Antimicrobial resistance (AMR) is concerning because it limits antimicrobial drug treatment options. AMR occurs by the overuse and misuse of antimicrobial drugs. In environmental settings, AMR can disseminate from places of high use, which leads to increased exposure to humans and animals. A previous study from our laboratory group showed extended-spectrum cephalosporinase-producing Escherichia coli/Klebsiella pneumoniae were isolated from fecal samples obtained in rural Cambodian community settings. Based on these isolates, this study has two aims. The first aim was characterization of selected Cambodian isolates with random amplification polymorphic DNA (RAPD) and antibiotic susceptibility test. From RAPD, the selected six isolates are diverse, except for C61 and C66 bacteria isolates with potential clonality. Additionally, the selected isolates are multidrug resistant (MDR) with reduced susceptibility to beta-lactams and fluoroquinolones. The second aim was to assess two developed methodologies, multiplex automated genome engineering (MAGE) and One-Step Curing Plasmid, by validation in bacteria laboratory strain and development for six Cambodian isolates. To modify AMR genetic elements, MAGE uses pMA7-SacB for homologous recombination with oligos for chromosomal gene disruption. Meanwhile, One-Step Curing Plasmid uses pFREE with the CRISPR/Cas9 system for plasmid and self-curing. Validation showed that MAGE can modify 8% of E. coli MG1655 with lacZ control screening oligos and almost 90% are cured from pFREE. Selected Cambodian isolates have antibiotic-resistance plasmids of IncR or IncFII replicon. For usage in Cambodian isolates, pFREE was modified to be pCAM-FREE by cloning IncR and IncFII plasmid as gRNA1 and gRNA5, respectively. Sequencing results showed pCAM-FREE have gRNA5. In conclusion, our study managed to characterize selected Cambodian isolates as MDR and diverse. In a laboratory strain, MAGE and One-Step Curing Plasmid are functional methods. Furthermore, pCAM-FREE was constructed to target IncFII and in the future, MAGE and pCAM-FREE could be tested in Cambodian isolates.

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Background: The human gut microbiota is the complex microbial community that lives in our gut. The gut microbiota has a key role in health and disease and its disruption has been linked to several chronic diseases such as cardiovascular diseases. As antibiotics are well known disruptors of gut microbiota, the aim of this thesis work was to identify associations between previous antibiotic consumption and the abundance of seven gut microbiota species previously linked to subclinical coronary atherosclerosis in the large population-based Swedish CArdioPulmonary bioImage Study (SCAPIS) cohort. Materials and Methods: Faecal samples of 9,794 individuals from the SCAPIS Uppsala and Malmö cohorts were analysed by deep shotgun metagenomics sequencing in a cross-sectional study. Previous antibiotic use was retrieved using the Swedish Drug Prescribed Register and divided into three periods: one year, between one and five years, and between five and nine years before faecal sampling. Associations between antibiotic consumption and the gut microbiota species were evaluated using linear regression adjusted for covariates and corrected for multiple testing. Results: Our results showed that antibiotic consumption was associated with an increased abundance of Ligilactobacillus salivarius, Bifidobacterium dentium, Rothia mucilaginosa, Streptococcus parasanguinis and Streptococcus oralis subsp. oralis. Often these positive associations were present for antibiotic consumed between one and five years before sampling.  The strongest associations were for broad-spectrum antibiotics and lincosamides with L. salivarius, B. dentium, R. mucilaginosa and S. parasanguinis; and for nitrofurantoin with S. oralis subsp. oralis.   Conclusions: This study provides insights on how antibiotic consumption is associated with enrichment and higher abundance of species previously linked with subclinical coronary atherosclerosis in the gut. Hence, this study provides insights on unintended effects of using antibiotics for managing infections, which underscores antibiotic use as not only a concern for development of antibiotic resistance but also for disrupting the gut microbiota, which may contribute to disease development. Knowledge about effect of antibiotics in gut microbiota may help to adequate this therapy according to comorbidities of individual profiles and to design better diagnostic tools for the risk population with the goal of preventing cardiovascular events in the general population.

Abstract  Aggregatibacter aphrophilus, a Gram negative bacterium, found in the oral cavity, causing cerebral abscesses and infective endocarditis, has been shown to be serum resistant in previous studies. Bacterial secretion systems are important for bacteria as they transfer virulence factors into other bacteria or host cells as an attack. A. aphrophilus encodes a type VI secretion system, which is a spike-like membrane protein, mainly consisting of a hemolysin co-regulated protein (Hcp). In this work, it was tested if Hcp would contribute to serum resistance of A. aphrophilus. Firstly, to assess Hcp contribution to serum resistance, a bacterial serum killing assay-method was used and data was collected from three independent experiments. Two strains of A. aphrophilus were used in the experiments: the laboratory strain HK83 and a HK83 hcp mutant strain. The results showed that Hcp provided no significant effect on serum resistance of A. aphrophilus. Secondly, optical density measurements were made for growth curve analysis, to determine if the HK83 hcp mutant strain had an impact in growth compared to HK83. The results indicated that the HK83 hcp mutant strain had a somewhat reduced growth compared to its parental strain.

Evolution in bacteria occurs through the combined effects of spontaneous mutations and horizontal gene transfer (HGT). Several mechanisms can lead to HGT: (i) transformation, the uptake of DNA from the environment; (ii) transduction, the transfer of DNA carried by a bacteriophage into another bacterium during infection; and (iii) conjugation, bacterial mating mediated by a conjugative plasmid like the F-factor. HGT through conjugation can lead to the transfer of resistance and virulence genes, which often reside on conjugative plasmids. Conjugation can occur both within a species or between different species. The F-factor plasmid may sometimes integrate into the chromosome by recombination if there is homology between IS elements on the plasmid and the chromosome. Cells with an integrated F-factor can transfer chromosomal DNA with high efficiency and are called Hfr-cells. There are two clinical pathogens (Klebsiella pneumoniae ST258 and Escherichia coli ST1193) that are highly successful (pathogenicity-wise) and thought to originate through the transfer of chromosomal DNA via conjugation creating unique strains with hybrid chromosomes.  Our question was how frequently the transfer of chromosomal DNA occurs when we use clinical isolates of E. coli with a plasmid and mate them with an E. coli recipient. We hypothesized that any conjugative plasmid might integrate into the chromosome, thus creatingHfr-cells with the potential for transfer of chromosomal DNA to create hybrid strains. Our prediction was that some clinical isolates should be able to transfer chromosomal DNA to another bacterial strain. By plating conjugation mixtures on selective medium where neither donor nor recipient could grow, we were able to isolate 15 possible transconjugants with hybridgenotypes occurring at a frequency of ~10-10.

Symbiont intestinal microbiomes contribute to host immunity, but may also contribute to autoimmune diseases. Segmented filamentous bacteria (SFB), designated Candidatus Arthromitus, are one of the key players in the gut microbiome. They have a unique cell cycle and are thought to play a role in immune establishment in infancy.  This research explored the feasibility of non-human primate infants as animal models for elucidating SFB function by analyzing previously published 16S rRNA gene sequencing data with the Divisive Amplicon Denoising Algorithm 2 (DADA2) algorithm and statistical methods.  Consequently, non-human primate infants as animal models for SFB investigation were seen as a potential option. However, the study also brought up questions about the species-specificity and transmission modes of SFB, thus additional research is needed.

Inhibitors belonging to the serpin (serine protease inhibitor) family control proteases involved in various physiological processes. All serpins have a common tertiary structure based on the dominant b-sheet A, but they have different inhibitory specificity. The specificity of a serpin is determined by the Pl-Pl’ peptide bond acting as a bait for the target protease which is made up of an exposed reactive centre loop (RCL). The serpin plasminogen activator inhibitor type-1 (PAI-1) is the main physiological inhibitor of urokinase-type and tissue-type plasminogen activators (uPA and tPA, respectively). Elevated plasma levels of PAI-l have been correlated with a higher risk of deep venous thrombosis, and PAI-1 is a risk factor for recurrent myocardial infarction. Furthermore, PAI-1 has a role in cell migration and has been suggested to regulate tumor growth and angiogenesis. PAI-1 is unique among the serpins in that it can spontaneously and rapidly convert into its latent form. This involves full insertion of the RCL into b-sheet A. There were two partially overlapping goals for this thesis. The first was to use latent PAI-1 as model for development of a fluorescence-based method, Donor-Donor Energy Migration for intramolecular distance measurements. The second goal was to use DDEM, together with other biochemical methods, to reveal the structure of the PAI-1/uPA complex, the conformation of the RCL in active PAI-1, and molecular determinants responsible for the conversion of PAI-1 from the active to the latent form. The use of molecular genetics for introduction of fluorescent molecules enables the use of DDEM to determine intramolecular distances in a variety of proteins. This approach can be applied to examin the overall molecular dimensions of proteins and to investigate structural changes upon interactions with specific target molecules. In this work, the accuracy of the DDEM method has been evaluated by experiments with the latent PAI-1 for which X-ray structure is known. Our data show that distances approximating the Förster radius (57±1 Å) obtained by DDEM are in good agreement (within 5.5 Å) with the distances obtained by X-ray crystallography. The molecular details of the inhibitory mechanism of serpins and the structure of the serpin/protease complex have remained unclear. To obtain the structural insights required to discriminate between different models of serpin inhibition, we used fluorescence spectroscopy and cross-linking techniques to map sites of PAI-1/uPA interaction, and distance measurement by DDEM to triangulate the position of the uPA in the complex. The data have demonstrated clearly that in the covalent PAI-1/uPA complex, the uPA is located at the distal end of the PAI-1 molecule relative to the initial docking site. This indicates that serpin inhibition involves reactive center cleavage followed by full loop insertion, whereby the covalently linked protease is translocated from one pole of the inhibitor to the opposite one. To search for molecular determinants that could be responsible for conversion of PAI-1 to the latent form, we studied the conformation of the RCL in active PAI-1 in solution. Intramolecular distance measurements by DDEM, the newly a developed method based on probe quenching and biochemical methods revealed that the RCL in PAI-1 is located much closer to the core of PAI-1 than has been suggested by the recently resolved X-ray structures of stable PAI-1 mutants, and it can be partially inserted. This possibly explains for the ability of PAI-1 to convert spontaneously to its latent form.

Allergic diseases, for example asthma and eczema, are nowadays considered belonging to the most common chronic diseases amongst children in the West, but the cause for this increase in allergy prevalence is unknown. Since studies have indicated a connection between children's exposure of microorganisms during infancy and risk of developing allergic disease, it is suggested that this exposure is a crucial factor in question of allergy development or not. Other studies have established differences in microflora composition between healthy children and children with allergic disease, and several studies have shown that probiotic therapy can give positive results in both prevention and treatment of allergic diseases. The aim of this master's thesis was to develop a method, using PCR and denaturing gradient gel electrophoresis, to study the diversity of Lactobacillus spp. in fecal samples retrieved from a study of the probiotic strain L. reuteri ATCC 55730. The developed method was successful in detecting lactobacilli in fecal samples, but three other bacterial genera commonly found in humans were also amplified. Comparison of average numbers of detected bacterial strains and lactobacilli strains between samples belonging to the probiotics and placebo groups, respectively, showed higher numbers for the probiotics group. Also, the only fecal samples that contained L. reuteri belonged to the probiotics group. Although the results are far from statistically significant, they support the theories that probiotics may influence the intestinal microbiota.

Sepsis är ett allvarligt tillstånd som uppstår när bakterier går från vävnad till blodbanan. Positiva blododlingar odlas på agarplattor och bakterier analyseras med Matrix Assisted Laser Desorption Ionisation Time-of-flight Mass spectrometry (MALDI-TOF MS) där prov blandas med en matrix och sedan bestrålas med laser. Proteinerna i provet joniseras och rör sig mot en detektor, vilket ger ett m/z-spektrum som jämförs med referensspektrum i en databas och ett score-värde erhålls över hur väl analyten liknar referensen. Arbetets syfte var att undersöka möjligheten att direktidentifiera bakterier från blod med en viss preparation innan analys med MALDI-TOF MS och på så vis möjliggöra snabbare preliminära svar samt undersöka möjligheten att särskilja Staphylocoocus aureus och koagulasnegativa stafylokocker. Innan analys med MALDI-TOF MS centrifugerades blod från positiva blododlingar blod i flera steg med 5 % natriumkloridlösning (NaCl-metoden). Dessutom testades ett kommersiellt kit (Sepsityper, Bruker Daltonics). Med NaCl-metoden sågs korrekt identifiering hos 66 % av inokulerade proverna. Av blododlingar innehållande med S. aureus respektive koagulasnegativa stafylokocker identifierades 60 % respektive 43 % av bakterierna korrekt. Med Sepsiptyper erhöll 58 % av proverna godkänt score-värde. Slutsatsen blev att det är möjligt att identifiera bakterier direkt från blod efter viss preparation, men metoden bör utvecklas mer då det fanns en signifikant skillnad i score mellan NaCl-metoden och nuvarande metod. Det är dock möjligt att skilja mellan Staphylococcus aureus och koagulasnegativa stafylokocker. Fler studier är nödvändiga för att avgöra möjligheten att föra in någon av metoderna i rutindiagnostiken.

Invasive Candida infection is an increasing cause of morbidity and mortality in the immunocompromised patient. Molecular diagnosis based on genomic amplification methods, such as real time PCR, has been reported as an alternative to conventional culture for early detection of invasive candidiasis. The template DNA extraction step has been the major limitation in most reported nucleic acid based assays, due to problems in breaking fungal cell walls and incomplete purification in PCR inhibitor substances. The aim of this study was to compare enzymatic cell wall disruption using recombinant lyticase with mechanical disruption using glass beads. The QIAamp tissue kit was compared with two automated DNA extraction robots, the BioRobot M48 and NucliSens easyMAG, to determine their sensitivity, reliability and duration for DNA release of C. albicans. Mechanical cell wall disruption shortened and facilitated the extraction procedure, but the quantity of released DNA was significantly lower than when enzymatic cell wall disruption was used. Use of robots did not significantly shorten the DNA extraction time, compared with manual DNA extraction. However the NucliSens easyMAG resulted in a higher yield of target DNA compared to the BioRobot M48 and the manual QIAamp tissue kit. / Invasiva svampinfektioner är ett stort problem hos patienter med dåligt immunförsvar. Förekomst av invasiva svampinfektioner har ökat under senare år och medför hög dödlighet. En svampinfektion som inte snabbt diagnostiseras och behandlas kan bli livshotande om patientens kondition är dålig. Candida albicans är den vanligaste orsaken till invasiva svampinfektioner. Med traditionell svampidentifiering kan det ta dagar till veckor att isolera och artbestämma svampen. En snabbare metod att detektera Candida är att använda sig av molekylärbiologiska metoder som påvisar svampens arvsmassa, DNA. Svampar har en cellvägg som är svår att bryta ner och därför är DNA extraktionssteget ett av de mest rapporterade problemen vid DNA svampdiagnostik. Syftet med denna studie var att jämföra enzymatisk och mekanisk cellväggsnedbrytning av C. albicans med hjälp av enzymet lyticase respektive glaskulor. Vi jämförde också en manuell metod med två automatiska robotar för att bestämma deras känslighet, tillförlitlighet och tidsåtgång för DNA-extraktion från C. albicans. De slutsatser som nåtts är att den enzymatiska cellväggsnedbrytningen var känsligare men betydligt mer tidskrävande än den mekaniska cellväggsnedbrytningen. Denna studie visade även att en av de automatiska systemen extraherade signifikant mer DNA än den manuella metoden.