. All Rights Reserved.

Kim J.,Stanford University | Tang J.Y.,Stanford University | Tang J.Y.,Childrens Hospital Oakland Research Institute | Gong R.,Howard Hughes Medical Institute | And 15 more authors.
Cancer Cell | Year: 2010

In a screen of drugs previously tested in humans we identified itraconazole, a systemic antifungal, as a potent antagonist of the Hedgehog (Hh) signaling pathway that acts by a mechanism distinct from its inhibitory effect on fungal sterol biosynthesis. Systemically administered itraconazole, like other Hh pathway antagonists, can suppress Hh pathway activity and the growth of medulloblastoma in a mouse allograft model and does so at serum levels comparable to those in patients undergoing antifungal therapy. Mechanistically, itraconazole appears to act on the essential Hh pathway component Smoothened (SMO) by a mechanism distinct from that of cyclopamine and other known SMO antagonists, and prevents the ciliary accumulation of SMO normally caused by Hh stimulation. © 2010 Elsevier Inc. All rights reserved.

News Article | November 12, 2015

Scientists know a lot about bacteriophages, viruses that infect bacteria. Medical practitioners likewise understand the clinical dangers of biofilms: slimy, antibiotic-defying aggregates of bacteria and organic substances that can stick to the walls and inner linings of infected organs and to chronic wounds, making infections excruciatingly hard to eradicate. But any link between bacteriophages and biofilms was unsuspected. Now, in a series of experiments prompted by a chance discovery, Stanford University School of Medicine investigators and their colleagues at three other research institutes have shown that a bacteriophage, or phage for short, is critical to the formation of biofilms by Pseudomonas, a bacterial pathogen behind numerous hospital-acquired infections, pneumonia cases and cystic fibrosis fatalities. The experiments are described in a study published Nov. 11 in Cell Host & Microbe. The study, the first to show that a phage can drive the formation of bacterial biofilms, is also the first to implicate any type of phage in causing chronic infections. The study also explains why biofilms can resist certain antibiotics, a discovery that could yield entirely novel therapeutic interventions. The researchers studied members of a family of long, filamentous phages known as Inoviruses. Other related phage species of the Inovirus family probably contribute to biofilm formation by diverse bacteria, said Paul Bollyky, M.D., Ph.D., assistant professor of infectious diseases at Stanford. Bollyky shares senior authorship of the study with William Parks, Ph.D., a professor of medicine at Cedars-Sinai Medical Center in Los Angeles. Biofilms factor into 75 to 80 percent of hospital-acquired infections, such as those of the urinary tract, heart valves and knee-replacement prostheses, Bollyky said. “A familiar example of a biofilm is the plaque that forms on our teeth,” he said. “You can brush twice a day, but once that plaque’s in place you’re never going to get rid of it.” Like all viruses, a phage can reproduce itself only by climbing into a cell — in this case, a bacterial cell — and commandeering its replicative machinery. Usually that’s lethal to the invaded cell, because the viruses’ offspring break out of the cell by puncturing its outer membrane, destroying the cell. Leaving host cells alive But Inoviruses don’t do that. Instead, these long, thin viruses are extruded from the bacterial cell without causing damage. Indeed, as the study shows, in the presence of organic substances called polymers, they shelter the bacteria they’ve infected by forming goopy lattices — biofilms — able to repel or sequester electrically-charged small molecules, including many drugs. Members of the Inovirus family of phages infect a broad class of bacteria, encompassing Escherichia (for example, E. coli, which can aggregate into treacherous biofilms) as well as Pseudomonas. One Pseudomonas species alone, P. aeruginosa, accounts for about 10 percent of all hospital-acquired infections, many chronic pneumonia cases, a large fraction of wound infections associated with diabetes and much of the air-passage obstruction that afflicts cystic fibrosis patients. Serendipity played a major part in the revelation of a phage’s role in bacterial biofilm generation. Patrick Secor, Ph.D., a senior fellow in microbiology at the University of Washington and the lead author of the study, was growing P. aeruginosa in culture and wondered if a substance called hyaluronan might be a good energy source for the bacteria. To test this, Secor mixed hyaluronan into the culture medium. Before his very eyes, a biofilm sprang up and spread rapidly through the culture. Hyaluronan is a polymer — a large organic molecule composed of many repeated subunits — and one of many made by living creatures. Other examples include DNA and mucin, the main constituent of mucus. A prominent feature of cystic fibrosis is the presence of high levels of extremely viscous mucus in the sputum. Cystic fibrosis, a genetic disease affecting one in 2,500 people, is deadly chiefly because of biofilms formed by P. aeruginosa, said Bollyky. “These biofilms fill up all the air spaces, and antibiotics can’t seem to penetrate them,” he said. “So, patients eventually succumb to infectious pneumonia.” By adulthood, virtually all cystic fibrosis patients are colonized by P. aeruginosa, Bollyky said. Resulting biofilms eventually render their sputum extremely viscous, sticky and tough to get rid of short of a lung transplant, he said. Teaming up Bollyky, a polymer-chemistry expert, is a good friend of Secor’s, and they began working together. With their associates, they demonstrated that several polymers, including bacterial DNA and the mucin of cystic fibrosis patients, could trigger biofilm formation in P. aeruginosa — but only if the Inovirus was present. “The long, filamentous phages made by the bacteria interact with these polymers to form orderly structures that help biofilms stick to surfaces and resist removal,” Bollyky said. “I always assumed that biofilms were chaotic networks of polymers and bacteria that look like the hairball plug you pull from the bottom of your shower drain. We were surprised to see that actually, in the presence of these phages, biofilm architecture is more like a crystal than a hairball. That higher-order organization makes these biofilms much more tenacious and formidable.” Examining sputum from CF patients, some infected with P. aeruginosa and others not, the investigators identified phage particles in the infected patients’ sputum. Adding phage particles to uninfected sputum samples induced the rapid generation and spread of highly organized biofilms in those samples. Further experiments may also explain why certain antibiotics work better than others against chronic infections. “The same physical properties that allow phage to organize biofilms also make them very efficient at sticking to antibiotics and trapping them within the biofilm. They never get close to the bacteria,” Bollyky said. “These phages may be one reason why chronic infections with P. aeruginosa require long treatment courses of high-dose antibiotics.” Phages are particularly good at binding some antibiotics, such as tobramycin, penicillin and azithromycin, while others, such as ciprofloxacin, are able to pass right through, the researchers found. The researchers documented similar biofilm dynamics using other bacterial species, including E. coli. All in all, bacteria carrying similar phages are responsible for about half of all hospital-acquired infections, Bollyky said. “If these findings can be validated, it could open the door to entirely new therapeutic targets for combatting hospital-acquired infections, complications of cystic fibrosis and much more,” Bollyky said. His group is exploring approaches to target phages therapeutically, such as chelating agents that might disrupt biofilms’ integrity and antiviral compounds that prevent Inovirus family members from reproducing. Researchers from the Benaroya Research Institute and the University of Washington, both in Seattle, and the California Institute for Medical Research, in San Jose, also contributed to the study. The study was funded by the National Institutes of Health and the Cystic Fibrosis Foundation. Stanford’s Department of Medicine also supported the work.

Brummer E.,California Institute for Medical Research | Brummer E.,Stanford University | Stevens D.A.,California Institute for Medical Research | Stevens D.A.,Stanford University
Medical Mycology | Year: 2010

Collectins, collagenous carbohydrate-binding proteins (C-type lectins), are recognized as important factors in non-specific innate immune responses to pathogens. By binding surface carbohydrate structures of pathogens, collectins modify the interaction between pathogens and the immune system. We review the structure of the lung surfactant proteins (SP) SP-A and SP-D, and the serum collectins, mannose binding lectins; the binding of these collectins to pathogen associated molecular patterns or ligands on pathogenic fungi; and the effect of collectin binding to opportunistic and primary fungal pathogens on the interaction with host defense cells, which can result in enhancement or inhibition of resistance. The result of collectin binding to opportunistic fungal pathogens (Aspergillus fumigatus, Candida albicans, Cryptococcus neoformans, Pneumocystis) or primary fungal pathogens (Blastomyces dermatitidis, Coccidioides, Histoplasma capsulatum, Paracoccidioides brasiliensis) on interaction with host defense cells relative to complement fixation, phagocytosis, and stimulation of cytokine/chemokine production is reviewed. Increased understanding of these relationships in future will help understand fungal pathogenesis and host defenses against mycoses. © 2010 ISHAM.

Hotson J.R.,Stanford University | Hotson J.R.,California Institute for Medical Research
PLoS ONE | Year: 2014

The peroneal nerve anatomy of the rabbit distal hindlimb is similar to humans, but reports of distal peroneal nerve conduction studies were not identified with a literature search. Distal sensorimotor recordings may be useful for studying rabbit models of length-dependent peripheral neuropathy. Surface electrodes were adhered to the dorsal rabbit foot overlying the extensor digitorum brevis muscle and the superficial peroneal nerve. The deep and superficial peroneal nerves were stimulated above the ankle and the common peroneal nerve was stimulated at the knee. The nerve conduction studies were repeated twice with a one-week intertest interval to determine measurement variability. Intravenous vincristine was used to produce a peripheral neuropathy. Repeat recordings measured the response to vincristine. A compound muscle action potential and a sensory nerve action potential were evoked in all rabbits. The compound muscle action potential mean amplitude was 0.29 mV (SD ± 0.12) and the fibula head to ankle mean motor conduction velocity was 46.5 m/s (SD ± 2.9). The sensory nerve action potential mean amplitude was 22.8 μV (SD ± 2.8) and the distal sensory conduction velocity was 38.8 m/s (SD ± 2.2). Sensorimotor latencies and velocities were least variable between two test sessions (coefficient of variation = 2.6-5.9%), sensory potential amplitudes were intermediate (coefficient of variation = 11.1%) and compound potential amplitudes were the most variable (coefficient of variation = 19.3%). Vincristine abolished compound muscle action potentials and reduced sensory nerve action potential amplitudes by 42-57% while having little effect on velocity. Rabbit distal hindlimb nerve conduction studies are feasible with surface recordings and stimulation. The evoked distal sensory potentials have amplitudes, configurations and recording techniques that are similar to humans and may be valuable for measuring large sensory fiber function in chronic models of peripheral neuropathies. © 2014 Hotson.

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