| 1. |
- Kampmann, Christian, 1975-
(författare)
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Go with your gut : The human intestinal microbiota, international travel, Campylobacter and ESBL-producing Enterobacteriaceae
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Up to 100 million people travel annually from industrialized countries to resource-limited ones. Each traveller contains an internal ecosystem composed of tens of trillions of microbes, known as the intestinal microbiota, which has a large effect on health. The microbiota seems to be highly individual and mostly stable but can be significantly affected by several factors. Many international travellers are at high risk of getting infected by Campylobacter, the most common cause of bacterial enteritis worldwide. Campylobacter infection can cause a wide range of symptoms, with varying severity, for reasons largely unknown. Travel also radically increases the risk of colonization by antibiotic-resistant intestinal bacteria, notably Extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (EPE). To date, there are no therapies available for EPE-decolonization. In this thesis, it was investigated whether the bacterial intestinal microbiota affected susceptibility to Campylobacter and if international travel as such had an impact on the microbiota. In a prospective, observational study, 67 healthy Swedes, travelling in groups to countries with a high risk of Campylobacter infection, were followed. The travellers answered questionnaires and delivered two faecal samples before and three samples after the trip. These samples were cultured for enteropathogens and analysed for the microbiota composition. Low diversity of microbiota seemed to increase the risk of Campylobacter jejuni infection, whereas a high relative abundance of Lachnospiraceae might decrease the risk (Paper I). Furthermore, the overall bacterial diversity did not seem to change in connection with travelling. However, the bacterial family Enterobacteriaceae (otherwise connected with inflammation, infection and antibiotic-resistance) was shown to be dramatically increased in abundance immediately after travel, and the family Christensenellaceae (otherwise connected with beneficial health conditions) simultaneously decreased (Paper II). Eight travellers, from two different destinations, were infected with closely related C. jejuni isolates (ST353CC). The bacterial analysis of genomic and phenotypic characteristics revealed that the C. jejuni isolates of the travellers returning from one of the destinations and with more severe symptoms actually showed less pathogenic potential, compared to the isolates of travellers from the other destination and with milder symptoms. However, the travellers with more severe symptoms had much higher relative abundances of Bacteroidetes in their intestinal microbiota and, in contrast to the other travellers, excluded meat from their diet. (Paper III) Finally, we investigated in a randomized, placebo-controlled clinical trial of 80 established intestinal carriers of EPE, whether the oral probiotic product Vivomixx® could eradicate EPE. Vivomixx® was not superior to placebo (Paper IV).
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| 2. |
- Byenfeldt, Marie, 1967-
(författare)
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Ultrasound based shear wave elastography of the liver : a non-invasive method for evaluation of liver disease
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Background: Detecting liver disease at an early stage is important, given that early intervention decreases the risk of developing cirrhosis and subsequently hepatocellular cancer (HCC). The non-invasive ultrasound-based shear wave elastography (SWE) has been used clinically for a decade to assess liver stiffness. This method is reliable, rapid and can be performed in an outpatient setting without known risks for the patient. However, increased variance in SWE results has been detected, without clear explanation. Factors that affect SWE results needs to be identified. Data are insufficient regarding the reliability of SWE with different body positions and probe pressures. Men have higher SWE results than women, also for unclear reasons. Increasing the reliability of SWE is crucial for understanding how factors such as overweight and obesity, cardiovascular and antiviral medication, age, sex, smoking habits, hepatic steatosis and cirrhosis affect SWE results.Aims: The overall aim of the studies included in this thesis was to increase the reliability of SWE liver. The specific aims were to investigate patient-related factors associated with increased uncertainty in SWE results. Another aim was to investigate the influence of increased intercostal probe pressure on liver stiffness assessment with SWE liver. The final aims were to investigate the influence of postural changes, sagittal abdominal diameter (SAD) and skin-to-liver capsule distance (SCD) on SWE results, along with sex-based differences for SWE results and cardiovascular medication.Methods: All enrolled participants in these studies were consecutive patients with various liver diseases presenting at the radiology department Östersunds Hospital. The patients were examined using SWE liver method at the ultrasound unit between April 2014 and May 2018. Inclusion criteria were that participants be adults (age ≥18 years) who had provided written consent for participating in the study. The exclusion criterion was an inability to communicate. Current guidelines for SWE of the liver were used in the thesis with the following exceptions: In study II, increased intercostal probe pressure was used, and in study III, postural change was used. Study I included 188 patients; study II included 112 patients, and studies III and IV involved 200 patients. The four studies were conducted as cross-sectional and clinical trial, using quantitative methods.Results: Factors associated with low variance for SWE results were age, sex, and presence of cirrhosis, the use of antiviral and/or cardiovascular medication, smoking habits, and body mass index. Factors associated with increased uncertainty in SWE results were increased SCD and the presence of steatosis. With increased probe pressure SCD decreased and the quality of shear wave increased. The results showed that the number of required measurements can be reduced. A postural change to left decubitus decreased SCD. For patients with increased SAD and increased SWE result in the supine position, SWE result decreased with a postural change to left decubitus. The SWE results, SCD and SAD significantly differed between women and men. SWE results was higher in the presence of increased SAD (≥23 cm) among men, but not among women.Conclusions: SWE of the liver is a reliable, non-invasive method for diagnosing liver disease. Results in this thesis suggest that for patients with SCD ≥2.5 cm, shear wave measures could be of poor quality and the SWE exam less reliable. In these cases, increased probe pressure may facilitate a reliable SWE exam. With such adjustments in probe pressure, the ultrasound-based SWE method can be superior for examination in patients with overweight or obesity. An effect of SAD ≥23 cm was seen for men with liver fibrosis only, which may explain the higher SWE result for men compared to women. Depending on the severity of liver disease and SAD, a postural change to left decubitus can produce a different outcome. As SAD increased, liver stiffness did, as well. Increased SAD thus is linked to increased liver stiffness, indicating that SAD should be taken into account when performing SWE of the liver.
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| 3. |
- Brundin, Peik M. A., 1975-
(författare)
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Sex differences in immune response and sex hormone receptor expression in healthy individuals and during viral infection
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- There is sex-bias in morbidity and mortality from infectious diseases. Infections kill more men than women and several studies have pointed out differences in the immune system as a reason. The sex hormones estrogen, progesterone and testosterone all shape the effect of the immune response on multiple levels. Women at fertile age have been suggested to have higher proinflammatory responses from inflammatory stimuli compared to men and post-menopausal women, which has been ascribed to their higher estrogen levels. This could possibly lead to a more active pathogen response but may also result in a detrimental immunopathology to infections or development of autoimmune reaction.The overall aim of this thesis is to study the contribution of sex hormones and sex hormone receptors (SHR) to sex differences in immune response. We focus on peripheral blood mononuclear cells (PBMCs) to study such relationships in healthy individuals, as well as in individuals with asymptomatic Torque Teno Virus infection, and individuals with acute Puumala virus infection.In Paper I, we investigated expression of SHR and immune response genes in PBMC from healthy premenopausal (pre-MP) women during the menstrual cycle. The expression levels were estimated using a qPCR Array (Taqman low-density array, TLDA). SHR expression did not change significantly during the menstrual cycle, but several key immune regulatory genes were significantly more expressed during the ovulatory and mid luteal phase. Further, we separated PBMC into cell subsets (CD4+ T-cells, CD8+ T-cells, CD56+ NK-cells, CD14+ monocytes and CD19+ B-cells) and analyzed the expression through qPCR of estrogen receptors (ERs), ERα, ERβ1 (wildtype) and the isoform ERβ2. For the first time and unexpectedly, we demonstrate that the isoform ERβ2 was more abundant than wildtype ERβ1. The data from this paper provides new knowledge on the contribution of the menstrual cycle on immune response.In Paper II, we explored the use of Torque Teno Virus as a secondary functional immune marker in men and women. Expression of viral TTV DNA in PBMCs was estimated using a qPCR kit from Argene (R-gene) and analyzed in relation to serum sex hormone levels. The results showed that 50% of the men, 25% the post-MP women, and 18% of the pre-MP women were TTV+. Interestingly, all pre-MP women that were TTV+ had hormonal aberrances and were either anovulatory and/or hypothyroid. TTV+ pre-MP women also had significantly lower progesterone levels than TTV- pre-MP women. This paper indicates that the prevalence of TTV in PBMC differs between men, pre-MP and post-MP women. Furthermore, hormonal aberrances (at least in pre-MP women) will lead to increased prevalence of TTV.In Paper III we investigated the expression of ERα, ERβ1 and ERβ2 in PBMC from patients with Nephropathia epidemica, the viral zoonotic disease caused by Puumala virus, a Hanta virus known to affect more men than women. Expression of ERs in PBMCs and clinical laboratory results during the acute and convalescent phases were analyzed using a principal component analysis (PCA). The results show differences in ER expression and support previous findings that men and women have a different clinical pictureIn conclusion, the results in this thesis reveal distinct patterns of immune response related to sex hormone levels, SHR expression and the phases of the menstrual cycle supporting that there a link between sex hormone levels and immune responses. Further, we show that the ER isoform ERβ2 is more abundant in PBMCs than what was previously described. The data in this thesis adds to the knowledge to the sex differences in immune response and exemplifies the importance of taking these differences into account in the clinic.
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| 4. |
- Lindskog Bergström, Cecilia, 1981-
(författare)
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Tissue Microarrays for Analysis of Expression Patterns
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Proteins are essential building blocks in every living cell, and since the complete human genome was sequenced in 2004, researchers have attempted to map the human proteome, which is the functional representation of the genome. One such initiative is the Human Protein Atlas programme (HPA), which generates monospecific antibodies towards all human proteins and uses these for high-throughput tissue profiling on tissue microarrays (TMAs). The results are publically available at the website www.proteinatlas.org.In this thesis, TMAs were used for analysis of expression patterns in various research areas. Different search queries in the HPA were tested and evaluated, and a number of potential biomarkers were identified, e.g. proteins exclusively expressed in islets of Langerhans, but not in exocrine glandular cells or other abdominal organs close to pancreas. The identified candidates were further analyzed on TMAs with pancreatic tissues from normal and diabetic individuals, and colocalization studies with insulin and glucagon revealed that several of the investigated proteins (DGCR2, GBF1, GPR44 and SerpinB10) appeared to be beta cell specific. Moreover, a set of proteins differentially expressed in lung cancer stroma was further analyzed on a clinical lung cancer cohort in the TMA format, and one protein (CD99) was significantly associated with survival. In addition, TMAs with tissue samples from different species were generated, e.g. for mapping of influenza virus attachment in various human and avian tissues. The results showed that the gull influenza virus H16N3 attached to human respiratory tract and eye, suggesting possible transmission of the virus between gull and human. TMAs were also used for analysis of protein expression differences between humans and other primates, and two proteins (TCF3 and SATB2) proved to be significantly differentially expressed on the human lineage at both the protein level and the RNA level. In conclusion, this thesis exemplifies the potential of the TMA technology, which can be used for analysis of expression patterns in a large variety of research fields, such as biomarker discovery, influenza virus research or further understanding of human evolution.
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| 5. |
- Ingman, Mikael
(författare)
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The hepatitis B virus – Insights into genetic variability, evolution and Bayesian phylogeographic inference
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In terms of genome size, the hepatitis B virus is the smallest virus known to infect humans and its compactness with multiple overlapping reading frames puts restraints on the emergence of mutations. In the papers included in this thesis we aimed to investigate genetic variation within the precore and core promoter region and to describe the origin, spread and diversification of HBV genotype A. We described a novel insertion in precore causing a frameshift and the abolishment of HBeAg secretion. Through the process of seroconversion viral load decreased by three logs and ALT values normalized concomitantly with the emergence of the mutated variant which could be detected early during the process as a minor variant along with the wildtype. The position of the insertion lies within the functionally important encapsidation signal necessary for the packaging of the HBV genome into core particles. Prediction of the structure of the encapsidation signal in the mutant was performed and revealed that functionally important parts of the structure remained intact.The variability in the core promoter and precore region was described in paper II. Genotypes A-D were studied and mutations were found to occur at key positions as A1762T, G1764A, G1896A and G1899A. The proportions of strains originating in seroconverted patients differed between the four genotypes. A number of rare mutations were found, notably the double mutations C1857T along with G1897A and C1856T together with G1898A.The evolution, global transmission and expansion of HBV/A has previously been described using a variety of different phylogenetic approaches. The main differences lie in the choice of method for calibrating the molecular clock – the correlation of the observed root-to tip divergence in the tree with units of time. We used a GenBank dataset supplemented with sequence material from the early 70’s and a tip-dating approach with a local clock model that allowed for rate variation between lineages. We showed that the deeper temporal distribution the added sequence material provided was necessary for a statistically robust calculation of tMRCA and evolutionary rate. The main finding in our study indicated a diversification of HBV/A in East Africa/Asia, Europe and West Africa in the 19th century followed by a rapid expansion during the mid-20th century. HBV/A has previously been proposed to have been introduced to Haiti through the trans-Atlantic slave trade, but our study indicated that these strains appear to have been introduced later in an historical contest similar to that describing how HIV was introduced to the Americas.
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| 6. |
- Sigmundsdottir, Gudrun
(författare)
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D-arabinitol in the diagnosis of invasive candidiasis
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Invasive candidiasis (IC) is a serious condition and timely diagnosis with early initiation of antifungal therapy is imerative for improving outcomes. Arabinitol is a sugar alcohol with two stereoisomers, D-arabinitol (DA) and L-arabintiol (LA). Several pathogenic Candida species produce DA in vitro and high DA levels have been detected in serum and urine in patients with IC. Renal dysfunction affects serum DA levels, serum and urine DA/LA or serum DA/creatinine are therefore measured to correct for kidney dysfunction. DA/LA ratio in urine was examined in neonatal infants in Lund, in patients with hematologic malignancies in Brisbane, Australia, and in HIV patients. Urine samples were collected on filter paper, which was found easy to apply and facilitated shipment of samples. DA/LA ratio is a reliable diagnostic method of IC in neonatal infants, all six infants with IC had elevated DA/LA ratios. Additionally five of eight infants receiving empirical antifungal treatment had elevated DA/LA ratios. The DA/LA ratio had lower sensitivity in hematology patients in Australia probably reflecting local changes in the epidemiology of candidemia with increased proportion of fungemias caused by C. krusei. HIV patients had normal DA/LA ratios and elevated ratios were not detected in five patients with Candida esophagitis. Clinical usage of DA/LA ratio in urine was studied iat the pediatric oncology unit (POU) and at the neonatal intensive care unit (NICU) in Lund. Screening of neutropenic children with cancer at the POU was found to decrease the number of IC but at the NICU the number of IC remained unchanged where the DA/LA ration was obtained only when IC was suspected. In vitro studies on DA production showed DA production in C. dubliniensis and C. krusei although C. krusei was found to produce low levels of DA. Neither in vitro nor in vivo DA production was detected in C. glabrata. DA production rate was highest in C. albicans and both intra and inter species variation of in vitro DA production was observed, which warrants further studies on the DA production rate and the sensitivity of DA/LA ratio in clinical use.
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| 7. |
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| 8. |
- Elfving, Kristina
(författare)
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Acute febrile illness in preschool children in Zanzibar - Infectious aetiologies, diagnosis and treatment
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Background: A majority of the three million children in Africa that do not survive their fifth birthday die from infections that often start as a seemingly uncomplicated febrile illness. Primary health care workers frequently encounter febrile children with a negative malaria rapid diagnostic test (mRDT), in particular in places like Zanzibar with a considerable decline in malaria prevalence. In recent years, accurate and sensitive molecular techniques like the polymerase chain reaction (PCR) have revealed increased detection of pathogens not only in ill patients but also in asymptomatic subjects. These factors underline the importance of re-evaluating the infectious disease aetiology and pathogen dynamics in febrile children and to assess whether existing diagnostic tools like mRDT and fever management guidelines like the IMCI (Integrated Management for childhood illness) remain useful and safe.Methods and Findings: The thesis is based on two field studies, both conducted on patients with acute uncomplicated febrile illness (by history or axillary temperature) in primary health care facilities April-July 2010 and 2011 in Zanzibar, Tanzania. In study 1 (paper I), 3890 febrile patients ≥2 months were included. Malaria prevalence by mRDT was 3.1%, with the highest prevalence, 6.1% in children aged 5-14 years old. Malaria microscopy and PCR were conducted on all mRDT positive and a randomly selected 20% of the mRDT negative patients. The sensitivities of mRDT versus malaria microscopy and PCR were below 80%, respectively. Study 2 (paper II-IV) included 677 febrile children aged 2-59 months of age that depending on the clinical picture were subjected to point-of-care tests, PCR analyses (on inclusion and day 14), urine culture and radiological analyses. For comparison, 167 geographically- and age-matched asymptomatic controls from the surrounding communities were recruited for selected PCR analyses. More than one pathogen was detected by PCR in 98% of patients and 93% of healthy controls. After application of study specific diagnostic criteria using clinical characteristics and laboratory results, including a comparison with detection in healthy controls, a cause of fever was assigned to 86%. The most common were respiratory syncytial virus (RSV), influenza A or B, rhinoviruses, enteroviruses, and S. pyogenes (Group A Streptococcus) (paper II and III). C-reactive Protein (CRP) was the only variable significantly associated with radiological pneumonia. Antibiotics were prescribed to 74% of patients whereas 22% had an infection that required antibiotics (paper II). On follow-up after two weeks >80% of the infections were cleared, but almost half of the sampled patients had a new infection on day 14 (paper IV).Conclusion: The sensitivity of the malaria RDT was relatively low. Thus, more sensitive tools than histidine-rich protein 2 (HRP-2) based mRDTs are warranted. Most of the uncomplicated febrile illness in children in Zanzibar was caused by a viral respiratory tract infection. Comparison of pathogen detection in febrile and healthy children was crucial for identifying cause of disease. The accuracy of the IMCI guidelines to guide antibiotic prescription was suboptimal with both over- as well as underprescription of antibiotics. However, the study did not find any diagnostic tool to help in guiding antibiotic prescription although C-reactive Protein might be a promising biomarker for future intervention studies. Respiratory infections usually cleared within two weeks. However, many children had acquired a new viral infection, suggesting that prolonged symptoms often are due to acquisition of new infections rather than to persistence.
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| 9. |
- Entezarjou, Artin
(författare)
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eVisits in the digital era of Swedish primary care
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Objective: To evaluate asynchronous digital visits (eVisits) with regard to digital communication, clinical decisionmaking,and subsequent care utilization in the digital era of primary care in Sweden.Methods: A mixed-methods approach was adopted across the various papers in the thesis, with all studiesevaluating the eVisit platform Flow in various clinical contexts.- Paper I was a comparative study of digital triage decisions when presented with automated patienthistory reports generated by the platform. Inter-rater reliability of triage decisions by majority vote in apanel of five physicians was compared to triage decisions by a machine learning model trained usingdata labelled by an expert primary care physician.- Paper II was a qualitative focus group study of nurse and physician experiences of digitalcommunication at three primary health care centers using the platform. Themes were generated usingqualitative content analysis as described by Graneheim and Lundman.- Papers III and IV were observational studies comparing office visits in the Skåne Region from Capio,a large private health care provider, to eVisit patients from Capio Go, a national eVisit service. Adultpatients with a chief complaint of sore throat, dysuria, or cough/common cold/influenza were recruited.eVisit patients were recruited prospectively digitally prior to their eVisit, while the office visit controlgroup was recruited retrospectively using letters. Paper III primarily compared antibiotic prescriptionrates per sore throat visit, while paper IV primarily compared subsequent physical health careutilization within two weeks for patients in the Skåne Region.Results: Interrater reliability was low (Cohen κ 0.17) between the panel majority vote and the machine learningmodel. Physicians and nurses experienced digitally filtered primary care, adjusting to a novel medium ofcommunication highlighting challenges in interpreting symptoms through text as well as alterations in practiceworkflow using asynchronous communication. Antibiotics prescription rate within three days was not higher aftereVisits compared to office visits (169/798 (21.2%) vs. 124/312 (39.7%) for sore throat, respectively; P<.001). Nosignificant differences in subsequent physical visits within two weeks (excluding the first 48 h of expected “digi-physical”care) were noted following eVisits compared to office visits (179 (18.0%) vs. 102 (17.6%); P = .854).Conclusions: eVisits do not seem to be associated with over-prescription of antibiotics, or over-utilization ofphysical health care when assessing common infectious symptoms. Given staff experiencing uncertainties ininterpretation of symptoms and triage decisions being inconsistent, eVisits may be best used as one of manymodalities to access primary care, with focus placed on facilitating patient-centered professional judgement bystaff, rather than automation of complex decisions.
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| 10. |
- Gunnarsson, Ronny K, 1955
(författare)
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Microbiologic diagnostic tests when asymptomatic carriers are present. Aspects of the use of conventional throat and nasopharyngeal culture as examples
- 2001
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Carriers of potentially pathogenic bacteria simultaneously ill from a viral infection complicatethe diagnostic procedure in respiratory tract infections. The present statistical methodsavailable to evaluate common diagnostic tests either ignore the phenomenon of carriers orprovide test characteristics that are difficult to apply in clinical decision making. In thisdissertation, the influence of carriers on the diagnostic process has been elucidated.· The etiologic predictive value (EPV) is a new statistical method developed to predictdisease caused by the bacteriological findings, taking carriers into consideration. Tocalculate EPV, it is necessary to have the proportion of positive tests among patients, theproportion of positive tests among a healthy control population and the sensitivity of thetest. This enables calculating the positive and negative EPV with a 95% confidenceinterval.· A throat culture was found to be a reliable indicator for illness caused by group A beta-haemolyticstreptococci (GABHS) in adult patients with a sore throat. Positive EPV(PEPV) was 99% (95% confidence interval is 94-100%). A seasonal variation, however,was found in pre-school children (0-6 years of age). A throat culture with growth ofGABHS was found to be reliable only in the winter season, with a PEPV of 94% (75-100%) as opposed to only 61% (0-91%) in the summer. However, our data did not permitus to conclude that this seasonal variation will be found every year.· Findings of Haemophilus influenzae in a nasopharyngeal culture, taken from patients witha sore throat, may indicate the true etiology of the disease. The prediction in regard todisease caused by H. influenzae (PEPV) was 93% (73-99%) for adults ³16 years of ageand 86% (28-99%) for pre-school children 0-6 years of age.· In adults with a long-standing cough combined with other symptoms of a respiratory tractinfection, it was found that growth of H. influenzae in a nasopharyngeal culture wouldindicate the etiology for infection with PEPV 90% (30-99%). Growth of Moraxellacatarrhalis in a nasopharyngeal sample, taken from a pre-school child with a long-standingcough 0-6 years of age, will indicate the etiology for infection with a PEPV of90% (66-99%).· A questionnaire sent to different microbiologic laboratories revealed a substantialvariation between different geographical areas propensity to perform a throat ornasopharyngeal culture. There was also a large variation between the different areas in theoutcome of these cultures. It could be shown that the variation in outcome of the culturesmakes it difficult to directly apply predictive values calculated from many scientificstudies.
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