Between adaptation and virulence:A proteomics view on Staphylococcus aureus infections

Staphylococcus aureus is one of the commonly encountered bacteria of the human microbiome. Although mostly a seemingly harmless commensal microbe, S. aureus can act as an invasive pathogen with seriously devastating effects on its host’s health and wellbeing. A wide range of infections caused by this bacterium has been reported to affect diverse parts of the human body, including the skin, soft tissues and bones, as well as important organs like the heart, kidneys and lungs. Particularly, S. aureus is infamous for being a major causative agent of respiratory tract infections that may escalate up to necrotizing pneumonia. Due to its clinical relevance, this pathogen has been intensively studied for many years. Nonetheless, further research in this field is still needed, because of the high capacity of S. aureus to evolve drug resistance, its high genomic plasticity and adaptability and, not in the last place, the plethora of niches within the human body where it can thrive and survive. In this regard, there are still many uncertainties concerning the specific adaptations carried out by S. aureus during colonization and infection of the human body, the transition between both stages, and upon the invasion of different types of host cells. To shed more light on some of these adaptations, the research described in this thesis has employed in vitro models of infection that mimic particular conditions during the infectious process with special focus on the lung epithelium. The adaptations displayed by S. aureus were monitored using advanced proteomics. Furthermore, the analyses documented in this thesis included S. aureus strains with diverse backgrounds and epidemiology to take into account the genetic diversity encountered in this species.Staphylococcus aureus ist eines der am häufigsten vorkommenden Bakterien im menschlichen Mikrobiom. Auch wenn sich S.aureus meist eher harmlos verhält, kann diese Mikrobe als invasiver Krankheitserreger bedrohliche Auswirkungen auf die Gesundheit und das Wohlbefinden von Patienten haben. Ein breites Spektrum an Infektionen, die durch dieses Bakterium ausgelöst werden, kann verschiedenste Körperteile des Menschens wie Haut, Weichteile und Knochen, sowie Lebenswichtige Organe wie das Herz, die Nieren und die Lunge betreffen. S. aureus ist insbesondere als ein Haupterreger von Atemwegsinfekten bekannt, welche sich bis zu einer nekrotisierenden Lungenentzündung entwickeln können. Aufgrund seiner klinischen Bedeutung wird dieser Kranksheitserrger bereits seit Jahren intensiv untersucht. Dennoch ist eine Erforschung von S. aureus wegen dessen Fähigkeiten Antibiotikaresistenzen zu entwickeln, der hohen genomischen Plastizität und Anpassungsfähigkeit und nicht zuletzt, der Vielzahl an Nischen im menschlichen Körper, wo es gedeihen und überleben kann, weiter notwendig. Die spezifischen Anpassungen von S. aureus während der Besiedlung und Kolonisierung des menschlichen Körpers, während des Übergangs zwischen diesen beiden Phasen sowie nach Eindringen in verschiedene Wirtszelltypen sind bisher nur unvollständig aufgeklärt. Um im Rahmen dieser Doktorabeit einige Einblicke in diese Anpassungen zu erhalten, wurden in vitro Infektionsmodelle eingesetzt, die bestimmte Bedingungen des Infektionsprozesses speziell im Lungenepithel widerspiegeln. Diese Anpassungen von S. aureus wurden mittels moderner Proteomanalysen untersucht. Weiterhin wurden im Rahmen dieser Arbeit S. aureus Stämme verschiedenen Ursprungs in die Analysen einbezogen, um auch die genetische Vielfalt dieser Spezies zu berücksichtigen

Between adaptation and virulence:A proteomics view on Staphylococcus aureus infections

Staphylococcus aureus is een reguliere bewoner van het menselijke lichaam. Ongeveer 30% van de gezonde volwassenen is drager van deze bacterie, meestal in de neus. Hoewel S. aureus dragerschap meestal symptoomloos is kan deze bacterie ziektes verwekken die in ernst variëren van een milde huidinfectie tot een levensbedreigende longontsteking. Dergelijke infecties kunnen moeilijk behandelbaar zijn, niet alleen omdat de bacterie gemakkelijk resistent wordt tegen antibiotica, maar ook omdat hij zich erg goed kan aanpassen aan de verschillende omstandigheden in en op ons lichaam. De aanpassingsmechanismen die S. aureus benut worden sinds vele jaren bestudeerd onder goed controleerbare laboratoriumcondities. Op grond hiervan kennen we veel van de basisprincipes die ten grondslag liggen aan het aanpassingsvermogen van S. aureus. Desondanks weten we nog steeds te weinig van de uitdagingen die de bacterie ondervindt, wanneer hij onze cellen en weefsels infecteert. Dit komt, doordat die condities erg complex en veranderlijk zijn en de bacterie dientengevolge vele functies tegelijk moet aanpassen. In het onderhavige promotie-onderzoek werden nieuwe technologieën ingezet om de eiwitsamenstelling van de bacterie precies te quantificeren, allereerst gedurende een infectie van humaan longepitheel en vervolgens in bacterie-isolaten die zich hebben aangepast aan infectiecondities in een ziekenhuisomgeving of onder de gezonde bevolking. De waargenomen veranderingen in eiwitsamenstelling zijn representatief voor de beslissingen die de bacterie neemt onder verschillende omstandigheden. De resultaten van dit promotie-onderzoek laten zien, dat met name aanpassingen in de bacteriële stofwisseling van eminent belang zijn tijdens een infectie en dat deze aanpassingen bepalend zijn voor de uitkomst van S. aureus infecties.Staphylococcus aureus is a regular resident of the human body. This bacterium is carried by around 30% of the healthy population, most frequently in the nasal cavity. Although carriage of S. aureus is generally asymptomatic, it is a renowned pathogen capable of causing diseases that range from mild skin infections to necrotizing pneumonia. Such infections may be difficult to treat, not only because this bacterium rapidly develops resistance to antibiotics, but also because it can effectively adapt to different environments within and around the human body. The adaptive mechanisms of S. aureus have been studied for many years in well-controlled laboratory settings. This has deepened our understanding of bacterial adaptations. Yet, the challenges imposed on the bacterium during infection of human cells and tissues are more complex, and the respective bacterial responses are still poorly understood especially since the bacterium needs to activate and modulate several adaptive pathways simultaneously. In the present PhD research, new technologies allowing precise quantification of proteins have been employed to assess the adaptive behavior of S. aureus, firstly upon invasion of lung epithelial cells, but also in response to different epidemiological conditions in the hospital and the general population. Importantly, the changes in protein abundance reflect the “decisions” taken by the pathogen in these widely differing conditions. The results presented in this thesis highlight the importance of adaptations in bacterial metabolism during infection, and they show that metabolic adaptations play critical roles in the outcome of infections caused by S. aureus

A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions.

Data-independent acquisition mass spectrometry promises higher performance in terms of quantification and reproducibility compared to data-dependent acquisition mass spectrometry methods. To enable high-accuracy quantification of Staphylococcus aureus proteins, we have developed a global ion library for data-independent acquisition approaches employing high-resolution time of flight or Orbitrap instruments for this human pathogen. We applied this ion library resource to investigate the time-resolved adaptation of S. aureus to the intracellular niche in human bronchial epithelial cells and in a murine pneumonia model. In epithelial cells, abundance changes for more than 400 S. aureus proteins were quantified, revealing, e.g., the precise temporal regulation of the SigB-dependent stress response and differential regulation of translation, fermentation, and amino acid biosynthesis. Using an in vivo murine pneumonia model, our data-independent acquisition quantification analysis revealed for the first time the in vivo proteome adaptation of S. aureus. From approximately 2.15 × 1

Long-term outcomes of the global tuberculosis and COVID-19 co-infection cohort

Background: Longitudinal cohort data of patients with tuberculosis (TB) and coronavirus disease 2019 (COVID-19) are lacking. In our global study, we describe long-term outcomes of patients affected by TB and COVID-19. Methods: We collected data from 174 centres in 31 countries on all patients affected by COVID-19 and TB between 1 March 2020 and 30 September 2022. Patients were followed-up until cure, death or end of cohort time. All patients had TB and COVID-19; for analysis purposes, deaths were attributed to TB, COVID-19 or both. Survival analysis was performed using Cox proportional risk-regression models, and the log-rank test was used to compare survival and mortality attributed to TB, COVID-19 or both. Results: Overall, 788 patients with COVID-19 and TB (active or sequelae) were recruited from 31 countries, and 10.8% (n=85) died during the observation period. Survival was significantly lower among patients whose death was attributed to TB and COVID-19 versus those dying because of either TB or COVID-19 alone (p<0.001). Significant adjusted risk factors for TB mortality were higher age (hazard ratio (HR) 1.05, 95% CI 1.03-1.07), HIV infection (HR 2.29, 95% CI 1.02-5.16) and invasive ventilation (HR 4.28, 95% CI 2.34-7.83). For COVID-19 mortality, the adjusted risks were higher age (HR 1.03, 95% CI 1.02-1.04), male sex (HR 2.21, 95% CI 1.24-3.91), oxygen requirement (HR 7.93, 95% CI 3.44-18.26) and invasive ventilation (HR 2.19, 95% CI 1.36-3.53). Conclusions: In our global cohort, death was the outcome in >10% of patients with TB and COVID-19. A range of demographic and clinical predictors are associated with adverse outcomes

Kinetic and bioinformatics characterization of cellulases from the metagenomic library of GEBIX specific to African oil palm (Elaeis guineensis Jacq.) empty fruit bunch

Magíster en Ingeniería QuímicaMaestrí

In vitro and in silico characterization of metagenomic soil-derived cellulases capable of hydrolyzing oil palm empty fruit bunch

Diversification of raw material for biofuel production is of interest to both academia and industry. One attractive substrate is a renewable lignocellulosic material such as oil palm (Elaeis guineensis Jacq.) empty fruit bunch (OPEFB), which is a byproduct of the palm oil industry. This study aimed to characterize cellulases active against this substrate. Cellulases with activity against OPEFB were identified from a metagenomic library obtained from DNA extracted from a high-Andean forest ecosystem. Our findings show that the highest cellulolytic activities were obtained at pH and temperature ranges of 4–10 and 30 °C–60 °C, respectively. Due to the heterogeneous character of the system, degradation profiles were fitted to a fractal-like kinetic model, evidencing transport mass transfer limitations. The sequence analysis of the metagenomic library inserts revealed three glycosyl hydrolase families. Finally, molecular docking simulations of the cellulases were carried out corroborating possible exoglucanase and β-glucosidase activity

Promoción de la salud y entornos saludables

Acné juvenil, presentación de 2 casos clínicosAlta ingesta de proteínas y su relación con el aumento de tejido adiposo en preescolaresAnálisis para la integración entre salud y educación para el desarrollo de programas de promociónCalidad de los estilos de vida de funcionarios académicos de la Universidad del BiobíoCambios en el patrón de consumo de alimentos en niños con un kiosco saludableCaracterísticas del sueño habitual y su relación con el nivel de somnolencia diurna en adolescentesCaracterización de información acerca de promoción de salud población urbana de Temuco, Región de la Araucanía, ChileComportamiento sexual durante el embarazo en usuarias de centros de salud, La Florida, Santiago, 2006Estado nutricional y actividad física en escolares de 1º, 5º y 8º básico de Arica¿Están los padres informados si sus hijos tienen miedo a la atención dental?Evaluación cualitativa del componente promocional de un programa psicosocial en población escolar vulnerableEvaluación de la efectividad de la aplicación del Programa Educativo "Quiero mi boca siempre sana"Evaluación estadística del uso de edulcorantes alimentarios en una población de SantiagoEvolución de la prematurez y características sociodemográficas de la población materna en ChileFactores de riesgo asociados a prevalencia de caries en alumnos del Ejército de ChileHábitos alimentarios en escolares de distinto tipo de establecimientos educacionalesNivel de conocimientos de los habitantes de Loncoche sobre enfermedades parasitarias, IX, Región, Chile 2009Nutrición y condiciones socioeconómicas de escolares de la escuela Jesús María Sifontes, Los Teques, VenezuelaRelación entre dificultad para comprar cigarrillos, lugares de venta y curso en adolescente

Promoción de la salud y entornos saludables

Acné juvenil, presentación de 2 casos clínicosAlta ingesta de proteínas y su relación con el aumento de tejido adiposo en preescolaresAnálisis para la integración entre salud y educación para el desarrollo de programas de promociónCalidad de los estilos de vida de funcionarios académicos de la Universidad del BiobíoCambios en el patrón de consumo de alimentos en niños con un kiosco saludableCaracterísticas del sueño habitual y su relación con el nivel de somnolencia diurna en adolescentesCaracterización de información acerca de promoción de salud población urbana de Temuco, Región de la Araucanía, ChileComportamiento sexual durante el embarazo en usuarias de centros de salud, La Florida, Santiago, 2006Estado nutricional y actividad física en escolares de 1º, 5º y 8º básico de Arica¿Están los padres informados si sus hijos tienen miedo a la atención dental?Evaluación cualitativa del componente promocional de un programa psicosocial en población escolar vulnerableEvaluación de la efectividad de la aplicación del Programa Educativo "Quiero mi boca siempre sana"Evaluación estadística del uso de edulcorantes alimentarios en una población de SantiagoEvolución de la prematurez y características sociodemográficas de la población materna en ChileFactores de riesgo asociados a prevalencia de caries en alumnos del Ejército de ChileHábitos alimentarios en escolares de distinto tipo de establecimientos educacionalesNivel de conocimientos de los habitantes de Loncoche sobre enfermedades parasitarias, IX, Región, Chile 2009Nutrición y condiciones socioeconómicas de escolares de la escuela Jesús María Sifontes, Los Teques, VenezuelaRelación entre dificultad para comprar cigarrillos, lugares de venta y curso en adolescente