Phi Based Research Articles

Candidate Resistant Genes of Sand Pear (Pyrus pyrifolia Nakai) to Alternaria alternata Revealed by Transcriptome Sequencing.

Pear black spot (PBS) disease, which is caused by Alternaria alternata (Aa), is one of the most serious diseases affecting sand pear (Pyrus pyrifolia Nakai) cultivation worldwide. To investigate the defense mechanisms of sand pear in response to Aa, the transcriptome of a sand pear germplasm with differential resistance to Aa was analyzed using Illumina paired-end sequencing. Four libraries derived from PBS-resistant and PBS-susceptible sand pear leaves were characterized through inoculation or mock-inoculation. In total, 20.5 Gbp of sequence data and 101,632,565 reads were generated, representing 44717 genes. Approximately 66% of the genes or sequenced reads could be aligned to the pear reference genome. A large number (5213) of differentially expressed genes related to PBS resistance were obtained; 34 microsatellites were detected in these genes, and 28 genes were found to be closely related to PBS resistance. Using a transcriptome analysis in response to PBS inoculation and comparison analysis to the PHI database, 4 genes (Pbr039001, Pbr001627, Pbr025080 and Pbr023112) were considered to be promising candidates for sand pear resistance to PBS. This study provides insight into changes in the transcriptome of sand pear in response to PBS infection, and the findings have improved our understanding of the resistance mechanism of sand pear to PBS and will facilitate future gene discovery and functional genome studies of sand pear.

Using the pathogen-host interactions database (PHI-base) to investigate plant pathogen genomes and genes implicated in virulence.

New pathogen-host interaction mechanisms can be revealed by integrating mutant phenotype data with genetic information. PHI-base is a multi-species manually curated database combining peer-reviewed published phenotype data from plant and animal pathogens and gene/protein information in a single database.

The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum.

BackgroundAccurate genome assembly and gene model annotation are critical for comparative species and gene functional analyses. Here we present the completed genome sequence and annotation of the reference strain PH-1 of Fusarium graminearum, the causal agent of head scab disease of small grain cereals which threatens global food security. Completion was achieved by combining (a) the BROAD Sanger sequenced draft, with (b) the gene predictions from Munich Information Services for Protein Sequences (MIPS) v3.2, with (c) de novo whole-genome shotgun re-sequencing, (d) re-annotation of the gene models using RNA-seq evidence and Fgenesh, Snap, GeneMark and Augustus prediction algorithms, followed by (e) manual curation.ResultsWe have comprehensively completed the genomic 36,563,796 bp sequence by replacing unknown bases, placing supercontigs within their correct loci, correcting assembly errors, and inserting new sequences which include for the first time complete AT rich sequences such as centromere sequences, subtelomeric regions and the telomeres. Each of the four F. graminearium chromosomes was found to be submetacentric with respect to centromere positioning. The position of a potential neocentromere was also defined. A preferentially higher frequency of genetic recombination was observed at the end of the longer arm of each chromosome. Within the genome 1529 gene models have been modified and 412 new gene models predicted, with a total gene call of 14,164. The re-annotation impacts upon 69 entries held within the Pathogen-Host Interactions database (PHI-base) which stores information on genes for which mutant phenotypes in pathogen-host interactions have been experimentally tested, of which 59 are putative transcription factors, 8 kinases, 1 ATP citrate lyase (ACL1), and 1 syntaxin-like SNARE gene (GzSYN1). Although the completed F. graminearum contains very few transposon sequences, a previously unrecognised and potentially active gypsy-type long-terminal-repeat (LTR) retrotransposon was identified. In addition, each of the sub-telomeres and centromeres contained either a LTR or MarCry-1_FO element. The full content of the proposed ancient chromosome fusion sites has also been revealed and investigated. Regions with high recombination previously noted to be rich in secretome encoding genes were also found to be rich in tRNA sequences. This study has identified 741 F. graminearum species specific genes and provides the first complete genome assembly for a Sordariomycetes species.ConclusionsThis fully completed F. graminearum PH-1 genome and manually curated annotation, available at Ensembl Fungi, provides the optimum resource to perform interspecies comparative analyses and gene function studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1756-1) contains supplementary material, which is available to authorized users.

Factors associated with age at pyeloplasty in children with ureteropelvic junction obstruction.

Our objectives were to: (1) delineate factors associated with surgery at <1 year and (2) determine if early intervention was associated with increased risk of readmission. We conducted a retrospective review of children age 0-18 years with a diagnosis of UPJ obstruction who underwent pyeloplasty from 1/1/1999 to 9/1/2009 using the PHIS database. Data collected included patient factors (race, gender, insurance type, APR-DRG severity of illness) and hospital factors (annual case volume, census region, academic status). Outcomes assessed were: age at surgery and hospital readmission within 1 year of surgery. Data were analyzed using logistic regression and Cox PH for multivariate analyses. 4499 children met study criteria. Minority race (OR 1.55), male gender (OR 1.49), public insurance (OR 1.37), high severity of illness (OR 3.60), Southern region (OR 1.44), and low hospital volume (OR 1.37) were significant predictors of early surgery (p < 0.05). Only early surgery (HR 2.42; 95% CI 1.67-3.49 2.42) was associated with increased risk of readmission. In children with UPJ obstruction, age at surgery is associated with patient demographic and hospital factors. Early surgery is associated with higher rates of readmission, suggesting that variations in age at surgery may be associated with significant differences in outcomes.

A review on computational systems biology of pathogen-host interactions.

Pathogens manipulate the cellular mechanisms of host organisms via pathogen–host interactions (PHIs) in order to take advantage of the capabilities of host cells, leading to infections. The crucial role of these interspecies molecular interactions in initiating and sustaining infections necessitates a thorough understanding of the corresponding mechanisms. Unlike the traditional approach of considering the host or pathogen separately, a systems-level approach, considering the PHI system as a whole is indispensable to elucidate the mechanisms of infection. Following the technological advances in the post-genomic era, PHI data have been produced in large-scale within the last decade. Systems biology-based methods for the inference and analysis of PHI regulatory, metabolic, and protein–protein networks to shed light on infection mechanisms are gaining increasing demand thanks to the availability of omics data. The knowledge derived from the PHIs may largely contribute to the identification of new and more efficient therapeutics to prevent or cure infections. There are recent efforts for the detailed documentation of these experimentally verified PHI data through Web-based databases. Despite these advances in data archiving, there are still large amounts of PHI data in the biomedical literature yet to be discovered, and novel text mining methods are in development to unearth such hidden data. Here, we review a collection of recent studies on computational systems biology of PHIs with a special focus on the methods for the inference and analysis of PHI networks, covering also the Web-based databases and text-mining efforts to unravel the data hidden in the literature.

Identification and characterization of a serious multidrug resistant Stenotrophomonas maltophilia strain in China.

An S. maltophilia strain named WJ66 was isolated from a patient; WJ66 showed resistance to more antibiotics than the other S. maltophilia strains. This bacteraemia is resistant to sulphonamides, or fluoroquinolones, while the representative strain of S. maltophilia, K279a, is sensitive to both. To explore drug resistance determinants of this strain, the draft genome sequence of WJ66 was determined and compared to other S. maltophilia sequences. Genome sequencing and genome-wide evolutionary analysis revealed that WJ66 was highly homologous with the strain K279a, but strain WJ66 contained additional antibiotic resistance genes. Further analysis confirmed that strain WJ66 contained an amino acid substitution (Q83L) in fluoroquinolone target GyrA and carried a class 1 integron, with an aadA2 gene in the resistance gene cassette. Homology analysis from the pathogen-host interaction database showed that strain WJ66 lacks raxST and raxA, which is consistent with K279a. Comparative genomic analyses revealed that subtle nucleotide differences contribute to various significant phenotypes in close genetic relationship strains.

The Pathogen-Host Interactions database (PHI-base): additions and future developments.

Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens. Mutant phenotypes are associated with gene information. The included pathogens infect a wide range of hosts including humans, animals, plants, insects, fish and other fungi. The current version, PHI-base 3.6, available at http://www.phi-base.org, stores information on 2875 genes, 4102 interactions, 110 host species, 160 pathogenic species (103 plant, 3 fungal and 54 animal infecting species) and 181 diseases drawn from 1243 references. Phenotypic and gene function information has been obtained by manual curation of the peer-reviewed literature. A controlled vocabulary consisting of nine high-level phenotype terms permits comparisons and data analysis across the taxonomic space. PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes. Virulence genes and hotspots can be visualized directly in genome browsers. Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s).

Flecainide use in children with cardiomyopathy or structural heart disease.

Flecainide is frequently used for treatment of cardiac arrhythmias in children. Due to concerns regarding increased mortality, there has been hesitancy to use flecainide in children with congenital heart disease (CHD) or cardiomyopathy (CM). The objective of this study was to describe trends in use of flecainide in children with CHD or CM and assess its association with cardiac arrest or death. Data from 42 children's hospitals contained in the PHIS database (2004-2011) were analyzed. All patients with CHD or CM receiving anti-arrhythmic therapy for supraventricular arrhythmias were reviewed. Trends in flecainide use were analyzed, and the incidence of cardiac arrest or death was compared to patients receiving other anti-arrhythmics. There were 3,544 pts with CHD or CM who received anti-arrhythmic therapy (median age 73 days). Flecainide was administered in 229 pts (6.5%). There was a trend toward increased use of flecainide in this population, increasing from 4.6% in 2004 to 8.7% in 2011 (p = 0.07). The incidence of cardiac arrest in patients with CHD or CM receiving flecainide was 3.0% with an overall mortality of 4.3%. The mortality was 2.9% in pts with CM and nobody with single ventricle physiology died. Based on multivariable analysis, when compared to pts with CHD or CM receiving other anti-arrhythmics, there was no difference in the incidence of cardiac arrest (p = 0.31) or death (p = 0.28). Flecainide use in children with CHD or CM has increased in recent years. The incidence of cardiac arrest or death with flecainide administration in this cohort appears comparable to other anti-arrhythmic agents.

Genome sequence and virulence variation-related transcriptome profiles of Curvularia lunata, an important maize pathogenic fungus.

BackgroundCurvularia lunata is an important maize foliar fungal pathogen that distributes widely in maize growing area in China. Genome sequencing of the pathogen will provide important information for globally understanding its virulence mechanism.ResultsWe report the genome sequences of a highly virulent C. lunata strain. Phylogenomic analysis indicates that C. lunata was evolved from Bipolaris maydis (Cochliobolus heterostrophus). The highly virulent strain has a high potential to evolve into other pathogenic stains based on analyses on transposases and repeat-induced point mutations. C. lunata has a smaller proportion of secreted proteins as well as B. maydis than entomopathogenic fungi. C. lunata and B. maydis have a similar proportion of protein-encoding genes highly homologous to experimentally proven pathogenic genes from pathogen-host interaction database. However, relative to B. maydis, C. lunata possesses not only many expanded protein families including MFS transporters, G-protein coupled receptors, protein kinases and proteases for transport, signal transduction or degradation, but also many contracted families including cytochrome P450, lipases, glycoside hydrolases and polyketide synthases for detoxification, hydrolysis or secondary metabolites biosynthesis, which are expected to be crucial for the fungal survival in varied stress environments. Comparative transcriptome analysis between a lowly virulent C. lunata strain and its virulence-increased variant induced by resistant host selection reveals that the virulence increase of the pathogen is related to pathways of toxin and melanin biosynthesis in stress environments, and that the two pathways probably have some overlaps.ConclusionsThe data will facilitate a full revelation of pathogenic mechanism and a better understanding of virulence differentiation of C. lunata.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-627) contains supplementary material, which is available to authorized users.

De novo sequencing and transcriptome analysis of Ustilaginoidea virens by using Illumina paired-end sequencing and development of simple sequence repeat markers.

Ustilaginoidea virens is the causal agent of rice false smut, which is a rice disease of increasing importance worldwide that has caused with the quantitative and qualitative rice losses. However, research on the pathogenic mechanism of U. virens is limited. In this study, we reported a de novo assembling, annotation, and characterization of the transcriptome and developed simple sequence repeat (SSR) markers of U. virens. U. virens transcripts of the mycelia and conidia mixture were sequenced using Illumina RNA-seq technology. A total of 52,554,142 clean reads were assembled into 36,496 transcripts representing 18,534 unigenes. Assembled unigenes were annotated through sequence comparison with known protein databases, and 48.48% of the unigenes were without hits in any of these databases. Clusters of orthologous groups for eukaryotic complete genome analysis identified the largest set of genes associated with posttranslational modification, protein turnover and chaperones. Kyoto Encyclopedia of Genes and Genomes pathway analyses identified the number of genes associated with mitogen-activated protein kinase and calcium-calcineurin pathways. The study also identified several putative pathogenicity determinants and candidate effectors in U. virens by using the pathogen-host interaction database. In addition, bioinformatics analysis revealed the presence of 12,298 SSR markers. This study provides a better understanding of the biology of U. virens and is an excellent resource for candidate genes required for pathogenesis discovery.

Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics

Ustilaginoidea virens (Cooke) Takah is an ascomycetous fungus that causes rice false smut, a devastating emerging disease worldwide. Here we report a 39.4 Mb draft genome sequence of U. virens that encodes 8,426 predicted genes. The genome has ~25% repetitive sequences that have been affected by repeat-induced point mutations. Evolutionarily, U. virens is close to the entomopathogenic Metarhizium spp., suggesting potential host jumping across kingdoms. U. virens possesses reduced gene inventories for polysaccharide degradation, nutrient uptake and secondary metabolism, which may result from adaptations to the specific floret infection and biotrophic lifestyles. Consistent with their potential roles in pathogenicity, genes for secreted proteins and secondary metabolism and the pathogen-host interaction database genes are highly enriched in the transcriptome during early infection. We further show that 18 candidate effectors can suppress plant hypersensitive responses. Together, our analyses offer new insights into molecular mechanisms of evolution, biotrophy and pathogenesis of U. virens.

Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia

Pochonia chlamydosporia is a worldwide-distributed soil fungus with a great capacity to infect and destroy the eggs and kill females of plant-parasitic nematodes. Additionally, it has the ability to colonize endophytically roots of economically-important crop plants, thereby promoting their growth and eliciting plant defenses. This multitrophic behavior makes P. chlamydosporia a potentially useful tool for sustainable agriculture approaches. We sequenced and assembled ∼41Mb of P. chlamydosporia genomic DNA and predicted 12,122 gene models, of which many were homologous to genes of fungal pathogens of invertebrates and fungal plant pathogens. Predicted genes (65%) were functionally annotated according to Gene Ontology, and 16% of them found to share homology with genes in the Pathogen Host Interactions (PHI) database. The genome of this fungus is highly enriched in genes encoding hydrolytic enzymes, such as proteases, glycoside hydrolases and carbohydrate esterases. We used RNA-Seq technology in order to identify the genes expressed during endophytic behavior of P. chlamydosporia when colonizing barley roots. Functional annotation of these genes showed that hydrolytic enzymes and transporters are expressed during endophytism. This structural and functional analysis of the P. chlamydosporia genome provides a starting point for understanding the molecular mechanisms involved in the multitrophic lifestyle of this fungus. The genomic information provided here should also prove useful for enhancing the capabilities of this fungus as a biocontrol agent of plant-parasitic nematodes and as a plant growth-promoting organism.

The Genome Sequence of the Fungal Pathogen Fusarium virguliforme That Causes Sudden Death Syndrome in Soybean

Fusarium virguliforme causes sudden death syndrome (SDS) of soybean, a disease of serious concern throughout most of the soybean producing regions of the world. Despite the global importance, little is known about the pathogenesis mechanisms of F. virguliforme. Thus, we applied Next-Generation DNA Sequencing to reveal the draft F. virguliforme genome sequence and identified putative pathogenicity genes to facilitate discovering the mechanisms used by the pathogen to cause this disease.Methodology/Principal FindingsWe have generated the draft genome sequence of F. virguliforme by conducting whole-genome shotgun sequencing on a 454 GS-FLX Titanium sequencer. Initially, single-end reads of a 400-bp shotgun library were assembled using the PCAP program. Paired end sequences from 3 and 20 Kb DNA fragments and approximately 100 Kb inserts of 1,400 BAC clones were used to generate the assembled genome. The assembled genome sequence was 51 Mb. The N50 scaffold number was 11 with an N50 Scaffold length of 1,263 Kb. The AUGUSTUS gene prediction program predicted 14,845 putative genes, which were annotated with Pfam and GO databases. Gene distributions were uniform in all but one of the major scaffolds. Phylogenic analyses revealed that F. virguliforme was closely related to the pea pathogen, Nectria haematococca. Of the 14,845 F. virguliforme genes, 11,043 were conserved among five Fusarium species: F. virguliforme, F. graminearum, F. verticillioides, F. oxysporum and N. haematococca; and 1,332 F. virguliforme-specific genes, which may include pathogenicity genes. Additionally, searches for candidate F. virguliforme pathogenicity genes using gene sequences of the pathogen-host interaction database identified 358 genes.ConclusionsThe F. virguliforme genome sequence and putative pathogenicity genes presented here will facilitate identification of pathogenicity mechanisms involved in SDS development. Together, these resources will expedite our efforts towards discovering pathogenicity mechanisms in F. virguliforme. This will ultimately lead to improvement of SDS resistance in soybean.

PHISTO: pathogen–host interaction search tool

Knowledge of pathogen-host protein interactions is required to better understand infection mechanisms. The pathogen-host interaction search tool (PHISTO) is a web-accessible platform that provides relevant information about pathogen-host interactions (PHIs). It enables access to the most up-to-date PHI data for all pathogen types for which experimentally verified protein interactions with human are available. The platform also offers integrated tools for visualization of PHI networks, graph-theoretical analysis of targeted human proteins, BLAST search and text mining for detecting missing experimental methods. PHISTO will facilitate PHI studies that provide potential therapeutic targets for infectious diseases. http://www.phisto.org. saliha.durmus@boun.edu.tr Supplementary data are available at Bioinformatics online.

Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era.

Infectious diseases comprise some of the leading causes of death and disability worldwide. Interactions between pathogen and host proteins underlie the process of infection. Improved understanding of pathogen‐host molecular interactions will increase our knowledge of the mechanisms involved in infection, and allow novel therapeutic solutions to be devised. Complete genome sequences for a number of pathogenic microorganisms, as well as the human host, has led to the revelation of their protein‐protein interaction (PPI) networks. In this post‐genomic era, pathogen‐host interactions (PHIs) operating during infection can also be mapped. Detailed systematic analyses of PPI and PHI data together are required for a complete understanding of pathogenesis of infections. Here we review the striking results recently obtained during the construction and investigation of these networks. Emphasis is placed on studies producing large‐scale interaction data by high‐throughput experimental techniques.

Large scale expressed sequence tag (EST) analysis of Metarhizium acridum infecting Locusta migratoria reveals multiple strategies for fungal adaptation to the host cuticle

To infect its insect host, the entomopathogenic fungus Metarhizium acridum has to breach the physical barrier of the host cuticle to gain entry into insect tissue. To identify virulence-associated genes to improve the biocontrol efficacy of M. acridum, it is necessary to understand the genes expressed by M. acridum during its infection of the insect host cuticle. In this study, we performed a large scale gene expression analysis of M. acridum during locust cuticle infection. We report the identification of 4,739 unique expressed sequence tags (ESTs), of which 80 % have not been previously identified. Analysis of the ESTs provided evidence that M. acridum may employ several different adaptation strategies to infect locust cuticle, such as metabolism reprogramming, protein secretion, endocytosis, cell-cycle-regulated morphogenesis and effector-dependent suppression of host immune responses. By searching against the pathogen-host interaction database, several genes associated with different adaptation processes were found to potentially encode important virulence genes. Gene expression pattern analysis by semi-quantitative RT-PCR revealed that M. acridum differentially regulates subsets of genes in response to different infection niches between the host cuticle and hemolymph. The present study provides novel candidate genes to investigate the biology of insect infection by M. acridum.

Risk factors for clostridium difficile infection in children with malignancy.

9533 Background: Clostridium difficile, the most common cause of nosocomial diarrhea, can lead to significant morbidity and mortality. 25% of all pediatric nosocomial C. difficile Infections (CDI) occur in children with cancer. Although the epidemiology of CDI in adults is well described, risk factors for CDI in children with malignancy have not been fully studied. Methods: Using the PHIS database, we created a retrospective cohort of patients ≥1 year old with an ICD-9 code for malignancy who were admitted to participating children’s hospitals from 2001-09. CDI was defined by an ICD-9 code, a charge for C. difficile toxin assay and antibiotic treatment for CDI. Pharmaceutical data was analyzed for the 7 days prior to each CDI. A Cox proportional hazards model, adjusted by site and clustered by patient, was created to measure the risk of developing CDI for each hospital admission. The model censored on discharge, stem cell transplantation or death. Results: Of 40,638 admissions of 21,248 children among 41 hospitals, 1,048 CDIs occurred. Analysis by drug class showed that exposure to 3rd and 4th generation cephalosporins was associated with increased risk of CDI. Exposure to 1st generation cephalosporins, macrolides, and H2 acid blockers showed a protective effect. Proton pump inhibitors, fluoroquinolones and clindamycin were not significantly associated with CDI. Individual drug analyses were also performed (Table). Conclusions: This study reports the first risk factor analysis for CDI among children with cancer in an administrative database. Similar to adult studies, risk of CDI increased with broad spectrum antibiotics. Unlike prior studies, ciprofloxacin showed a protective effect against CDI in children with cancer. Further study and confirmation of risk factors for CDI in children with malignancy may help guide antibiotic use and CDI screening programs. Risk factors for CDI. Risk factor Hazard ratio P value 95% confidence interval Ceftizoxime 14.4 <0.001 5.4 – 38.2 Ticarcillin 8.9 0.033 1.2 – 66.2 Cefepime 2.1 <0.001 1.8 – 2.5 Cefotaxime 1.6 0.032 1.04 – 2.4 Ceftazidime 1.5 <0.001 1.2 – 1.8 Hospital days in last month 1.04 <0.001 1.03 – 1.05 Ranitidine 0.86 0.047 0.73 – 0.998 Cefazolin 0.72 0.015 0.55 – 0.94 Ciprofloxacin 0.59 0.019 0.37 – 0.92

Blame the Boletus? Demystifying Mushrooms in Latin Literature

Keeping in mind Emily Gowers's dictum that ‘food, for the Roman writer who chose to discuss it, was simultaneously important and trivial’, let us go on a mushroom hunt through the fragmented habitat of Latin literature, with some preliminary nosing about in the Greek. We are looking for μύκαι and μύκητες in Greek, and fungi in Latin, and we are keeping an eye open for one kind in particular, the boletus, although we also will stumble upon the occasional interesting fungus suillus (‘pig fungus’). We are not truffle hunting: tubera (Greek ὕδνα) are a topic for another day. Although no survey, however comprehensive, of the appearances of one foodstuff in Latin literature can do full justice to the individual sources, we can still gain something from an overview of the tradition; and although what we learn may be trivial, even the trivial can make its own small contribution to our understanding of a larger matter, in this case the representation of time and change in the Roman world.Ahead of us with knife and collecting basket roams the ghost of the Reverend William Houghton M.A., F.L.S., Victorian parson, Rector of Wellington parish in Preston township, Shropshire, a man with time on his hands—and at least two cats—who in 1885 compiled a list titled, ‘Notices of Fungi in Greek and Latin Authors’. Dr Denis Benjamin, author of Mushrooms: Poisons and Panaceas, says that ‘it would take the persistence of another classical scholar to discover if he [Houghton] missed or misrepresented anything’. Persistence, in the form of the TLL—in its infancy when Houghton was doing his research—the RE entry ‘Pilze’, Maggiulli's Nomenclatura Micologica Latina, and the PHI database, has indeed added to the good Rector's basket a few more specimens on the Latin side, some of which are useful for our inquiry.

Induction Mortality In Pediatric Acute Lymphoblastic Leukemia (ALL): a Retrospective Cohort Analysis From the Pediatric Health Systems Information (PHIS) Database, 1999–2009

AbstractAbstract 3239We sought to define factors identifying children at increased risk for mortality during the induction phase of chemotherapy for ALL. We identified a cohort of 11,145 pediatric patients with newly diagnosed ALL using PHIS data from 1999–2009. The PHIS database contains de-identified records of all admissions from 42 children's hospitals across the United States, representing 85% of pediatric admissions to freestanding children's hospitals. Data are internally validated by PHIS, and participating hospitals must have an error rate of <2%. Patients were further validated by manual comparison of induction chemotherapy to published ALL induction standards. Information included in the database are patient demographics, ICD-9 codes, and resource utilization codes for pharmacy, radiology and other procedures. Our strategy to identify newly diagnosed ALL patients included all patients from birth to age 18.99 years with an ICD-9 code for ALL (204.xx) who received one of a series of 3- or 4-drug induction chemotherapy regimens based on standard practices for the era studied. Data were analyzed from the first 30 days after initial admission for ALL. Table 1 shows demographic characteristics, as well as clinical characteristics hypothesized to predict increased mortality. There were 172 patients who died during the study period (1.54%; Table 2). Age <1 year was associated with markedly increased mortality compared to ages 1–9.99 years; patients ages 10–18.99 also had increased mortality. Sex, race and Hispanic ethnicity were not predictive of mortality. We hypothesized that Down syndrome, anthracycline exposure and dexamethasone exposure would be risk factors; however, none of these exposures significantly predicted increased mortality compared to patients without these exposures. Certain interventions were strong predictors of mortality, such as intubation, use of pressors, intubation with concomitant pressors, extracorporeal membrane oxygenation (ECMO), and hemodialysis (Table 2). We tabulated the frequency of ICD-9 codes during the admission in which mortality was observed. The most commonly associated diagnoses were: respiratory failure, acidosis, aplastic anemia, pleural effusion, hemorrhagic stroke, renal failure, sepsis, coagulopathy, complications of a vascular device, hyponatremia, hypotension/shock, pneumonia, and seizure. We are in the process of further analyzing these diagnostic codes for prediction of mortality risk. In summary, we present the largest published dataset of induction mortality in pediatric ALL. Additionally, this is the first use of a nationally representative pediatric ALL dataset that includes patients irrespective of clinical trial enrollment. We are currently performing multivariate analyses using ICD-9 discharge, procedure and utilization codes to define risk factors for induction mortality. Using these analyses, we will develop a model that may allow practitioners to intervene against poor outcomes in high-risk patients. Finally, these data can provide national benchmarks for ALL induction mortality and complication rates that will be critically important in this era of increasing emphasis on patient safety.Table 1:Demographic characteristics of PHIS ALL cohort, 1999–2009Patient characteristicN(%)Age at diagnosis, median 5.7 years<1 year410(3.68)1-9.99 years7543(67.68)10-18.99 years3192(28.64)Female4835(43.38)RaceCaucasian8430(75.66)African American938(8.42)Asian/Pacific Islander327(2.93)Native American78(0.70)Other/unknown808(7.25)Missing562(5.04)Hispanic ethnicity2376(21.32)Down syndrome304(2.73)Anthracycline exposure4645(41.68)Dexamethasone exposure5393(48.39)Hospitalization dataMean ± SDMedian (range)Duration of 1st admission13.31 ± 14.829 (1-283)Number of hospitalizations in 1st 30 days1.35 ± 0.591 (1-5)Table 2:Risk of mortality by demographics and need for interventionRisk factorMortality rate, N (%)RR (95% CI)Overall172 (1.54)–Age at diagnosis<1 year23 (5.61)7.17 (4.48, 11.49)1-9.99 years59 (0.78)1.010-18.99 years90 (2.82)3.61 (2.60, 4.99)Any IntubationYes99 (26.68)39.38 (29.64, 52.32)No73 (0.68)1.0PressorsYes74 (16.34)17.82 (13.38, 23.74)No98 (0.92)1.0Any Intubation + pressorsYes60 (45.11)44.36 (34.10, 57.69)No112 (1.02)1.0ECMOYes6 (75.00)50.32 (32.81, 77.17)No166 (1.49)1.0HemodialysisYes29 (15.59)11.95 (8.24, 17.33)No143 (1.30)1.0 Disclosures:No relevant conflicts of interest to declare.

Expressed sequence tags from the flower pathogen Claviceps purpurea.

SUMMARY The ascomycete Claviceps purpurea (ergot) is a biotrophic flower pathogen of rye and other grasses. The deleterious toxic effects of infected rye seeds on humans and grazing animals have been known since the Middle Ages. To gain further insight into the molecular basis of this disease, we generated about 10 000 expressed sequence tags (ESTs)-about 25% originating from axenic fungal culture and about 75% from tissues collected 6-20 days after infection of rye spikes. The pattern of axenic vs. in planta gene expression was compared. About 200 putative plant genes were identified within the in planta library. A high percentage of these were predicted to function in plant defence against the ergot fungus and other pathogens, for example pathogenesis-related proteins. Potential fungal pathogenicity and virulence genes were found via comparison with the pathogen-host interaction database (PHI-base; http://www.phi-base.org) and with genes known to be highly expressed in the haustoria of the bean rust fungus. Comparative analysis of Claviceps and two other fungal flower pathogens (necrotrophic Fusarium graminearum and biotrophic Ustilago maydis) highlighted similarities and differences in their lifestyles, for example all three fungi have signalling components and cell wall-degrading enzymes in their arsenal. In summary, the analysis of axenic and in planta ESTs yielded a collection of candidate genes to be evaluated for functional roles in this plant-microbe interaction.