Entwicklung und Evaluierung von Methoden zur zeitnahen Identifizierung weinrelevanter Mikroorganismen

Hefen der Gattung Saccharomyces und Milchsäurebakterien sind bei der Weinbereitung von besonderer Bedeutung. Neben der alkoholischen Gärung sind Hefen an der Ausbildung von Aromastoffen beteiligt. Milchsäurebakterien spielen eine Rolle beim biologischen Säureabbau (malolaktische Fermentation), können jedoch aufgrund ihrer Stoffwechseleigenschaft weitere Aromamodifikationen bewirken. Die Zusammensetzung der mikrobiellen Flora zu verschiedenen Zeitpunkten der Weinbereitung hat einen direkten Einfluss auf die Qualität der Weine, welche sich sowohl positiv als auch negativ verändern kann. Daher ist die zuverlässige Identifizierung und Differenzierung verschiedener Mikroorganismen auf Art- aber auch Stamm-Ebene während der Vinifikation von Bedeutung.rnDer erste Teil dieser Arbeit beschäftigte sich mit der Differenzierung von Hefearten der Gattung Saccharomyces, welche mit Hilfe konventioneller Methoden nicht eindeutig identifiziert werden können. Unter Verwendung des DNA-Fingerprintverfahrens Specifically Amplified Polymorphic DNA (SAPD)-PCR sowie der Matrix-Assisted-Laser-Desorption/Ionization-Time-Of-Flight-Mass-Spectrometry (MALDI-TOF-MS) war eine Differenzierung dieser taxonomisch sehr nah verwandten Arten möglich. Weiterhin konnten interspezifische Hybridstämme detektiert werden. In diesem Zusammenhang wurde der Hybridcharakter des Stammes NCYC 3739 (S. cerevisiae x kudriavzevii) entdeckt. Um die Elternspezies eines Hybridstamms zuverlässig zu bestimmen, sind weiterführende Genanalysen notwendig. Hierzu konnte eine Restriktionsfragmentlängenpolymorphismus (RFLP)-Analyse verschiedener genetischer Marker erfolgreich herangezogen werden.rnIm Rahmen dieser Arbeit wurde weiterhin ein Schnellidentifizierungssystem zum Nachweis weinrelevanter Milchsäurebakterien entwickelt. Mit Hilfe der Sequence Characterized Amplified Region (SCAR)-Technik konnten artspezifische Primer generiert werden, welche auf der Grundlage charakteristischer Fragmente der SAPD-PCR abgeleitet wurden. Durch die Anwendung dieser Primer in einer Multiplex-PCR-Reaktion war die Detektion verschiedener, einerseits häufig in Wein vorkommender und andererseits potentiell an der Ausbildung von Weinfehlern beteiligter Milchsäurebakterien-Arten möglich. Die ermittelte Nachweisgrenze dieser Methode lag mit 10^4 - 10^5 Zellen/ml im Bereich der Zelltiter, die in Most und Wein anzutreffen sind. Anhand der Untersuchung verschiedener Weinproben von Winzern in Rheinhessen wurde die Praxistauglichkeit dieser Methode demonstriert. rnUm die gesamten Milchsäurebakterien-Population im Verlauf der Weinbereitung zu kontrollieren, kann die Denaturierende Gradienten-Gelelektrophorese herangezogen werden. Hierzu wurden in dieser Arbeit Primer zur Amplifikation eines Teilbereichs des rpoB-Gens abgeleitet, da dieses Gen eine Alternative zur 16S rDNA darstellt. Die DNA-Region erwies sich als geeignet, um zahlreiche weinrelevante Milchsäurebakterien-Arten zu differenzieren. In einigen ersten Versuchen konnte gezeigt werden, dass diese Methode für eine praktische Anwendung in Frage kommt.rnOenococcus oeni ist das wichtigste Milchsäurebakterien während der malolaktischen Fermentation und wird häufig in Form kommerzieller Starterkulturen eingesetzt. Da verschiedene Stämme unterschiedliche Eigenschaften aufweisen können, ist es von Bedeutung, die Identität eines bestimmten Stammes zweifelsfrei feststellen zu können. Anhand der Analyse verschiedener O. oeni-Stämme aus unterschiedlichen Weinbaugebieten konnte gezeigt werden, dass sowohl die nested SAPD-PCR als auch die MALDI-TOF-MS genügend Sensitivität aufweisen, um eine Unterscheidung auf Stamm-Ebene zu ermöglichen, wobei die mittels nSAPD-PCR ermittelten Distanzen der Stämme zueinander mit deren geographischer Herkunft korrelierte.rnDie in der vorliegenden Arbeit entwickelten Methoden können dazu beitragen, den Prozess der Weinherstellung besser zu kontrollieren und so eine hohe Qualität des Endproduktes zu gewährleisten.rn

Entwicklung eines biologischen Verfahrens zur Reduktion des Methanschlupfes von Gasaufbereitungsanlagen mittels Einsatz methanotropher Mikroorganismen

Im Rahmen dieser Arbeit wurde ein biologisches Verfahren zur Reduzierung des Methanschlupfes in Gasaufbereitungsanlagen entwickelt. Der Methanschlupf entsteht, wenn das in Biogasanlagen produzierte Biogas auf normierte Erdgasqualität aufgereinigt wird, welches notwendig ist, um es in das bestehende Erdgasnetz einleiten zu können. Bei dieser Aufreinigung wird aus dem Biogas auch ein Teil des Methans mit ausgewaschen und gelangt mit dem Abgas der Gasaufbereitungsanlage in die Umwelt. Bisher wird dieses methanhaltige Abgas verbrannt, da eine Freisetzung des starken Treibhausgases Methan durch das Erneuerbare-Energien-Gesetz untersagt ist. Dies reduziert die ökologische Bilanz und setzt die Wirtschaftlichkeit der gesamten Biogasanlage herab. rnUm das Methan mit Hilfe eines biologischen Verfahrens zu entfernen, wurden zunächst methanoxidierende Bakterien (MOB) aus verschiedenen Habitaten isoliert, darunter auch erstmalig aus Termiten. Der Nachweis erfolgte durch (quantitative) Polymerase-Kettenreaktion und Fluoreszenz-in-situ-Hybridisierung anhand spezifischer Primer bzw. Sonden für das Gen der partikulären Methanmonoxygenase, ein MOB kennzeichnendes Enzym. Ihr Titer wurde durch qPCR auf 10^2 - 10^3 MOB pro Termitendarm durch qPCR bestimmt. Mit Hilfe einer 16S rDNA Sequenzierung, der (n)SAPD-PCR, der Bestimmung der zellulären Fettsäurezusammensetzung sowie MALDI-TOF-MS-Analysen konnten die Termitenisolate der Gattung Methylocystis zugeordnet werden. Die fehlende Artzuweisung spricht jedoch für die Isolierung einer neuen Art. rnFür den Einsatz der Isolate in Gasaufbereitungsanlagen wurde in Zusammenarbeit mit dem Prüf- und Forschungsinstitut in Pirmasens ein Reaktor im Technikumsmaßstab entwickelt und konstruiert. Der Reaktor wurde mit synthetischen Aufwuchskörper befüllt, diese mit einem neu gewonnenen potenten Termitenisolat besiedelt und der methanhaltige Abgasstrom der Gasaufbereitungsanlage darüber geleitet. Es wurde eine Reduktion des Methans um 68 % innerhalb von 30 Stunden erzielt. Medienoptimierungen wiesen das Potential auf, diesen Verbrauch um das bis zu 4-fache weiter zu steigern. Da durch die Oxidation des Methans im Abgasstrom der Gasaufbereitungsanlage Zellmasse und Polyhydroxybuttersäure (PHB) aufgebaut wurde, können diese als Substrat zurück in die Biogasanlagen geleitet werden und die Wirtschaftlichkeit weiter verbessern. Die Wirksamkeit des in diesem Projekt entwickelten Verfahrens wurde somit eindeutig demonstriert.

Podredumbre parda del melocotonero (Monilinia spp.) : detección, identificación de especies y contribución a la epidemiología de la enfermedad

Monilinia spp. (M. laxa, M. fructigena y M. fructicola) causa marchitez en brotes y flores, chancros en ramas y podredumbre de la fruta de hueso provocando pérdidas económicas importantes en años con climatología favorable para el desarrollo de la enfermedad, particularmente en variedades tardías de melocotonero y nectarino. En estos huéspedes en España, hasta el momento, la especie predominante es M. laxa y, en menor proporción, M. fructigena. La reciente introducción en Europa de la especie de cuarentena M. fructicola hace necesaria una detección e identificación rápida de cada una de las especies. Además, hay diversos aspectos de la etiología y epidemiología de la enfermedad que no se conocen en las condiciones de cultivo españolas. En un primer objetivo de esta Tesis se ha abordado la detección e identificación de las especies de Monilinia spp. causantes de podredumbre parda. El estudio de las bases epidemiológicas para el control de la enfermedad constituye el fin del segundo objetivo. Para la detección del género Monilinia en material vegetal por PCR, diferenciándolo de otros hongos presentes en la superficie del melocotonero, se diseñaron una pareja de cebadores siguiendo un análisis del ADN ribosomal. La discriminación entre especies de Monilinia se consiguió utilizando marcadores SCAR (región amplificada de secuencia caracterizada), obtenidos después de un estudio de marcadores polimórficos de ADN amplificados al azar (RAPDs). También fue diseñado un control interno de amplificación (CI) basado en la utilización de un plásmido con secuencias de los cebadores diferenciadores del género, para ser utilizado en el protocolo de diagnóstico de la podredumbre parda con el fin de reconocer falsos negativos debidos a la inhibición de PCR por componentes celulares del material vegetal. Se disponía de un kit comercial que permitía distinguir Monilinia de otros géneros y M. fructicola del resto de especies mediante anticuerpos monoclonales utilizando la técnica DAS-ELISA. En esta Tesis se probaron diferentes fuentes de material como micelio ó conidias procedentes de cultivos en APD, o el micelio de la superficie de frutas o de momias frescas, como formas de antígeno. Los resultados obtenidos con ELISA se compararon con la identificación por métodos morfológico-culturales y por PCR con los cebadores desarrollados en esta Tesis. Los resultados demostraron la posibilidad de una detección temprana en frutas frescas por este método, realzando las posibilidades de una diagnosis temprana para una prevención más eficaz de M. fructicola en fruta de hueso. El estudio epidemiológico de la enfermedad comenzó con la determinación de las principales fuentes de inóculo primario y su importancia relativa en melocotoneros y nectarinos del valle del Ebro. Para ello se muestrearon 9 huertos durante los años 2003 a 2005 recogiendo todas las momias, frutos abortados, gomas, chancros, y brotes necróticos en los árboles. También se recogieron brotes aparentemente sanos y muestras de material vegetal situados en el suelo. En estas muestras se determinó la presencia de Monilinia spp. Los resultados mostraron que la fuente principal de inóculo son las momias que se quedan en los árboles en las que la supervivencia del hongo tras el invierno es muy alta. También son fuentes de inóculo las momias del suelo y los brotes necróticos. De aquí se deriva que una recomendación importante para los agricultores es que deben eliminar este material de los huertos. Un aspecto no estudiado en melocotonero o nectarino en España es la posible relación que puede darse entre la incidencia de infecciones latentes en los frutos inmaduros a lo largo del cultivo y la incidencia de podredumbre en los frutos en el momento de la recolección y en postcosecha. Esta relación se había observado previamente en otros frutales de hueso infectados con M. fructicola en diversos países del mundo. Para estudiar esta relación se realizaron ensayos en cinco huertos comerciales de melocotonero y nectarino situados en el Valle del Ebro en cuatro estados fenológicos durante los años 2000-2002. No se observaron infecciones latentes en botón rosa, dándose la máxima incidencia en precosecha, aunque en algunos huertos se daba otro pico en el endurecimiento del embrión. La especie prevaleciente fue M. laxa. Se obtuvo una correlación positiva significativa entre la incidencia de infecciones latentes y la incidencia de podredumbre en postcosecha. Se desarrolló también un modelo de predicción de las infecciones latentes en función de la temperatura (T) y el periodo de humectación (W). Este modelo indicaba que T y W explicaban el 83% de la variación en la incidencia de infecciones latentes causadas por Monilinia spp. Por debajo de 8ºC no se predecían latentes, necesitándose más de 22h de W para predecir la ocurrencia de latentes con T = 8ºC, mientras que solo se necesitaban 5h de W a 25ºC. Se hicieron también ensayos en condiciones controladas para determinar la relación entre la incidencia de las infecciones latentes, las condiciones ambientales (T y W), la concentración de inóculo del patógeno (I) y el estado de desarrollo del huésped (S) y para validar el modelo de predicción desarrollado con los experimentos de campo. Estos ensayos se llevaron cabo con flores y frutos de nectarino procedentes de un huerto comercial en seis estados fenológicos en los años 2004 y 2005, demostrándose que la incidencia de podredumbre en postcosecha y de infecciones latentes estaba afectada por T, W, I y S. En los frutos se producían infecciones latentes cuando la T no era adecuada para el desarrollo de podredumbre. Una vez desarrollado el embrión eran necesarias más de 4-5h de W al día y un inóculo superior a 104 conidias ml-1 para que se desarrollase o podredumbre o infección latente. La ecuación del modelo obtenido con los datos de campo era capaz de predecir los datos observados en estos experimentos. Para evaluar el efecto del inóculo de Monilinia spp. en la incidencia de infecciones latentes y de podredumbre de frutos en postcosecha se hicieron 11 experimentos en huertos comerciales de melocotonero y nectarino del Valle del Ebro durante 2002 a 2005. Se observó una correlación positiva entre los números de conidias de Monilinia spp. en la superficie de los frutos y la incidencia de infecciones latentes De los estudios anteriores se deducen otras dos recomendaciones importantes para los agricultores: las estrategias de control deben tener en cuenta las infecciones latentes y estimar el riesgo potencial de las mismas basándose en la T y W. Deben tener también en cuenta la concentración de esporas de Monilinia spp. en la superficie de los frutos para disminuir el riesgo de podredumbre parda. El conocimiento de la estructura poblacional de los patógenos sienta las bases para establecer métodos más eficaces de manejo de las enfermedades. Por ello en esta Tesis se ha estudiado el grado de diversidad genética entre distintas poblaciones de M. laxa en diferentes localidades españolas utilizando 144 marcadores RAPDs (59 polimórficos y 85 monomórficos) y 21 aislados. El análisis de la estructura de la población reveló que la diversidad genética dentro de las subpoblaciones (huertos) (HS) representaba el 97% de la diversidad genética (HT), mientras que la diversidad genética entre subpoblaciones (DST) sólo representaba un 3% del total de esta diversidad. La magnitud relativa de la diferenciación génica entre subpoblaciones (GST) alcanzaba 0,032 y el número estimado de migrantes por generación (Nm) fue de 15,1. Los resultados obtenidos en los dendrogramas estaban de acuerdo con el análisis de diversidad génica. Las agrupaciones obtenidas eran independientes del huerto de procedencia, año o huésped. En la Tesis se discute la importancia relativa de las diferentes fuentes evolutivas en las poblaciones de M. laxa. Finalmente se realizó un muestreo en distintos huertos de melocotonero y nectarino del Valle del Ebro para determinar la existencia o no de aislados resistentes a los fungicidas del grupo de los benzimidazoles y las dicarboximidas, fungicidas utilizados habitualmente para el control de la podredumbre parda y con alto riesgo de desarrollar resistencia en las poblaciones patógenas. El análisis de 114 aislados de M. laxa con los fungicidas Benomilo (bencimidazol) (1Bg m.a ml-1), e Iprodiona (dicarboximida) (5Bg m.a ml-1), mostró que ninguno era resistente en las dosis ensayadas. Monilinia spp. (M. laxa, M. fructigena and M. fructicola) cause bud and flower wilt, canker in branches and stone fruit rot giving rise important economic losses in years with appropriate environmental conditions, it is particularly important in late varieties of peach and nectarine. Right now, M. laxa is the major species for peach and nectarine in Spain followed by M. fructigena, in a smaller proportion. The recent introduction of the quarantine organism M. fructicola in Europe makes detection and identification of each one of the species necessary. In addition, there are different aspects of disease etiology and epidemiology that are not well known in Spain conditions. The first goal of this Thesis was the detection and identification of Monilinia spp. causing brown rot. Study of the epidemiology basis for disease control was the second objective. A pair of primers for PCR detection was designed based on the ribosomal DNA sequence in order to detect Monilinia spp. in plant material and to discriminate it from other fungi colonizing peach tree surface. Discrimination among Monilinia spp. was successful by SCAR markers (Sequence Characterized Amplified Region), obtained after a random amplified polymorphic DNA markers (RAPDs) study. An internal control for the PCR (CI) based on the use of a mimic plasmid designed on the primers specific for Monilinia was constructed to be used in diagnosis protocol for brown rot in order to avoid false negatives due to the inhibition of PCR as consequence of remained plant material. A commercial kit based on DAS-ELISA and monoclonals antibodies was successfully tested to distinguish Monilinia from other fungus genera and M. fructicola from other Monilinia species. Different materials such as micelium or conidias from APD cultures, or micelium from fresh fruit surfaces or mummies were tested in this Thesis, as antigens. Results obtained by ELISA were compared to classical identification by morphologic methods and PCR with the primers developed in this Thesis. Results demonstrated the possibility of an early detection in fresh fruits by this method for a more effective prevention of M. fructicola in stone fruit. The epidemiology study of the disease started with the determination of the main sources of primary inoculum and its relative importance in peach trees and nectarines in the Ebro valley. Nine orchards were evaluated during years 2003 to 2005 collecting all mummies, aborted fruits, rubbers, cankers, and necrotic buds from the trees. Apparently healthy buds and plant material located in the ground were also collected. In these samples presence of Monilinia spp. was determined. Results showed that the main inoculum sources are mummies that stay in the trees and where fungus survival after the winter is very high. Mummies on the ground and the necrotics buds are also sources of inoculum. As consequence of this an important recommendation for the growers is the removal of this material of the orchards. An important issue not well studied in peach or nectarine in Spain is the possible relationship between the incidence of latent infections in the immature fruits and the incidence of fruit rot at harvesting and postharvesting. This relationship had been previously shown in other stone fruit trees infected with M. fructicola in different countries over the world. In order to study this relationship experiments were run in five commercial peach and nectarine orchards located in the Ebro Valley in four phenologic states from 2000 to 2002. Latent infections were not observed in pink button, the maxima incidence arise in preharvest, although in some orchards another increase occurred in the embryo hardening. The most prevalence species was M. laxa. A significant positive correlation between the incidence of latent infections and the incidence of rot in postharvest was obtained. A prediction model of the latent infections based on the temperature (T) and the wetness duration (W) was also developed. This model showed that T and W explained 83% of the variation in latent infection incidence caused by Monilinia spp. Below 8ºC latent infection was not predicted, more than 22h of W with T = 8ºC were needed to predict latent infection occurrence of, whereas at 25ºC just 5h of W were enough. Tests under controlled conditions were also made to determine the relationship among latent infections incidence, environmental conditions (T and W), inoculum concentration of the pathogen (I) and development state of the host (S) to validate the prediction model developed on the field experiments. These tests were made with flowers and fruits of nectarine coming from a commercial orchard, in six phenologic states in 2004 and 2005, showing that incidence of rot in postharvest and latent infections were affected by T, W, I and S. In fruits latent infections took place when the T was not suitable for rot development. Once developed the embryo, more than 4-5h of W per day and higher inoculums (104 conidia ml-1) were necessary for rot or latent infection development. The equation of the model obtained with the field data was able to predict the data observed in these experiments. In order to evaluate the effect of inoculum of Monilinia spp. in the incidence of latent infections and of rot of fruits in postharvest, 11 experiments in commercial orchards of peach and nectarine of the Ebro Valley were performed from 2002 to 2005. A positive correlation between the conidial numbers of Monilinia spp. in the surface of the fruits and the incidence of latent infections was observed. Based on those studies other two important recommendations for the agriculturists are deduced: control strategies must consider the latent infections and potential risk based on the T and W. Spores concentration of Monilinia spp. in the surface of fruits must be also taken in concern to reduce the brown rot risk. The knowledge of the population structure of the pathogens determines the bases to establish more effective methods of diseases handling. For that reason in this Thesis the degree of genetic diversity among different M. laxa populations has been studied in different Spanish locations using 144 RAPDs markers (59 polymorphic and 85 monomorphics) on 21 fungal isolates. The analysis of the structure of the population revealed that the genetic diversity within the subpopulations (orchards) (HS) represented 97% of the genetic diversity (HT), whereas the genetic diversity between subpopulations (DST) only represented a 3% of the total of this diversity. The relative magnitude of the genic differentiation between subpopulations (GST) reached 0.032 and the considered number of migrantes by generation (Nm) was of 15.1. The results obtained in dendrograms were in agreement with the analysis of genic diversity. The obtained groupings were independent of the orchard of origin, year or host. In the Thesis the relative importance of the different evolutionary sources in the populations from M. laxa is discussed. Finally a sampling of resistant isolates in different orchards from peach and nectarine of Ebro Valley was made to determine the existence of fungicide resistance of the group of benzimidazoles and the dicarboximidas, fungicides used habitually for the control of rot brown and with high risk of resistance developing in the pathogenic populations. The analysis of 114 isolated ones of M. laxa with the fungicides Benomilo (bencimidazol) (1Bg m.a ml-1), and Iprodiona (dicarboximida) (5Bg m.a ml-1), showed no resistant in the doses evaluated.

Aluminum-Resistant Arabidopsis Mutants That Exhibit Altered Patterns of Aluminum Accumulation and Organic Acid Release from Roots1

Al-resistant (alr) mutants of Arabidopsis thaliana were isolated and characterized to gain a better understanding of the genetic and physiological mechanisms of Al resistance. alr mutants were identified on the basis of enhanced root growth in the presence of levels of Al that strongly inhibited root growth in wild-type seedlings. Genetic analysis of the alr mutants showed that Al resistance was semidominant, and chromosome mapping of the mutants with microsatellite and random amplified polymorphic DNA markers indicated that the mutants mapped to two sites in the Arabidopsis genome: one locus on chromosome 1 (alr-108, alr-128, alr-131, and alr-139) and another on chromosome 4 (alr-104). Al accumulation in roots of mutant seedlings was studied by staining with the fluorescent Al-indicator dye morin and quantified via inductively coupled argon plasma mass spectrometry. It was found that the alr mutants accumulated lower levels of Al in the root tips compared with wild type. The possibility that the mutants released Al-chelating organic acids was examined. The mutants that mapped together on chromosome 1 released greater amounts of citrate or malate (as well as pyruvate) compared with wild type, suggesting that Al exclusion from roots of these alr mutants results from enhanced organic acid exudation. Roots of alr-104, on the other hand, did not exhibit increased release of malate or citrate, but did alkalinize the rhizosphere to a greater extent than wild-type roots. A detailed examination of Al resistance in this mutant is described in an accompanying paper (J. Degenhardt, P.B. Larsen, S.H. Howell, L.V. Kochian [1998] Plant Physiol 117: 19–27).

Development of PCR-based markers for detection of Leifsonia xyli subsp. xyli in fibrovascular fluid of infected sugarcane plants

DNA of Leifsonia xyli subsp. xyli (Lxx), the causal agent of ratoon stunting disease of sugarcane, was detected in the fibrovascular fluid of sugarcane plants using random amplified polymorphic DNA PCR-based amplification using two 10-mer oligonucleotide primers. The primers OPC-02 and OPC-11 produced Lxx-specific markers of approximately 800 bp and 1000 bp, respectively. A cloned DNA fragment from the 800 bp PCR product (pSKC2-800) hybridised to a single genomic DNA fragment from Lxx when used as a probe in Southern hybridisation. This cloned fragment did not hybridise to L. xyli subsp. cynodontis (Lxc), or L. xyli-like bacteria isolated from grasses in Australia, indicating the usefulness of this DNA fragment as a specific probe for Lxx. A cloned fragment from the 1000 bp PCR product ( pSKC11-1000) hybridised to three genomic fragments in Lxx isolates, one genomic fragment in two of the four isolates of L. xyli-like bacteria, and in two of the four isolates of Lxc isolated from the USA. These results indicate that L. xyli-like bacteria are more likely to be related to Lxc than Lxx. These probes did not hybridise to the DNA from strains of the species of Clavibacter, Rathayibacter, Acidovorax, Ralstonia, Pseudomonas and Xanthomonas tested. Two oligonucleotide primers (21-mer) designed from the pSKC2-800 sequences specifically amplified template DNA from Lxx and detected as few as 5 x 10(4) cells/mL in fibrovascular fluid from sugarcane plants infected with Lxx.

An outbreak of Serratia marcescens on the neonatal unit:a tale of two clones

Serratia spp. are an important cause of hospital-acquired infections and outbreaks in high-risk settings. Twenty-one patients were infected or colonized over a nine-month period during 2001-2002 on a neonatal unit. Twenty-two isolates collected were examined for antibiotic susceptibility, β-lactamase production and genotype. Random-amplified polymorphic DNA polymerase chain reaction and pulsed-field gel electrophoresis revealed that two clones were present. The first clone caused invasive clinical infection in four babies, and was subsequently replaced by a non-invasive clone that affected 14 babies. Phenotypically, the two strains also differed in their prodigiosin production; the first strain was non-pigmented whereas the second strain displayed pink-red pigmentation. Clinical features suggested a difference in their pathogenicity. No environmental source was found. The outbreak terminated following enhanced compliance with infection control measures and a change of antibiotic policy. Although S. marcescens continued to be isolated occasionally for another five months of follow-up, these were sporadic isolates with distinct molecular typing patterns. © 2005 The Hospital Infection Society.

Phenotypic and genotypic characterisation of Clostrum Difficile

Clostridium difficile is at present one of the most common nosocomial infections in the developed world. Hypervirulent strains (PCR ribotype 027) of C. difficile which produce enhanced levels of toxins have also been associated with other characteristics such as a greater rate of sporulation and resistance to fluoroquinolones. Infection due to C. difficile PCR ribotype 027 has also been associated with greater rates of morbidity and mortality. The aim of this thesis was to investigate both the phenotypic and genotypic characteristics of two populations of toxigenic clinical isolates of C. difficile which were recovered from two separate hospital trusts within the UK. Phenotypic characterisation of the isolates was undertaken using analytical profile indexes (APIs), minimum inhibitory concentrations(MICs) and S-layer protein typing. In addition to this, isolates were also investigated for the production of a range of extracellular enzymes as potential virulence factors. Genotypic characterisation was performed using a random amplification of polymorphic DNA(RAPD) PCR protocol which was fully optimised in this study, and the gold standard method, PCR ribotyping. The discriminatory power of both methods was compared and the similarity between the different isolates also analysed. Associations between the phenotypic and genotypic characteristics and the recovery location of the isolate were then investigated. Extracellular enzyme production and API testing revealed little variation between the isolates; with S-layer typing demonstrating low discrimination. Minimum inhibitory concentrations did not identify any resistance towards either vancomycin or metronidazole; there were however significant differences in the distribution of antibiogram profiles of isolates recovered from the two different trusts. The RAPD PCR protocol was successfully optimised and alongside PCR ribotyping, effectively typed all of the clinical isolates and also identified differences in the number of types defined between the two locations. Both PCR ribotyping and RAPD demonstrated similar discriminatory power; however, the two genotyping methods did not generate amplicons that mapped directly onto each other and therefore clearly characterised isolates based on different genomic markers. The RAPD protocol also identified different subtypes within PCR ribotypes, therefore demonstrating that all isolates defined as a particular PCR ribotype were not the same strain. No associations could be demonstrated between the phenotypic and genotypic characteristics observed; however, the location from which an isolate was recovered did appear to influence antibiotic resistance and genotypic characteristics. The phenotypic and genotypic characteristics observed amongst the C. difficile isolates in this study, may provide a basis for the identification of further targets which may be potentially incorporated into future methods for the characterisation of C. difficile isolates.

Characterisation of propionibacterium acnes

Propionibacterium acnes forms part of the normal flora of the skin, oral cavity, large intestine and the external ear. Historically, P. acnes is considered to be of low virulence; however, in recent years it has been found as the aetiological agent in various pathologies including acne vulgaris, endophthalmitis, endocarditis, osteomyelitis, sarcoidosis, prosthetic hip infections and sciatica. It currently remains unclear why this normally harmless commensal can cause infection and contribute to a number of clinically significant conditions. This thesis has sought to investigate the phenotypic, genetic and antigenic properties of P.acnes strains isolated from sciatica patients undergoing microdiscectomy, normal skin, blood cultures, prosthetic hips and acne lesions. Isolates' phenotype was examined by determining their biotype by analytical profile index, antimicrobial susceptibility, virulence factor expression and serotype. A molecular typing method for P.acnes was developed using random amplification of polymorphic DNA (RAPD). Patient serum was used to screen P.acnes strains for antigens expressed in vivo and the chemical composition determined. The serodiagnostic potential and inflammatory properties of identified antigens were assessed. The optimised and reproducible RAPD protocol classified strains into three major clusters and was found to distinguish between the serotypes I and II for a large number of clinical isolates. Molecular typing by RAPD also enabled the identification of a genotype that did not react with the type I or II monoclonal antibodies and these strains may therefore constitute a previously undiscovered subspecies of P.acnes with a genetic background different from the type I and II serotypes. A major cell associated antigen produced by all strains was identified and characterised. A serological assay based on the antigen was used to measure IgG and IgM levels in serum from patients with acne, sciatica and controls. No difference in levels of antibodies was detected. Inflammatory properties of the antigen were measured by exposing murine macrophage-like cells and measuring the release of nitric oxide and tumour necrosis factor-alpha (TNF-α). Only TNF-α was elicited in response to the antigen. The phenotypic, genotypic and antigenic properties of this organism may provide a basis for future studies on P.acnes virulence and provide an insight into its mechanisms of pathogenesis.

First isolation and characterization of Chryseobacterium shigense from rainbow trout

BACKGROUND There have been an increasing number of infections in fish associated with different species of Chryseobacterium, being considered potentially emerging pathogens. Nevertheless the knowledge of the diversity of species associated with fish disease is partial due to the problems for a correct identification at the species level based exclusively on phenotypic laboratory methods. RESULTS Chryseobacterium shigense was isolated from the liver, kidney and gills of diseased rainbow trout in different disease episodes that occurred in a fish farm between May 2008 and June 2009. Identity of the isolates was confirmed by 16 S rRNA gene sequencing and phenotypic characterization. Isolates represented a single strain as determined by random amplified polymorphic DNA analysis. CONCLUSIONS This is the first description of the recovery of C. shigense from clinical specimens in trout, a very different habitat to fresh lactic acid beverage where it was initially isolated.

Gene and genotypic diversity of Phytophthora cinnamomi in South Africa and Australia revealed by DNA polymorphisms

Phytophthora cinnamomi isolates from South Africa and Australia were compared to assess genetic differentiation between the two populations. These two populations were analysed for levels of phenotypic diversity using random amplified polymorphic DNAs (RAPDs) and gene and genotypic diversity using restriction fragment length polymorphisms (RFLPs). Sixteen RAPD markers from four decanucleotide Operon primers and 34 RFLP alleles from 15 putative loci were used. A few isolates from Papua New Guinea known to posses alleles different from Australian isolates were also included for comparative purposes. South African and Australian P. cinnamomi populations were almost identical with an extremely low level of genetic distance between them (D-m = 0.003). Common features for the two populations include shared alleles, low levels of phenotypic/genotypic diversity, high clonality, and low observed and expected levels of heterozygosity. Furthermore, relatively high levels of genetic differentiation between mating type populations (D-m South Africa = 0.020 and D-m Australia = 0.025 respectively), negative fixation indices, and significant deviations from Hardy-Weinberg equilibrium, all provided evidence for the lack of frequent sexual reproduction in both populations. The data strongly suggest that both the South African and Australian P. cinnamomi populations are introduced.

A DNA fingerprinting procedure for ultra high-throughput genetic analysis of insects

Existing procedures for the generation of polymorphic DNA markers are not optimal for insect studies in which the organisms are often tiny and background molecular Information is often non-existent. We have used a new high throughput DNA marker generation protocol called randomly amplified DNA fingerprints (RAF) to analyse the genetic variability In three separate strains of the stored grain pest, Rhyzopertha dominica. This protocol is quick, robust and reliable even though it requires minimal sample preparation, minute amounts of DNA and no prior molecular analysis of the organism. Arbitrarily selected oligonucleotide primers routinely produced similar to 50 scoreable polymorphic DNA markers, between individuals of three Independent field isolates of R. dominica. Multivariate cluster analysis using forty-nine arbitrarily selected polymorphisms generated from a single primer reliably separated individuals into three clades corresponding to their geographical origin. The resulting clades were quite distinct, with an average genetic difference of 37.5 +/- 6.0% between clades and of 21.0 +/- 7.1% between individuals within clades. As a prelude to future gene mapping efforts, we have also assessed the performance of RAF under conditions commonly used in gene mapping. In this analysis, fingerprints from pooled DNA samples accurately and reproducibly reflected RAF profiles obtained from Individual DNA samples that had been combined to create the bulked samples.

Novel polymorphic microsatellite markers in section Caulorrhizae (Arachis, Fabaceae)

This work reports the characterization of 11 polymorphic microsatellite loci in section Caulorrhizae. The primer pairs were designed from Arachis pintoi and showed full transferability to Arachis repens species. These new markers were used to evaluate the genetic diversity in germplasm (accessions and cultivars) of section Caulorrhizae. This new set of markers detected greater gene diversity than morphological and molecular markers such as AFLP (amplified fragment length polymorphism) and RAPD (rapid analysis of polymorphic DNA) previously used in this germplasm.

Avaliação do envolvimento das bombas de efluxo na fármaco-resistência ao Praziquantel em Schistosoma Mansonii

O Praziquantel (PZQ) é o fármaco de primeira linha no tratamento da schistosomose, com alta taxa de cura e sem efeitos secundários significativos. Têm sido reportados cada vez mais casos de resistência ou de aumento de tolerância a este fármaco, aumentando as preocupações de emergência de estirpes resistentes ao PZQ. O Verapamil, um bloqueador de canais de cálcio, inibe o fluxo de fármaco activo e tem sido descrito como um bom inibidor das glicoproteínas-P (P-gp), sendo, por isso, utilizado em diversos estudos de fármaco-resistência. No laboratório de Helmintologia da Unidade de Ensino e Investigação em Parasitologia Médica do Instituto de Higiene e Medicina Tropical, foi seleccionada uma linha de S. mansoni, resistente a 800 mg/Kg de PZQ, após pressão de fármaco constante e crescente ao longo de vários ciclos. Para confirmar a existência de diferenças polimórficas entre a estirpes sensível e resistente de S. mansoni, extraiu-se o DNA de parasitas adultos de ambas as estirpes de S. mansoni e analisou-se por Random Amplified Polymorphic DNAPolymerase Chain Reaction (RAPD-PCR). As diferenças polimórficas entre a estirpe sensível e a resistente foram observadas e calculou-se o coeficiente de similaridade (Dice’s coefficient). Após confirmar a existência de polimorfismos entre as duas estirpes, a atividade das bombas de efluxo foi avaliada em ambas as estirpes. A avaliação foi realizada num ensaio de acumulação usando o composto Brometo de Etídio na presença e ausência de Verapamil. O papel das bombas de efluxo na resistência ao PZQ, foi ainda investigado comparando a resposta dos parasitas da estirpe sensível e resistente ao fármaco na ausência e na presença de diferentes doses de Verapamil, em cultura in vitro. Os resultados obtidos foram reforçados comparando os níveis e expressão do gene SmMDR2 em ambas as estirpes isogénicas por Real-Time PCR (qPCR). A estirpe resistente de S. mansoni, necessitou de concentrações mais elevadas de inibidor quando comparada com a estirpe sensível para obter níveis significativos de fluorescência de Brometo de Etídio. A cultura in vitro mostrou uma dose letal de PZQ mais elevada na estirpe resistente do que na estirpe sensível na ausência de Verapamil. Na presença de Verapamil houve uma redução na dose letal de PZQ nos machos de ambas as estirpes, sendo esta redução mais acentuada nos machos da estirpe resistente. As fêmeas não mostraram alterações significativas na dose letal de PZQ na presença e ausência e inibidor. Os resultados foram reforçados pela observação dos níveis do gene SmMDR2, onde os machos da estirpe resistente mostraram ter os maiores níveis de expressão e pelo aumento de expressão nos machos de ambas as estirpes após exposição ao PZQ. As fêmeas de ambas as estirpes não tiveram diferenças significativas na expressão do gene após exposição ao PZQ e as fêmeas da estirpe resistente tiveram mostraram ter os níveis de expressão do gene SmMDR2 mais baixos entre os machos e fêmeas de ambas as estirpes. Os resultados obtidos neste trabalho mostraram que os machos da estirpe resistente têm maior atividade de bombas de efluxo do que os machos da estirpe sensível e que as bombas P-gp estão envolvidas na resposta e no aumento de tolerância dos machos de S. mansoni ao PZQ.

Assessment of silver-stained AFLP markers for studying DNA polymorphism in proso millet (Panicum miliaceum L.)

Proso millet (Panicum miliaceum L.) is a serious weed in North America. A high number of wild proso millet biotypes are known but the genetic basis of its phenotypic variation is poorly understood. In the present study, a non-radioactive silver staining method for PCR-Amplified Fragment Length Polymorphism (AFLP) was evaluated for studying genetic polymorphism in American proso millet biotypes. Twelve biotypes and eight primer combinations with two/three and three/three selective nucleotides were used. Pair of primers with two/three selective nucleotides produced the highest number of amplified DNA fragments, while pair of primers with three/three selective nucleotides were more effective for revealing more polymorphic DNA fragments. The two better primer combinations were EcoR-AAC/Mse-CTT and EcoR-ACT/Mse-CAA with seven and eleven polymorphic DNA fragments, respectively. In a total of 450 amplified fragments, at least 339 appeared well separated in a silver stained acrylamide gel and 39 polymorphic DNA bands were scored. The level of polymorphic DNA (11.5%) using only eight pairs of primers were effective for grouping proso millet biotypes in two clusters but insufficient for separating hybrid biotypes from wild and crop. Nevertheless, the present result indicates that silver stained AFLP markers could be a cheap and important tool for studying genetic relationships in proso millet.