Sepsis-induced organ failure is associated with high morbidity and mortality rates. The onset of an exaggerated host response to microbial invasion and/or trauma, is believed to be the primary cause of excessive inflammation and the subsequent tissue hypoperfusion observed in patients with severe sepsis. In our mouse model of sepsis induced by cecal ligation and perforation (CLP), symptoms indicative of the disease, including diarrhea, increased ventilation and persistent hypothermia, are present at six hours after the surgery (T6). In the untreated CLP mice, mortality occurs starting at T15. As induced hypothermia has shown to exert immunomodulatory effects, this study is aimed at assessing its potential in attenuating inflammation and improving survival in experimental sepsis. Our data has shown that deep hypothermia initiated at T6, by means of cold chamber-induced cooling, prolongs survival. Plasma cytokine quantification by enzyme-linked immunosorbent assays (ELISA) also reveals that induced deep hypothermia reduces tumour necrosis factor(TNF)-α and interleukin (IL)-6 production in untreated CLP mice. In contrast, induced moderate hypothermia does not have such effect. Antibiotic (cefotaxime) and saline resuscitation initiated immediately following CLP ensures survival. However, when these supportive treatments are initiated at T6, >50% mortality is observed in the CLP mice with or without induced hypothermia. In summary, this preliminary study provides proof for a downregulated inflammatory response mediated by external cooling. However, to achieve a survival benefit, treatment strategies in addition to cooling and antibiotics may be required.

Sepsis-induced organ failure is associated with high morbidity and mortality rates. The onset of an exaggerated host response to microbial invasion and/or trauma, is believed to be the primary cause of excessive inflammation and the subsequent tissue hypoperfusion observed in patients with severe sepsis. In our mouse model of sepsis induced by cecal ligation and perforation (CLP), symptoms indicative of the disease, including diarrhea, increased ventilation and persistent hypothermia, are present at six hours after the surgery (T6). In the untreated CLP mice, mortality occurs starting at T15. As induced hypothermia has shown to exert immunomodulatory effects, this study is aimed at assessing its potential in attenuating inflammation and improving survival in experimental sepsis. Our data has shown that deep hypothermia initiated at T6, by means of cold chamber-induced cooling, prolongs survival. Plasma cytokine quantification by enzyme-linked immunosorbent assays (ELISA) also reveals that induced deep hypothermia reduces tumour necrosis factor(TNF)-α and interleukin (IL)-6 production in untreated CLP mice. In contrast, induced moderate hypothermia does not have such effect. Antibiotic (cefotaxime) and saline resuscitation initiated immediately following CLP ensures survival. However, when these supportive treatments are initiated at T6, >50% mortality is observed in the CLP mice with or without induced hypothermia. In summary, this preliminary study provides proof for a downregulated inflammatory response mediated by external cooling. However, to achieve a survival benefit, treatment strategies in addition to cooling and antibiotics may be required.

In the first study, three different transport systems for bacteria were evaluated. The CLSI M40-A guideline was used to monitor the maintenance of both mono- and polymicrobial samples during a simulated transportation at room temperature that lasted 0-48 h. All systems were able to maintain the viability of all organisms for 24 h, but none of them could support all tested species after 48 h.  The most difficult species to recover was Neisseria gonorrhoeae, and in polymicrobial samples overgrowth was an observed problem. The aim of the second study was to study the presence of TSST-1 and three other important toxin genes in invasive isolates of Staphylococcus aureus collected during the years 2000-2012 at two tertiary hospitals. The genes encoding the staphylococcal toxins were detected by PCR, and whole-genome sequencing was used for analyzing the genetic relatedness between isolates. The results showed that the most common toxin was TSST-1, and isolates positive for this toxin exhibited a clear clonality independent of year and hospital. The typical patient was a male aged 55-74 years and with a bone or a joint infection. The third study was a clinical study of the effect of silver-based wound dressings on the bacterial flora in chronic leg ulcers. Phenotypic and genetic silver-resistance were investigated before and after topical silver treatment, by determining the silver nitrate MICs and by detecting sil genes with PCR. The silver-based dressings had a limited effect on primary wound pathogens, and the activity of silver nitrate on S. aureus was mainly bacteriostatic. A silver-resistant Enterobacter cloacae strain was identified after only three weeks of treatment, and cephalosporin-resistant members of the Enterobacteriaceae family were relatively prone to developed silver-resistance after silver exposure in vitro. The last study was undertaken in order to develop an easy-to-use method for simulating the laundering process of hospital textiles, and apply the method when evaluating the decontaminating efficacy of two different washing temperatures. The laundering process took place at professional laundries, and Enterococcus faecium was used as a bioindicator. The results showed that a lowering of the washing temperature from 70°C to 60°C did not affect the decontamination efficacy; the washing cycle alone reduced the number of bacteria with 3-5 log10 CFU, whereas the following tumble drying reduced the bacterial numbers with another 3-4 log10 CFU, yielding the same final result independent of the washing temperature. To ensure that sufficient textile hygiene is maintained, the whole laundering process needs to be monitored. The general conclusion is that all developmental work in the bacterial field requires time and a large strain collection.

Sepsis-induced organ failure is associated with high morbidity and mortality rates. The onset of an exaggerated host response to microbial invasion and/or trauma, is believed to be the primary cause of excessive inflammation and the subsequent tissue hypoperfusion observed in patients with severe sepsis. In our mouse model of sepsis induced by cecal ligation and perforation (CLP), symptoms indicative of the disease, including diarrhea, increased ventilation and persistent hypothermia, are present at six hours after the surgery (T6). In the untreated CLP mice, mortality occurs starting at T15. As induced hypothermia has shown to exert immunomodulatory effects, this study is aimed at assessing its potential in attenuating inflammation and improving survival in experimental sepsis. Our data has shown that deep hypothermia initiated at T6, by means of cold chamber-induced cooling, prolongs survival. Plasma cytokine quantification by enzyme-linked immunosorbent assays (ELISA) also reveals that induced deep hypothermia reduces tumour necrosis factor(TNF)-α and interleukin (IL)-6 production in untreated CLP mice. In contrast, induced moderate hypothermia does not have such effect. Antibiotic (cefotaxime) and saline resuscitation initiated immediately following CLP ensures survival. However, when these supportive treatments are initiated at T6, >50% mortality is observed in the CLP mice with or without induced hypothermia. In summary, this preliminary study provides proof for a downregulated inflammatory response mediated by external cooling. However, to achieve a survival benefit, treatment strategies in addition to cooling and antibiotics may be required.

Meningitis is an infection of the meninges, a layer of tissue surrounding the brain. In cases of pneumococcal meningitis (where the bacterium Streptococcus pneumoniae is the causat- ive agent) this causes severe inflammation, requiring intensive care and rapid antibiotic treatment. The contribution of variation in host and pathogen genetics to pneumococcal meningitis is unknown. In this thesis I develop and apply statistical genetics techniques to identify genomic variation associated with the various stages of pneumococcal meningitis, including colonisation, invasion and severity. I start by describing the development of a method to perform genome-wide association studies (GWAS) in bacteria, which can find variation in bacterial genomes associated with bacterial traits such as antibiotic resistance and virulence. I then applied this method to longitudinal samples from asymptomatic carriage, and found lineages and specific variants associated with altered duration of carriage. To assess meningitis versus carriage samples I applied similar analysis techniques, and found that the bacterial genome is crucial in determining invasive potential. As well as bacterial serotype, which I found to be the main effect, I discovered many independent sequence variants associated with disease. Separately, I analysed within host-diversity during the invasive phase of disease and found it to be of less relevance to disease progression. Finally, I analysed host genotype data from four independent studies using GWAS and heritability estimates to determine the contribution of human sequence variation to pneumococcal meningitis. Host sequence accounted for some variation in susceptibility to and severity of meningitis. The work concludes with a combined analysis of pairs of bacterial and human sequences from meningitis cases, and finds variation correlated between the two.

Neutropenia febril (NF) constitui complicação frequente do tratamento quimioterápico do câncer e está associada a altas taxas de morbimortalidade. O reconhecimento dos principais fatores associados ao desenvolvimento de desfechos clínicos desfavoráveis na NF é fundamental, uma vez que estes podem ser utilizados como marcadores prognósticos ou alvos terapêuticos. Este estudo objetiva determinar os principais fatores associados com mortalidade, tempo de hospitalização, incidência de bacteremia por patógenos multirresistentes e incidência de choque séptico no início da febre em pacientes hospitalizados com NF secundária à quimioterapia citotóxica para o câncer. Na presente coorte prospectiva composta por 305 episódios consecutivos de NF (em 169 pacientes com câncer) realizada em um hospital terciário no período de outubro de 2009 a agosto de 2011, as seguintes questões de pesquisa foram avaliadas: impacto do tempo de início da antibioticoterapia na mortalidade em 28 dias; fatores relacionados com tempo de hospitalização; impacto dos fatores microbiológicos da bacteremia no desenvolvimento de choque séptico no início do episódio de NF; fatores de risco para bacteremia por patógenos multirresistentes; impacto da bacteremia por Staphylococcus coagulase-negativo na mortalidade em 28 dias. Em 5 publicações distintas, os seguintes resultados foram notados: o atraso do início da antibioticoterapia está associado a maiores taxas de mortalidade em 28 dias; neoplasia hematológica, regimes quimioterápicos de altas doses, duração da neutropenia e bacteremia por Gram-negativos multirresistentes estão associados com períodos prolongados de internação por NF; infecção de corrente sanguínea polimicrobiana, bacteremia por Escherichia coli e bacteremia por Streptococcus viridans estão associados a choque séptico no início do episódio de NF; idade avançada, duração da neutropenia e presença de cateter venoso central estão associados com bacteremia por patógenos multirresistentes; bacteremia por Staphylococcus coagulase-negativo está associada a menores taxas de mortalidade em 28 dias quando comparado à bacteremia por outros patógenos. / Febrile neutropenia (FN) is a common complication of cancer chemotherapy and is associated with high morbidity and mortality rates. Recognition of the main factors associated with the development of adverse clinical outcomes in FN is crucial, given that these factors can be used as prognostic markers or therapeutic targets. This study aims to determine the main factors associated with mortality, length of hospital stay, incidence of bacteremia by multidrug-resistant pathogens and incidence of septic shock at the onset of fever in hospitalized patients with FN secondary to cancer cytotoxic chemotherapy. In the present prospective cohort of 305 FN episodes (in 169 cancer patients) conducted at a tertiary hospital from October 2009 to August 2011, the following research questions were evaluated: impact of time to antibiotic administration on 28-day mortality; factors associated with length of hospital stay; impact of microbiological factors of bacteremia on the development of septic shock at the onset of FN; risk factors for bacteremia by multidrug-resistant pathogens; impact of coagulasenegative Staphylococcus bacteremia on 28-day mortality. In 5 distinct publications, the following results were noted: delay of antibiotic administration is associated with higher 28-day mortality rates; hematologic malignancy, high-dose chemotherapy regimens, duration of neutropenia and bacteremia by multidrug-resistant Gram-negative bacteria are associated with prolonged length of hospital stay; polymicrobial bloodstream infection, bacteremia by Escherichia coli, and bacteremia by viridans sreptococci are associated with septic shock at the onset of FN; advanced age, duration of neutropenia and presence of indwelling central venous catheters are associated with bacteremia by multidrug-resistant pathogens; coagulase-negative Staphylococcus bacteremia is associated with lower 28-day mortality rates compared with bacteremia by other pathogens.

Neutropenia febril (NF) constitui complicação frequente do tratamento quimioterápico do câncer e está associada a altas taxas de morbimortalidade. O reconhecimento dos principais fatores associados ao desenvolvimento de desfechos clínicos desfavoráveis na NF é fundamental, uma vez que estes podem ser utilizados como marcadores prognósticos ou alvos terapêuticos. Este estudo objetiva determinar os principais fatores associados com mortalidade, tempo de hospitalização, incidência de bacteremia por patógenos multirresistentes e incidência de choque séptico no início da febre em pacientes hospitalizados com NF secundária à quimioterapia citotóxica para o câncer. Na presente coorte prospectiva composta por 305 episódios consecutivos de NF (em 169 pacientes com câncer) realizada em um hospital terciário no período de outubro de 2009 a agosto de 2011, as seguintes questões de pesquisa foram avaliadas: impacto do tempo de início da antibioticoterapia na mortalidade em 28 dias; fatores relacionados com tempo de hospitalização; impacto dos fatores microbiológicos da bacteremia no desenvolvimento de choque séptico no início do episódio de NF; fatores de risco para bacteremia por patógenos multirresistentes; impacto da bacteremia por Staphylococcus coagulase-negativo na mortalidade em 28 dias. Em 5 publicações distintas, os seguintes resultados foram notados: o atraso do início da antibioticoterapia está associado a maiores taxas de mortalidade em 28 dias; neoplasia hematológica, regimes quimioterápicos de altas doses, duração da neutropenia e bacteremia por Gram-negativos multirresistentes estão associados com períodos prolongados de internação por NF; infecção de corrente sanguínea polimicrobiana, bacteremia por Escherichia coli e bacteremia por Streptococcus viridans estão associados a choque séptico no início do episódio de NF; idade avançada, duração da neutropenia e presença de cateter venoso central estão associados com bacteremia por patógenos multirresistentes; bacteremia por Staphylococcus coagulase-negativo está associada a menores taxas de mortalidade em 28 dias quando comparado à bacteremia por outros patógenos. / Febrile neutropenia (FN) is a common complication of cancer chemotherapy and is associated with high morbidity and mortality rates. Recognition of the main factors associated with the development of adverse clinical outcomes in FN is crucial, given that these factors can be used as prognostic markers or therapeutic targets. This study aims to determine the main factors associated with mortality, length of hospital stay, incidence of bacteremia by multidrug-resistant pathogens and incidence of septic shock at the onset of fever in hospitalized patients with FN secondary to cancer cytotoxic chemotherapy. In the present prospective cohort of 305 FN episodes (in 169 cancer patients) conducted at a tertiary hospital from October 2009 to August 2011, the following research questions were evaluated: impact of time to antibiotic administration on 28-day mortality; factors associated with length of hospital stay; impact of microbiological factors of bacteremia on the development of septic shock at the onset of FN; risk factors for bacteremia by multidrug-resistant pathogens; impact of coagulasenegative Staphylococcus bacteremia on 28-day mortality. In 5 distinct publications, the following results were noted: delay of antibiotic administration is associated with higher 28-day mortality rates; hematologic malignancy, high-dose chemotherapy regimens, duration of neutropenia and bacteremia by multidrug-resistant Gram-negative bacteria are associated with prolonged length of hospital stay; polymicrobial bloodstream infection, bacteremia by Escherichia coli, and bacteremia by viridans sreptococci are associated with septic shock at the onset of FN; advanced age, duration of neutropenia and presence of indwelling central venous catheters are associated with bacteremia by multidrug-resistant pathogens; coagulase-negative Staphylococcus bacteremia is associated with lower 28-day mortality rates compared with bacteremia by other pathogens.

Neutropenia febril (NF) constitui complicação frequente do tratamento quimioterápico do câncer e está associada a altas taxas de morbimortalidade. O reconhecimento dos principais fatores associados ao desenvolvimento de desfechos clínicos desfavoráveis na NF é fundamental, uma vez que estes podem ser utilizados como marcadores prognósticos ou alvos terapêuticos. Este estudo objetiva determinar os principais fatores associados com mortalidade, tempo de hospitalização, incidência de bacteremia por patógenos multirresistentes e incidência de choque séptico no início da febre em pacientes hospitalizados com NF secundária à quimioterapia citotóxica para o câncer. Na presente coorte prospectiva composta por 305 episódios consecutivos de NF (em 169 pacientes com câncer) realizada em um hospital terciário no período de outubro de 2009 a agosto de 2011, as seguintes questões de pesquisa foram avaliadas: impacto do tempo de início da antibioticoterapia na mortalidade em 28 dias; fatores relacionados com tempo de hospitalização; impacto dos fatores microbiológicos da bacteremia no desenvolvimento de choque séptico no início do episódio de NF; fatores de risco para bacteremia por patógenos multirresistentes; impacto da bacteremia por Staphylococcus coagulase-negativo na mortalidade em 28 dias. Em 5 publicações distintas, os seguintes resultados foram notados: o atraso do início da antibioticoterapia está associado a maiores taxas de mortalidade em 28 dias; neoplasia hematológica, regimes quimioterápicos de altas doses, duração da neutropenia e bacteremia por Gram-negativos multirresistentes estão associados com períodos prolongados de internação por NF; infecção de corrente sanguínea polimicrobiana, bacteremia por Escherichia coli e bacteremia por Streptococcus viridans estão associados a choque séptico no início do episódio de NF; idade avançada, duração da neutropenia e presença de cateter venoso central estão associados com bacteremia por patógenos multirresistentes; bacteremia por Staphylococcus coagulase-negativo está associada a menores taxas de mortalidade em 28 dias quando comparado à bacteremia por outros patógenos. / Febrile neutropenia (FN) is a common complication of cancer chemotherapy and is associated with high morbidity and mortality rates. Recognition of the main factors associated with the development of adverse clinical outcomes in FN is crucial, given that these factors can be used as prognostic markers or therapeutic targets. This study aims to determine the main factors associated with mortality, length of hospital stay, incidence of bacteremia by multidrug-resistant pathogens and incidence of septic shock at the onset of fever in hospitalized patients with FN secondary to cancer cytotoxic chemotherapy. In the present prospective cohort of 305 FN episodes (in 169 cancer patients) conducted at a tertiary hospital from October 2009 to August 2011, the following research questions were evaluated: impact of time to antibiotic administration on 28-day mortality; factors associated with length of hospital stay; impact of microbiological factors of bacteremia on the development of septic shock at the onset of FN; risk factors for bacteremia by multidrug-resistant pathogens; impact of coagulasenegative Staphylococcus bacteremia on 28-day mortality. In 5 distinct publications, the following results were noted: delay of antibiotic administration is associated with higher 28-day mortality rates; hematologic malignancy, high-dose chemotherapy regimens, duration of neutropenia and bacteremia by multidrug-resistant Gram-negative bacteria are associated with prolonged length of hospital stay; polymicrobial bloodstream infection, bacteremia by Escherichia coli, and bacteremia by viridans sreptococci are associated with septic shock at the onset of FN; advanced age, duration of neutropenia and presence of indwelling central venous catheters are associated with bacteremia by multidrug-resistant pathogens; coagulase-negative Staphylococcus bacteremia is associated with lower 28-day mortality rates compared with bacteremia by other pathogens.

L'endocardite infectieuse (EI) est une complication rare mais gravissime de la bactériémie à Staphylococcus aureus. Bien que certains facteurs de risque liés à l'hôte aient été décrits, l'implication de facteurs bactériens dans la survenue de l'EI est encore inconnue. Ces travaux de thèse ont visé à chercher tout élément bactérien associé à l'EI. Les facteurs phénotypiques décrits ou supposés comme potentiellement impliqués dans l'EI ont été testés. En parallèle, les profils génotypiques des souches obtenus par puces ADN ont été analysés par différents outils statistiques. L'analyse statistique univariée n'a montré aucune différence significative entre souches d'EI et souches de bactériémie, suggérant un processus complexe et multifactoriel. En effet, l'analyse discriminante en composante principale appliquée sur les données de puces ADN a permis de mettre en évidence une distinction entre les deux groupes de souches, confirmée sur une collection indépendante de souches. De plus, une fonction linéaire simplifiée, basée sur seulement 8 marqueurs génétiques, a permis d'obtenir des performances similaires, sur la collection de souches initiale ainsi que la collection indépendante de validation. En dernier lieu, les souches d'EI et de bactériémie ont été comparées à partir de séquences du génome complet (n = 40 (20 EI, 20 bactériémies)). L'analyse statistique par analyse discriminante en composante principale réalisée sur ces données génomiques confirme une distinction possible entre les deux groupes de souches. Au total, ces travaux de thèse apportent la preuve de concept que les facteurs bactériens sont impliqués dans la survenue de l'EI au cours de bactériémie à S. aureus / Infective endocarditis (IE) is a severe condition complicating 10-25% of Staphylococcus aureus bacteremia. Although host-related IE risk factors have been identified, the involvement of bacterial features in IE complication is still unclear. This PhD work aimed to characterize strictly defined IE and bacteremia isolates and searched for discriminant features. Phenotypic traits previously reported or hypothesized to be involved in staphylococcal IE pathogenesis were tested. In parallel, the genotypic profiles of all isolates, obtained by microarray, were analyzed. No significant difference was observed between IE and bacteremia strains, regarding either phenotypic or genotypic univariate analyses, suggesting a multifactorial process. However, the discriminant analysis of principal components (DAPC), applied on microarray data, segregated IE and bacteremia isolates. The performance of this model was confirmed with an independent collection of IE and bacteremia isolates. Finally, a simple linear discriminant function based on a subset of 8 genetic markers retained valuable performance both in study collection and in the independent validation collection. At last, IE and bacteremia isolates were compared based on whole genome sequence data from a subset of 40 isolates. When applied to this dataset, DAPC confirmed a possible segregation between the two groups of isolates. All in all, this PhD work provides the proof of concept that bacterial characteristics may contribute to the occurrence of IE in patients with S. aureus bacteremia

Sepsis-induced organ failure is associated with high morbidity and mortality rates. The onset of an exaggerated host response to microbial invasion and/or trauma, is believed to be the primary cause of excessive inflammation and the subsequent tissue hypoperfusion observed in patients with severe sepsis. In our mouse model of sepsis induced by cecal ligation and perforation (CLP), symptoms indicative of the disease, including diarrhea, increased ventilation and persistent hypothermia, are present at six hours after the surgery (T6). In the untreated CLP mice, mortality occurs starting at T15. As induced hypothermia has shown to exert immunomodulatory effects, this study is aimed at assessing its potential in attenuating inflammation and improving survival in experimental sepsis. Our data has shown that deep hypothermia initiated at T6, by means of cold chamber-induced cooling, prolongs survival. Plasma cytokine quantification by enzyme-linked immunosorbent assays (ELISA) also reveals that induced deep hypothermia reduces tumour necrosis factor(TNF)-α and interleukin (IL)-6 production in untreated CLP mice. In contrast, induced moderate hypothermia does not have such effect. Antibiotic (cefotaxime) and saline resuscitation initiated immediately following CLP ensures survival. However, when these supportive treatments are initiated at T6, >50% mortality is observed in the CLP mice with or without induced hypothermia. In summary, this preliminary study provides proof for a downregulated inflammatory response mediated by external cooling. However, to achieve a survival benefit, treatment strategies in addition to cooling and antibiotics may be required.