<p>The obligate intracellular bacterium <i>Chlamydia pneumoniae (Cp</i>), a common human pathogen, has been associated with atherosclerotic cardiovascular disease. The aetiology of non-rheumatic aortic valve sclerosis has, however, not been clarified. In two prospective studies of 42 and 46 patients undergoing surgical valve replacement because of aortic valve stenosis, the presence of <i>Cp </i>DNA could be demonstrated by polymerase chain reaction (PCR) in 49% and 35% of the sclerotic valves as compared to 9 % and 0%, respectively, of valves from forensic control cases with no heart valve disease. Some inflammatory and infectious diseases are associated with trace element changes. Eleven of 15 trace elements showed changed concentrations in sclerotic valve tissue compared to control valves in support of an active process in the sclerotic valves. Notable was an increased iron concentration in the patients´ valves suggesting a possible link to <i>Cp</i>. Furthermore, a disturbed trace element balance existed in the patients´ sera, the pattern of which was compatible with ongoing infection. In a prospective study of 38 patients operated on for thoracic aortic aneurysm or dissection, <i>Cp</i> DNA <i>w</i>as detected byPCR in 12 % of the aneurysms and the result was confirmed byelectron microscopy(EM<i>).</i> In none of the dissection patients could <i>Cp </i>be demonstratedin the removed tissues. The minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) values for doxycycline and azithromycin increased with longer <i>Cp </i>preincubation times when tested in vitro<i>.</i> EMwas performed to visualise the inactivation at a cellular level.Thus, the results demonstrate <i>Cp </i>in the tissues in non-rheumatic aortic valve sclerosis and in thoracic aortic aneurysm but not in aortic dissection.</p>

<p>The first hospital outbreak of vancomycin-resistant enterococci (VRE) and carriage rates of VRE and ampicillin-resistant enterococci (ARE) in Sweden were investigated. Clonal relationships and mutations in fluoroquinolone resistance determining regions among ARE collected nation-wide were studied. Risk factors for ARE infection, shedding of ARE and the presence of the virulence gene <i>esp</i> in ARE isolates and patients on a hematology unit and other units at Uppsala University Hospital were further investigated. </p><p>The first Swedish hospital VRE outbreak was due to clonal spread of <i>E. faecium, vanA</i>. The nation wide carriage rates of ARE and VRE were 21.5% / 1% and 6% / 0%, among hospitalized patients and non-hospitalized individuals respectively. All ARE and VRE were <i>E. faecium</i> and >90% resistant to ciprofloxacin. All VRE carried<i> vanB</i>. Carriage of ARE was independently associated with >5 days of antibiotic treatment. Phenotypic and genetic typing showed a significantly higher homogeneity among ARE compared to matched ASE <i>E. faecium</i> isolates. Mutations conferring high-level ciprofloxacin resistance were found only in ARE. Risk factors for ARE infection included long duration of hospital stay and exposure to antibiotics. Skin carriage was associated with ARE shedding. ARE bacteremia was independently associated with prior ARE colonization and hematopoietic stem cell transplantation. Death was more common in ARE septicemia cases compared to controls. <i>Esp</i> was significantly more common in ARE surveillance compared to ARE blood isolates from patients on the hematology ward.</p><p>In conclusion, VRE were rare but clonally related multi-resistant ARE <i>E. faecium</i> were highly prevalent in Swedish hospitals. Spread of ARE in hospitals during the 1990s is suggested to be the main explanation for the emergence of ARE in Sweden. Spread was facilitated by use of antibiotics and probably by the presence of virulence genes in<i> E. faecium</i> isolates.</p>

<p>Toxic products, such as endotoxin from the gram-negative and exotoxin from the gram-positive bacteria, are the most important initiators of the inflammatory host response in sepsis. In addition to antibacterial treatment, numerous attempts have been made to interfere with the exaggerated proinflammatory cascade initiated by the toxins. As most antitoxic and anti-inflammatory agents have shown no clear efficacy, an attractive alternative has been to prevent or minimise their release. Therefore, it was of interest to further study the antibiotic-induced release of toxins after exposure to antibiotics used for the treatment of the most severe infections, especially if protein synthesis inhibitors could reduce the release induced by PBP 3-specific β-lactam antibiotics.</p><p>There were significant reductions in endotoxin release from gram-negative bacteria when the combination of the PBP 3-specific β-lactam antibiotic, cefuroxime, and the protein synthesis inhibitor, tobramycin, was compared with cefuroxime alone. Increasing doses of tobramycin reduced endotoxin release and increased the killing rate. In a kinetic <i>in vitro</i> model the endotoxin release from <i>E.coli</i> was higher after the second dose of cefuroxime. Nevertheless, it was reduced after addition of tobramycin.</p><p>No binding of tobramycin to endotoxin was observed, either <i>in vivo</i> or <i>in vitro</i>. In a porcine sepsis model, a possible anti-inflammatory effect of ceftazidime and tobramycin, expressed as late cytokine inhibition, was seen.</p><p>The protein synthesis inhibitor, clindamycin, released less streptococcal pyrogenic exotoxin A (SpeA) from a group A streptococcus strain than penicillin, and addition of clindamycin to penicillin resulted in less toxin production than penicillin alone. The SpeA production was dependent on the bacterial number at the start of treatment. Higher doses of penicillin also led to less SpeA. </p><p>The choice of antibiotic class and dose may be important in the severely ill septic patient in whom an additional toxin release could be deleterious. A combination of a β-lactam antibiotic and a protein synthesis inhibitor seems beneficial but further investigations are needed.</p>

<p>In patients with sepsis, the activation of the cascade systems, for example the complement system with the generation of C5a, is followed by a state of immunosuppression with impaired bactericidal capacity caused by suppression of the neutrophil granulocytes. To inhibit the C5a-induced systemic inflammatory and the following anti-inflammatory responses, different anti-C5a strategies have been successful in experimental models of sepsis. In animals and in healthy volunteers after injection of lipopolysaccharide (LPS), an up-regulation of the C5a receptor (C5aR) has been reported. Before designing clinical studies, it was of importance to increase the knowledge of C5a and C5aR regulation in humans. </p><p>At the time when the diagnosis of severe sepsis or septic shock can be established clinically, granulocyte C5aR expression, analysed by flow cytometer, was shown to be reduced, whereas monocyte C5aR expression was unchanged. There was a correlation between granulocyte C5aR expression and the severity of disease, as measured by the APACHE II score. </p><p><i>Ex vivo</i> incubation of whole blood with LPS resulted in a reduction in granulocyte C5aR expression. Such a reduction was not found in isolated cells, indicating that the effect was mediated via plasma factors, such as C5a, IL-8 and TNF-α which all were shown to reduce C5aR expression <i>ex vivo</i>.</p><p>Although there was a trend between chemotaxis, as measured by migration in a modified Boyden chamber, and C5aR expression on granulocytes from patients with severe sepsis or septic shock or from healthy individuals, the correlation failed to reach statistical significance.</p><p>It is concluded that granulocyte C5aR expression is affected by several plasma factors and that a reduction is clinically evident at the time of the sepsis diagnosis. Reduced granulocyte C5aR expression is associated with an impaired chemotaxis but does not alone limit the chemotactic response.</p>

The obligate intracellular bacterium Chlamydia pneumoniae (Cp), a common human pathogen, has been associated with atherosclerotic cardiovascular disease. The aetiology of non-rheumatic aortic valve sclerosis has, however, not been clarified. In two prospective studies of 42 and 46 patients undergoing surgical valve replacement because of aortic valve stenosis, the presence of Cp DNA could be demonstrated by polymerase chain reaction (PCR) in 49% and 35% of the sclerotic valves as compared to 9 % and 0%, respectively, of valves from forensic control cases with no heart valve disease. Some inflammatory and infectious diseases are associated with trace element changes. Eleven of 15 trace elements showed changed concentrations in sclerotic valve tissue compared to control valves in support of an active process in the sclerotic valves. Notable was an increased iron concentration in the patients´ valves suggesting a possible link to Cp. Furthermore, a disturbed trace element balance existed in the patients´ sera, the pattern of which was compatible with ongoing infection. In a prospective study of 38 patients operated on for thoracic aortic aneurysm or dissection, Cp DNA was detected byPCR in 12 % of the aneurysms and the result was confirmed byelectron microscopy(EM). In none of the dissection patients could Cp be demonstratedin the removed tissues. The minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) values for doxycycline and azithromycin increased with longer Cp preincubation times when tested in vitro. EMwas performed to visualise the inactivation at a cellular level.Thus, the results demonstrate Cp in the tissues in non-rheumatic aortic valve sclerosis and in thoracic aortic aneurysm but not in aortic dissection.

The first hospital outbreak of vancomycin-resistant enterococci (VRE) and carriage rates of VRE and ampicillin-resistant enterococci (ARE) in Sweden were investigated. Clonal relationships and mutations in fluoroquinolone resistance determining regions among ARE collected nation-wide were studied. Risk factors for ARE infection, shedding of ARE and the presence of the virulence gene esp in ARE isolates and patients on a hematology unit and other units at Uppsala University Hospital were further investigated. The first Swedish hospital VRE outbreak was due to clonal spread of E. faecium, vanA. The nation wide carriage rates of ARE and VRE were 21.5% / 1% and 6% / 0%, among hospitalized patients and non-hospitalized individuals respectively. All ARE and VRE were E. faecium and &gt;90% resistant to ciprofloxacin. All VRE carried vanB. Carriage of ARE was independently associated with &gt;5 days of antibiotic treatment. Phenotypic and genetic typing showed a significantly higher homogeneity among ARE compared to matched ASE E. faecium isolates. Mutations conferring high-level ciprofloxacin resistance were found only in ARE. Risk factors for ARE infection included long duration of hospital stay and exposure to antibiotics. Skin carriage was associated with ARE shedding. ARE bacteremia was independently associated with prior ARE colonization and hematopoietic stem cell transplantation. Death was more common in ARE septicemia cases compared to controls. Esp was significantly more common in ARE surveillance compared to ARE blood isolates from patients on the hematology ward. In conclusion, VRE were rare but clonally related multi-resistant ARE E. faecium were highly prevalent in Swedish hospitals. Spread of ARE in hospitals during the 1990s is suggested to be the main explanation for the emergence of ARE in Sweden. Spread was facilitated by use of antibiotics and probably by the presence of virulence genes in E. faecium isolates.

Toxic products, such as endotoxin from the gram-negative and exotoxin from the gram-positive bacteria, are the most important initiators of the inflammatory host response in sepsis. In addition to antibacterial treatment, numerous attempts have been made to interfere with the exaggerated proinflammatory cascade initiated by the toxins. As most antitoxic and anti-inflammatory agents have shown no clear efficacy, an attractive alternative has been to prevent or minimise their release. Therefore, it was of interest to further study the antibiotic-induced release of toxins after exposure to antibiotics used for the treatment of the most severe infections, especially if protein synthesis inhibitors could reduce the release induced by PBP 3-specific β-lactam antibiotics. There were significant reductions in endotoxin release from gram-negative bacteria when the combination of the PBP 3-specific β-lactam antibiotic, cefuroxime, and the protein synthesis inhibitor, tobramycin, was compared with cefuroxime alone. Increasing doses of tobramycin reduced endotoxin release and increased the killing rate. In a kinetic in vitro model the endotoxin release from E.coli was higher after the second dose of cefuroxime. Nevertheless, it was reduced after addition of tobramycin. No binding of tobramycin to endotoxin was observed, either in vivo or in vitro. In a porcine sepsis model, a possible anti-inflammatory effect of ceftazidime and tobramycin, expressed as late cytokine inhibition, was seen. The protein synthesis inhibitor, clindamycin, released less streptococcal pyrogenic exotoxin A (SpeA) from a group A streptococcus strain than penicillin, and addition of clindamycin to penicillin resulted in less toxin production than penicillin alone. The SpeA production was dependent on the bacterial number at the start of treatment. Higher doses of penicillin also led to less SpeA. The choice of antibiotic class and dose may be important in the severely ill septic patient in whom an additional toxin release could be deleterious. A combination of a β-lactam antibiotic and a protein synthesis inhibitor seems beneficial but further investigations are needed.

In patients with sepsis, the activation of the cascade systems, for example the complement system with the generation of C5a, is followed by a state of immunosuppression with impaired bactericidal capacity caused by suppression of the neutrophil granulocytes. To inhibit the C5a-induced systemic inflammatory and the following anti-inflammatory responses, different anti-C5a strategies have been successful in experimental models of sepsis. In animals and in healthy volunteers after injection of lipopolysaccharide (LPS), an up-regulation of the C5a receptor (C5aR) has been reported. Before designing clinical studies, it was of importance to increase the knowledge of C5a and C5aR regulation in humans. At the time when the diagnosis of severe sepsis or septic shock can be established clinically, granulocyte C5aR expression, analysed by flow cytometer, was shown to be reduced, whereas monocyte C5aR expression was unchanged. There was a correlation between granulocyte C5aR expression and the severity of disease, as measured by the APACHE II score. Ex vivo incubation of whole blood with LPS resulted in a reduction in granulocyte C5aR expression. Such a reduction was not found in isolated cells, indicating that the effect was mediated via plasma factors, such as C5a, IL-8 and TNF-α which all were shown to reduce C5aR expression ex vivo. Although there was a trend between chemotaxis, as measured by migration in a modified Boyden chamber, and C5aR expression on granulocytes from patients with severe sepsis or septic shock or from healthy individuals, the correlation failed to reach statistical significance. It is concluded that granulocyte C5aR expression is affected by several plasma factors and that a reduction is clinically evident at the time of the sepsis diagnosis. Reduced granulocyte C5aR expression is associated with an impaired chemotaxis but does not alone limit the chemotactic response.

Puumala viruses, a member of the Hantavirus genus in the Bunyaviridae family, are enveloped by a lipid bilayer and possesses a tripartite single stranded RNA genome with negative polarity. The hantaviruses encode four proteins: a nucleocapsid protein (N), two membrane spanning glycoproteins (GN and GC) and a RNA dependent RNA polymerase (RdRp). Hantaviruses cause two forms of diseases, hemorrhagic fever with renal syndrome (HFRS) in Europe and Asia, and hantavirus pulmonary syndrome (HPS) in the Americas. The hantaviruses are mainly rodent borne, and humans are mostly infected by inhalation of aerosolized rodent secrete. Human Puumala virus infection results in nephropathia epidemica (NE), a mild haemorrhagic disease. It is of importance to have a good understanding of the epidemiology and genetics of these viruses for the development of new diagnostic methods and for future vaccine development. In this thesis we determined the complete viral genome sequence and characterized the structural proteins based on studies of expression and glycosylation patterns, for a unique human virus isolate; performed a genomic analysis of local Puumala viruses and their individual rodent host, Clethrionomys glareolus, from six different locations was performed. It was seen that the virus genetic variation between different locations could be stable over relatively large distances while there could be large variation over a short distance. For the bank voles no such variation could be seen; developed and evaluated Genetic vaccines, based on PCR-generated linear DNA. We showed that it was important to protect these fragments against nuclease degradation at that attachment of a nuclear localization signal peptide further improved the immune response. We also designed, fabricated and evaluated a 2000 probe cDNA-microarray for identification and differentiation of hantaviruses. The chips was based on 12 different strains of six hantaviruses and could differentiate between both different hantaviruses and strains within one hantavirus serotype.

In this thesis, we study three emerging applications of OR/MS, namely, (i) disease spread modeling, intervention strategies, and food supply chain management during an influenza pandemic, (ii) the practical applications of production planning and scheduling in the commercial lithographic printing industry, and (iii) packing/placement problems in chip design in the semiconductor industry. In the first part of the thesis, we study an emergency response planning problem motivated by discussions with the American Red Cross, which has taken on a responsibility to feed people in case of an influenza pandemic. During an emergency such as an influenza pandemic or a bioterror attack, regular distribution channels of critical products and services including food and water may be disrupted, or some of the infected individuals may not be able to go to grocery stores. We analyze the geographical spread of the disease and develop solution approaches for designing the food distribution supply chain network in case of an influenza pandemic. In addition, we investigate the effect of voluntary quarantine on the disease spread and food distribution supply chain network. Finally, we analyze the effect of influenza pandemic on the workforce level. In the second part, we study a real life scheduling/packing problem motivated by the practices in the commercial lithographic printing industry which make up the largest segment of the printing industry. We analyze the problem structure and develop efficient algorithms to form cost effective production schedules. In addition, we propose a new integer programming formulation, strengthen it by adding cuts and propose several preprocessing steps to solve the problem optimally. In the last part of the thesis, motivated by the chip design problem in the semiconductor industry, we study a rectangle packing/placement problem. We discuss the hardness of the problem, explore the structural properties, and discuss a special case which is polynomially solvable. Then, we develop an integer programming formulation and propose efficient algorithms to find a ``good' placement.