In diesem Jahrhundert haben neue experimentelle Techniken und Computer-Verfahren enorme Mengen an Information erzeugt, die bereits viele biologische Rätsel enthüllt haben. Doch die Komplexität biologischer Systeme wirft immer weitere neue Fragen auf. Um ein System zu verstehen, bestand der Hauptansatz bis jetzt darin, es in Komponenten zu zerlegen, die untersucht werden können. Ein neues Paradigma verknüpft die einzelnen Informationsteile, um sie auf globaler Ebene verstehen zu können. In der vorgelegten Doktorarbeit habe ich deshalb versucht, infektiöse Krankheiten mit globalen Methoden („Systembiologie“) bioinformatisch zu untersuchen. Im ersten Teil wird der Apoptose-Signalweg analysiert. Apoptose (Programmierter Zelltod) wird bei verschiedenen Infektionen, zum Beispiel bei Viruserkrankungen, als Abwehrmaßnahme eingesetzt. Die Interaktionen zwischen Proteinen, die ‚death’ Domänen beinhalten, wurden untersucht, um folgende Fragen zu klären: i) wie wird die Spezifität der Interaktionen erzielt? –sie wird durch Adapter erreicht, ii) wie werden Proliferation/ Überlebenssignale während der Aktivierung der Apoptose eingeleitet? – wir fanden Hinweise für eine entscheidende Rolle des RIP Proteins (Rezeptor-Interagierende Serine/Threonine-Proteinkinase 1). Das Modell erlaubte uns, die Interaktions-Oberflächen von RIP vorherzusagen. Der Signalweg wurde anschließend auf globaler Ebene mit Simulationen für verschiedene Zeitpunkte analysiert, um die Evolution der Aktivatoren und Inhibitoren des Signalwegs und seine Struktur besser zu verstehen. Weiterhin wird die Signalverarbeitung für Apoptosis-Signalwege in der Maus detailliert modelliert, um den Konzentrationsverlauf der Effektor-Kaspasen vorherzusagen. Weitere experimentelle Messungen von Kaspase-3 und die Überlebenskurven von Zellen bestätigen das Modell. Der zweite Teil der Resultate konzentriert sich auf das Phagosom, eine Organelle, die eine entscheidende Rolle bei der Eliminierung von Krankheitserregern spielt. Dies wird am Beispiel von M. tuberculosis veranschaulicht. Die Fragestellung wird wiederum in zwei Aspekten behandelt: i) Um die Prozesse, die durch M. tuberculosis inhibiert werden zu verstehen, haben wir uns auf das Phospholipid-Netzwerk konzentriert, das bei der Unterdrückung oder Aktivierung der Aktin-Polymerisation eine große Rolle spielt. Wir haben für diese Netzwerkanalyse eine Simulation für verschiedene Zeitpunkte ähnlich wie in Teil eins angewandt. ii) Es wird vermutet, dass Aktin-Polymere bei der Fusion des Phagosoms mit dem Lysosom eine Rolle spielen. Um diese Hypothese zu untersuchen, wurde ein in silico Modell von uns entwickelt. Wir fanden heraus, dass in der Anwesenheit von Aktin-Polymeren die Suchzeit für das Lysosom um das Fünffache reduziert wurde. Weiterhin wurden die Effekte der Länge der Aktin-Polymere, die Größe der Lysosomen sowie der Phagosomen und etliche andere Modellparameter analysiert. Nach der Untersuchung eines Signalwegs und einer Organelle führte der nächste Schritt zur Untersuchung eines komplexen biologischen Systems der Infektabwehr. Dies wurde am Beispiel der Wirt-Pathogen Interaktion bei Bordetella pertussis und Bordetella bronchiseptica dargestellt. Die geringe Menge verfügbarer quantitativer Daten war der ausschlaggebende Faktor bei unserer Modellwahl. Für die dynamische Simulation wurde ein selbst entwickeltes Bool’sches Modell verwendet. Die Ergebnisse sagen wichtige Faktoren bei der Pathologie von Bordetellen hervor, besonders die Bedeutung der Th1 assoziierten Antworten und dagegen nicht der Th2 assoziierten Antworten für die Eliminierung des Pathogens. Einige der quantitativen Vorhersagen wurden durch Experimente wie die Untersuchung des Verlaufs einer Infektion in verschiedenen Mutanten und Wildtyp-Mäusen überprüft. Die begrenzte Verfügbarkeit kinetischer Daten war der kritische Faktor bei der Auswahl der computer-gestützten Modelle. Der Erfolg unserer Modelle konnte durch den Vergleich mit experimentellen Beobachtungen belegt werden. Die vergleichenden Modelle in Kapitel 6 und 9 können zur Untersuchung neuer Wirt-Pathogen Interaktionen verwendet werden. Beispielsweise führt in Kapitel 6 die Analyse von Inhibitoren und inhibitorischer Signalwege aus drei Organismen zur Identifikation wichtiger regulatorischer Zentren in komplexen Organismen und in Kapitel 9 ermöglicht die Identifikation von drei Phasen in B. bronchiseptica und der Inhibition von IFN-γ durch den Faktor TTSS die Untersuchung ähnlicher Phasen und die Inhibition von IFN-γ in B. pertussis. Eine weitere wichtige Bedeutung bekommen diese Modelle durch die mögliche Identifikation neuer, essentieller Komponenten in Wirt-Pathogen Interaktionen. In silico Modelle der Effekte von Deletionen zeigen solche Komponenten auf, die anschließend durch experimentelle Mutationen weiter untersucht werden können. / In this century new experimental and computational techniques are adding an enormous amount of information, revealing many biological mysteries. The complexities of biological systems still broach new questions. Till now the main approach to understand a system has been to divide it in components that can be studied. The upcoming new paradigm is to combine the pieces of information in order to understand it at a global level. In the present thesis we have tried to study infectious diseases with such a global ‘Systems Biology’ approach. In the first part the apoptosis pathway is analyzed. Apoptosis (Programmed cell death) is used as a counter measure in different infections, for example viral infections. The interactions between death domain containing proteins are studied to address the following questions: i) How specificity is maintained - showing that it is induced through adaptors, ii) how proliferation/ survival signals are induced during activation of apoptosis – suggesting the pivotal role of RIP. The model also allowed us to detect new possible interacting surfaces. The pathway is then studied at a global level in a time step simulation to understand the evolution of the topology of activators and inhibitors of the pathway. Signal processing is further modeled in detail for the apoptosis pathway in M. musculus to predict the concentration time course of effector caspases. Further, experimental measurements of caspase-3 and viability of cells validate the model. The second part focuses on the phagosome, an organelle which plays an essential role in removal of pathogens as exemplified by M. tuberculosis. Again the problem is addressed in two main sections: i) To understanding the processes that are inhibited by M. tuberculosis; we focused on the phospholipid network applying a time step simulation in section one, which plays an important role in inhibition or activation of actin polymerization on the phagosome membrane. ii) Furthermore, actin polymers are suggested to play a role in the fusion of the phagosome with lysosome. To check this hypothesis an in silico model was developed; we find that the search time is reduced by 5 fold in the presence of actin polymers. Further the effect of length of actin polymers, dimensions of lysosome, phagosome and other model parameter is analyzed. After studying a pathway and then an organelle, the next step was to move to the system. This was exemplified by the host pathogen interactions between Bordetella pertussis and Bordetella bronchiseptica. The limited availability of quantitative information was the crucial factor behind the choice of the model type. A Boolean model was developed which was used for a dynamic simulation. The results predict important factors playing a role in Bordetella pathology especially the importance of Th1 related responses and not Th2 related responses in the clearance of the pathogen. Some of the quantitative predictions have been counterchecked by experimental results such as the time course of infection in different mutants and wild type mice. All these computational models have been developed in presence of limited kinetic data. The success of these models has been validated by comparison with experimental observations. Comparative models studied in chapters 6 and 9 can be used to explore new host pathogen interactions. For example in chapter 6, the analysis of inhibitors and inhibitory paths in three organism leads to the identification of regulatory hotspots in complex organisms and in chapter 9 the identification of three phases in B. bronchiseptica and inhibition of IFN-γ by TTSS lead us to explore similar phases and inhibition of IFN-γ in B. pertussis. Further an important significance of these models is to identify new components playing an essential role in host-pathogen interactions. In silico deletions can point out such components which can be further analyzed by experimental mutations.

Trotz deutlich zunehmender Durchimpfungsraten bei Kindern und Jugendlichen tritt Pertussis in Deutschland weiterhin als Ursache signifikanter Morbidität auf, v. a. bei ungeimpften Kindern und Säuglingen. Die Datenlage zur Pertussis-Epidemiologie ist vor allem in den alten Bundesländern aufgrund der bis 2013 fehlenden Meldepflicht sehr begrenzt. Das Ziel dieser Studie war die Ermittlung der Inzidenz und des Schweregrades von ICD-10-dokumentierten Bordetella pertussis-Hospitalisationen bei Kindern in Bayern. 27 (73%) von insgesamt 37 bayerischen Kinderkliniken beteiligten sich an der Surveillance-Studie. Sie führten eine Datenabfrage für im Jahr 2007 und 2008 stationär aufgenommene Kinder unter 17 Jahren mit einem ICD- 10-Code für Pertussis (A37.0 oder A37.9) als Haupt- oder Nebendiagnose bei Entlassung durch. Zu diesen Kindern wurden demographische Basisdaten sowie Jahr und Monat der Hospitalisation, Haupt- und alle Nebendiagnosen, Aufenthaltsdauer und Behandlung (OPS-Codes) erhoben. Im 2-Jahres-Zeitraum 2007/2008 wurden insgesamt 171 Fälle identifiziert (2007:109 Fälle; 2008: 62 Fälle), mit 0-17 gemeldeten Fällen pro Klinik. Mädchen waren mit 51% (n=88) etwas häufiger betroffen als Jungen. Der Altersmedian lag bei vier Monaten (IQR: 1-14 Monate); 121 (70.7%) Kinder waren Säuglinge <1 Jahr, 102 (59.6%) <6 Monate und 41 (24.0%) <2 Monate alt. Die jährliche Inzidenz bei Säuglingen <1 Jahr wurde auf 67/100.000 Hospitalisationen geschätzt, bei Säuglingen <2 Monate auf 22/100.000. Respiratorische Komplikationen einschließlich Pneumonien und Apnoen traten bei 31% (n=53) aller Kinder auf; von diesen waren 82% (n=39) <1 Jahr bzw. 44% (n=21) <2 Monate alt. Fünf Kinder (3%) mussten intensivstationär behandelt werden, davon waren 4 jünger als 4 Monate. Bei einem Säugling (0.6%) war ein Krampfanfall dokumentiert, kardio-respiratorische Komplikationen kamen bei 2% und Dehydratation bei 8% aller Kinder vor. Sowohl die Inzidenz der Hospitalisationen als auch die Komplikationsrate waren am höchsten bei Säuglingen <1 Jahr bzw. <2 Monaten. Die Ergebnisse belegen die Bedeutung der zeitgerechten Umsetzung der Impfempfehlung, d.h. den rechtzeitigen Start der Grundimmunisierung im Alter von 2, 3 und 4 Monaten. Auch die bereits 2004 empfohlene Impfung von Kontaktpersonen ist für die Prävention von Pertussis bei Säuglingen von hoher Wichtigkeit. Die bisher nicht allgemein empfohlene Impfung für Schwangere bzw. für Neugeborene könnte ggf. die Hospitalisationszahlen weiter senken; weitere Studien dazu werden dringend benötigt. / Despite high vaccination coverage among infants and adolescents, pertussis remains a reason for a high rate of morbidity and mortality, especially in unvaccinated infants. The data available on regard to pertussis epidemiology is very limited due to the fact that, until 2013, there was no reporting obligation for pertussis in the states of former West Germany. The aim of this study is to investigate the hospitalization rate and severity of ICD-10 documented Bordetella pertussis infections in Bavarian children. 27 (73%) of a total of 37 Bavarian children`s hospitals participated in the surveillance study. They carried out data retrieval for children under 17 years of age hospitalized in 2007 or 2008 with an ICD-10-pertussis-code (A37.0 or A37.9) as the primary or secondary diagnosis at discharge. The collected database included basic demographic data, year and month of hospital admission, all primary and secondary diagnoses, duration of hospital stay and treatment (OPS- and DRG-codes). From 2007 to 2008 a total of 171 cases were reported (2007: 109 cases; 2008: 62 cases), with 0-17 cases reported per hospital. At 51%, girls were more frequently affected than boys. The median age was 4 months (IQR: 1-14 months). 121 (70,7%) children were infants <1 year, 102 (59,6%) <6 months and 41 (24%) <2 months of age. The annual incidence for infants <1 year was estimated at 67 pertussis hospitalizations/100,000 children < 1 year, and for infants <2 months at 109 pertussis hospitalizations/100,000 children <2 months. Respiratory complications, including pneumonia and apnea, developed in 31% (n=53) of the children: whereby 82% (n=39) of them were <1 year old and 44% (n=21) <2 months of age. Five children (3%) required intensive care treatment, four of them were younger than 4 months of age. Convulsions were observed in one infant (0,6%). Further complications were cardio-respiratory complications (2%) and dehydration (8%). Both the incidence and complication rate were highest among children under 1 year of age and for infants under 2 months of age. The results prove the importance of timely implementation of vaccination recommendations i. e. the punctual beginning of basic immunization at the age of 2, 3 and 4 months. Furthermore, the vaccination of contact persons, which was recommended in 2004, is also extremely important for pertussis prevention in infants. Until now there has been no general recommendation for the vaccination of pregnant women or neonates as yet. However, these vaccinations could possibly reduce hospitalization rates even more; further studies are urgently required in this area.

Thesis (Ph. D.)--University of Virginia, 2001. / Includes bibliographical references (leaves 146-168). Also available online through Digital Dissertations.

En este trabajo de tesis doctoral y bajo la hipótesis de la utilización por parte la bacteria de Bordetella pertussis del desarrollo en biofilm como un posible mecanismo de persistencia en el hospedador se evaluó la capacidad de formación de biofilm por parte de aislados clínicos de Bordetella pertussis obtenidos de pacientes infectados y tratados en el Hospital Sor María Ludovica de la ciudad de La Plata. Todos los aislados clínicos estudiados, incluyendo cepas aisladas entre los años 2001 y 2007 presentaron mayor capacidad de formación de biofilm en superficies abióticas cuando se las comparó con la cepa de referencia Bordetella pertussis Tohama I, cepa adaptada al laboratorio y utilizada en la producción de vacunas contra la enfermedad. De los ocho aislados clínicos estudiados se seleccionó uno, debido a una exacerbada producción de biofilm (produjo 5 veces más biomasa en las mismas condiciones de cultivo cuando se la comparó con la cepa de referencia) y se realizó un estudio de proteómica comparativa para establecer un posible fenotipo adaptado a la condición de cultivo en estudio. Los experimentos se llevaron a cabo en colaboración con el grupo de la Dra. Monika Elingh Schulz de la Universidad de Veterinaria de Viena, Austria y se utilizó la tecnología 2D-DIGE para evaluar la expresión diferencial de proteínas de la fracción soluble entre ambas cepas en condiciones de cultivo líquido y biofilm. Un análisis de componente principal indicó que las diferencias más significativas entre los fenotipos expresados es consecuencia de la diferencia de cepas y posteriormente consecuencia de la condición de cultivo. Se identificaron 32 proteínas diferencialmente expresadas (mayor de 3 veces de diferencia) entre ambas cepas, las cuales fueron asignadas a las categorías: metabolismo y obtención de energía, síntesis de aminoácidos y proteínas, transporte y virulencia (Bcrh2, OmpQ, Vag8 y BrkA). Todos los factores de virulencia identificados corresponden a proteínas reguladas por el sistema de dos componentes BVGAS. Sabiendo que dicho sistema regula la expresión de importantes adhesinas en Bordetella pertussis y que su inactividad provoca la incapacidad de formación de biofilm es que se decidió estudiar a través de la técnica de PCR en tiempo real la expresión del ARN mensajero de un conjunto mayor de factores de virulencia regulados por este sistema incluyendo adhesinas tales como FHA, PRN, Fim, BipA y la proteína de secreción del sistema tipo III Bsp22 que ha sido reportada en la bibliografía como participante junto a Fim en la producción de filamentos que brindarían estructura a la matriz extracelular del biofilm de B. pertussis. Los resultados obtenidos indicaron un aumento en la expresión de ARN mensajero para la totalidad de los genes estudiados indicando que posiblemente el aumento en la expresión de adhesinas reguladas por el sistema BvgAS, sumado a la expresión de enzimas involucradas en la producción de energía que podrían explicar la alta velocidad de duplicación de la cepa clínica Bp2723 le conferirían la capacidad de formar un biofilm más robusto comparado con la cepa de referencia en las condiciones de cultivo estudiadas.

: Filamentous hemagglutinin (FHA) is adhesive protein molecule that is secreted by Gram- negative bacterium Bordetella pertusis, the causative agent of whooping cough (pertussis). The C-terminal segment of FHA plays a crucial role in host-pathogen interaction, however, the structural features are still unknown. Here, we identified the C-terminal residue of FHA and processed form of FHA (FHA*) as alanine residues in position 2304 and 2228, respectively. Circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy demonstrated that the C-terminal segment of FHA(FHA 1995-2228) is characterized by alpha-helical contribution without any compact protein fold. Moreover, suppression of transcription of small regulatory RNA pairing to the 5'-end of fhaB transcript resulted in two- fold increase of FHA production. These data suggested that the C-terminal segment of FHA appear to be an unstructured protein and FHA secretion is negatively regulated by small regulatory RNA. (In Czech) Keywords: Bordetella pertussis, filamentous hemagglutinin, small RNA

The Gram-negative pathogen bacterium Bordetella pertussis is the infectious agent causing pertussis or whooping cough. The infection is dangerous to infants, often being deadly if untreated. Since whole-cell pertussis vaccines have been replaced by acellular pertussis vaccines, pertussis has become the most prevalent vaccine-preventable disease in developed countries. Therefore, the development of a new generation of pertussis vaccines has become a high priority. Opsonophagocytic assays are one method used to assess the efficacy of new vaccines. The main objective of the thesis is to develop opsonophagocytic killing and uptake assays for the measurement of functional antibody activity against Bordetella pertussis. Neutrophils from mice and humans were isolated by three different methods and used for the assessment of different human and mouse sera in opsonophagocytic killing and uptake assays. Different experimental conditions were tested, including multiplicity of infection and serum dilutions. The opsonophagocytic uptake assay proved to discriminate between naïve and immune sera. Serum from mice vaccinated with the whole-cell pertussis vaccine enhanced opsonophagocytic uptake of B. pertussis cells into neutrophils, while serum from mice immunized with the acellular pertussis vaccine did not....

Pertussis is an infectious disease caused by the Gram-negative bacterium Bordetella pertussis. In Peru, actual public health programs indicate that vaccination against B. pertussis must be mandatory and generalized, besides all detected cases must be reported. The objective of this study was to determine the prevalence of B. pertussis among children under five years of age with a presumptive diagnosis of whopping cough in Cajamarca, a region located in northern Peru. / Background and Objectives: Pertussis is an infectious disease caused by the Gram-negative bacterium Bordetella pertussis. In Peru, actual public health programs indicate that vaccination against B. pertussis must be mandatory and generalized, be-sides all detected cases must be reported. The objective of this study was to determine the prevalence of B. pertussis among children under five years of age with a presumptive diagnosis of whopping cough in Cajamarca, a region located in northern Peru. Materials and Methods: The population of this cross-sectional study were children under 5 years old hospitalized as presumptive cases of pertussis during December 2017 to December 2018. The nasopharyngeal samples were analyzed by real-time PCR for the detection of B. pertussis. Results: B. pertussis was identified as PCR + in 42.3% of our sample (33/78). The clinical presentation that was observed most frequently includes paroxysmal coughing (97%), difficulty breathing (69.7%), cyanosis (72.7%) and post-tussive em-esis (60.6%). Additionally, pneumonia was the most observed complication (33.3%). Four of the patients with PCR+ for B. pertussis presented only lymphocytosis, five only leukocytosis, two patients with decreased leukocytosis and lymphocytes and only one patient with leukopenia and relative lymphocytosis. There was a percentage of 84.8% of unvaccinated children in the PCR+ group. Finally, the mother was the most frequent symptom carrier (18.2%). Conclusion: In conclusion, in the studied population there is a high rate of PCR+ cases for B. pertussis. Laboratory values may show leukopenia or lymphopenia in patients with pertussis. It is necessary to use appropriate laboratory diagnostic tests in all infants with respiratory symptoms for B. pertussis. Since, the clinical diagnosis overestimates the diagnosis of pertussis. / Revisión por pares

Background: Acute respiratory infections (ARIs) represent an important cause of morbidity and mortality in children, remaining a major public health concern, especially affecting children under 5 years old from low-income countries. Unfortunately, information regarding their epidemiology is still limited in Peru. Methods: A secondary data analysis was performed from a previous cross-sectional study conducted in children with a probable diagnosis of Pertussis from January 2010 to July 2012. All samples were analyzed via Polymerase Chain Reaction (PCR) for the following etiologies: Influenza-A, Influenza-B, RSV-A, RSV-B, Adenovirus, Parainfluenza 1 virus, Parainfluenza 2 virus, Parainfluenza 3 virus, Mycoplasma pneumoniae and Chlamydia pneumoniae. Results: A total of 288 patients were included. The most common pathogen isolated was Adenovirus (49%), followed by Bordetella pertussis (41%) from our previous investigation, the most prevelant microorganisms were Mycoplasma pneumonia (26%) and Influenza-B (19.8%). Coinfections were reported in 58% of samples and the most common association was found between B. pertussis and Adenovirus (12.2%). Conclusions: There was a high prevalence of Adenovirus, Mycoplasma pneumoniae and other etiologies in patients with a probable diagnosis of pertussis. Despite the presence of persistent cough lasting at least two weeks and other clinical characteristics highly suspicious of pertussis, secondary etiologies should be considered in children under 5 years-old in order to give a proper treatment. / Revisión por pares

Objective: This study aimed to determine the prevalence of A. baumannii in children aged less than 1 year admitted with a clinical diagnosis of whooping cough. Results: A total of 225 nasopharyngeal samples from children under 1 year old hospitalized with clinical diagnosis of whooping cough were studied from January 2010 to July 2012. The presence of A. baumannii was detected in 20.89% (47/225) of the nasopharyngeal swab samples. Among the 47 patients with A. baumannii: 5 were diagnosed with A. baumannii monoinfection, 17 co-infection with bacteria, 7 co-infection with virus and 18 co-infection with bacteria + virus. It was observed that 51.6% (116/225) were children between 29 days and 3 months old, this same group had the highest overall prevalence with 53.3%. The most common co-infecting pathogens were Bordetella pertussis in 55.3%, Adenovirus in 42.6% and Mycoplasma pneumoniae in 23.4%. / Revisión por pares

Background and Objectives: Pertussis is an infectious disease caused by the Gram-negative bacterium Bordetella pertussis. In Peru, actual public health programs indicate that vaccination against B. pertussis must be mandatory and generalized, be-sides all detected cases must be reported. The objective of this study was to determine the prevalence of B. pertussis among children under five years of age with a presumptive diagnosis of whopping cough in Cajamarca, a region located in northern Peru. Materials and Methods: The population of this cross-sectional study were children under 5 years old hospitalized as presumptive cases of pertussis during December 2017 to December 2018. The nasopharyngeal samples were analyzed by real-time PCR for the detection of B. pertussis. Results: B. pertussis was identified as PCR + in 42.3% of our sample (33/78). The clinical presentation that was observed most frequently includes paroxysmal coughing (97%), difficulty breathing (69.7%), cyanosis (72.7%) and post-tussive em-esis (60.6%). Additionally, pneumonia was the most observed complication (33.3%). Four of the patients with PCR+ for B. pertussis presented only lymphocytosis, five only leukocytosis, two patients with decreased leukocytosis and lymphocytes and only one patient with leukopenia and relative lymphocytosis. There was a percentage of 84.8% of unvaccinated children in the PCR+ group. Finally, the mother was the most frequent symptom carrier (18.2%). Conclusion: In conclusion, in the studied population there is a high rate of PCR+ cases for B. pertussis. Laboratory values may show leukopenia or lymphopenia in patients with pertussis. It is necessary to use appropriate laboratory diagnostic tests in all infants with respiratory symptoms for B. pertussis. Since, the clinical diagnosis overestimates the diagnosis of pertussis. / Revisión por pares